Atomic Reference Data for Electronic Structure Calculations
Kotochigova, S; Shirley, E L
We have generated data for atomic electronic structure calculations, to provide a standard reference for results of specified accuracy under commonly used approximations. Results are presented here for total energies and orbital energy eigenvalues for all atoms from H to U, at microHartree accuracy in the total energy, as computed in the local-density approximation (LDA) the local-spin-density approximation (LSD); the relativistic local-density approximation (RLDA); and scalar-relativistic local-density approximation (ScRLDA).
Efficient evaluation of atom tunneling combined with electronic structure calculations
Ásgeirsson, Vilhjálmur; Arnaldsson, Andri; Jónsson, Hannes
2018-03-01
Methodology for finding optimal tunneling paths and evaluating tunneling rates for atomic rearrangements is described. First, an optimal JWKB tunneling path for a system with fixed energy is obtained using a line integral extension of the nudged elastic band method. Then, a calculation of the dynamics along the path is used to determine the temperature at which it corresponds to an optimal Feynman path for thermally activated tunneling (instanton) and a harmonic approximation is used to estimate the transition rate. The method is illustrated with calculations for a modified two-dimensional Müller-Brown surface but is efficient enough to be used in combination with electronic structure calculations of the energy and atomic forces in systems containing many atoms. An example is presented where tunneling is the dominant mechanism well above room temperature as an H3BNH3 molecule dissociates to form H2. Also, a solid-state example is presented where density functional theory calculations of H atom tunneling in a Ta crystal give close agreement with experimental measurements on hydrogen diffusion over a wide range in temperature.
Multi-million atom electronic structure calculations for quantum dots
Usman, Muhammad
Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.
2004-01-01
framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....
Calculation of atomic structures and radiative properties of fusion plasmas
Jarrah, Walid; Pain, Jean-Christophe; Benredjem, Djamel
2017-03-01
The opacity is an important issue in the knowledge of the radiative properties of Inertial Confinement Fusion (ICF) and astrophysical plasmas. In this work we present the opacity of the mixture C+Si, composing the ablator of some ICF capsules. We have used Cowan's code to calculate the atomic structure of carbon and silicon. We also have developed a collisional-radiative model in order to obtain the opacity of the mixture. Line broadening, line shift and ionization potential depression are taken into account in the opacity profile. Comparisons to other calculations are carried out. NLTE and LTE opacity calculations show discrepancies mainly in the range 1900-2000 eV for the bound-bound contribution to the total opacity and in the range 50-350 eV for the bound-free contribution. We have also accounted for photoexcitation and photoionization processes. The corresponding rates are obtained by modeling the Hohlraum radiation by a Planckian distribution at a radiative temperature of 300 eV.
Elantkowska, Magdalena; Ruczkowski, Jarosław; Sikorski, Andrzej; Dembczyński, Jerzy
2017-11-01
A parametric analysis of the hyperfine structure (hfs) for the even parity configurations of atomic terbium (Tb I) is presented in this work. We introduce the complete set of 4fN-core states in our high-performance computing (HPC) calculations. For calculations of the huge hyperfine structure matrix, requiring approximately 5000 hours when run on a single CPU, we propose the methods utilizing a personal computer cluster or, alternatively a cluster of Microsoft Azure virtual machines (VM). These methods give a factor 12 performance boost, enabling the calculations to complete in an acceptable time.
Energy Technology Data Exchange (ETDEWEB)
Lin, Lin; Chen, Mohan; Yang, Chao; He, Lixin
2012-02-10
We describe how to apply the recently developed pole expansion plus selected inversion (PEpSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating charge density, total energy, Helmholtz free energy and atomic forces without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEpSI is that it has a much lower computational complexity than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEpSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEpSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundreds. Both the wall clock time and the memory requirement of PEpSI is modest. This makes it even possible to perform Kohn-Sham DFT calculations for 10,000-atom nanotubes on a single processor. We also show that the use of PEpSI does not lead to loss of accuracy required in a practical DFT calculation.
Atomic structure calculations and identification of EUV and SXR spectral lines in Sr XXX
Goyal, Arun; Khatri, Indu; Aggarwal, Sunny; Singh, A. K.; Mohan, Man
2015-08-01
We report an extensive theoretical study of atomic data for Sr XXX in a wide range with L-shell electron excitations to the M-shell. We have calculated energy levels, wave-function compositions and lifetimes for lowest 113 fine structure levels and wavelengths of an extreme Ultraviolet (EUV) and soft X-ray (SXR) transitions. We have employed multi-configuration Dirac Fock method (MCDF) approach within the framework of Dirac-Coulomb Hamiltonian including quantum electrodynamics (QED) and Breit corrections. We have also presented the radiative data for electric and magnetic dipole (E1, M1) and quadrupole (E2, M2) transitions from the ground state. We have made comparisons with available energy levels compiled by NIST and achieve good agreement. But due to inadequate data in the literature, analogous relativistic distorted wave calculations have also been performed using flexible atomic code (FAC) to assess the reliability and accuracy of our results. Additionally, we have provided new atomic data for Sr XXX which is not published elsewhere in the literature and we believe that our results may be beneficial in fusion plasma research and astrophysical investigations and applications.
Marks, Laurence D.
2010-06-01
In his editorial in this issue, the editor-in-chief emphasizes the editorial policy that any paper which involves a crystallographic structure (whether experimentally measured or theoretically calculated) must also include a complete listing of all the atomic positions within the crystal structure, either as supporting information or directly within the paper itself. He also strongly recommends that the complete crystallographic data set be included as supporting information. At the request of the editor-in-chief, I outline here the reasons why this is scientifically desirable. Furthermore, I propose here that the Surface Science community adopt the same standard format for reporting these as is already widely used in bulk crystallography publications, namely the inclusion of a Crystallographic Information Format file (or CIF file) as supporting information. Finally, I describe the details of this specific file format, with illustrative examples.
Quantum chemical calculation of the equilibrium structures of small metal atom clusters
Kahn, L. R.
1982-01-01
Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.
GRASP92: a package for large-scale relativistic atomic structure calculations
Parpia, F. A.; Froese Fischer, C.; Grant, I. P.
2006-12-01
of CSFs sharing the same quantum numbers is determined using the configuration-interaction (CI) procedure that results upon varying the expansion coefficients to determine the extremum of a variational functional. Radial functions may be determined by numerically solving the multiconfiguration Dirac-Fock (MCDF) equations that result upon varying the orbital radial functions or some subset thereof so as to obtain an extremum of the variational functional. Radial wavefunctions may also be determined using a screened hydrogenic or Thomas-Fermi model, although these schemes generally provide initial estimates for MCDF self-consistent-field (SCF) calculations. Transition properties for pairs of ASFs are computed from matrix elements of multipole operators of the electromagnetic field. All matrix elements of CSFs are evaluated using the Racah algebra. Reasons for the new version: During recent studies using the general relativistic atomic structure package (GRASP92), several errors were found, some of which might have been present already in the earlier GRASP92 version (program ABJN_v1_0, Comput. Phys. Comm. 55 (1989) 425). These errors were reported and discussed by Froese Fischer, Gaigalas, and Ralchenko in a separate publication [C. Froese Fischer, G. Gaigalas, Y. Ralchenko, Comput. Phys. Comm. 175 (2006) 738-744. [7
Directory of Open Access Journals (Sweden)
Elmar Träbert
2014-03-01
Full Text Available The interpretation of atomic observations by theory and the testing of computational predictions by experiment are interactive processes. It is necessary to gain experience with “the other side” before claims of achievement can be validated and judged. The discussion covers some general problems in the field as well as many specific examples, mostly organized by isoelectronic sequence, of what level of accuracy recently has been reached or which atomic structure or level lifetime problem needs more attention.
Theoretical Calculations of Atomic Data for Spectroscopy
Bautista, Manuel A.
2000-01-01
Several different approximations and techniques have been developed for the calculation of atomic structure, ionization, and excitation of atoms and ions. These techniques have been used to compute large amounts of spectroscopic data of various levels of accuracy. This paper presents a review of these theoretical methods to help non-experts in atomic physics to better understand the qualities and limitations of various data sources and assess how reliable are spectral models based on those data.
Gidofalvi, Gergely
2014-01-01
Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multi-referenced) electrons. We use a low-cost approximate solution of the anti-Hermitian contracted Schr{\\"o}dinger equation (ACSE) for the one- and two-electron reduced density matrices (RDMs) to generate an approximate set of natural orbitals for strongly correlated quantum systems. The natural-orbital basis set is truncated to generate a molecule-optimized basis set whose rank matches that of a standard correlation-consistent basis set optimized for the atoms. We show that basis-set truncation by approximate natural orbitals can be viewed as a one-electron unitary transformation of the Hamiltonian operator and suggest an extension of approximate natural-orbital truncations through two-electron unitary transformations of the Hamiltonian operator, such as those employed in the solution of the ACSE. The molecule-optimized basis set from the ACS...
Rafique, Muhammad; Shuai, Yong; Xu, Meng; Zhang, Guohua; Guo, Yanming
2017-09-01
Graphene-based magnetic materials have revealed great potential for developing high-performance electronic units at sub-nanometer such as spintronic data storage devices. However, a significant ferromagnetism behavior and ample band gap in the electronic structure of graphene is required before it can be used for actual engineering applications. Based on first-principles calculations, here we demonstrate the structural, electronic and magnetic behaviors of 5d transition metal (TM) atom-substituted nitrogenized monolayer graphene. We find that, during TMN(3)4 cluster-substitution, tight bonding occurs between impurity atoms and graphene with significant binding energies. Charge transfer occurs from graphene layer to the TMN(3)4 clusters. Interestingly, PtN3, TaN4 and ReN4 cluster-doped graphene structures exhibit dilute magnetic semiconductor behavior with 1.00 μB, 1.04 μB and 1.05 μB magnetic moments, respectively. While, OsN4 and PtN4 cluster-doped structures display nonmagnetic direct band gap semiconductor behavior. Remaining, TMN(3)4 cluster-doped graphene complexes exhibit half metal properties. Detailed analysis of density of states (DOS) plots indicate that d orbitals of TM atoms should be responsible for arising magnetic moments in graphene. Given results pave a new route for potential applications of dilute magnetic semiconductors and half-metals in spintronic devices by employing TMN(3)4 cluster-doped graphene complexes.
Dirac-Fock atomic electronic structure calculations using different nuclear charge distributions
Visscher, L; Dyall, KG
1997-01-01
Numerical Hartree-Fock calculations based on the Dirac-Coulomb Hamiltonian for the first 109 elements of the periodic table are presented. The results give the total electronic energy, as a function of the nuclear model that is used, for four different models of the nuclear charge distribution. The
Energy Technology Data Exchange (ETDEWEB)
Lim, Suh Yeon
2006-08-15
This book is written to teach atom structure in very easy way. It is divided into nine chapters, which indicates what is the components of matter? when we divide matter continuously, it becomes atom, what did atom look like? particles comprised of matter is not only atom, discover of particles comprised of atom, symbol of element, various radiation, form alchemy to nuclear transmutation, shape of atom is evolving. It also has various pictures in each chapters to explain easily.
Calculated Atomic Volumes of the Actinide Metals
DEFF Research Database (Denmark)
Skriver, H.; Andersen, O. K.; Johansson, B.
1979-01-01
The equilibrium atomic volume is calculated for the actinide metals. It is possible to account for the localization of the 5f electrons taking place in americium.......The equilibrium atomic volume is calculated for the actinide metals. It is possible to account for the localization of the 5f electrons taking place in americium....
Lin, Xiao; Nilius, Niklas; Sterrer, Martin; Koskinen, Pekka; Häkkinen, Hannu; Freund, Hans-Joachim
2010-04-01
The perimeter of oxide-supported metal particles is suggested to be of pivotal importance for various catalytic processes. To elucidate the underlying effects, the electronic properties of edge and corner atoms of planar Au clusters on MgO/Ag(001) thin films have been analyzed with scanning tunneling microscopy and electronic structure calculations. The low-coordinated perimeter atoms are characterized by a high density of s -derived states at the Fermi level. Those states accommodate transfer electrons from the MgO/Ag substrate, which render the perimeter atoms negatively charged. In contrast, the inner atoms of the island are not affected by the charge transfer and remain neutral. This combination of charge accumulation and high state-density explains the specific relevance of the cluster perimeter in adsorption and reaction processes.
Energy Technology Data Exchange (ETDEWEB)
Benedek, R.; Thackeray, M.M. [Argonne National Lab., IL (United States). Chemical Technology Div.; Yang, L.H. [Lawrence Livermore National Lab., CA (United States)
1999-09-01
Interest in the {gamma}-bronze, Li{sub 1+x}V{sub 3}O{sub 8}, as a possible electrode material in rechargeable Li batteries has stimulated several experimental studies on this system. Detailed interpretation of the electrochemical and physical-property measurements is complicated by uncertainties regarding the structural arrangement of Li atoms as a function of x and by a phase transition between two monoclinic structures ({gamma}{sub a}, {gamma}{sub b}) during intercalation. To elucidate the atomic structures and the phase transition, first-principles calculations re performed with the local-density-functional-theory (LDFT) planewave pseudopotential method for both {gamma}{sub a} and {gamma}{sub b} as a function of lithiation. Calculations for the compositions 1+x=1.5 and 1+x=4 confirm that the Li configuration determined in the existing X-ray diffraction structure refinements (at 1+x=1.2 and 1+x=4, respectively), coincide with the predicted low-energy configurations. Structure predictions were made at intermediate compositions, for which no experimental structure measurement is available. The order in which the tetrahedrally coordinated Li sites are filled at equilibrium as a function of x in {gamma}{sub a} was predicted. Calculated electrochemical potentials as a function of composition agree well with experimental data. (orig.)
Ab initio calculations on structural and electronic transport properties of six-atom GaN clusters
Song, Jinfeng; Long, Xiaojiang; Hao, Yanjun; Zhu, Jun; Guo, Yundong
2017-11-01
The structural and electronic transport properties of GaxNy (x + y = 6) clusters are investigated in the framework of density functional theory (DFT). To get their most stable structures, a strategy of particle swarm optimization (PSO) algorithm is adopted. It is found that the most stable cluster’s binding energy and HOMO-LUMO gap energy decrease with Ga atom’s number in cluster increasing. The electronic transport properties of the clusters connected with two Al(100) electrodes are obtained by a method of combining nonequilibrium Green’s function (NEGF) with DFT. Equilibrium conductance of all six-atom GaN cluster is low (less than 0.65 G0), and Ga2N4 has the highest one (0.635 G0). Significant negative differential resistance (NDR) phenomenon is observed in configurations with cluster Ga2N4, Ga3N3 and Ga5N1, and these three clusters have almost the same current value in voltage region from 0.8 V to 1.3 V.
Energy Technology Data Exchange (ETDEWEB)
Madjet, Mohamed E., E-mail: mmadjet@qf.org.qa; El-Mellouhi, Fedwa; Carignano, Marcelo A.; Berdiyorov, Golibjon R. [Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, P. O. Box 5825, Doha (Qatar)
2016-04-28
We calculated the partial charges in methylammonium (MA) lead-iodide perovskite CH{sub 3}NH{sub 3}PbI{sub 3} in its different crystalline phases using different first-principles electronic charge partitioning approaches, including the Bader, ChelpG, and density-derived electrostatic and chemical (DDEC) schemes. Among the three charge partitioning methods, the DDEC approach provides chemically intuitive and reliable atomic charges for this material, which consists of a mixture of transition metals, halide ions, and organic molecules. The DDEC charges are also found to be robust against the use of hybrid functionals and/or upon inclusion of spin–orbit coupling or dispersive interactions. We calculated explicitly the atomic charges with a special focus on the dipole moment of the MA molecules within the perovskite structure. The value of the dipole moment of the MA is reduced with respect to the isolated molecule due to charge redistribution involving the inorganic cage. DDEC charges and dipole moment of the organic part remain nearly unchanged upon its rotation within the octahedral cavities. Our findings will be of both fundamental and practical importance, as the accurate and consistent determination of the atomic charges is important in order to understand the average equilibrium distribution of the electrons and to help in the development of force fields for larger scale atomistic simulations to describe static, dynamic, and thermodynamic properties of the material.
Energy Technology Data Exchange (ETDEWEB)
Dorado, B.
2010-09-15
Uranium dioxide UO{sub 2} is the standard nuclear fuel used in pressurized water reactors. During in-reactor operation, the fission of uranium atoms yields a wide variety of fission products (FP) which create numerous point defects while slowing down in the material. Point defects and FP govern in turn the evolution of the fuel physical properties under irradiation. In this study, we use electronic structure calculations in order to better understand the fuel behavior under irradiation. In particular, we investigate point defect behavior, as well as the stability of three volatile FP: iodine, krypton and xenon. In order to take into account the strong correlations of uranium 5f electrons in UO{sub 2}, we use the DFT+U approximation, based on the density functional theory. This approximation, however, creates numerous metastable states which trap the system and induce discrepancies in the results reported in the literature. To solve this issue and to ensure the ground state is systematically approached as much as possible, we use a method based on electronic occupancy control of the correlated orbitals. We show that the DFT+U approximation, when used with electronic occupancy control, can describe accurately point defect and fission product behavior in UO{sub 2} and provide quantitative information regarding point defect transport properties in the oxide fuel. (author)
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.S.
1977-11-01
The effects of the 4f shell of electrons and the relativity of valence electrons are compared. The effect of 4f shell (lanthanide contraction) is estimated from the numerical Hartree-Fock (HF) calculations of pseudo-atoms corresponding to Hf, Re, Au, Hg, Tl, Pb and Bi without 4f electrons and with atomic numbers reduced by 14. The relativistic effect estimated from the numerical Dirac-Hartree-Fock (DHF) calculations of those atoms is comparable in the magnitude with that of the 4f shell of electrons. Both are larger for 6s than for 5d or 6p electrons. The various relativistic effects on valence electrons are discussed in detail to determine the proper level of the approximation for the valence electron calculations of systems with heavy elements. An effective core potential system has been developed for heavy atoms in which relativistic effects are included in the effective potentials.
BOOK REVIEW: Computational Atomic Structure
Post, Douglass E.
1998-02-01
The primary purpose of `Computational Atomic Structure' is to give a potential user of the Multi-Configuration Hartree-Fock (MCHF) Atomic Structure Package an outline of the physics and computational methods in the package, guidance on how to use the package, and information on how to interpret and use the computational results. The book is successful in all three aspects. In addition, the book provides a good overview and review of the physics of atomic structure that would be useful to the plasma physicist interested in refreshing his knowledge of atomic structure and quantum mechanics. While most of the subjects are covered in greater detail in other sources, the book is reasonably self-contained, and, in most cases, the reader can understand the basic material without recourse to other sources. The MCHF package is the standard package for computing atomic structure and wavefunctions for single or multielectron ions and atoms. It is available from a number of ftp sites. When the code was originally written in FORTRAN 77, it could only be run on large mainframes. With the advances in computer technology, the suite of codes can now be compiled and run on present day workstations and personal computers and is thus available for use by any physicist, even those with extremely modest computing resources. Sample calculations in interactive mode are included in the book to illustrate the input needed for the code, what types of results and information the code can produce, and whether the user has installed the code correctly. The user can also specify the calculational level, from simple Hartree-Fock to multiconfiguration Hartree-Fock. The MCHF method begins by finding approximate wavefunctions for the bound states of an atomic system. This involves minimizing the energy of the bound state using a variational technique. Once the wavefunctions have been determined, other atomic properties, such as the transition rates, can be determined. The book begins with an
Can atom-surface potential measurements test atomic structure models?
Lonij, Vincent P A; Klauss, Catherine E; Holmgren, William F; Cronin, Alexander D
2011-06-30
van der Waals (vdW) atom-surface potentials can be excellent benchmarks for atomic structure calculations. This is especially true if measurements are made with two different types of atoms interacting with the same surface sample. Here we show theoretically how ratios of vdW potential strengths (e.g., C₃(K)/C₃(Na)) depend sensitively on the properties of each atom, yet these ratios are relatively insensitive to properties of the surface. We discuss how C₃ ratios depend on atomic core electrons by using a two-oscillator model to represent the contribution from atomic valence electrons and core electrons separately. We explain why certain pairs of atoms are preferable to study for future experimental tests of atomic structure calculations. A well chosen pair of atoms (e.g., K and Na) will have a C₃ ratio that is insensitive to the permittivity of the surface, whereas a poorly chosen pair (e.g., K and He) will have a ratio of C₃ values that depends more strongly on the permittivity of the surface.
DEFF Research Database (Denmark)
Bork, Nicolai Christian; Eurenius, K. E. J.; Rossmeisl, Jan
2012-01-01
) oxygen atoms closely associated with a Ca dopant. Further, the unexpected presence of Ho hydride defects in undoped, oxygen deficient Sm2Sn2O7 is reported. Finally, the stretching frequencies and relative intensities for these and other sites are calculated. The main features of the Fourier transform...
Monte Carlo calculations of atoms and molecules
Schmidt, K. E.; Moskowitz, J. W.
1986-06-01
The variational and Green's function Monte Carlo (GFMC) methods can treat many interesting atomic and molecular problems. These methods can give chemical accuracy for up to 10 or so electrons. The various implementations of the GFMC method, including the domain Green's function method and the short-time approximation, are discussed. Results are presented for several representative atoms and molecules.
Introduction to Density Functional Theory: Calculations by Hand on the Helium Atom
Baseden, Kyle A.; Tye, Jesse W.
2014-01-01
Density functional theory (DFT) is a type of electronic structure calculation that has rapidly gained popularity. In this article, we provide a step-by-step demonstration of a DFT calculation by hand on the helium atom using Slater's X-Alpha exchange functional on a single Gaussian-type orbital to represent the atomic wave function. This DFT…
Universal bosonic tetramers of dimer-atom-atom structure
Deltuva, A.
2012-01-01
Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.
Theoretical Calculation of Absolute Radii of Atoms and Ions. Part 1. The Atomic Radii
Directory of Open Access Journals (Sweden)
Raka Biswas
2002-02-01
Full Text Available Abstract. A set of theoretical atomic radii corresponding to the principal maximum in the radial distribution function, 4ÃÂ€r2R2 for the outermost orbital has been calculated for the ground state of 103 elements of the periodic table using Slater orbitals. The set of theoretical radii are found to reproduce the periodic law and the Lother MeyerÃ¢Â€Â™s atomic volume curve and reproduce the expected vertical and horizontal trend of variation in atomic size in the periodic table. The d-block and f-block contractions are distinct in the calculated sizes. The computed sizes qualitatively correlate with the absolute size dependent properties like ionization potentials and electronegativity of elements. The radii are used to calculate a number of size dependent periodic physical properties of isolated atoms viz., the diamagnetic part of the atomic susceptibility, atomic polarizability and the chemical hardness. The calculated global hardness and atomic polarizability of a number of atoms are found to be close to the available experimental values and the profiles of the physical properties computed in terms of the theoretical atomic radii exhibit their inherent periodicity. A simple method of computing the absolute size of atoms has been explored and a large body of known material has been brought together to reveal how many different properties correlate with atomic size.
Calculation of tin atomic data and plasma properties.
Energy Technology Data Exchange (ETDEWEB)
Morozov, V.; Tolkach, V.; Hassanein, A.
2005-08-26
This report reviews the major methods and techniques we use in generating basic atomic and plasma properties relevant to extreme ultraviolet (EUV) lithography applications. The basis of the work is the calculation of the atomic energy levels, transitions probabilities, and other atomic data by various methods, which differ in accuracy, completeness, and complication. Later on, we calculate the populations of atomic levels and ion states in plasmas by means of the collision-radiation equilibrium (CRE) model. The results of the CRE model are used as input to the thermodynamic functions, such as pressure and temperature from the internal energy and density (equation of state), electric resistance, thermal conduction, and other plasma properties. In addition, optical coefficients, such as emission and absorption coefficients, are generated to resolve a radiation transport equation (RTE). The capabilities of our approach are demonstrated by generating the required atomic and plasma properties for tin ions and plasma within the EUV region near 13.5 nm.
Investigation of atomic processes during film growth using semiempirical calculations
Leonardelli, G
2001-01-01
Growth of thin films on solid surfaces is strongly determined by the rates of the individual atomic processes and therefore depends on the energy barriers which must be surmounted during these processes. The diffusion barriers of interlayer diffusion processes are calculated in this work using embedded atom method (EAM) potentials. Great attention is paid to effects of small simulation cells preventing the atoms near the step edge from relaxing completely and thereby modifying the barriers for step descent on steps of the Pt(111) surface. Calculations in this work can also explain experimental data which show Co atoms sitting in special sites like corners and kinks when small amounts of Co are deposited on the Pt(111) surface. The results show why these sites are occupied and why configurations along A-steps are different from those on B-steps. Furthermore, calculations explain the intermixing of adlayer and substrate atoms on fcc(111) surfaces in the vicinity of rough steps occurring when these steps smoothe...
Calculation of Rydberg energy levels for the francium atom
Huang, Shi-Zhong; Chu, Jin-Min
2010-06-01
Based on the weakest bound electron potential model theory, the Rydberg energy levels and quantum defects of the np2Po1/2 (n = 7-50) and np2Po3/2 (n = 7-50) spectrum series for the francium atom are calculated. The calculated results are in excellent agreement with the 48 measured levels, and 40 energy levels for highly excited states are predicted.
Calculation of magnetic response properties using atoms in molecules
Keith, T. A.; Bader, R. F. W.
1992-06-01
A new method (IGAIM — individual gauges for atoms in molecules) is presented for relatively accurate ab initio calculations of molecular magnetic response properties. The current density induced within an atom in a molecule by an external magnetic field is well described by the coupled, perturbed Hartree—Fock method when the gauge origin of the vector potential is placed at its nucleus, the natural origin for the free atom, even though it may be poorly described in the rest of the molecule. Since the molecular magnetic susceptibility and nuclear magnetic shielding tensors can be expressed in terms of the induced current density as a sum of separately determined atomic contributions, these properties are, in general, accurately predicted even with basis sets that are insufficient for conventional CPHF.
Calculation of growth per cycle (GPC) of atomic layer deposited ...
Indian Academy of Sciences (India)
2014-03-06
Mar 6, 2014 ... Calculation of growth per cycle (GPC) of atomic layer deposited aluminium oxide nanolayers and dependence of GPC on surface OH concentration. ANU PHILIP, SUBIN THOMAS and K RAJEEV KUMAR*. Department of Instrumentation, Cochin University of Science and Technology,. Cochin 682 022, India.
Calculation of growth per cycle (GPC) of atomic layer deposited ...
Indian Academy of Sciences (India)
Home; Journals; Pramana – Journal of Physics; Volume 82; Issue 3. Calculation of growth per cycle (GPC) of atomic layer deposited aluminium oxide nanolayers and dependence of GPC on surface OH concentration. Anu Philip Subin Thomas K Rajeev Kumar. Research Articles Volume 82 Issue 3 March 2014 pp 563-569 ...
Schwinger variational calculation of ionization of hydrogen atoms for ...
Indian Academy of Sciences (India)
Schwinger variational calculation of ionization of hydrogen atoms for large momentum transfers. K CHAKRABARTI. Department of Mathematics, Scottish Church College, 1 & 3 Urquhart Square,. Kolkata 700 006, India. MS received 7 July 2001; revised 10 October 2001. Abstract. Schwinger variational principle is used here ...
Golafrooz Shahri, S.; Roknabadi, M. R.; Radfar, R.
2017-12-01
In this present paper, the non-equilibrium Green function (NEGF) method along with the density functional theory (DFT) were used to investigate the effect of doping a single transition-metal atom on transport and electronic properties of armchair graphyne (γ-graphyne) nanoribbons. It can be deduced from the results that among the doped TM atoms, Mn and Fe cause stronger polarized currents comparing to Co and Ni. Mn-AGyNR represents the features of a half-semiconductor and behaves like a semiconductor in both up and down spin channels. On the other hand, Fe-AGyNR shows a great potential in spintronic applications due to its half-metal properties. Also our results show the promising application of armchair graphyne nanoribbons in nano-electrical devices.
Update on nuclear structure effects in light muonic atoms
Energy Technology Data Exchange (ETDEWEB)
Hernandez, Oscar Javier, E-mail: javierh@triumf.ca; Dinur, Nir Nevo; Ji, Chen; Bacca, Sonia [TRIUMF (Canada); Barnea, Nir [The Hebrew University, Racah Institute of Physics (Israel)
2016-12-15
We present calculations of the nuclear structure corrections to the Lamb shift in light muonic atoms, using state-of-the-art nuclear potentials. We outline updated results on finite nucleon size contributions.
VIBRATIONAL RAMAN OPTICAL-ACTIVITY CALCULATIONS USING LONDON ATOMIC ORBITALS
DEFF Research Database (Denmark)
Helgaker, T.; Ruud, K.; Bak, Keld L.
1994-01-01
Ab initio calculations of Raman differential intensities are presented at the self-consistent field (SCF) level of theory. The electric dipole-electric dipole, electric dipole-magnetic dipole and electric dipole-electric quadrupole polarizability tensors are calculated at the frequency of the inc...... of the incident light, using SCF linear response theory. London atomic orbitals are employed, imposing gauge origin invariance on the calculations. Calculations have been carried out in the harmonic approximation for CFHDT and methyloxirane.......Ab initio calculations of Raman differential intensities are presented at the self-consistent field (SCF) level of theory. The electric dipole-electric dipole, electric dipole-magnetic dipole and electric dipole-electric quadrupole polarizability tensors are calculated at the frequency...
High-accuracy coupled cluster calculations of atomic properties
Energy Technology Data Exchange (ETDEWEB)
Borschevsky, A. [School of Chemistry, Tel Aviv University, 69978 Tel Aviv, Israel and Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, Private Bag 102904, 0745 Auckland (New Zealand); Yakobi, H.; Eliav, E.; Kaldor, U. [School of Chemistry, Tel Aviv University, 69978 Tel Aviv (Israel)
2015-01-22
The four-component Fock-space coupled cluster and intermediate Hamiltonian methods are implemented to evaluate atomic properties. The latter include the spectra of nobelium and lawrencium (elements 102 and 103) in the range 20000-30000 cm{sup −1}, the polarizabilities of elements 112-114 and 118, required for estimating their adsorption enthalpies on surfaces used to separate them in accelerators, and the nuclear quadrupole moments of some heavy atoms. The calculations on superheavy elements are supported by the very good agreement with experiment obtained for the lighter homologues.
Calculation of the Rydberg Energy Levels for Francium Atom
Directory of Open Access Journals (Sweden)
Huang Shizhong
2010-01-01
Full Text Available Based on the weakest bound electron potential model theory, the Rydberg energy levels and quantum defects of nsS21/2(n=8--50, ndD23/2(n=6--50, and ndD25/2(n=6--50 spectrum series for francium atom are calculated. The calculated results are in excellent agreement with the 74 known experimentally measured levels (the absolute difference is less than 0.03 cm-1 and 58 energy levels for highly excited states are predicted.
Calculation of the Rydberg Energy Levels for Francium Atom
Huang Shizhong; Sun Qiufeng
2010-01-01
Based on the weakest bound electron potential model theory, the Rydberg energy levels and quantum defects of nsS21/2(n=8--50), ndD23/2(n=6--50), and ndD25/2(n=6--50) spectrum series for francium atom are calculated. The calculated results are in excellent agreement with the 74 known experimentally measured levels (the absolute difference is less than 0.03 cm-1) and 58 energy levels for highly excited states are predicted.
Calculations of optical rotation: Influence of molecular structure
Directory of Open Access Journals (Sweden)
Yu Jia
2012-01-01
Full Text Available Ab initio Hartree-Fock (HF method and Density Functional Theory (DFT were used to calculate the optical rotation of 26 chiral compounds. The effects of theory and basis sets used for calculation, solvents influence on the geometry and values of calculated optical rotation were all discussed. The polarizable continuum model, included in the calculation, did not improve the accuracy effectively, but it was superior to γs. Optical rotation of five or sixmembered of cyclic compound has been calculated and 17 pyrrolidine or piperidine derivatives which were calculated by HF and DFT methods gave acceptable predictions. The nitrogen atom affects the calculation results dramatically, and it is necessary in the molecular structure in order to get an accurate computation result. Namely, when the nitrogen atom was substituted by oxygen atom in the ring, the calculation result deteriorated.
DEFF Research Database (Denmark)
Avery, John Scales; Avery, James Emil; Aquilanti, Vincenzo
2004-01-01
The generalized Sturmian method for atomic and molecular electronic structure calculations is a direct configuration interaction method in which the configurations are chosen to be isoenergetic solutions of an approximate N-electron Schrödinger equation with a weighted potential, $\\beta_\
Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy.
Krivanek, Ondrej L; Chisholm, Matthew F; Nicolosi, Valeria; Pennycook, Timothy J; Corbin, George J; Dellby, Niklas; Murfitt, Matthew F; Own, Christopher S; Szilagyi, Zoltan S; Oxley, Mark P; Pantelides, Sokrates T; Pennycook, Stephen J
2010-03-25
Direct imaging and chemical identification of all the atoms in a material with unknown three-dimensional structure would constitute a very powerful general analysis tool. Transmission electron microscopy should in principle be able to fulfil this role, as many scientists including Feynman realized early on. It images matter with electrons that scatter strongly from individual atoms and whose wavelengths are about 50 times smaller than an atom. Recently the technique has advanced greatly owing to the introduction of aberration-corrected optics. However, neither electron microscopy nor any other experimental technique has yet been able to resolve and identify all the atoms in a non-periodic material consisting of several atomic species. Here we show that annular dark-field imaging in an aberration-corrected scanning transmission electron microscope optimized for low voltage operation can resolve and identify the chemical type of every atom in monolayer hexagonal boron nitride that contains substitutional defects. Three types of atomic substitutions were found and identified: carbon substituting for boron, carbon substituting for nitrogen, and oxygen substituting for nitrogen. The substitutions caused in-plane distortions in the boron nitride monolayer of about 0.1 A magnitude, which were directly resolved, and verified by density functional theory calculations. The results demonstrate that atom-by-atom structural and chemical analysis of all radiation-damage-resistant atoms present in, and on top of, ultra-thin sheets has now become possible.
Electronic structure of atoms: atomic spectroscopy information system
Kazakov, V. V.; Kazakov, V. G.; Kovalev, V. S.; Meshkov, O. I.; Yatsenko, A. S.
2017-10-01
The article presents a Russian atomic spectroscopy, information system electronic structure of atoms (IS ESA) (http://grotrian.nsu.ru), and describes its main features and options to support research and training. The database contains over 234 000 records, great attention paid to experimental data and uniform filling of the database for all atomic numbers Z, including classified levels and transitions of rare earth and transuranic elements and their ions. Original means of visualization of scientific data in the form of spectrograms and Grotrian diagrams have been proposed. Presentation of spectral data in the form of interactive color charts facilitates understanding and analysis of properties of atomic systems. The use of the spectral data of the IS ESA together with its functionality is effective for solving various scientific problems and training of specialists.
Finite Bias Calculations to Model Interface Dipoles in Electrochemical Cells at the Atomic Scale
DEFF Research Database (Denmark)
Hansen, Martin Hangaard; Jin, Chengjun; Thygesen, Kristian Sommer
2016-01-01
The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure t...... to satisfy the thermodynamic constraints imposed by the environment. This is captured by the generalized computational hydrogen electrode model, which enables us to make efficient first-principles calculations of atomic scale properties of the electrochemical interface.......The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure...
Partial atomic multipoles for internally consistent microelectrostatic calculations.
Snamina, Mateusz; Mazur, Grzegorz; Petelenz, Piotr
2017-10-30
An extension of the extant microelectrostatic methodologies, based on the concept of distributed generalized polarizability matrix derived from the Coupled Perturbed Hartree-Fock (CPHF) equations, is proposed for self-consistent calculation of charge carrier and charge-transfer (CT) state electrostatic energies in molecular solids, including the doped, defected and disordered ones. The CPHF equations are solved only once and the generalized molecular polarizability they yield enables low cost iterations that mutually adjust the molecular electronic distributions and the local electric field in which the molecules are immersed. The approach offers a precise picture of molecular charge densities, accounting for atomic partial multipoles up to order 2, which allows one to reproduce the recently reported large charge-quadrupole contributions to CT state energies in low-symmetry local environments. It is particularly well suited for repetitive calculations for large clusters (up to 300,000 atoms), and may potentially be useful for describing electrostatic solvent effects. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Efficient Calculation of Molecular Integrals over London Atomic Orbitals.
Irons, Tom J P; Zemen, Jan; Teale, Andrew M
2017-08-08
The use of London atomic orbitals (LAOs) in a nonperturbative manner enables the determination of gauge-origin invariant energies and properties for molecular species in arbitrarily strong magnetic fields. Central to the efficient implementation of such calculations for molecular systems is the evaluation of molecular integrals, particularly the electron repulsion integrals (ERIs). We present an implementation of several different algorithms for the evaluation of ERIs over Gaussian-type LAOs at arbitrary magnetic field strengths. The efficiencies of generalized McMurchie-Davidson (MD), Head-Gordon-Pople (HGP), and Rys quadrature schemes are compared. For the Rys quadrature implementation, we avoid the use of high precision arithmetic and interpolation schemes in the computation of the quadrature roots and weights, enabling the application of this algorithm seamlessly to a wide range of magnetic fields. The efficiency of each generalized algorithm is compared by numerical application, classifying the ERIs according to their total angular momenta and evaluating their performance for primitive and contracted basis sets. In common with zero-field integral evaluation, no single algorithm is optimal for all angular momenta; thus, a simple mixed scheme is put forward that selects the most efficient approach to calculate the ERIs for each shell quartet. The mixed approach is significantly more efficient than the exclusive use of any individual algorithm.
Electronic Structure Calculations and the Ising Hamiltonian.
Xia, Rongxin; Bian, Teng; Kais, Sabre
2017-11-20
Obtaining exact solutions to the Schrödinger equation for atoms, molecules, and extended systems continues to be a "Holy Grail" problem which the fields of theoretical chemistry and physics have been striving to solve since inception. Recent breakthroughs have been made in the development of hardware-efficient quantum optimizers and coherent Ising machines capable of simulating hundreds of interacting spins with an Ising-type Hamiltonian. One of the most vital questions pertaining to these new devices is, "Can these machines be used to perform electronic structure calculations?" Within this work, we review the general procedure used by these devices and prove that there is an exact mapping between the electronic structure Hamiltonian and the Ising Hamiltonian. Additionally, we provide simulation results of the transformed Ising Hamiltonian for H2 , He2 , HeH+, and LiH molecules, which match the exact numerical calculations. This demonstrates that one can map the molecular Hamiltonian to an Ising-type Hamiltonian which could easily be implemented on currently available quantum hardware. This is an early step in developing generalized methods on such devices for chemical physics.
Relativistic calculations of screening parameters and atomic radii of neutral atoms
Guerra, M.; Amaro, P.; Santos, J. P.; Indelicato, P.
2017-09-01
Calculations of the effective nuclear charge for elements with 1 ≤ Z ≤ 118 have been performed in a Dirac-Fock approach including all relativistic effects as well as contributions from quantum electrodynamics. Maximum charge density for every subshell of every element in the periodic table was also computed in the same framework as well as atomic radii based on the total charge density. Results were compared with the extensively cited works of Clementi et al., obtained in the 1960s with Roothan's self-consistent-field method.
DEFF Research Database (Denmark)
Falkenberg, G.; Bunk, O.; Johnson, R.L.
2002-01-01
. Sci. 123/124, 104 (1998) for In on Si(001). For the (4x4) subunit, we propose a model that includes the main features of the (3x4) subunit together with additional mixed Ge-In dimers. The atomic positions were optimized using ab initio total-energy calculations. The calculated local densities......Using scanning-tunneling microscopy (STM) and first-principles total-energy calculations, we have determined the atomic geometry of the superstructures formed by the adsorption of up to 0.5 monolayer of indium on Ge(001) and annealing at temperatures above 200 degreesC. A strong interaction between...... indium adatoms and the germanium substrate atoms leads to the formation of two different In-Ge subunits on the Ge(001) surface. In the subsaturation regime separate (nx4) subunits are observed where n can be either 3 or 4 and the STM images resemble those of the Si(001)-(3x4)-In and -Al reconstructions...
Energy Technology Data Exchange (ETDEWEB)
Jiang, Jun, E-mail: phyjiang@yeah.net [Key Laboratory of Atomic and Molecular Physics and Functional Materials of Gansu Province, College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070 (China); School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Mitroy, J. [School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Cheng, Yongjun, E-mail: cyj83mail@gmail.com [School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin 150080 (China); Bromley, M.W.J., E-mail: brom@physics.uq.edu.au [School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland 4075 (Australia)
2015-01-15
Effective oscillator strength distributions are systematically generated and tabulated for the alkali atoms, the alkaline-earth atoms, the alkaline-earth ions, the rare gases and some miscellaneous atoms. These effective distributions are used to compute the dipole, quadrupole and octupole static polarizabilities, and are then applied to the calculation of the dynamic polarizabilities at imaginary frequencies. These polarizabilities can be used to determine the long-range C{sub 6}, C{sub 8} and C{sub 10} atom–atom interactions for the dimers formed from any of these atoms and ions, and we present tables covering all of these combinations.
Electronic structure of crystalline uranium nitride: LCAO DFT calculations
Energy Technology Data Exchange (ETDEWEB)
Evarestov, R.A.; Losev, M.V.; Panin, A.I. [Department of Quantum Chemistry, St. Petersburg State University, 26 University Prospekt, Stary Peterghof, 198504 (Russian Federation); Mosyagin, N.S. [Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg District, 188300 (Russian Federation); Titov, A.V. [Department of Quantum Chemistry, St. Petersburg State University, 26 University Prospekt, Stary Peterghof, 198504 (Russian Federation); Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg District, 188300 (Russian Federation)
2008-01-15
The results of the first LCAO DFT calculations of cohesive energy, band structure and charge distribution in uranium nitride (UN) crystal are presented and discussed. The calculations are made with the uranium atom relativistic effective core potentials, including 60, 78 and 81 electrons in the core. It is demonstrated that the chemical bonding in UN crystal has a metallic-covalent nature. Three 5f-electrons are localized on the U atom and occupy the states near the Fermi level. The metallic nature of the crystal is due to the f-character of both the valence-band top and the conduction-band bottom. The covalent bonds are formed by the interaction of 7s- and 6d-states of the uranium atom with the 2p-states of the nitrogen atom. It is shown that the inclusion of 5f-electrons in the atomic core introduces small changes in the calculated cohesive energy of UN crystal and electron charge distribution. However, the inclusion of 5s-, 5p-, 5d-electrons in the valence shell allows the better agreement with the calculated and experimental cohesive-energy value. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Energy Technology Data Exchange (ETDEWEB)
Tian Shanxi; Kishimoto, Naoki; Ohno, Koichi
2002-12-15
He I ultraviolet photoelectron spectra and He*(2{sup 3}S) Penning ionization electron spectra have been measured for 1-adamantanol, cyclohexanol and cyclohexanone. Four stable isomeric conformers of cyclohexanol were predicted by Becke's three-parameter hybrid density functional B3LYP/6-31+G(d,p) calculations. Since the orbital reactivity in Penning ionizations is simply related to the electron density extending outside the molecular surface, the theoretical Penning ionization electron spectra were synthesized using the calculated molecular orbital wave functions and ionization potentials. They were in good agreement with the experimental spectra except for the low-electron-energy bands. Collision energy dependence of partial ionization cross sections for the oxygen lone pair orbitals exhibited that there are strong steric hindrances by the neighboring hydrogen atoms in 1-adamantanol and cyclohexanol.
Geminal embedding scheme for optimal atomic basis set construction in correlated calculations
Energy Technology Data Exchange (ETDEWEB)
Sorella, S., E-mail: sorella@sissa.it [International School for Advanced Studies (SISSA), Via Beirut 2-4, 34014 Trieste, Italy and INFM Democritos National Simulation Center, Trieste (Italy); Devaux, N.; Dagrada, M., E-mail: mario.dagrada@impmc.upmc.fr [Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05 (France); Mazzola, G., E-mail: gmazzola@phys.ethz.ch [Theoretische Physik, ETH Zurich, 8093 Zurich (Switzerland); Casula, M., E-mail: michele.casula@impmc.upmc.fr [CNRS and Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05 (France)
2015-12-28
We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.
Geminal embedding scheme for optimal atomic basis set construction in correlated calculations
Sorella, S.; Devaux, N.; Dagrada, M.; Mazzola, G.; Casula, M.
2015-12-01
We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.
Niels Bohr and the Atomic Structure
Indian Academy of Sciences (India)
IAS Admin
Christien Bohr, was a professor of physiology in the Copenhagen. University. Niels received his education in Copenhagen, obtain- ing his masters degree in 1909, and the doctoral degree in 1911. M Durga Prasad ... Inelastic scattering of electrons from mercury atoms. 1914. J Franck, G Hertz. Interpretation of fine structure.
Atomic Structure and Properties of Extended Defects in Silicon
Energy Technology Data Exchange (ETDEWEB)
Buczko, R.; Chisholm, M.F.; Kaplan, T.; Maiti, A.; Mostoller, M.; Pantelides, S.T.; Pennycook, S.J.
1998-10-15
The Z-contrast technique represents a new approach to high-resolution electron microscopy allowing for the first time incoherent imaging of materials on the atomic scale. The key advantages of the technique, an intrinsically higher resolution limit and directly interpretable, compositionally sensitive imaging, allow a new level of insight into the atomic configurations of extended defects in silicon. This experimental technique has been combined with theoretical calculations (a combination of first principles, tight binding, and classical methods) to extend this level of insight by obtaining the energetic and electronic structure of the defects.
Autoionizing states of atoms calculated using generalized sturmians
DEFF Research Database (Denmark)
Avery, James Emil; Avery, John Scales
2005-01-01
energies. A large-Z approximation is discussed, and simple formulas are derived which are valid not only for autoionizing states, but for all states of an isoelectronic atomic series. Diagonalization of a small block of the interelectron repulsion matrix yields roots that can be used for a wide range of Z...
Structure and properties of atomic nanoclusters
Alonso, Julio A
2005-01-01
Atomic clusters are the bridge between molecules and the bulk matter. Following two key experiments - the observation of electronic shells in metallic clusters and the discovery of the C60 fullerence - the field of atomic clusters has experienced a rapid growth, and is now considered a mature field. The electrons of the cluster are confined to a small volume, hence, quantum effects are manifested on many properties of the clusters. Another interesting feature is that the properties often change in a non-smooth way as the number of atoms in the cluster increases. This book provides an updated overview of the field, and presents a detailed description of the structure and electronic properties of different types of clusters: Van der Waals clusters, metallic clusters, clusters of ionic materials and network clusters. The assembling of clusters is also considered, since specially stable clusters are expected to play a role in the future design and synthesis of new materials.
Numerical calculation of the ground state of Helium atom using ...
African Journals Online (AJOL)
Hylleraas did the calculation of the ground state in 1926 using the variational parameter a. In this paper we trace Hylleraas historic calculation, the use of computer enables us to improve the approximation found by Hylleraas . The program was written in FORTRAN language, designed in such away that for a particular value ...
Atomic and electronic structure of exfoliated black phosphorus
Energy Technology Data Exchange (ETDEWEB)
Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok; Wentzcovitch, Renata M.; Mkhoyan, K. Andre, E-mail: mkhoyan@umn.edu [Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Low, Tony; Robbins, Matthew C.; Haratipour, Nazila; Koester, Steven J. [Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)
2015-11-15
Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolution view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO{sub 3} or H{sub 3}PO{sub 3} during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time.
Imaging DNA Structure by Atomic Force Microscopy.
Pyne, Alice L B; Hoogenboom, Bart W
2016-01-01
Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometre resolution. For biological applications, one of its key advantages is its ability to visualize substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine superstructure and secondary structure of surface-bound DNA. The method is also readily applicable to probe DNA-DNA interactions and DNA-protein complexes.
Atomic structure of a decagonal Al-Pd-Mn phase
Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer
2017-12-01
We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.
A piecewise lookup table for calculating nonbonded pairwise atomic interactions.
Luo, Jinping; Liu, Lijun; Su, Peng; Duan, Pengbo; Lu, Daihui
2015-11-01
A critical challenge for molecular dynamics simulations of chemical or biological systems is to improve the calculation efficiency while retaining sufficient accuracy. The main bottleneck in improving the efficiency is the evaluation of nonbonded pairwise interactions. We propose a new piecewise lookup table method for rapid and accurate calculation of interatomic nonbonded pairwise interactions. The piecewise lookup table allows nonuniform assignment of table nodes according to the slope of the potential function and the pair interaction distribution. The proposed method assigns the nodes more reasonably than in general lookup tables, and thus improves the accuracy while requiring fewer nodes. To obtain the same level of accuracy, our piecewise lookup table accelerates the calculation via the efficient usage of cache memory. This new method is straightforward to implement and should be broadly applicable. Graphical Abstract Illustration of piecewise lookup table method.
Directory of Open Access Journals (Sweden)
Yingfeng Li
2013-05-01
Full Text Available The ways in which carbon atoms coalesce over the steps on copper (111 surface are ascertained by density functional theory (DFT calculations in the context of chemical vapor deposition (CVD growth of graphene. Two strategies, (1 by putting carbon atoms on and under the steps separately and (2 by importing additional carbon atoms between the ones separated by the steps, have been attempted to investigate if an over-step coalescence of carbon atoms could take place. Based on analyses about the optimized configurations and adsorption energies of carbon atoms nearby the steps, as well as the energy evolution curve of the system throughout the geometry optimizations process, we determined the main way in which graphene grows over the steps continuously: the carbon atoms, adsorbed additionally on the locations between the already existing ones which are separated by the steps, link them (these carbon atoms separated by the steps together. The direct over-step coalescence of the carbon atoms separated by the steps is very difficult, although the energy barrier preventing their coalescence can be weakened by importing carbon atoms on and under the steps gradually. Our results imply potential applications in directing the fabrication of graphene with particular structure by controlling the surface topography of copper substrate.
Precision of calculated static polarizabilities: Ga, In and Tl atoms
Energy Technology Data Exchange (ETDEWEB)
Borschevsky, Anastasia, E-mail: A.Borschevsky@massey.ac.nz [School of Chemistry, Tel Aviv University, 69978 Tel Aviv (Israel); Centre for Theoretical Chemistry and Physics, New Zealand Institute for Advanced Study, Massey University Auckland, Private Bag 102904, 0745 Auckland (New Zealand); Zelovich, Tamar, E-mail: tamizilo@gmail.com [School of Chemistry, Tel Aviv University, 69978 Tel Aviv (Israel); Eliav, Ephraim, E-mail: ephraim@tau.ac.il [School of Chemistry, Tel Aviv University, 69978 Tel Aviv (Israel); Kaldor, Uzi, E-mail: kaldor@tau.ac.il [School of Chemistry, Tel Aviv University, 69978 Tel Aviv (Israel)
2012-02-20
Graphical abstract: The polarizabilities of Ga, In and Tl are calculated with high precision. The In and Tl values fall within experimental error bars, with precision four times better than experiment. A value for Ga with error bars is obtained for the first time. Highlights: Black-Right-Pointing-Pointer Polarizabilities of Ga, In and Tl are calculated by relativistic coupled cluster methods. Black-Right-Pointing-Pointer Relativity and correlation are treated at high level. Black-Right-Pointing-Pointer Large, converged basis sets are used. Black-Right-Pointing-Pointer Results agree with available experimental values. Black-Right-Pointing-Pointer Calculated error bars are 4 times smaller than experimental. - Abstract: The static dipole polarizabilities of the group 13 elements Ga, In and Tl in the three {sup 2}P{sub JM{sub J}} substates are calculated by the Fock space coupled cluster method. The ground {sup 2}P{sub 1/2} states are also studied by the single reference coupled cluster approach, with triple excitations included perturbatively. Very large basis sets are employed and extended to convergence. The effects of different parameters in the calculation (2- vs. 4-component Hamiltonian, basis sets, coupled cluster expansion) are explored. The effect of the Gaunt interaction, which approximates the lowest order relativistic correction to the two-electron interaction, is also studied. Error bounds are estimated at 3% for the ground states and 5% for the J = 3/2 states. The final recommended values for the ground states are {alpha}(Ga) = 51.1(1.5) a.u., {alpha}(In) = 62.0(1.9) a.u., and {alpha}(Tl) = 52.1(1.6) a.u. The last two are in agreement with the experimental {alpha}(In) = 69(8) a.u. and {alpha}(Tl) = 51(7) a.u., and have error bars 4 times smaller. No experimental value is available for Ga, and the present calculations provide the first error bars for this element.
Implementation of highly parallel and large scale GW calculations within the OpenAtom software
Ismail-Beigi, Sohrab
The need to describe electronic excitations with better accuracy than provided by band structures produced by Density Functional Theory (DFT) has been a long-term enterprise for the computational condensed matter and materials theory communities. In some cases, appropriate theoretical frameworks have existed for some time but have been difficult to apply widely due to computational cost. For example, the GW approximation incorporates a great deal of important non-local and dynamical electronic interaction effects but has been too computationally expensive for routine use in large materials simulations. OpenAtom is an open source massively parallel ab initiodensity functional software package based on plane waves and pseudopotentials (http://charm.cs.uiuc.edu/OpenAtom/) that takes advantage of the Charm + + parallel framework. At present, it is developed via a three-way collaboration, funded by an NSF SI2-SSI grant (ACI-1339804), between Yale (Ismail-Beigi), IBM T. J. Watson (Glenn Martyna) and the University of Illinois at Urbana Champaign (Laxmikant Kale). We will describe the project and our current approach towards implementing large scale GW calculations with OpenAtom. Potential applications of large scale parallel GW software for problems involving electronic excitations in semiconductor and/or metal oxide systems will be also be pointed out.
Directory of Open Access Journals (Sweden)
Raiker Witter
2015-01-01
Full Text Available Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT. Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.
Perturbation calculations of the interaction energies between non-bonded hydrogen atoms - Part 2
Laidlaw, W.G.; Lekkerkerker, H.N.W.; Wieser, H.
1971-01-01
Calculations of the interaction energy between non-bonded hydrogen atoms in the fragments A—H---H'—A' for selected displacements of the hydrogen atoms enable one to evaluate corrections to the force field due to the non-bonded interactions and to discuss the changes in the stretching vibration
Seldam, C.A. ten; Groot, S.R. de
1952-01-01
From Jensen's and Gombás' modification of the statistical Thomas-Fermi atom model, a theory for compressed atoms is developed by changing the boundary conditions. Internal kinetic energy and polarizability of argon are calculated as functions of pressure. At 1000 atm. an internal kinetic energy of
Systematic reduction of sign errors in many-body calculations of atoms and molecules
Kent, P. R. C.; Bajdich, M.; Tiago, M. L.; Hood, R. Q.; Reboredo, F. A.
2010-03-01
We apply the self-healing diffusion Monte Carlo algorithm (SHDMC) [Phys. Rev. B 79 195117 (2009), ibid. 80 125110 (2009)] to the calculation of ground states of atoms and molecules. By comparing with configuration interaction results we show the method yields systematic convergence towards the exact ground state wave function and reduction of the fixed-node DMC sign error. We present results for atoms and light molecules, obtaining, e.g. the binding of N2 to chemical accuracy. Moreover, we demonstrate that the algorithm is robust enough to be used for the systems as large as the fullerene C20 starting from a set of random coefficients. SHDMC thus constitutes a practical method for systematically reducing the Fermion sign problem in electronic structure calculations. Research sponsored by the ORNL LDRD program (MB), U.S. DOE BES Divisions of Materials Sciences & Engineering (FAR, MLT) and Scientific User Facilities (PRCK). LLNL research was performed under U.S. DOE contract DE-AC52-07NA27344 (RQH).
All-atom calculation of protein free-energy profiles
Orioli, S.; Ianeselli, A.; Spagnolli, G.; Faccioli, P.
2017-10-01
The Bias Functional (BF) approach is a variational method which enables one to efficiently generate ensembles of reactive trajectories for complex biomolecular transitions, using ordinary computer clusters. For example, this scheme was applied to simulate in atomistic detail the folding of proteins consisting of several hundreds of amino acids and with experimental folding time of several minutes. A drawback of the BF approach is that it produces trajectories which do not satisfy microscopic reversibility. Consequently, this method cannot be used to directly compute equilibrium observables, such as free energy landscapes or equilibrium constants. In this work, we develop a statistical analysis which permits us to compute the potential of mean-force (PMF) along an arbitrary collective coordinate, by exploiting the information contained in the reactive trajectories calculated with the BF approach. We assess the accuracy and computational efficiency of this scheme by comparing its results with the PMF obtained for a small protein by means of plain molecular dynamics.
Energy Technology Data Exchange (ETDEWEB)
Kohn, S.; Weare, J.; Ong, E.; Baden, S.
1997-05-01
We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradient with FAC multigrid preconditioning. We have parallelized our solver using an object- oriented adaptive mesh refinement framework.
Aggarwal, Kanti M.
2015-11-01
Recently, Goyal et al. [1] reported energies and lifetimes (τ) for the lowest 113 levels of the 2s22p5, 2s2p6, 2s22p43ℓ, 2s2p53ℓ and 2p63ℓ configurations of F-like Sr XXX. For the calculations they adopted the multi-configuration Dirac-Fock (MCDF) and the flexible atomic code (FAC). Additionally, they also listed radiative rates (A- values), oscillator strengths (f- values) and line strengths (S- values) for four types of transitions, namely electric dipole (E1), electric quadrupole (E2), magnetic dipole (M1) and magnetic quadrupole (M2), but only from the ground to the higher excited levels. However, there are two clear anomalies in their reported data. Firstly, the f-values listed from FAC in their Tables 3-6 are larger than from MCDF by a factor of two, for all transitions. This is because they have blindly listed the output from FAC without realising that, unlike MCDF, FAC lists ωf where ω is the statistical weight, and happens to be exactly 2 in the present case. Secondly, their lifetime for level 2 (2s22p51/2 o 2P) is incorrect. This is because the dominant contributing transition for this level is 1-2 M1 for which A=3.25×106 s-1, listed (correctly) in their Table 5, and this leads to τ=3.08×10-7 s, and not 1.54×10-7 s, as listed in their Table 1.
The generalized sturmian method for calculating spectra of atoms and ions
DEFF Research Database (Denmark)
Avery, James Emil; Avery, John Scales
2003-01-01
The properties of generalized Sturmian basis sets are reviewed, and functions of this type are used to perform direct configuration interaction calculations on the spectra of atoms and ions. Singlet excited states calculated in this way show good agreement with experimentally measured spectra. When...... the generalized Sturmian method is applied to atoms, the configurations are constructed from hydrogenlike atomic orbitals with an effective charge which is characteristic of the configuration. Thus, orthonormality between the orbitals of different configurations cannot be assumed, and the generalized Slater...
DEFF Research Database (Denmark)
Ruud, Kenneth; Helgaker, Trygve; Kobayashi, Rika
1994-01-01
to corresponding individual gauges for localized orbitals (IGLO) results. The London results show better basis set convergence than IGLO, especially for heavier atoms. It is shown that the choice of active space is crucial for determination of accurate nuclear shielding constants.......Nuclear shielding calculations are presented for multiconfigurational self-consistent field wave functions using London atomic orbitals (gauge invariant atomic orbitals). Calculations of nuclear shieldings for eight molecules (H2O, H2S, CH4, N2, CO, HF, F2, and SO2) are presented and compared...
First-principles calculations of atomic and electronic properties of ZnO nanostructures
Energy Technology Data Exchange (ETDEWEB)
Xu, H.; Fan, W.; Fang, D. [Nano-organic Photoelectronic Laboratory, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing (China); Graduate University of Chinese Academy of Sciences, Beijing (China); Rosa, A.L.; Frauenheim, T. [BCCMS, University of Bremen (Germany); Zhang, R.Q. [Center of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR (China)
2010-10-15
We employ density-functional theory within the generalized-gradient approximation to investigate the formation energies and atomic and electronic structure of ZnO nanowires and nanotubes (NTs). We find that relaxations on the facets of the bare wires are very similar to those in nonpolar (10 anti 10) surfaces and play an important role in stabilizing the nanowires. All bare wires are found to be semiconducting, with band gaps larger than that in bulk ZnO. We further investigated hydrogen and water adsorption on ZnO nanowires. We find that the electronic structure of ZnO nanowires can be tuned by hydrogen adsorption and that adsorption of water leads to dissociation of a half-monolayer. Next, the stability of ZnO NTs has been investigated. We show that multiwall NTs are more stable than single-walled tubes. Finally, point defects in ZnO NTs have been investigated using spin-polarized calculations. All calculations were shown to introduce defect levels in the band gap, thus changing the electronic structure of the NTs drastically. (Abstract Copyright [2010], Wiley Periodicals, Inc.)
Abdullahi, Yusuf Zuntu; Leong, Yoon Tiem; Halim, Mohd Mahadi; Hashim, Md. Roslan; Leng, Lim Thong; Uebayashi, Kazuhiko
2017-11-01
The mechanical, structural, electronic and magnetic properties of s-triazine sheet (C6N6) with embedded Mn atom (Mn -C6N6) is investigated under the influence of external environment (symmetric deformation and perpendicular electric field) using density-functional theory (DFT) with the spin polarized generalized gradient approximation (GGA) and Hubbard U correction (GGA + U). Our results show that Mn -C6N6 system is structurally and mechanically stable. The binding energy of Mn embedded in C6N6 sheet can be modulated under the influence of external environment. Moreover, the semiconducting and magnetic properties of the Mn -C6N6 systems under external fields are preserved. We also explore the geometries, electronic and magnetic properties of Mn -C6N6 with adsorbed atoms and molecules. The Mn -C6N6 with adsorbed O atom and O2 molecule systems shows half-metallic character whereas the remaining systems preserve their semiconducting property. The total magnetic moment per unit cell in most of the systems is found to reduce as compared to that of the Mn -C6N6 sheet. The reduction in the magnetic moment can be related to the strong interactions among the Mn atom and the surrounding atoms which lead to the formation of low-spin configurations. Overall, our results indicate that the Mn -C6N6 systems with and without adsorbed atoms and molecules can serve as potential candidates for future spintronics and catalysis applications.
Block Tridiagonal Matrices in Electronic Structure Calculations
DEFF Research Database (Denmark)
Petersen, Dan Erik
This thesis focuses on some of the numerical aspects of the treatment of the electronic structure problem, in particular that of determining the ground state electronic density for the non–equilibrium Green’s function formulation of two–probe systems and the calculation of transmission...
Shevlin, S A
2001-01-01
transport properties of the line are also calculated. Finally we find which of the two models of the (4x1)-Si(111)-ln reconstruction is thermodynamically favoured in a supercell geometry. We use ab initio plane wave techniques in the Local-Density-Approximation, and calculate and compare the electronic structure of the two models with respect to the characteristic energies for electron dispersion along and across the chain structures. We also consider the effects of electronic structure on the in-plane transport properties of the indium lines. The structural and electronic properties of several candidate atomic scale wires are analysed. Three candidates are studied: the trans-polyacetylene molecule, the silicon line on the (001) face of cubic silicon carbide (the (nx2) series of reconstructions) and the indium chain on the (111) face of silicon carbide (the (4x1) reconstruction). We use the polyacetylene molecule as a test-bed for the techniques that we use to calculate transport properties in an empirically ...
Studying atomic structures by aberration-corrected transmission electron microscopy.
Urban, Knut W
2008-07-25
Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy-loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli-electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations.
Dimakis, Nicholas; Valdez, Danielle; Flor, Fernando Antonio; Salgado, Andres; Adjibi, Kolade; Vargas, Sarah; Saenz, Justin
2017-08-01
The adsorption of the alkali Li, K, and Na and the alkaline Ca on graphene is studied using periodic density functional theory (DFT) under various adatom coverages. The charge transfers between the adatom and the graphene sheet and the almost unchanged densities-of-states spectra in the energy region near and below the Fermi level support an ionic bond pattern between the adatom and the graphene atoms. However, the presence of small orbital overlap between the metal and the nearest graphene atom is indicative of small covalent bonding. Van der Waals interactions are examined through a semiempirical correction in the DFT functional and by comparing adatom-graphene calculations between 3% and 1.4% adatom coverages. Optimized adatom-graphene geometries identify the preferred adatom sites, whereas the adatom-graphene strength is correlated with the adsorption energy and the adatom distance from the graphene plane. Calculated electronic properties and structural parameters are obtained using hybrid functionals and a generalized gradient approximation functional paired with basis sets of various sizes. We found that due to long range electrostatic forces between the alkali/alkaline adatoms and the graphene monolayer, the adatom-graphene structural and electronic properties could be well-described by specific DFT functionals paired with high-quality adatom basis sets. For Li, K, and Na adsorbed on graphene, increased adatom surface coverage weakens the adatom-graphene interaction. However, this statement does not apply for Ca adsorbed on graphene. In this case, the Ca adsorption strength, which is stronger at higher coverages, is opposite to increases in the Ca-4s orbital population.
The electronic structure of small nickel atom clusters
Basch, Harold; Newton, M. D.; Moskowitz, J. W.
1980-11-01
The ground state electronic structure of small nickel atom clusters (Nin, n=1-6) has been calculated using the ab initio effective core potential self-consistent field (SCF) method in a Gaussian expansion basis. The electronic configuration of the nickel atoms in the clusters is found to be very close to 3d94s1. The ground state electronic configurations for Nin generally have n unpaired 3d electrons in molecular orbitals (MO's) spanning the same irreducible representations as the 4s atomic orbitals while the n 4s electrons fill their MO's in accord with a simple three-dimensional Hückel model with overlap. Exceptions to this description are found in the cases of linear systems where the 3d holes prefer δ over σ symmetry and in octahedral Ni6 where a different preferred set of 3d holes is obtained. The SCF ground state wave functions correspond roughly to a model in which the 3d electrons can be viewed as weakly interacting localized 3d9 units. The clusters are bound together primarily by the 4s electrons with the 4p orbital contribution increasing in importance with cluster size and dimensionality. The binding energy per nickel atom generally increases as the size of the cluster increases, although at six atoms this quantity has not yet converged with cluster size. The density of states diagram for the occupied one electron energy levels in Ni6 is found to be very different from the corresponding types of diagrams obtained in the muffin tin (MT)-Xα method for small nickel atom clusters. This difference is examined in detail, with consideration given to the effects of relaxation energy and to the different orbital level filling criteria used in the two methods.
Equilibrium structure and atomic vibrations of Nin clusters
Borisova, Svetlana D.; Rusina, Galina G.
2017-12-01
The equilibrium bond lengths and binding energy, second differences in energy and vibrational frequencies of free clusters Nin (2 ≤ n ≤ 20) were calculated with the use of the interaction potential obtained in the tight-binding approximation (TBA). The results show that the minimum vibration frequency plays a significant role in the evaluation of the dynamic stability of the clusters. A nonmonotonic dependence of the minimum vibration frequency of clusters on their size and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 are demonstrated. This result agrees with the theoretical and experimental data on stable structures of small metallic clusters.
Ab initio calculation of the real contact area on the atomic scale
Wolloch, M.; Feldbauer, G.; Mohn, P.; Redinger, J.; Vernes, A.
2015-05-01
We present an approach to determine the onset of contact between a tip and a surface. The real contact area depending on the distance is calculated using Bader's quantum theory of atoms in molecules. The jump to contact, which is often observed in atomic force microscopy experiments, is used as an indicator for the initial point of contact, which in turn is defined by atomic relaxations and thus without the need of external parameters. Within our approach the contact area is estimated by evaluating the zero flux surfaces between the touching Bader atoms, where the necessary electronic density cutoff for the Bader partitioning is calculated to depend on the initial point of contact. Our proposed approach is therefore completely ab initio and we are able to define and calculate the real area of contact without imposing restrictions or free parameters. As a prototype system we choose a tip made of a ten-atom tungsten pyramid above a moiré layer of graphene on an fcc iridium (111) substrate. We find that the contact area depends exponentially on the effective distance between the tip apex and the surface atom directly below within the atomically relaxed nanosystem.
Calculated Structural Phase-Transitions in the Alkaline-Earth Metals
DEFF Research Database (Denmark)
Skriver, Hans Lomholt
1982-01-01
The local-density approximation and the linear muffin-tin orbital method have been used within the atomic-sphere approximation to calculate structural energy differences for all the alkaline earth metals at zero temperature. At ordinary pressure the calculations predict the crystal structure...
Relativistic calculations of quasi-one-electron atoms and ions using Laguerre and Slater spinors
Jiang, Jun; Cheng, Yongjun; Bromley, Michael W J
2016-01-01
A relativistic description of the structure of heavy alkali atoms and alkali-like ions using S-spinors and L-spinors has been developed. The core wavefunction is defined by a Dirac-Fock calculation using an S-spinors basis. The S-spinor basis is then supplemented by a large set of L-spinors for the calculation of the valence wavefunction in a frozen-core model. The numerical stability of the L-spinor approach is demonstrated by computing the energies and decay rates of several low-lying hydrogen eigenstates, along with the polarizabilities of a $Z=60$ hydrogenic ion. The approach is then applied to calculate the dynamic polarizabilities of the $5s$, $4d$ and $5p$ states of Sr$^+$. The magic wavelengths at which the Stark shifts between different pairs of transitions are zero are computed. Determination of the magic wavelengths for the $5s \\to 4d_{\\frac32}$ and $5s \\to 4d_{\\frac52}$ transitions near $417$~nm (near the wavelength for the $5s \\to 5p_j$ transitions) would allow a determination of the oscillator s...
Directory of Open Access Journals (Sweden)
Isabella Natali Sora
2012-01-01
Full Text Available Quantum mechanics density functional calculations provided gas-phase electron distributions and proton affinities for several mono- and diaza[5]helicenes; computational results, together with experimental data concerning crystal structures and propensity to methylation of the nitrogen atom(s, provide a basis for designing azahelicene complexes with transition metal ions.
Inner Space: The Structure of the Atom
Energy Technology Data Exchange (ETDEWEB)
Glasstone, Samuel
1972-01-01
The atom is now regarded as the smallest possible particle of an element that retains the identity of that element. The atoms of an element determine the characteristics of that particular element. One of the purposes of this booklet is to explain how the atoms of various elements differ from one another.
Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J
2014-08-07
Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the
Structurally uniform and atomically precise carbon nanostructures
Segawa, Yasutomo; Ito, Hideto; Itami, Kenichiro
2016-01-01
Nanometre-sized carbon materials consisting of benzene units oriented in unique geometric patterns, hereafter named nanocarbons, conduct electricity, absorb and emit light, and exhibit interesting magnetic properties. Spherical fullerene C60, cylindrical carbon nanotubes and sheet-like graphene are representative forms of nanocarbons, and theoretical simulations have predicted several exotic 3D nanocarbon structures. At present, synthetic routes to nanocarbons mainly lead to mixtures of molecules with a range of different structures and properties, which cannot be easily separated or refined into pure forms. Some researchers believe that it is impossible to synthesize these materials in a precise manner. Obtaining ‘pure’ nanocarbons is a great challenge in the field of nanocarbon science, and the construction of structurally uniform nanocarbons, ideally as single molecules, is crucial for the development of functional materials in nanotechnology, electronics, optics and biomedical applications. This Review highlights the organic chemistry approach — more specifically, bottom-up construction with atomic precision — that is currently the most promising strategy towards this end.
Yu.S. Nagornov; I.V. Zhilyaev
2016-01-01
The present work is devoted to the analysis of three-dimensional data of atomic force microscopy for research of the morphology of red blood cells. In this paper we built a biomechanical model of the erythrocyte, which allowed calculating the intracellular pressure of erythrocyte based on data of atomic force microscopy. As a result, we obtained the dependence intracellular pressure on the morphology of red blood cell. We have proposed a method of estimating of intracellular pressure of eryth...
Effects of NMR spectral resolution on protein structure calculation.
Directory of Open Access Journals (Sweden)
Suhas Tikole
Full Text Available Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.
First principles calculations of interlayer exchange coupling in bcc Fe/Cu/Fe structures
Energy Technology Data Exchange (ETDEWEB)
Kowalewski, M.; Heninrich, B. [Simon Fraser Univ., Burnaby, British Columbia (Canada); Schulthess, T.C.; Butler, W.H. [Oak Ridge National Lab., TN (United States)
1998-01-01
The authors report on theoretical calculations of interlayer exchange coupling between two Fe layers separated by a modified Cu spacer. These calculations were motivated by experimental investigations of similar structures by the SFU group. The multilayer structures of interest have the general form: Fe/Cu(k)/Fe and Fe/Cu(m)/X(1)/Cu(n)/Fe where X indicates one AL (atomic layer) of foreign atoms X (Cr, Ag, or Fe) and k, m, n represent the number of atomic layers of Cu. The purpose of the experimental and theoretical work was to determine the effect of modifying the pure Cu spacer by replacing the central Cu atomic layer with the atomic layer of foreign atoms X. The first principles calculation were performed using the Layer Korringa-Kohn-Rostoker (LKKR) method. The theoretical thickness dependence of the exchange coupling between two semi-infinite Fe layers was calculated for pure Cu spacer thicknesses in the range of 0 < k < 16. The effect of the foreign atoms X on the exchange coupling was investigated using the structure with 9 AL Cu spacer as a reference sample. The calculated changes in the exchange coupling are in qualitative agreement with experiment.
MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES
Energy Technology Data Exchange (ETDEWEB)
D. M. PARKIN; L. CHEN; ET AL
2000-09-01
We explored both experimentally and theoretically the behavior of materials at stresses close to their theoretical strength. This involves the preparation of ultra fine scale structures by a variety of fabrication methods. In the past year work has concentrated on wire drawing of in situ composites such as Cu-Ag and Cu-Nb. Materials were also fabricated by melting alloys in glass and drawing them into filaments at high temperatures by a method known as Taylor wire technique. Cu-Ag microwires have been drawn by this technique to produce wires 10 {micro}m in diameter that consist of nanoscale grains of supersaturated solid solution. Organogels formed from novel organic gelators containing cholesterol tethered to squaraine dyes or trans-stilbene derivatives have been studied from several different perspectives. The two types of molecules are active toward several organic liquids, gelling in some cases at w/w percentages as low as 0.1. While relatively robust, acroscopically dry gels are formed in several cases, studies with a variety of probes indicate that much of the solvent may exist in domains that are essentially liquid-like in terms of their microenvironment. The gels have been imaged by atomic force microscopy and conventional and fluorescence microscopy, monitoring both the gelator fluorescence in the case of the stilbene-cholesterol gels and, the fluorescence of solutes dissolved in the solvent. Remarkably, our findings show that several of the gels are composed of similarly appearing fibrous structures visible at the nano-, micro-, and macroscale.
The atomic and electronic structure of amorphous silicon nitride
Alvarez, F
2002-01-01
Using a novel approach to the ab initio generation of random networks we constructed two nearly stoichiometric samples of amorphous silicon nitride with the same content x= 1.29. The two 64-atom periodically-continued cubic diamond-like cells contain 28 silicons and 36 nitrogens randomly substituted, and were amorphized with a 6 f s time step by heating them to just below their melting temperature with a Harris-functional based, molecular dynamics code in the LDA approximation. The averaged total radial distribution function (RDF) obtained is compared with some existing Tersoff-like potential simulations and with experiment; ours agree with experiment. All the partial radial features are calculated and the composition of the second peak also agrees with experiment. The electronic structure is calculated and the optical gaps obtained using both a HOMO-LUMO approach and the Tauc-like procedure developed recently that gives reasonable gaps. (Author)
Coupled-cluster calculations of properties of Boron atom as a monovalent system
Gharibnejad, H
2015-01-01
We present relativistic coupled-cluster (CC) calculations of energies, magnetic-dipole hyperfine constants, and electric-dipole transition amplitudes for low-lying states of atomic boron. The trivalent boron atom is computationally treated as a monovalent system. We explore performance of the CC method at various approximations. Our most complete treatment involves singles, doubles and the leading valence triples. The calculations are done using several approximations in the coupled-cluster (CC) method. The results are within 0.2-0.4% of the energy benchmarks. The hyperfine constants are reproduced with 1-2% accuracy.
Modulated structure calculated for superconducting hydrogen sulfide
Energy Technology Data Exchange (ETDEWEB)
Majumdar, Arnab; Tse, John S.; Yao, Yansun [Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, SK (Canada)
2017-09-11
Compression of hydrogen sulfide using first principles metadynamics and molecular dynamics calculations revealed a modulated structure with high proton mobility which exhibits a diffraction pattern matching well with experiment. The structure consists of a sublattice of rectangular meandering SH{sup -} chains and molecular-like H{sub 3}S{sup +} stacked alternately in tetragonal and cubic slabs forming a long-period modulation. The novel structure offers a new perspective on the possible origin of the superconductivity at very high temperatures in which the conducting electrons in the SH chains are perturbed by the fluxional motions of the H{sub 3}S resulting in strong electron-phonon coupling. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)
Cipolla, Laura; Ferrari, Lia A.
2016-01-01
A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).
Teo, Boon K.; Li, Wai-Kee
2011-01-01
This article is divided into two parts. In the first part, the atomic unit (au) system is introduced and the scales of time, space (length), and speed, as well as those of mass and energy, in the atomic world are discussed. In the second part, the utility of atomic units in quantum mechanical and spectroscopic calculations is illustrated with…
Magnetism, microstructure and First Principles calculations of atomized and annealed Ni{sub 3}Al
Energy Technology Data Exchange (ETDEWEB)
García-Escorial, A., E-mail: age@cenim.csic.es [CENIM-CSIC, Avda. Gregorio del Amo, 8, 28040 Madrid (Spain); Crespo, P.; Hernando, A. [Instituto de Magnetismo Aplicado, IMA-UCM, P.O. Box 155, 28230 Madrid (Spain); Lieblich, M. [CENIM-CSIC, Avda. Gregorio del Amo, 8, 28040 Madrid (Spain); Marín, P.; Velasco, V. [Instituto de Magnetismo Aplicado, IMA-UCM, P.O. Box 155, 28230 Madrid (Spain); Ynduráin, F. [Dpto. de Física de la Materia Condensada, UAM, Cantoblanco, 28049 Madrid (Spain)
2014-12-05
Highlights: • The microstructure and order of as-atomized Ni{sub 3}Al powder change with annealing. • The change of the magnetic properties shows the influence of the chemical order. • First Principles calculations show the effect of the density of states to the order. - Abstract: In this work Ni{sub 3}Al powder particles obtained by atomization were characterized magnetically and microstructurally in as-atomized state and after annealing. Upon annealing the X-ray diffraction patterns show a noticeable increase of the signal of the ordered phase γ′-Ni{sub 3}Al, L1{sub 2}, phase and the microstructure evolves from a lamellar and dendrite to a large grain microstructure. The Curie temperature of the as-atomized powder particles is 85 K and decreases after annealing down to 50 K. First Principles calculations were carried out to correlate the experimental observations with local order of Ni and Al atoms and illustrate the importance of the local order in the density of states at the Fermi level, showing how the magnetic moment depends on the Ni and Al atomic position.
Cobalamins uncovered by modern electronic structure calculations
DEFF Research Database (Denmark)
Kepp, Kasper Planeta; Ryde, Ulf
2009-01-01
This review describes how computational methods have contributed to the held of cobalamin chemistry since the start of the new millennium. Cobalamins are cobalt-dependent cofactors that are used for alkyl transfer and radical initiation by several classes of enzymes. Since the entry of modern...... electronic-structure calculations, in particular density functional methods, the understanding of the molecular mechanism of cobalamins has changed dramatically, going from a dominating view of trans-steric strain effects to a much more complex view involving an arsenal of catalytic strategies. Among...
Lattice QCD Calculation of Nucleon Structure
Energy Technology Data Exchange (ETDEWEB)
Liu, Keh-Fei [University of Kentucky, Lexington, KY (United States). Dept. of Physics and Astronomy; Draper, Terrence [University of Kentucky, Lexington, KY (United States). Dept. of Physics and Astronomy
2016-08-30
It is emphasized in the 2015 NSAC Long Range Plan that "understanding the structure of hadrons in terms of QCD's quarks and gluons is one of the central goals of modern nuclear physics." Over the last three decades, lattice QCD has developed into a powerful tool for ab initio calculations of strong-interaction physics. Up until now, it is the only theoretical approach to solving QCD with controlled statistical and systematic errors. Since 1985, we have proposed and carried out first-principles calculations of nucleon structure and hadron spectroscopy using lattice QCD which entails both algorithmic development and large-scale computer simulation. We started out by calculating the nucleon form factors -- electromagnetic, axial-vector, πNN, and scalar form factors, the quark spin contribution to the proton spin, the strangeness magnetic moment, the quark orbital angular momentum, the quark momentum fraction, and the quark and glue decomposition of the proton momentum and angular momentum. The first round of calculations were done with Wilson fermions in the `quenched' approximation where the dynamical effects of the quarks in the sea are not taken into account in the Monte Carlo simulation to generate the background gauge configurations. Beginning in 2000, we have started implementing the overlap fermion formulation into the spectroscopy and structure calculations. This is mainly because the overlap fermion honors chiral symmetry as in the continuum. It is going to be more and more important to take the symmetry into account as the simulations move closer to the physical point where the u and d quark masses are as light as a few MeV only. We began with lattices which have quark masses in the sea corresponding to a pion mass at ~ 300 MeV and obtained the strange form factors, charm and strange quark masses, the charmonium spectrum and the D_{s} meson decay constant f_{Ds}, the strangeness and charmness, the meson mass
Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality
Labushev, Mikhail M.
2012-01-01
The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.
Boll, Torben
2012-10-01
In this article the Cu-Au binding energy in Cu3Au is determined by comparing experimental atom probe tomography (APT) results to simulations. The resulting bonding energy is supported by density functional theory calculations. The APT simulations are based on the Müller-Schottky equation, which is modified to include different atomic neighborhoods and their characteristic bonds. The local environment is considered up to the fifth next nearest neighbors. To compare the experimental with simulated APT data, the AtomVicinity algorithm, which provides statistical information about the positions of the neighboring atoms, is applied. The quality of this information is influenced by the field evaporation behavior of the different species, which is connected to the bonding energies. © Microscopy Society of America 2012.
Post, D; Clark, R E H; Putvinskaya, N
1995-01-01
Reduction of the peak heat loads on the plasma facing components is essential for the success of the next generation of high fusion power tokamaks such as the International Thermonuclear Experimental Reactor (ITER) 1 . Many present concepts for accomplishing this involve the use of atomic processes to transfer the heat from the plasma to the main chamber and divertor chamber walls and much of the experimental and theoretical physics research in the fusion program is directed toward this issue. The results of these experiments and calculations are the result of a complex interplay of many processes. In order to identify the key features of these experiments and calculations and the relative role of the primary atomic processes, simple quasi-analytic models and the latest atomic physics rate coefficients and cross sections have been used to assess the relative roles of central radiation losses through bremsstrahlung, impurity radiation losses from the plasma edge, charge exchange and hydrogen radiation losses f...
Energy Technology Data Exchange (ETDEWEB)
Dimakis, Nicholas, E-mail: nicholas.dimakis@utrgv.edu [Department of Physics, University of Texas Rio Grande Valley, Edinburg, TX (United States); Valdez, Danielle; Flor, Fernando Antonio; Salgado, Andres; Adjibi, Kolade [Department of Physics, University of Texas Rio Grande Valley, Edinburg, TX (United States); Vargas, Sarah; Saenz, Justin [Robert Vela High School, Edinburg, TX (United States)
2017-08-15
Highlights: • Li, K, Na, and Ca graphene interaction is primarily ionic, whereas small covalent interactions also co-exist in these cases. • Van der Waals interactions are revealed by comparing adatom-graphene geometries between 1.4% and 3% adatom coverages and using Grimme corrections. • The Li, K, Na graphene interactions are accurately described by both PBE0 and PBE functionals. For Ca/graphene, the PBE0 functional should not be used. • For Li, K, and Na adsorbed on graphene, adatom-graphene interaction weakens as the adatom coverages increases. • The Ca-graphene interaction strength, which is stronger at high coverages, is opposite to increases in the Ca–4s orbital population. - Abstract: The adsorption of the alkali Li, K, and Na and the alkaline Ca on graphene is studied using periodic density functional theory (DFT) under various adatom coverages. The charge transfers between the adatom and the graphene sheet and the almost unchanged densities-of-states spectra in the energy region near and below the Fermi level support an ionic bond pattern between the adatom and the graphene atoms. However, the presence of small orbital overlap between the metal and the nearest graphene atom is indicative of small covalent bonding. Van der Waals interactions are examined through a semiempirical correction in the DFT functional and by comparing adatom-graphene calculations between 3% and 1.4% adatom coverages. Optimized adatom-graphene geometries identify the preferred adatom sites, whereas the adatom-graphene strength is correlated with the adsorption energy and the adatom distance from the graphene plane. Calculated electronic properties and structural parameters are obtained using hybrid functionals and a generalized gradient approximation functional paired with basis sets of various sizes. We found that due to long range electrostatic forces between the alkali/alkaline adatoms and the graphene monolayer, the adatom-graphene structural and electronic
Revealing and exploiting hierarchical material structure through complex atomic networks
Ahnert, Sebastian E.; Grant, William P.; Pickard, Chris J.
2017-08-01
One of the great challenges of modern science is to faithfully model, and understand, matter at a wide range of scales. Starting with atoms, the vastness of the space of possible configurations poses a formidable challenge to any simulation of complex atomic and molecular systems. We introduce a computational method to reduce the complexity of atomic configuration space by systematically recognising hierarchical levels of atomic structure, and identifying the individual components. Given a list of atomic coordinates, a network is generated based on the distances between the atoms. Using the technique of modularity optimisation, the network is decomposed into modules. This procedure can be performed at different resolution levels, leading to a decomposition of the system at different scales, from which hierarchical structure can be identified. By considering the amount of information required to represent a given modular decomposition we can furthermore find the most succinct descriptions of a given atomic ensemble. Our straightforward, automatic and general approach is applied to complex crystal structures. We show that modular decomposition of these structures considerably simplifies configuration space, which in turn can be used in discovery of novel crystal structures, and opens up a pathway towards accelerated molecular dynamics of complex atomic ensembles. The power of this approach is demonstrated by the identification of a possible allotrope of boron containing 56 atoms in the primitive unit cell, which we uncover using an accelerated structure search, based on a modular decomposition of a known dense phase of boron, γ-B28.
Atomic structure of self-organizing iridium induced nanowires on Ge(001)
Energy Technology Data Exchange (ETDEWEB)
Kabanov, N.S., E-mail: n.kabanov@utwente.nl [Faculty of Physics, Moscow State University, 119991 (Russian Federation); Physics of Interfaces and Nanomaterials, MESA+ Institute for Nanotechnology, University of Twente, P. O. Box 217, Enschede 7500 AE (Netherlands); Heimbuch, R.; Zandvliet, H.J.W. [Physics of Interfaces and Nanomaterials, MESA+ Institute for Nanotechnology, University of Twente, P. O. Box 217, Enschede 7500 AE (Netherlands); Saletsky, A.M.; Klavsyuk, A.L. [Faculty of Physics, Moscow State University, 119991 (Russian Federation)
2017-05-15
Highlights: • Ir/Ge(001) structure has been studied with DFT calculations and scanning tunneling microscopy. • Ir/Ge(001) nanowires are composed of Ge atoms and Ir atoms are located in subsurface positions. • The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. - Abstract: The atomic structure of self-organizing iridium (Ir) induced nanowires on Ge(001) is studied by density functional theory (DFT) calculations and variable-temperature scanning tunneling microscopy. The Ir induced nanowires are aligned in a direction perpendicular to the Ge(001) substrate dimer rows, have a width of two atoms and are completely kink-less. Density functional theory calculations show that the Ir atoms prefer to dive into the Ge(001) substrate and push up the neighboring Ge substrate atoms. The nanowires are composed of Ge atoms and not Ir atoms as previously assumed. The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. Time-resolved scanning tunneling microscopy measurements reveal that this dynamics is caused by buckled Ge substrate dimers that flip back and forth between their two buckled configurations.
Determination of atomic cluster structure with cluster fusion algorithm
DEFF Research Database (Denmark)
Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.
2005-01-01
We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....
Variational Monte Carlo calculations of lithium atom in strong magnetic field
Energy Technology Data Exchange (ETDEWEB)
Doma, S. B., E-mail: sbdoma@alexu.edu.eg [Alexandria University, Mathematics Department, Faculty of Science (Egypt); Shaker, M. O.; Farag, A. M. [Tanta University, Mathematics Department, Faculty of Science (Egypt); El-Gammal, F. N., E-mail: famta-elzahraa4@yahoo.com [Menofia University, Mathematics Department, Faculty of Science (Egypt)
2017-01-15
The variational Monte Carlo method is applied to investigate the ground state and some excited states of the lithium atom and its ions up to Z = 10 in the presence of an external magnetic field regime with γ = 0–100 arb. units. The effect of increasing field strength on the ground state energy is studied and precise values for the crossover field strengths were obtained. Our calculations are based on using accurate forms of trial wave functions, which were put forward in calculating energies in the absence of magnetic field. Furthermore, the value of Y at which ground-state energy of the lithium atom approaches to zero was calculated. The obtained results are in good agreement with the most recent values and also with the exact values.
Mapping energetics of atom probe evaporation events through first principles calculations
Energy Technology Data Exchange (ETDEWEB)
Peralta, Joaquín, E-mail: jperaltac@gmail.com [Department of Materials Science and Engineering and Institute for Combinatorial Discovery, Iowa State University, 2220 Hoover Hall, Iowa State University, Ames, IA 50011-2230 (United States); Broderick, Scott R., E-mail: sbroderick@iastate.edu [Department of Materials Science and Engineering and Institute for Combinatorial Discovery, Iowa State University, 2220 Hoover Hall, Iowa State University, Ames, IA 50011-2230 (United States); Rajan, Krishna, E-mail: krajan@iastate.edu [Department of Materials Science and Engineering and Institute for Combinatorial Discovery, Iowa State University, 2220 Hoover Hall, Iowa State University, Ames, IA 50011-2230 (United States)
2013-09-15
The purpose of this work is to use atomistic modeling to determine accurate inputs into the atom probe tomography (APT) reconstruction process. One of these inputs is evaporation field; however, a challenge occurs because single ions and dimers have different evaporation fields. We have calculated the evaporation field of Al and Sc ions and Al–Al and Al–Sc dimers from an L1{sub 2}-Al{sub 3}Sc surface using ab initio calculations and with a high electric field applied to the surface. The evaporation field is defined as the electric field at which the energy barrier size is calculated as zero, corresponding to the minimum field that atoms from the surface can break their bonds and evaporate from the surface. The evaporation field of the surface atoms are ranked from least to greatest as: Al–Al dimer, Al ion, Sc ion, and Al–Sc dimer. The first principles results were compared with experimental data in the form of an ion evaporation map, which maps multi-ion evaporations. From the ion evaporation map of L1{sub 2}-Al{sub 3}Sc, we extract relative evaporation fields and identify that an Al–Al dimer has a lower evaporation field than an Al–Sc dimer. Additionally, comparatively an Al–Al surface dimer is more likely to evaporate as a dimer, while an Al–Sc surface dimer is more likely to evaporate as single ions. These conclusions from the experiment agree with the ab initio calculations, validating the use of this approach for modeling APT energetics. - Highlights: ► Calculated evaporation field of monomer and dimer atom probe evaporations. ► Determined relative evaporation fields using ion evaporation maps. ► Compared the experimental and calculated results and found that they agreed.
Benchmark calculations of low-lying triplet states of Be atom
Bubin, Sergiy
Benchmark variational calculations of several lowest triplet states of the beryllium atom are reported. The wave functions of the states were expanded in terms of highly optimized explicitly correlated Gaussian basis sets and accurate energies are deterimed assuming finite nuclear mass of the atom. These wave functions were used to compute various expectation values, including those that appear in the leading relativistic and QED corrections. Density distributions and pair correlation functions are analyzed for both electrons an nucleus. This work has been supported by the Ministry of Education and Science of Kazakhstan.
The calculation of satellite line structures in highly stripped plasmas
Energy Technology Data Exchange (ETDEWEB)
Abdallah, J. Jr.; Kilcrease, D.P. [Los Alamos National Lab., NM (United States); Faenov, A.Ya.; Pikuz, T.A. [Multicharged Ion Spectra Data Center, Moscow (Russian Federation)
1998-11-01
This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Recently developed high-resolution x-ray spectrographs have made it possible to measure satellite structures from various plasma sources with great detail. These lines are weak optically thin lines caused by the decay of dielectronic states and generally accompany the resonance lines of H-like and He-like ions. The Los Alamos atomic physics and kinetics codes provide a unique capability for calculating the position and intensities of such lines. These programs have been used to interpret such highly resolved spectral measurements from pulsed power devices and laser produced plasmas. Some of these experiments were performed at the LANL Bright Source and Trident laser facilities. The satellite structures are compared with calculations to diagnose temperatures and densities. The effect of non-thermal electron distributions of electrons on calculated spectra was also considered. Collaborations with Russian scientists have added tremendous value to this research die to their vast experience in x-ray spectroscopy.
ARC: An open-source library for calculating properties of alkali Rydberg atoms
Šibalić, N.; Pritchard, J. D.; Adams, C. S.; Weatherill, K. J.
2017-11-01
We present an object-oriented Python library for the computation of properties of highly-excited Rydberg states of alkali atoms. These include single-body effects such as dipole matrix elements, excited-state lifetimes (radiative and black-body limited) and Stark maps of atoms in external electric fields, as well as two-atom interaction potentials accounting for dipole and quadrupole coupling effects valid at both long and short range for arbitrary placement of the atomic dipoles. The package is cross-referenced to precise measurements of atomic energy levels and features extensive documentation to facilitate rapid upgrade or expansion by users. This library has direct application in the field of quantum information and quantum optics which exploit the strong Rydberg dipolar interactions for two-qubit gates, robust atom-light interfaces and simulating quantum many-body physics, as well as the field of metrology using Rydberg atoms as precise microwave electrometers. Program Files doi:http://dx.doi.org/10.17632/hm5n8w628c.1 Licensing provisions: BSD-3-Clause Programming language: Python 2.7 or 3.5, with C extension External Routines: NumPy [1], SciPy [1], Matplotlib [2] Nature of problem: Calculating atomic properties of alkali atoms including lifetimes, energies, Stark shifts and dipole-dipole interaction strengths using matrix elements evaluated from radial wavefunctions. Solution method: Numerical integration of radial Schrödinger equation to obtain atomic wavefunctions, which are then used to evaluate dipole matrix elements. Properties are calculated using second order perturbation theory or exact diagonalisation of the interaction Hamiltonian, yielding results valid even at large external fields or small interatomic separation. Restrictions: External electric field fixed to be parallel to quantisation axis. Supplementary material: Detailed documentation (.html), and Jupyter notebook with examples and benchmarking runs (.html and .ipynb). [1] T.E. Oliphant
Chain-Branching Control of the Atomic Structure of Alkanethiol-Based Gold–Sulfur Interfaces
DEFF Research Database (Denmark)
Wang, Yun; Chi, Qijin; Zhang, Jingdong
2011-01-01
Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111...
Atomic and electronic structure of surfaces theoretical foundations
Lannoo, Michel
1991-01-01
Surfaces and interfaces play an increasingly important role in today's solid state devices. In this book the reader is introduced, in a didactic manner, to the essential theoretical aspects of the atomic and electronic structure of surfaces and interfaces. The book does not pretend to give a complete overview of contemporary problems and methods. Instead, the authors strive to provide simple but qualitatively useful arguments that apply to a wide variety of cases. The emphasis of the book is on semiconductor surfaces and interfaces but it also includes a thorough treatment of transition metals, a general discussion of phonon dispersion curves, and examples of large computational calculations. The exercises accompanying every chapter will be of great benefit to the student.
Energy Technology Data Exchange (ETDEWEB)
Piñera, Ibrahin, E-mail: ipinera@ceaden.edu.cu [Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, CEADEN, 30 St. 502, Playa 11300, Havana (Cuba); Cruz, Carlos M.; Leyva, Antonio; Abreu, Yamiel; Cabal, Ana E. [Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, CEADEN, 30 St. 502, Playa 11300, Havana (Cuba); Espen, Piet Van; Remortel, Nick Van [University of Antwerp, CGB, Groenenborgerlaan 171, 2020 Antwerpen (Belgium)
2014-11-15
Highlights: • We present a calculation procedure for dpa cross section in solids under irradiation. • Improvement about 10–90% for the gamma irradiation induced dpa cross section. • Improvement about 5–50% for the electron irradiation induced dpa cross section. • More precise results (20–70%) for thin samples irradiated with electrons. - Abstract: Several authors had estimated the displacements per atom cross sections under different approximations and models, including most of the main gamma- and electron-material interaction processes. These previous works used numerical approximation formulas which are applicable for limited energy ranges. We proposed the Monte Carlo assisted Classical Method (MCCM), which relates the established theories about atom displacements to the electron and positron secondary fluence distributions calculated from the Monte Carlo simulation. In this study the MCCM procedure is adapted in order to estimate the displacements per atom cross sections for gamma and electron irradiation. The results obtained through this procedure are compared with previous theoretical calculations. An improvement in about 10–90% for the gamma irradiation induced dpa cross section is observed in our results on regard to the previous evaluations for the studied incident energies. On the other hand, the dpa cross section values produced by irradiation with electrons are improved by our calculations in about 5–50% when compared with the theoretical approximations. When thin samples are irradiated with electrons, more precise results are obtained through the MCCM (in about 20–70%) with respect to the previous studies.
Efficient calculation of degenerate atomic rates by numerical quadrature on GPUs
Aslanyan, V.; Aslanyan, A. G.; Tallents, G. J.
2017-10-01
The rates of atomic processes in cold, dense plasma are governed strongly by effects of quantum degeneracy. The electrons follow Fermi-Dirac statistics and their high density limits the number of quantum states available for occupation after a collision. These factors preclude a direct solution to the usual rate coefficient integrals. We summarize the formulation of this problem and present a simple, but efficient method of evaluating collisional rate coefficients via direct numerical integration. Numerical quadrature has an intrinsically high level of parallelism, ideally suited for graphics processor units. GPUs are particularly suited to this problem because of the large number of integrals which must be carried out simultaneously for a given atomic model. A CUDA code to calculate the rates of significant atomic processes as part of a collisional-radiative model is presented and discussed. This approach may be readily extended to other applications where rapid and repeated evaluation of many integrals is required.
Quantum-mechanical calculations of cross sections for electron collisions with atoms and molecules
Bartschat, Klaus; Zatsarinny, Oleg
2016-01-01
An overview of quantum-mechanical methods to generate cross-section data for electron collisions with atoms and molecules is presented. Particular emphasis is placed on the time-independent close-coupling approach, since it is particularly suitable for low-energy collisions and also allows for systematic improvements as well as uncertainty estimates. The basic ideas are illustrated with examples for electron collisions with argon atoms and methane. For many atomic systems, such as e-Ar collisions, highly reliable cross sections can now be computed with quantified uncertainties. On the other hand, while electron collision calculations with molecules do provide key input data for plasma models, the methods and computer codes presently used require further development to make these inputs robust.
Dance, Ian
2011-06-28
The intramolecular hydrogenation paradigm for the reducing actions of the enzyme nitrogenase postulates that the iron-molybdenum cofactor (FeMo-co, Fe(7)MoS(9)N(homocitrate)) as active site contains H atoms bound to Fe and S during the catalytic cycle, and that these H atoms are the reducing agents. The reduction of N(2) and of all other non-physiological substrates is strongly inhibited by carbon monoxide, except for the formation of H(2) from protons. It has been recently reported that vanadium nitrogenase and modified molybdenum nitrogenase reduce CO to hydrocarbons. Therefore many questions now arise about relationships between CO and H on the nitrogenase cofactors. In order to assist the interpretation of kinetic infrared spectral data, vibrational frequencies and modes have been calculated for a variety of possible structures in which FeMo-co bears H atoms, or CO ligands, or both. Fe-H stretching frequencies occur in the same spectral window as the C-O stretching frequencies, with lesser intensity, and both stretches are strongly coupled in some structures. Symmetrical bridging of CO between two Fe atoms of FeMo-co is destabilised by the presence of other ligands on Fe, and the reason for this is evident. Two results for bound formyl, HCO, are reported. These calculations of reference structures allow some interpretation of existing experimental spectra, but, more significantly, they suggest further kinetic infrared experiments to elucidate the chemical mechanism of catalysis by nitrogenase under normal turnover conditions. This journal is © The Royal Society of Chemistry 2011
Density functional theory calculations on transition metal atoms adsorbed on graphene monolayers
Dimakis, Nicholas; Flor, Fernando Antonio; Salgado, Andres; Adjibi, Kolade; Vargas, Sarah; Saenz, Justin
2017-11-01
Transition metal atom adsorption on graphene monolayers has been elucidated using periodic density functional theory under hybrid and generalized gradient approximation functionals. More specifically, we examined the adsorption of Cu, Fe, Zn, Ru, and Os on graphene monolayers by calculating, among others, the electronic density-of-states spectra of the adatom-graphene system and the overlap populations of the adatom with the nearest adsorbing graphene carbon atoms. These calculations reveal that Cu form primarily covalent bonds with graphene atoms via strong hybridization between the adatom orbitals and the sp band of the graphene substrate, whereas the interaction of the Ru and Os with graphene also contain ionic parts. Although the interaction of Fe with graphene atoms is mostly covalent, some charge transfer to graphene is also observed. The interaction of Zn with graphene is weak. Mulliken population analysis and charge contour maps are used to elucidate charge transfers between the adatom and the substrate. The adsorption strength is correlated with the metal adsorption energy and the height of the metal adatom from the graphene plane for the geometrically optimized adatom-graphene system. Our analysis shows that show that metal adsorption strength follows the adatom trend Ru ≈ Os > Fe > Cu > Zn, as verified by corresponding changes in the adsorption energies. The increased metal-carbon orbital overlap for the Ru relative to Os adatom is attributed to hybridization defects.
Pereyaslavets, Leonid B; Finkelstein, Alexey V
2012-04-19
A detailed calculation of protein interactions with explicitly considered water molecules takes enormous time. If water is considered implicitly (as media rather than as molecules), calculations become faster. These calculations are less precise, unless one uses voluminous computations of solvent-accessible areas. Our goal is to obtain parameters for nonbonded atom-atom interactions in implicitly considered water without computation of solvent-accessible areas. Because the "in-vacuum" interactions of atoms are obtained from experimental structures of crystals and enthalpies of their sublimation, the "in-water" interactions must be corrected using solvation free energies obtained from Henry's constants. Thus, we obtained parameters for the in-water van der Waals, electrostatic, and polarized interactions for atoms typical of protein structures. Parameters of covalent interactions were taken from the ENCAD force field and partial charges of atoms from quantum-mechanical calculations. The sought parameters of the in-water nonbonded interactions were optimized to achieve the best description of crystal structures and their sublimation and solvation at the room temperature. With the optimized parameters, the correlation between the calculated and experimental cohesion of molecules in crystals is 98.3% in the in-vacuum case (the supplementary force field PFFSubl1.1) and 95.4% the in-water case (the sought force field PFFSol1.1).
Neutron and gamma ray calculation for Hiroshima-type atomic bomb
Energy Technology Data Exchange (ETDEWEB)
Hoshi, Masaharu; Endo, Satoru; Takada, Jun [Hiroshima Univ. (Japan). Research Inst. for Radiation Biology and Medicine; Iwatani, Kazuo; Oka, Takamitsu; Shizuma, Kiyoshi; Fujita, Shoichiro; Hasai, Hiromi
1998-03-01
We looked at the radiation dose of Hiroshima and Nagasaki atomic bomb again in 1986. We gave it the name of ``Dosimetry System 1986`` (DS86). We and other groups have measured the expose dose since 1986. Now, the difference between data of {sup 152}Eu and the calculation result on the basis of DS86 was found. To investigate the reason, we carried out the calculations of neutron transport and neutron absorption gamma ray for Hiroshima atomic bomb by MCNP3A and MCNP4A code. The problems caused by fast neutron {sup 32}P from sulfur in insulator of pole. To correct the difference, we investigated many models and found agreement of all data within 1 km. (S.Y.)
Energy Technology Data Exchange (ETDEWEB)
Maeta, Takahiro [Graduate School of System Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan); GlobalWafers Japan Co., Ltd., Higashikou, Seirou-machi, Kitakanbara-gun, Niigata 957-0197 (Japan); Sueoka, Koji [Department of Communication Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan)
2014-08-21
Ge-based substrates are being developed for applications in advanced nano-electronic devices because of their higher intrinsic carrier mobility than Si. The stability and diffusion mechanism of impurity atoms in Ge are not well known in contrast to those of Si. Systematic studies of the stable sites of 2nd to 6th row element impurity atoms in Ge crystal were undertaken with density functional theory (DFT) and compared with those in Si crystal. It was found that most of the impurity atoms in Ge were stable at substitutional sites, while transition metals in Si were stable at interstitial sites and the other impurity atoms in Si were stable at substitutional sites. Furthermore, DFT calculations were carried out to clarify the mechanism responsible for the diffusion of impurity atoms in Ge crystals. The diffusion mechanism for 3d transition metals in Ge was found to be an interstitial-substitutional diffusion mechanism, while in Si this was an interstitial diffusion mechanism. The diffusion barriers in the proposed diffusion mechanisms in Ge and Si were quantitatively verified by comparing them to the experimental values in the literature.
The 2003 update of antiproton mass by precision three-body calculation of antiprotonic helium atom
Kino, Y; Kudo, H
2004-01-01
The Particle Listings 2000 edition gave the recommended value of antiproton mass, for the first time, to be within 5 * 10/sup -7/ in the relative deviation from the proton mass; this can be a test of the CPT invariance. The value was derived by our precision 3-body calculation, using the Gaussian expansion method, to analyze the laser spectroscopy data of metastable states in antiprotonic helium atoms taken at CERN. The 2002 edition and the 2003 updated version reported an one-order smaller value, 6 * 10/sup -8/, based on further development of both the experiment and our calculation.
Controlling atomic structures and photoabsorption processes by an infrared laser
Tong, X. M.; Toshima, N.
2010-01-01
We propose a theoretical method to calculate the infrared (IR) laser-assisted photoabsorption cross sections over a broad energy range by a single calculation. In this method we define an initial wave function as the product of the dipole operator and the atomic ground state, propagate the initial wave function in the IR laser field with different initial phases, then calculate the generalized autocorrelation function, which is defined as the averaged value of the autocorrelation function ove...
The grasp2K relativistic atomic structure package
Jönsson, P.; He, X.; Froese Fischer, C.; Grant, I. P.
2007-10-01
This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a "make" facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report. Program summaryProgram title: grasp2K Catalogue identifier: ADZL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 213 524 No. of bytes in distributed program, including test data, etc.: 1 328 588 Distribution format: tar.gz Programming language: Fortran and C Computer: Intel
Build-up algorithm for atomic correspondence between chemical structures.
Kawabata, Takeshi
2011-08-22
Determining a one-to-one atom correspondence between two chemical compounds is important to measure molecular similarities and to find compounds with similar biological activities. This calculation can be formalized as the maximum common substructure (MCS) problem, which is well-studied and has been shown to be NP-complete. Although many rigorous and heuristic algorithms have been developed, none of these algorithms is sufficiently fast and accurate. We developed a new program, called "kcombu" using a build-up algorithm, which is a type of the greedy heuristic algorithms. The program can search connected and disconnected MCSs as well as topologically constrained disconnected MCS (TD-MCS), which is introduced in this study. To evaluate the performance of our program, we prepared two correct standards: the exact correspondences generated by the maximum clique algorithms and the 3D correspondences obtained from superimposed 3D structure of the molecules in a complex 3D structure with the same protein. For the five sets of molecules taken from the protein structure database, the agreement value between the build-up and the exact correspondences for the connected MCS is sufficiently high, but the computation time of the build-up algorithm is much smaller than that of the exact algorithm. The comparison between the build-up and the 3D correspondences shows that the TD-MCS has the best agreement value among the other types of MCS. Additionally, we observed a strong correlation between the molecular similarity and the agreement with the correct and 3D correspondences; more similar molecule pairs are more correctly matched. Molecular pairs with more than 40% Tanimoto similarities can be correctly matched for more than half of the atoms with the 3D correspondences.
Shu, Haibo; Li, Feng; Liang, Pei; Chen, Xiaoshuang
2016-09-15
Two-dimensional (2D) boron sheets (i.e., borophene) have a huge potential as a basic building block in nanoelectronics and optoelectronics; such a situation is greatly promoted by recent experiments on fabrication of borophene on silver substrates. However, the fundamental atomic structure of borophene on the Ag substrate is still under debate, which greatly impedes further exploration of its properties. Herein, the atomic structure and electronic properties of borophene on an Ag(111) surface have been studied using first-principles calculations and ab initio molecular dynamics simulations. Our results reveal that there exist three energetically favorable borophene structures (β5, χ1, and χ2) on the Ag(111) surface and their simulated STM images are in good agreement with experimental results, suggesting the coexistence of boron phases during the growth. All these stable borophene structures have a planar structure with slight surface buckling (∼0.15 Å) and relatively high hexagonal vacancy density (1/6 and 1/5) and exhibit typical metallic conductivity. These findings not only can be applied to solve the experimental controversies about the atomic structure of borophene on the Ag substrate but also provide a theoretical basis for exploring the fundamental properties and applications of 2D boron sheets.
DEFF Research Database (Denmark)
Johnsen, Kristinn; Yngvason, Jakob
1996-01-01
We report on a numerical study of the density matrix functional introduced by Lieb, Solovej, and Yngvason for the investigation of heavy atoms in high magnetic fields. This functional describes exactly the quantum mechanical ground state of atoms and ions in the limit when the nuclear charge Z...... and the electron number N tend to infinity with N/Z fixed, and the magnetic field B tends to infinity in such a way that B/Z4/3→∞. We have calculated electronic density profiles and ground-state energies for values of the parameters that prevail on neutron star surfaces and compared them with results obtained...... by other methods. For iron at B=1012 G the ground-state energy differs by less than 2% from the Hartree-Fock value. We have also studied the maximal negative ionization of heavy atoms in this model at various field strengths. In contrast to Thomas-Fermi type theories atoms can bind excess negative charge...
Relativistic calculations of double $K$-shell photoionization for neutral medium-$Z$ atoms
Yerokhin, V A; Fritzsche, S
2014-01-01
Fully relativistic calculations are presented for the double $K$-shell photoionization cross section for several neutral medium-$Z$ atoms, from magnesium ($Z = 10$) up to silver ($Z = 47$). The calculations take into account all multipoles of the absorbed photon as well as the retardation of the electron-electron interaction. The approach is based on the partial-wave representation of the Dirac continuum states and uses the Green-function technique to represent the full Dirac spectrum of intermediate states. The method is strictly gauge invariant, which is used as an independent cross check of the computational procedure. The calculated ratios of the double-to-single $K$-shell ionization cross sections are compared with the experimental data and with previous computations.
Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E
2017-04-07
The inclusion of atomic polarizations for describing molecular electronic structure changes on vibration is shown to be necessary for coherent infrared intensity modeling. Atomic charges from the ChelpG partition scheme and atomic charges and dipoles from Quantum Theory of Atoms in Molecules (QTAIM) were employed within two different models to describe the stretching and bending vibrational intensities of the C-H, C-F, and C=O groups. The model employing the QTAIM parameters was the Charge-Charge Transfer and Dipolar Polarization model (QTAIM/CCTDP), and the model employing the ChelpG charges was the Equilibrium Charge-Charge Flux (ChelpG/ECCF). The QTAIM/CCTDP models result in characteristic proportions of the charge-charge transfer-dipolar polarization contributions even though their sums giving the total intensities do not discriminate between these vibrations. According to the QTAIM/CCTDP model, the carbon monoxide intensity has electronic structure changes similar to those of the carbonyl stretches whereas they resemble those of the CH stretches for the ChelpG/ECCF model.
Brouwer, Darren H; Moudrakovski, Igor L; Darton, Richard J; Morris, Russell E
2010-12-01
Combining quantum-chemical calculations and ultrahigh-field NMR measurements of (29)Si chemical shielding (CS) tensors has provided a powerful approach for probing the fine details of zeolite crystal structures. In previous work, the quantum-chemical calculations have been performed on 'molecular fragments' extracted from the zeolite crystal structure using Hartree-Fock methods (as implemented in Gaussian). Using recently acquired ultrahigh-field (29) Si NMR data for the pure silica zeolite ITQ-4, we report the results of calculations using recently developed quantum-chemical calculation methods for periodic crystalline solids (as implemented in CAmbridge Serial Total Energy Package (CASTEP) and compare these calculations to those calculated with Gaussian. Furthermore, in the context of NMR crystallography of zeolites, we report the completion of the NMR crystallography of the zeolite ITQ-4, which was previously solved from NMR data. We compare three options for the 'refinement' of zeolite crystal structures from 'NMR-solved' structures: (i) a simple target-distance based geometry optimization, (ii) refinement of atomic coordinates in which the differences between experimental and calculated (29)Si CS tensors are minimized, and (iii) refinement of atomic coordinates to minimize the total energy of the lattice using CASTEP quantum-chemical calculations. All three refinement approaches give structures that are in remarkably good agreement with the single-crystal X-ray diffraction structure of ITQ-4. Copyright © 2010 John Wiley & Sons, Ltd.
Atomic Structure and Dynamics of Single Platinum Atom Interactions with Monolayer MoS2.
Li, Huashan; Wang, Shanshan; Sawada, Hidetake; Han, Grace G D; Samuels, Thomas; Allen, Christopher S; Kirkland, Angus I; Grossman, Jeffrey C; Warner, Jamie H
2017-03-28
We have studied atomic level interactions between single Pt atoms and the surface of monolayer MoS2 using aberration-corrected annular dark field scanning transmission electron microscopy at an accelerating voltage of 60 kV. Strong contrast from single Pt atoms on the atomically resolved monolayer MoS2 lattice enables their exact position to be determined with respect to the MoS2 lattice, revealing stable binding sites. In regions of MoS2 free from surface contamination, the Pt atoms are localized in S vacancy sites and exhibit dynamic hopping to nearby vacancy sites driven by the energy supplied by the electron beam. However, in areas of MoS2 contaminated with carbon surface layers, the Pt atoms appear at various positions with respect to the underlying MoS2 lattice, including on top of Mo and in off-axis positions. These variations are due to the Pt bonding with the surrounding amorphous carbon layer, which disrupts the intrinsic Pt-MoS2 interactions, leading to more varied positions. Density functional theory (DFT) calculations reveal that Pt atoms on the surface of MoS2 have a small barrier for migration and are stabilized when bound to either a single or double sulfur vacancies. DFT calculations have been used to understand how the catalytic activity of the MoS2 basal plane for hydrogen evolution reaction is influenced by Pt dopants by variation of the hydrogen adsorption free energy. This strong dependence of catalytic effect on interfacial configurations is shown to be common for a series of dopants, which may provide a means to create and optimize reaction centers.
Rittenhouse, Robert C.
2015-01-01
The "atoms first" philosophy, adopted by a growing number of General Chemistry textbook authors, places greater emphasis on atomic structure as a key to a deeper understanding of the field of chemistry. A pivotal concept needed to understand the behavior of atoms is the restriction of an atom's energy to specific allowed values. However,…
DWBA-G calculations of electron impact ionization of noble gas atoms
Energy Technology Data Exchange (ETDEWEB)
Kheifets, A S [Research School of Physical Sciences and Engineering, The Australian National University, Canberra ACT 0200 (Australia); Naja, A; Casagrande, E M Staicu; Lahmam-Bennani, A [Universite Paris-Sud 11, Laboratoire des Collisions Atomiques et Moleculaires (LCAM), Bat. 351, 91405 Orsay Cedex (France)], E-mail: A.Kheifets@anu.edu.au
2008-07-28
We perform calculations of electron impact ionization of noble gas atoms within the distorted wave Born approximation (DWBA) corrected by the Gamow factor (G) to account for the post-collision interaction. We make an extensive comparison with experimental data on He 1s{sup 2}, Ne 2s{sup 2}, 2p{sup 6} and Ar 3p{sup 6} under kinematics characterized by large energy transfer and close to minimum momentum transfer from the projectile to the target. For all atoms, good agreement between theory and experiment is achieved. In the case of Ar, the disagreement of experimental data with theory reported earlier by Catoire et al (2006 J. Phys. B: At. Mol. Opt. Phys. 39 2827) is reconciled.
Atomic structure of self-organizing iridium induced nanowires on Ge(001)
Kabanov, Nikolai; Heimbuch, Rene; Zandvliet, Henricus J.W.; Saletsky, A.M.; Klavsyuk, A.L.
2017-01-01
The atomic structure of self-organizing iridium (Ir) induced nanowires on Ge(001) is studied by density functional theory (DFT) calculations and variable-temperature scanning tunneling microscopy. The Ir induced nanowires are aligned in a direction perpendicular to the Ge(001) substrate dimer rows,
Pawlak, Rémy; Kisiel, Marcin; Klinovaja, Jelena; Meier, Tobias; Kawai, Shigeki; Glatzel, Thilo; Loss, Daniel; Meyer, Ernst
2016-11-01
Motivated by the striking promise of quantum computation, Majorana bound states (MBSs) in solid-state systems have attracted wide attention in recent years. In particular, the wavefunction localisation of MBSs is a key feature and is crucial for their future implementation as qubits. Here we investigate the spatial and electronic characteristics of topological superconducting chains of iron atoms on the surface of Pb(110) by combining scanning tunnelling microscopy and atomic force microscopy. We demonstrate that the Fe chains are mono-atomic, structured in a linear manner and exhibit zero-bias conductance peaks at their ends, which we interpret as signature for a MBS. Spatially resolved conductance maps of the atomic chains reveal that the MBSs are well localised at the chain ends (≲25 nm), with two localisation lengths as predicted by theory. Our observation lends strong support to use MBSs in Fe chains as qubits for quantum-computing devices.
Niels Bohr and the quantum atom the Bohr model of atomic structure 1913-1925
Kragh, Helge
2012-01-01
Niels Bohr and the Quantum Atom is the first book that focuses in detail on the birth and development of Bohr's atomic theory and gives a comprehensive picture of it. At the same time it offers new insight into Bohr's peculiar way of thinking, what Einstein once called his 'unique instinct and tact'. Contrary to most other accounts of the Bohr atom, the book presents it in a broader perspective which includes the reception among other scientists and the criticism launched against it by scientists of a more conservative inclination. Moreover, it discusses the theory as Bohr originally conceived it, namely, as an ambitious theory covering the structure of atoms as well as molecules. By discussing the theory in its entirety it becomes possible to understand why it developed as it did and thereby to use it as an example of the dynamics of scientific theories.
Understanding the proton radius puzzle: Nuclear structure effects in light muonic atoms
Directory of Open Access Journals (Sweden)
Ji Chen
2016-01-01
Full Text Available We present calculations of nuclear structure effects to the Lamb shift in light muonic atoms. We adopt a modern ab-initio approach by combining state-of-the-art nuclear potentials with the hyperspherical harmonics method. Our calculations are instrumental to the determination of nuclear charge radii in the Lamb shift measurements, which will shed light on the proton radius puzzle.
Unraveling the atomic structure of ultrafine iron clusters
Wang, Hongtao
2012-12-18
Unraveling the atomic structures of ultrafine iron clusters is critical to understanding their size-dependent catalytic effects and electronic properties. Here, we describe the stable close-packed structure of ultrafine Fe clusters for the first time, thanks to the superior properties of graphene, including the monolayer thickness, chemical inertness, mechanical strength, electrical and thermal conductivity. These clusters prefer to take regular planar shapes with morphology changes by local atomic shuffling, as suggested by the early hypothesis of solid-solid transformation. Our observations differ from observations from earlier experimental study and theoretical model, such as icosahedron, decahedron or cuboctahedron. No interaction was observed between Fe atoms or clusters and pristine graphene. However, preferential carving, as observed by other research groups, can be realized only when Fe clusters are embedded in graphene. The techniques introduced here will be of use in investigations of other clusters or even single atoms or molecules.
Atomic structure of clusters through chemical reactions
Energy Technology Data Exchange (ETDEWEB)
Riley, S.J.
1991-01-01
Techniques for the probing of isolated metal cluster structure through adsorbate binding patterns will be described. The saturation of clusters with reagents such as ammonia and nitrogen provides information on the number of preferred binding sites for these reagents. The dependence of this number on cluster size can suggest particular structural themes. The equilibrium reaction with water can be used to identify cluster sizes having especially enhanced binding for the water molecule. Again, the sequence of cluster sizes showing such enhancement can point to specific cluster structure. The reaction with oxygen can identify cluster sizes having particularly high ionization potentials, and these can be compared to simple models for the electronic structure of metal clusters. Representative applications of these probes to iron, cobalt, nickel, and copper clusters will be discussed. 5 figs.
AMORPHOUS SILICON ELECTRONIC STRUCTURE MODELING AND BASIC ELECTRO-PHYSICAL PARAMETERS CALCULATION
Directory of Open Access Journals (Sweden)
B. A. Golodenko
2014-01-01
Full Text Available Summary. The amorphous semiconductor has any unique processing characteristics and it is perspective material for electronic engineering. However, we have not authentic information about they atomic structure and it is essential knot for execution calculation they electronic states and electro physical properties. The author's methods give to us decision such problem. This method allowed to calculation the amorphous silicon modeling cluster atomics Cartesian coordinates, determined spectrum and density its electronic states and calculation the basics electro physical properties of the modeling cluster. At that determined numerical means of the energy gap, energy Fermi, electron concentration inside valence and conduction band for modeling cluster. The find results provides real ability for purposeful control to type and amorphous semiconductor charge carriers concentration and else provides relation between atomic construction and other amorphous substance physical properties, for example, heat capacity, magnetic susceptibility and other thermodynamic sizes.
A fully relativistic approach for calculating atomic data for highly charged ions
Energy Technology Data Exchange (ETDEWEB)
Zhang, Hong Lin [Los Alamos National Laboratory; Fontes, Christopher J [Los Alamos National Laboratory; Sampson, Douglas H [PENNSYLVANIA STATE UNIV
2009-01-01
We present a review of our fully relativistic approach to calculating atomic data for highly charged ions, highlighting a research effort that spans twenty years. Detailed discussions of both theoretical and numerical techniques are provided. Our basic approach is expected to provide accurate results for ions that range from approximately half ionized to fully stripped. Options for improving the accuracy and range of validity of this approach are also discussed. In developing numerical methods for calculating data within this framework, considerable emphasis is placed on techniques that are robust and efficient. A variety of fundamental processes are considered including: photoexcitation, electron-impact excitation, electron-impact ionization, autoionization, electron capture, photoionization and photorecombination. Resonance contributions to a variety of these processes are also considered, including discussions of autoionization, electron capture and dielectronic recombination. Ample numerical examples are provided in order to illustrate the approach and to demonstrate its usefulness in providing data for large-scale plasma modeling.
Structure and protonation of some indolizine derivatives studied by ab initio MO calculations
Wiench, J. W.; Stefaniak, L.; Webb, G. A.
2002-02-01
Some gauge invariant atomic orbitals-coupled-perturbed Hartree-Fock (GIAO-CPHF) calculations were performed for seven indolizine derivatives and their monoprotonated forms. Chemical shift, molecular geometry, and charge distribution data are reported for each molecule. The calculations support the results of nuclear magnetic resonance (NMR) spectroscopy measurements showing that protonation occurs preferentially at N1. The good agreement between the calculated and observed 13C and 15N chemical shifts show that such calculations can be used for chemical shift assignment purposes. Cation structures and probable sites for electrophilic reaction or second protonation are also discussed.
New version: GRASP2K relativistic atomic structure package
Jönsson, P.; Gaigalas, G.; Bieroń, J.; Fischer, C. Froese; Grant, I. P.
2013-09-01
, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 730252 No. of bytes in distributed program, including test data, etc.: 14808872 Distribution format: tar.gz Programming language: Fortran. Computer: Intel Xeon, 2.66 GHz. Operating system: Suse, Ubuntu, and Debian Linux 64-bit. RAM: 500 MB or more Classification: 2.1. Catalogue identifier of previous version: ADZL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 597 Does the new version supersede the previous version?: Yes Nature of problem: Prediction of atomic properties — atomic energy levels, oscillator strengths, radiative decay rates, hyperfine structure parameters, Landé gJ-factors, and specific mass shift parameters — using a multiconfiguration Dirac-Hartree-Fock approach. Solution method: The computational method is the same as in the previous GRASP2K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A
Energy Technology Data Exchange (ETDEWEB)
Kim, Young Soon; Nam, Baek Il [Myongji University, Seoul (Korea, Republic of)
1995-08-01
We have developed computer programs to calculate 2-and 3-step selective resonant multiphoton ionization of atoms. Autoionization resonances in the final continuum can be put into account via B-Spline basis set method. 8 refs., 5 figs. (author)
ISOTROPIC INELASTIC COLLISIONS IN A MULTITERM ATOM WITH HYPERFINE STRUCTURE
Energy Technology Data Exchange (ETDEWEB)
Belluzzi, Luca [Istituto Ricerche Solari Locarno, CH-6605 Locarno Monti (Switzerland); Landi Degl’Innocenti, Egidio [Dipartimento di Fisica e Astronomia, Università di Firenze, I-50125 Firenze (Italy); Bueno, Javier Trujillo [Instituto de Astrofísica de Canarias, E-38205 La Laguna, Tenerife (Spain)
2015-10-10
A correct modeling of the scattering polarization profiles observed in some spectral lines of diagnostic interest, the sodium doublet being one of the most important examples, requires taking hyperfine structure (HFS) and quantum interference between different J-levels into account. An atomic model suitable for taking these physical ingredients into account is the so-called multiterm atom with HFS. In this work, we introduce and study the transfer and relaxation rates due to isotropic inelastic collisions with electrons, which enter the statistical equilibrium equations (SEE) for the atomic density matrix of this atomic model. Under the hypothesis that the electron–atom interaction is described by a dipolar operator, we provide useful relations between the rates describing the transfer and relaxation of quantum interference between different levels (whose numerical values are in most cases unknown) and the usual rates for the atomic level populations, for which experimental data and/or approximate theoretical expressions are generally available. For the particular case of a two-term atom with HFS, we present an analytical solution of the SEE for the spherical statistical tensors of the upper term, including both radiative and collisional processes, and we derive the expression of the emission coefficient in the four Stokes parameters. Finally, an illustrative application to the Na i D{sub 1} and D{sub 2} lines is presented.
Single-atom based coherent quantum interference device structure.
Naydenov, Borislav; Rungger, Ivan; Mantega, Mauro; Sanvito, Stefano; Boland, John J
2015-05-13
We describe the fabrication, operation principles, and simulation of a coherent single-atom quantum interference device (QID) structure on Si(100) controlled by the properties of single atoms. The energy and spatial distribution of the wave functions associated with the device are visualized by scanning tunneling spectroscopy and the amplitude and phase of the evanescent wave functions that couple into the quantum well states are directly measured, including the action of an electrostatic gate. Density functional theory simulations were employed to simulate the electronic structure of the device structure, which is in excellent agreement with the measurements. Simulations of device transmission demonstrate that our coherent single-atom QID can have ON-OFF ratios in excess of 10(3) with potentially minimal power dissipation.
Atomic structure of intracellular amorphous calcium phosphate deposits.
Betts, F; Blumenthal, N C; Posner, A S; Becker, G L; Lehninger, A L
1975-01-01
The radial distribution function calculated from x-ray diffraction of mineralized cytoplasmic structures isolated from the hepatopancreas of the blue crab (Callinectes sapidus) is very similar to that previously found for synthetic amorphous calcium phosphate. Both types of mineral apparently have only short-range atomic order, represented as a neutral ion cluster of about 10 A in longest dimension, whose probable composition is expressed by the formula Ca9(PO4)6. The minor differences observed are attributed to the presence in the biological mineral of significant amounts of Mg-2+ and ATP. Synthetic amorphous calcium phosphate in contact with a solution containing an amount of ATP equivalent to that of the biological mineral failed to undergo conversion to the thermodynamically more stable hydroxyapatite. The amorphous calcium phosphate of the cytoplasmic mineral granules is similarly stable, and does not undergo conversion to hydroxyapatite, presumably owing to the presence of ATP and Mg-2+, known in inhibitors of the conversion process. The physiological implications of mineral deposits consisting of stabilized calcium phosphate ion clusters are discussed. PMID:1056015
Lobato, I.; Rojas, J.; Landauro, C.V.; Torres, J
2008-01-01
The structural evolution and dynamics of silver nanodrops Ag${}_{2896}$ (4.4 nm in diameter) during rapid cooling conditions has been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modeled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique is applied to reveal the structural transition in the process of solidifica...
Atomic force microscopy reveals hydroxyapatite-citrate interfacial structure at the atomic level.
Jiang, Wenge; Pan, Haihua; Cai, Yurong; Tao, Jinhui; Liu, Peng; Xu, Xurong; Tang, Ruikang
2008-11-04
An approach to organic-inorganic interfacial structure at the atomic level is a great challenge in the studies of biomineralization. We demonstrate that atomic force microscopy (AFM) is powerful tool to discover the biomineral interface in detail. By using a model system of (100) hydroxyapatite (HAP) face and citrate, it reveals experimentally that only a side carboxylate and a surface calcium ion are involved in the binding effect during the citrate adsorption, which is against the previous understandings by using Langmuir adsorption and computer simulation. Furthermore, the adsorbed citrate molecules can use their free carboxylate and hydroxyl groups to be self-assembled on the HAP surface. AFM examination also finds that the presence of citrate molecules on the HAP crystal faces can enhance the adhesion force of the HAP surface. We suggest that the established AFM method can be used for a precise and direct understanding of biointerfaces at the atomic level.
New crystal structure prediction of fully hydrogenated borophene by first principles calculations.
Wang, Zhiqiang; Lü, Tie-Yu; Wang, Hui-Qiong; Feng, Yuan Ping; Zheng, Jin-Cheng
2017-04-04
New crystal structures of fully hydrogenated borophene (borophane) have been predicted by first principles calculation. Comparing with the chair-like borophane (C-boropane) that has been reported in literature, we obtained four new borophane conformers with much lower total-energy. The most stable one, washboard-like borophane (W-borophane), has energy about 113.41 meV/atom lower than C-borophane. In order to explain the relative stability of different borophane conformers, the atom configuration, density of states, charge transfer, charge density distribution and defect formation energy of B-H dimer have been calculated. The results show that the charge transfer from B atoms to H atoms is crucial for the stability of borophane. In different borophane conformers, the bonding characteristics between B and H atoms are similar, but the B-B bonds in W-borophane are much stronger than that in C-borophane or other structures. In addition, we examined the dynamical stability of borophane conformers by phonon dispersions and found that the four new conformers are all dynamically stable. Finally the mechanical properties of borophane conformers along an arbitrary direction have been discussed. W-borophane possesses unique electronic structure (Dirac cone), good stability and superior mechanical properties. W-borophane has broad perspective for nano electronic device.
Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.
Torres, A E; Fomine, S
2015-04-28
The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.
Lens capsule structure assessed with atomic force microscopy
Sueiras, Vivian M.; Moy, Vincent T.
2015-01-01
Purpose To image the ultrastructure of the anterior lens capsule at the nanoscale level using atomic force microscopy (AFM). Methods Experiments were performed on anterior lens capsules maintained in their in situ location surrounding the lens from six human cadavers (donor age range: 44–88 years), four cynomolgus monkeys (Macaca fascicularis age range: 4.83–8.92 years), and seven pigs (<6 months). Hydration of all samples was maintained using Dulbecco’s Modified Eagle Medium (DMEM). Whole lenses were removed from the eye and placed anterior side up in agarose gel before gel hardening where only the posterior half of the lens was contained within the gel. After the gel hardened, the Petri dish was filled with DMEM until the point where the intact lens was fully submerged. AFM was used to image the anterior lens surface in contact mode. An integrated analysis program was used to calculate the interfibrillar spacing, fiber diameter, and surface roughness of the samples. Results The AFM images depict a highly ordered fibrous structure at the surface of the lens capsule in all three species. The interfibrillar spacing for the porcine, cynomolgus monkey, and human lens capsules was 0.68±0.25, 1.80±0.39, and 1.08±0.25 μm, respectively. In the primate, interfibrillar spacing significantly decreased linearly as a function of age. The fiber diameters ranged from 50 to 950 nm. Comparison of the root mean square (RMS) and average deviation demonstrate that the surface of the porcine lens capsule is the smoothest, and that the human and cynomolgus monkey capsules are significantly rougher. Conclusions AFM was successful in providing high-resolution images of the nanostructure of the lens capsule samples. Species-dependent differences were observed in the overall structure and surface roughness. PMID:25814829
Hédoux, Alain; Guinet, Yannick; Carpentier, Laurent; Paccou, Laurent; Derollez, Patrick; Brandán, Silvia Antonia
2017-06-01
In this work, three monomeric forms of arabinitol, usually named arabitol, and their dimeric species have been structural and vibrationally studied by using the micro-Raman spectra in the solid phase accomplished with theoretical calculations based on the theory of the functional of the density (DFT). The hybrid B3LYP method was used for all the calculations together with the 6-31G* and 6-311++g** basis sets. Two different L structures with minima energies were predicted in accordance to the two polymorphic structures revealed by recent X-ray diffraction experiments. The studies by natural bond orbital (NBO) calculations reveals high stabilities of the L form as compared with the D one but the topological properties by using the atoms in molecules (AIM) suggest a higher stability of the D form due to a strong H bond interactions. The scaled mechanical force fields (SQMFF) procedure was used to perform the complete vibrational assignments for the monomeric forms and their dimer. On the other hand, the similarity in the gap values computed for the three forms of arabitol with those observed for sucrose, trehalose, maltose and lactose in gas phase at the same level of theory could partially explain the sweetening property of this alcohol. In addition, the influences of the size of the basis set on some properties were evidenced.
Atomic scale structures of interfaces between kaolinite edges and water
Liu, X.; Lu, X.; Wang, R.; Meijer, E.J.; Zhou, H.; He, H.
2012-01-01
This paper reports the atomic scale structures of kaolinite edge surfaces in contact with water. The commonly occurring edge surfaces are investigated (i.e. (0 1 0) and (1 1 0)) by using first principles molecular dynamics (FPMD) technique. For (1 1 0)-type edge surface, there are two different
Pattern recognition approach to quantify the atomic structure of graphene
DEFF Research Database (Denmark)
Kling, Jens; Vestergaard, Jacob Schack; Dahl, Anders Bjorholm
2014-01-01
We report a pattern recognition approach to detect the atomic structure in high-resolution transmission electron microscopy images of graphene. The approach provides quantitative information such as carbon-carbon bond lengths and bond length variations on a global and local scale alike. © 2014...
Crystal structures and atomic model of NADPH oxidase
Magnani, Francesca; Nenci, Simone; Fananas, Elisa Millana; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W.; Mattevi, Andrea
2017-01-01
NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic
Workshop on foundations of the relativistic theory of atomic structure
Energy Technology Data Exchange (ETDEWEB)
None
1981-03-01
The conference is an attempt to gather state-of-the-art information to understand the theory of relativistic atomic structure beyond the framework of the original Dirac theory. Abstracts of twenty articles from the conference were prepared separately for the data base. (GHT)
Identifying local structural states in atomic imaging by computer vision.
Laanait, Nouamane; Ziatdinov, Maxim; He, Qian; Borisevich, Albina
2017-01-01
The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both local and nonlocal information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect-engineered multilayer graphene surface.
Toward the Atomic Structure of PrPSc.
Rodriguez, Jose A; Jiang, Lin; Eisenberg, David S
2017-09-01
In this review, we detail our current knowledge of PrP Sc structure on the basis of structural and computational studies. We discuss the progress toward an atomic resolution description of PrP Sc and results from the broader field of amyloid studies that may further inform our knowledge of this structure. Moreover, we summarize work that investigates the role of PrP Sc structure in its toxicity, transmissibility, and species specificity. We look forward to an atomic model of PrP Sc , which is expected to bring diagnostics and/or therapeutics to the field of prion disease. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.
Electronic band-structure calculations of some magnetic chromium compounds
VANBRUGGEN, CF; HAAS, C; DEGROOT, RA
1989-01-01
In this paper band-structure calculations of CrS, CrSe, Cr3Se4 and CrSb are presented. Together with our accompanying results for the chromium tellurides, these calculations give a coherent picture of the changes in the electronic structure caused by anion substitution and by introduction of cation
Soil structure interaction calculations: a comparison of methods
Energy Technology Data Exchange (ETDEWEB)
Wight, L.; Zaslawsky, M.
1976-07-22
Two approaches for calculating soil structure interaction (SSI) are compared: finite element and lumped mass. Results indicate that the calculations with the lumped mass method are generally conservative compared to those obtained by the finite element method. They also suggest that a closer agreement between the two sets of calculations is possible, depending on the use of frequency-dependent soil springs and dashpots in the lumped mass calculations. There is a total lack of suitable guidelines for implementing the lumped mass method of calculating SSI, which leads to the conclusion that the finite element method is generally superior for calculative purposes.
Revealing electronic structure in atomically-engineered manganite thin films
Monkman, Eric Justin
Semiconductor technology is based on tuning the properties of devices by manipulating thin films and interfaces. Recently, this approach has been extended to complex oxides, where quantum many-body interactions give rise to emergent ground states not present in the parent materials. Rationally controlling and engineering correlated electronic phases has the potential to revolutionize modern electronics, but is hindered by the inability of current theory to account for the effects of many-body interactions on the underlying electronic structure. Manganites provide a particularly model system for studying many-body effects due to their complex electronic and magnetic phase diagrams, which give rise to many potentially useful properties. Despite extensive work on manganite films demonstrating numerous electronic phase transitions, little is directly known about how the electronic structure responds to the 'control parameters' accessible in thin films. This dissertation presents direct measurements of the electronic structure in La1-- xSrxMnO3 based thin films and interfaces through several phase transitions using a unique integrated oxide molecular-beam epitaxy and angle-resolved photoemission spectroscopy system. We observe the full Fermi surface and near-EF electronic structure of the ferromagnetic and A-type antiferromagnetic metallic phases, reconciling first-principles calculations with experiment for the first time. Furthermore, our results provide key insights into the polaronic nature of the metallic charge carriers. We then explore the mechanism underlying the insulating ground state for La2/3Sr1/3MnO3 under strong tensile strain. Our measurements rule out the scenarios of bandwidth or localization-driven metal-insulator transitions, and reveal an instability of the strongly interacting metal towards an ordered insulating phase that can be accessed through epitaxial strain. By next studying atomically precise interfaces in (LaMnO3)2n/(SrMnO 3)n superlattices
Figgen, Detlev; Wedig, Anja; Stoll, Hermann; Dolg, Michael; Eliav, Ephraim; Kaldor, Uzi
2008-01-14
The four-component atomic intermediate-Hamiltonian Fock-space coupled cluster (IHFSCC) code of Landau et al. [J. Chem. Phys. 115, 6862 (2001)] has been adapted to two-component calculations with relativistic pseudopotentials of the energy-consistent variety. Recently adjusted energy-consistent pseudopotentials for group 11 and 12 transition elements as well as group 13 and 14 post-d main group elements, which were fitted to atomic valence spectra from four-component multiconfiguration Dirac-Hartree-Fock calculations, are tested in IHFSCC calculations for ionization potentials, electron affinities, and excitation energies of a variety of atoms and ions. Where comparison is possible, the deviations from experimental data are in good agreement with those found in previously published IHFSCC all-electron calculations: experimental data are usually reproduced within a few hundred wavenumbers.
Stanke, Monika; Adamowicz, Ludwik; Kedziera, Dariusz
2013-07-01
The inclusion of the leading quantum electrodynamic energy correction is unavoidable if one aims for sub 0.01 cm-1 accuracy in the calculations of atomic and molecular spectra. The important part of the calculation of the correction is the determination of the value of the so-called Bethe logarithm (ln k 0). In this work, we examine how to construct Gaussian basis sets for such calculations. While the testing is performed for the ground state of the hydrogen atom, the results allow us to suggest how the construction of appropriate basis sets can be handled in ln k 0 calculations of atoms and molecules with more than one electron performed with explicitly correlated all-electron Gaussian functions.
Directory of Open Access Journals (Sweden)
Jason M. Hudzik
2013-01-01
Full Text Available Entropy data are reported using different calculation methods for internal rotors on n-heptane, 2-methylhexane, and 2,3-dimethylpentane and on the different radical sites of each species corresponding to the loss of a hydrogen atom for temperatures between 298 and 1500 K. Structures, moments of inertia, vibration frequencies, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p level of theory. Comparisons with experimental literature data suggest limitations inuse of the rigid-rotor harmonic-oscillator (HO approximation and advantages to the use of internal rotation contributions for entropy relative to torsion frequencies. The comparisons suggest the need to include contributions from all internal rotors where the barriers are at or below those of the above molecules. Calculation of entropy from the use of internal rotor contributions provides acceptable approximations to available literature values. Entropy values for radicals corresponding to carbon sites on these hydrocarbons are presented.
Gao, Daqiang; Liu, Yonggang; Liu, Peitao; Si, Mingsu; Xue, Desheng
2016-10-20
Since the graphitic carbon nitride (g-C4N3), which can be seen as C-doped graphitic-C3N4 (g-C3N4), was reported to display ferromagnetic ground state and intrinsic half-metallicity (Du et al., PRL,108,197207,2012), it has attracted numerous research interest to tune the electronic structure and magnetic properties of g-C3N4 due to their potential applications in spintronic devices. In this paper, we reported the experimentally achieving of high temperature ferromagnetism in metal-free ultrathin g-C3N4 nanosheets by introducing of B atoms. Further, first-principles calculation results revealed that the current flow in such a system was fully spin-polarized and the magnetic moment was mainly attributed to the p orbital of N atoms in B doped g-C3N4 monolayer, giving the theoretic evidence of the ferromagnetism and half-metallicity. Our finding provided a new perspective for B doped g-C3N4 spintronic devices in future.
Energy Technology Data Exchange (ETDEWEB)
Kwon, Nam Ic [Hankuk University of foreign studies, Seoul (Korea)
2000-03-01
The source of anomalous broad linewidth of 3{sup 3}P{sub 1},{sub 2},{sub 3}-3{sup 3}D{sub 2},{sub 3},4(3s') transition was explained. The broad optogalvanic spectrum was consisted of two gaussian peaks of different linewidths, and they are separated by 250 MHz. The Narrow peak, which has linewidth of room temperature, is from oxygen atoms already separated, and the shifted broad peak, which has linewidth corresponding to a temperature of 9000 K, is from weakly bound molecular ions. Obtained hyperfine spectrum of fluorine atom at the expected frequency, was too weak to analyze hyperfine structure constants. Microwave discharge might be necessary for higher density of excited state. 16 refs., 11 figs. (Author)
Atomic Structure Control of Silica Thin Films on Pt(111)
Crampton, Andrew S
2015-05-27
Metal oxide thin films grown on metal single crystals are commonly used to model heterogeneous catalyst supports. The structure and properties of thin silicon dioxide films grown on metal single crystals have only recently been thoroughly characterized and their spectral properties well established. We report the successful growth of a three- dimensional, vitreous silicon dioxide thin film on the Pt(111) surface and reproduce the closed bilayer structure previously reported. The confirmation of the three dimensional nature of the film is unequivocally shown by the infrared absorption band at 1252 cm−1. Temperature programmed desorption was used to show that this three-dimensional thin film covers the Pt(111) surface to such an extent that its application as a catalyst support for clusters/nanoparticles is possible. The growth of a three-dimensional film was seen to be directly correlated with the amount of oxygen present on the surface after the silicon evaporation process. This excess of oxygen is tentatively attributed to atomic oxygen being generated in the evaporator. The identification of atomic oxygen as a necessary building block for the formation of a three-dimensional thin film opens up new possibilities for thin film growth on metal supports, whereby simply changing the type of oxygen enables thin films with different atomic structures to be synthesized. This is a novel approach to tune the synthesis parameters of thin films to grow a specific structure and expands the options for modeling common amorphous silica supports under ultra high vacuum conditions.
Modeling Protein Structure at Near Atomic Resolutions With Gorgon
Baker, Matthew L.; Abeysinghe, Sasakthi S.; Schuh, Stephen; Coleman, Ross A.; Abrams, Austin; Marsh, Michael P.; Hryc, Corey F.; Ruths, Troy; Chiu, Wah; Ju, Tao
2011-01-01
Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. PMID:21296162
Shen, Lin; Yang, Weitao
2016-04-12
We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.
DEFF Research Database (Denmark)
Bak, Keld L.; Hansen, Aage E.; Ruud, K.
1995-01-01
The second-quantization magnetic dipole operator that arises when London atomic orbitals are used as basis functions is derived. In atomic units, the magnetic dipole operator is defined as the negative of the first derivative of the electronic Hamiltonian containing the interaction with the exter......The second-quantization magnetic dipole operator that arises when London atomic orbitals are used as basis functions is derived. In atomic units, the magnetic dipole operator is defined as the negative of the first derivative of the electronic Hamiltonian containing the interaction...... that the length expression for the rotatory strength in linear response calculations gives gauge-origin-independent results. Sample calculations on ti ans-cyclooctene and its fragments are presented. Compared to conventional orbitals, the basis set convergence of the rotatory strengths calculated in the length...... form using London atomic orbitals is favourable. The rotatory strength calculated for trans-cyclooctene agrees nicely with the corresponding experimental circular dichroism spectrum, but the spectra for the fragment molecules show little resemblance with that of trans-cyclooctene....
Energy Technology Data Exchange (ETDEWEB)
Kaganovich, I. D., Shnidman, Ariel, Mebane, Harrison, Davidson, R.C.
2008-10-10
Evaluation of ion-atom charge-changing cross sections is needed for many accelerator applications. A classical trajectory Monte Carlo (CTMC) simulation has been used to calculate ionization and charge exchange cross sections. For benchmarking purposes, an extensive study has been performed for the simple case of hydrogen and helium targets in collisions with various ions. Despite the fact that the simulation only accounts for classical mechanics, the calculations are comparable to experimental results for projectile velocities in the region corresponding to the vicinity of the maximum cross section. Shortcomings of the CTMC method for multielectron target atoms are discussed.
Cavities and atomic packing in protein structures and interfaces.
Directory of Open Access Journals (Sweden)
Shrihari Sonavane
2008-09-01
Full Text Available A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively is presented. The total volume of cavities increases with the size of the protein (or the interface, though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 A(3 of cavity volume is found to accommodate single water, with another 40-45 A(3 needed for each additional solvent molecule. Polar atoms/residues have a higher propensity to line solvated cavities. Relative to the frequency of occurrence in the whole structure (or interface, residues in beta-strands are found more often lining the cavities, and those in turn and loop the least. Any depression in one chain not complemented by a protrusion in the other results in a cavity in the protein-protein interface. Through the use of the Voronoi volume, the packing of residues involved in protein-protein interaction has been compared to that in the protein interior. For a comparable number of atoms the interface has about twice the number of cavities relative to the tertiary structure.
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
Energy Technology Data Exchange (ETDEWEB)
Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Fujimoto, K. [Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nakagawa, A. [Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan); Nomoto, A. [Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)
2014-10-28
Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.
Stanke, Monika; Komasa, Jacek; Bubin, Sergiy; Adamowicz, Ludwik
2009-08-01
We have performed very accurate quantum mechanical calculations of the five lowest S states of the beryllium atom. In the nonrelativistic part of the calculations we used the variational method and we explicitly included the nuclear motion in the Schrödinger equation. The nonrelativistic wave functions of the five states were expanded in terms of explicitly correlated Gaussian functions. These wave functions were used to calculate the leading α2 relativistic correction ( α is the fine structure constant) and the α3 quantum electrodynamics (QED) correction. We also estimated the α4 QED correction by calculating its dominant component. A comparison of the experimental transition frequencies with the frequencies obtained based on the energies calculated in this work shows an excellent agreement.
Atom exchange between aqueous Fe(II) and structural Fe in clay minerals.
Neumann, Anke; Wu, Lingling; Li, Weiqiang; Beard, Brian L; Johnson, Clark M; Rosso, Kevin M; Frierdich, Andrew J; Scherer, Michelle M
2015-03-03
Due to their stability toward reductive dissolution, Fe-bearing clay minerals are viewed as a renewable source of Fe redox activity in diverse environments. Recent findings of interfacial electron transfer between aqueous Fe(II) and structural Fe in clay minerals and electron conduction in octahedral sheets of nontronite, however, raise the question whether Fe interaction with clay minerals is more dynamic than previously thought. Here, we use an enriched isotope tracer approach to simultaneously trace Fe atom movement from the aqueous phase to the solid ((57)Fe) and from the solid into the aqueous phase ((56)Fe). Over 6 months, we observed a significant decrease in aqueous (57)Fe isotope fraction, with a fast initial decrease which slowed after 3 days and stabilized after about 50 days. For the aqueous (56)Fe isotope fraction, we observed a similar but opposite trend, indicating that Fe atom movement had occurred in both directions: from the aqueous phase into the solid and from the solid into aqueous phase. We calculated that 5-20% of structural Fe in clay minerals NAu-1, NAu-2, and SWa-1 exchanged with aqueous Fe(II), which significantly exceeds the Fe atom layer exposed directly to solution. Calculations based on electron-hopping rates in nontronite suggest that the bulk conduction mechanism previously demonstrated for hematite1 and suggested as an explanation for the significant Fe atom exchange observed in goethite2 may be a plausible mechanism for Fe atom exchange in Fe-bearing clay minerals. Our finding of 5-20% Fe atom exchange in clay minerals indicates that we need to rethink how Fe mobility affects the macroscopic properties of Fe-bearing phyllosilicates and its role in Fe biogeochemical cycling, as well as its use in a variety of engineered applications, such as landfill liners and nuclear repositories.
Ground-state structures of atomic metallic hydrogen.
McMahon, Jeffrey M; Ceperley, David M
2011-04-22
Ab initio random structure searching using density functional theory is used to determine the ground-state structures of atomic metallic hydrogen from 500 GPa to 5 TPa. Including proton zero-point motion within the harmonic approximation, we estimate that molecular hydrogen dissociates into a monatomic body-centered tetragonal structure near 500 GPa (r(s)=1.23) that remains stable to 1 TPa (r(s)=1.11). At higher pressures, hydrogen stabilizes in an …ABCABC… planar structure that is similar to the ground state of lithium, but with a different stacking sequence. With increasing pressure, this structure compresses to the face-centered cubic lattice near 3.5 TPa (r(s)=0.92).
Partial structure factors reveal atomic dynamics in metallic alloy melts
Nowak, B.; Holland-Moritz, D.; Yang, F.; Voigtmann, Th.; Kordel, T.; Hansen, T. C.; Meyer, A.
2017-07-01
We investigate the dynamical decoupling of the diffusion coefficients of the different components in a metallic alloy melt, using a combination of neutron diffraction, isotopic substitution, and electrostatic levitation in Zr-Ni melts. We show that excess Ni atoms can diffuse more freely in a background of saturated chemical interaction, causing their dynamics to become much faster and thus decoupled than anticipated from the interparticle interactions. Based on the mode-coupling theory of the glass transition, the averaged structure as given by the partial static structure factors is able to explain the observed dynamical behavior.
On atom-bond connectivity molecule structure descriptors
Directory of Open Access Journals (Sweden)
Furtula Boris
2016-01-01
Full Text Available The atom-bond connectivity index (ABC is a degree-based molecular structure descriptor with well-documented chemical applications. In 2010 a distance-based new variant of this index (ABCGG has been proposed. Until now, the relation between ABC and ABCGG has not been analyzed. In this paper, we establish the basic characteristics of this relation. In particular, ABC and ABCGG are not correlated and both cases ABC > ABCGG and ABC < ABCGG may occur in the case of (structurally similar molecules. However, in the case of benzenoid hydrocarbons, ABC always exceeds ABCGG. [Projekat Ministarstva nauke Republike Srbije, br. 174033
Wang, Junmei; Cieplak, Piotr; Li, Jie; Hou, Tingjun; Luo, Ray; Duan, Yong
2011-03-31
In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, that is, whether the interactions of two atoms that form the bond, bond angle, and dihedral angle are turned off or scaled down. When 1-2 (bonded) and 1-3 (separated by two bonds) interactions are turned off, 1-4 (separated by three bonds) interactions are scaled down, or both, all models including the Applequist model achieved similar performance: the average percentage error (APE) ranges from 1.15 to 1.23%, and the average unsigned error (AUE) ranges from 0.143 to 0.158 Å(3). When the short-range 1-2, 1-3, and full 1-4 terms are taken into account (set D models), the APE ranges from 1.30 to 1.58% for the three Thole models, whereas the Applequist model (DA) has a significantly larger APE (3.82%). The AUE ranges from 0.166 to 0.196 Å(3) for the three Thole models, compared with 0.446 Å(3) for the Applequist model. Further assessment using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact have smaller errors than the models developed using this particular data set (set E models). The fact that A, B, and C model sets are notably more accurate than both D and E model sets strongly suggests that the inclusion of 1-2 and 1-3 interactions reduces the transferability and accuracy.
Atomic and electronic structures of novel silicon surface structures
Energy Technology Data Exchange (ETDEWEB)
Terry, J.H. Jr.
1997-03-01
The modification of silicon surfaces is presently of great interest to the semiconductor device community. Three distinct areas are the subject of inquiry: first, modification of the silicon electronic structure; second, passivation of the silicon surface; and third, functionalization of the silicon surface. It is believed that surface modification of these types will lead to useful electronic devices by pairing these modified surfaces with traditional silicon device technology. Therefore, silicon wafers with modified electronic structure (light-emitting porous silicon), passivated surfaces (H-Si(111), Cl-Si(111), Alkyl-Si(111)), and functionalized surfaces (Alkyl-Si(111)) have been studied in order to determine the fundamental properties of surface geometry and electronic structure using synchrotron radiation-based techniques.
Atomic structure of graphene supported heterogeneous model catalysts
Energy Technology Data Exchange (ETDEWEB)
Franz, Dirk
2017-04-15
Graphene on Ir(111) forms a moire structure with well defined nucleation centres. Therefore it can be utilized to create hexagonal metal cluster lattices with outstanding structural quality. At diffraction experiments these 2D surface lattices cause a coherent superposition of the moire cell structure factor, so that the measured signal intensity scales with the square of coherently scattering unit cells. This artificial signal enhancement enables the opportunity for X-ray diffraction to determine the atomic structure of small nano-objects, which are hardly accessible with any experimental technique. The uniform environment of every metal cluster makes the described metal cluster lattices on graphene/Ir(111) an attractive model system for the investigation of catalytic, magnetic and quantum size properties of ultra-small nano-objects. In this context the use of x-rays provides a maximum of flexibility concerning the possible sample environments (vacuum, selected gases, liquids, sample temperature) and allows in-situ/operando measurements. In the framework of the present thesis the structure of different metal clusters grown by physical vapor deposition in an UHV environment and after gas exposure have been investigated. On the one hand the obtained results will explore many aspects of the atomic structure of these small metal clusters and on the other hand the presented results will proof the capabilities of the described technique (SXRD on cluster lattices). For iridium, platinum, iridium/palladium and platinum/rhodium the growth on graphene/Ir(111) of epitaxial, crystalline clusters with an ordered hexagonal lattice arrangement has been confirmed using SXRD. The clusters nucleate at the hcp sites of the moire cell and bind via rehybridization of the carbon atoms (sp{sup 2} → sp{sup 3}) to the Ir(111) substrate. This causes small displacements of the substrate atoms, which is revealed by the diffraction experiments. All metal clusters exhibit a fcc structure
Stability and Strength of Atomically Thin Borophene from First Principles Calculations
Peng, Bo; Shao, Hezhu; Ning, Zeyu; Xu, Yuanfeng; Lu, Hongliang; Zhang, David Wei; Zhu, Heyuan
2016-01-01
A new two-dimensional (2D) material, borophene (2D boron sheet), has been grown successfully recently on single crystal Ag substrates by two parallel experiments [Mannix \\textit{et al., Science}, 2015, \\textbf{350}, 1513] [Feng \\textit{et al., Nature Chemistry}, 2016, \\textbf{advance online publication}]. Three main structures have been proposed ($\\beta_{12}$, $\\chi_3$ and striped borophene). However, the stability of three structures is still in debate. Using first principles calculations, we examine the dynamical, thermodynamical and mechanical stability of $\\beta_{12}$, $\\chi_3$ and striped borophene. Free-standing $\\beta_{12}$ and $\\chi_3$ borophene is dynamically, thermodynamically, and mechanically stable, while striped borophene is dynamically and thermodynamically unstable due to high stiffness along $a$ direction. The origin of high stiffness and high instability in striped borophene along $a$ direction can both be attributed to strong directional bonding. This work provides a benchmark for examining...
Atomic-Level Structural Dynamics of Polyoxoniobates during DMMP Decomposition.
Wang, Qi; Chapleski, Robert C; Plonka, Anna M; Gordon, Wesley O; Guo, Weiwei; Nguyen-Phan, Thuy-Duong; Sharp, Conor H; Marinkovic, Nebojsa S; Senanayake, Sanjaya D; Morris, John R; Hill, Craig L; Troya, Diego; Frenkel, Anatoly I
2017-04-10
Ambient pressure in situ synchrotron-based spectroscopic techniques have been correlated to illuminate atomic-level details of bond breaking and formation during the hydrolysis of a chemical warfare nerve agent simulant over a polyoxometalate catalyst. Specifically, a Cs8[Nb6O19] polyoxoniobate catalyst has been shown to react readily with dimethyl methylphosphonate (DMMP). The atomic-level transformations of all reactant moieties, the [Nb6O19]8- polyanion, its Cs+ counterions, and the DMMP substrate, were tracked under ambient conditions by a combination of X-ray absorption fine structure spectroscopy, Raman spectroscopy, and X-ray diffraction. Results reveal that the reaction mechanism follows general base (in contrast to specific base) hydrolysis. Together with computational results, the work demonstrates that the ultimate fate of DMMP hydrolysis at the Cs8[Nb6O19] catalyst is strong binding of the (methyl) methylphosphonic acid ((M)MPA) product to the polyanions, which ultimately inhibits catalytic turnover.
Deciphering Adsorption Structure on Insulators at the Atomic Scale
Energy Technology Data Exchange (ETDEWEB)
Thurmer, Konrad [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Materials Physics; Feibelman, Peter J. [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Integrated Nanotechnologies
2014-09-01
We applied Scanning Probe Microscopy and Density Functional Theory (DFT) to discover the basics of how adsorbates wet insulating substrates, addressing a key question in geochemistry. To allow experiments on insulating samples we added Atomic Force Microscopy (AFM) capability to our existing UHV Scanning Tunneling Microscope (STM). This was accomplished by integrating and debugging a commercial qPlus AFM upgrade. Examining up-to-40-nm-thick water films grown in vacuum we found that the exact nature of the growth spirals forming around dislocations determines what structure of ice, cubic or hexagonal, is formed at low temperature. DFT revealed that wetting of mica is controlled by how exactly a water layer wraps around (hydrates) the K^{+} ions that protrude from the mica surface. DFT also sheds light on the experimentally observed extreme sensitivity of the mica surface to preparation conditions: K atoms can easily be rinsed off by water flowing past the mica surface.
Yu, Rong Mei; Zan, Li Rong; Jiao, Li Guang; Ho, Yew Kam
2017-09-01
Spatially confined atoms have been extensively investigated to model atomic systems in extreme pressures. For the simplest hydrogen-like atoms and isotropic harmonic oscillators, numerous physical quantities have been established with very high accuracy. However, the expectation value of which is of practical importance in many applications has significant discrepancies among calculations by different methods. In this work we employed the basis expansion method with cut-off Slater-type orbitals to investigate these two confined systems. Accurate values for several low-lying bound states were obtained by carefully examining the convergence with respect to the size of basis. A scaling law for was derived and it is used to verify the accuracy of numerical results. Comparison with other calculations show that the present results establish benchmark values for this quantity, which may be useful in future studies.
Serov, Vladislav V; Sergeeva, Tatiana A; Vinitsky, Sergue I
2012-01-01
A review of some recently developed methods of calculating multiple differential cross-sections of photoionization and electron impactionization of atoms and molecules having two active electrons is presented. The methods imply original approaches to calculating three-particle Coulomb wave functions. The external complex scaling method and the formalism of the Schroedinger equation with a source in the right-hand side are considered. Efficiency of the time-dependent approaches to the scattering problem, such as the paraxial approximation and the time-dependent scaling, is demonstrated. An original numerical method elaborated by the authors for solving the 6D Schroedinger equation for an atom with two active electrons, based on the Chang-Fano transformation and the discrete variable representation, is formulated. Basing on numerical simulations, the threshold behavior of angular distributions of two-electron photoionization of the negative hydrogen ion and helium atom, and multiple differential cross-sections ...
Atomic Structure of Au−Pd Bimetallic Alloyed Nanoparticles
Ding, Yong
2010-09-08
Using a two-step seed-mediated growth method, we synthesized bimetallic nanoparticles (NPs) having a gold octahedron core and a palladium epitaxial shell with controlled Pd-shell thickness. The mismatch-release mechanism between the Au core and Pd shell of the NPs was systematically investigated by high-resolution transmission electron microscopy. In the NPs coated with a single atomic layer of Pd, the strain between the surface Pd layer and the Au core is released by Shockley partial dislocations (SPDs) accompanied by the formation of stacking faults. For NPs coated with more Pd (>2 nm), the stacking faults still exist, but no SPDs are found. This may be due to the diffusion of Au atoms into the Pd shell layers to eliminate the SPDs. At the same time, a long-range ordered L11 AuPd alloy phase has been identified in the interface area, supporting the assumption of the diffusion of Au into Pd to release the interface mismatch. With increasing numbers of Pd shell layers, the shape of the Au-Pd NP changes, step by step, from truncated-octahedral to cubic. After the bimetallic NPs were annealed at 523 K for 10 min, the SPDs at the surface of the NPs coated with a single atomic layer of Pd disappeared due to diffusion of the Au atoms into the surface layer, while the stacking faults and the L11 Au-Pd alloyed structure remained. When the annealing temperature was increased to 800 K, electron diffraction patterns and diffraction contrast images revealed that the NPs became a uniform Au-Pd alloy, and most of the stacking faults disappeared as a result of the annealing. Even so, some clues still support the existence of the L11 phase, which suggests that the L11 phase is a stable, long-range ordered structure in Au-Pd bimetallic NPs. © 2010 American Chemical Society.
Structure formation in atom lithography using geometric collimation
Meijer, T.; Beardmore, J.P.; Fabrie, C.G.C.H.M.; van Lieshout, J.P.; Notermans, R.P.M.J.W.; Sang, R.T.; Vredenbregt, E.J.D.; Van Leeuwen, K.A.H.
2011-01-01
Atom lithography uses standing wave light fields as arrays of lenses to focus neutral atom beams into line patterns on a substrate. Laser cooled atom beams are commonly used, but an atom beam source with a small opening placed at a large distance from a substrate creates atom beams which are locally
Structural Calculations for Amorphous Systems Using Structural Diffusion Model
2001-06-01
Dalg,9, S. Dalg&, N. Talip , I. Orug Department of Physics, Trakya University, 22030 Edirne, TURKEY We present the results of calculations of the...or the deduced pair distribution function 538 S. Dalg&, S. Dalg&, N. Talip , I. Orug g(r). Both these properties are one-dimensional constructs...S(k) are shown in figure(1-a). We note that the differences between the 540 S. Dalg3q, S. Dalg&, N. Talip , I. Orue experimental S(k) in a-Fe not very
SGO: A fast engine for ab initio atomic structure global optimization by differential evolution
Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang
2017-10-01
As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.
Partially Assembled Nucleosome Structures at Atomic Detail.
Rychkov, Georgy N; Ilatovskiy, Andrey V; Nazarov, Igor B; Shvetsov, Alexey V; Lebedev, Dmitry V; Konev, Alexander Y; Isaev-Ivanov, Vladimir V; Onufriev, Alexey V
2017-02-07
The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Snyder, David A.; Grullon, Jennifer; Huang, Yuanpeng J.; Tejero, Roberto; Montelione, Gaetano T.
2014-01-01
Maximizing the scientific impact of NMR-based structure determination requires robust and statistically sound methods for assessing the precision of NMR-derived structures. In particular, a method to define a core atom set for calculating superimpositions and validating structure predictions is critical to the use of NMR-derived structures as targets in the CASP competition. FindCore (D.A. Snyder and G.T. Montelione PROTEINS 2005;59:673–686) is a superimposition independent method for identifying a core atom set, and partitioning that set into domains. However, as FindCore optimizes superimposition by sensitively excluding not-well-defined atoms, the FindCore core may not comprise all atoms suitable for use in certain applications of NMR structures, including the CASP assessment process. Adapting the FindCore approach to assess predicted models against experimental NMR structures in CASP10 required modification of the FindCore method. This paper describes conventions and a standard protocol to calculate an “Expanded FindCore” atom set suitable for validation and application in biological and biophysical contexts. A key application of the Expanded FindCore method is to identify a core set of atoms in the experimental NMR structure for which it makes sense to validate predicted protein structure models. We demonstrate the application of this Expanded FindCore method in characterizing well-defined regions of 18 NMR-derived CASP10 target structures. The Expanded FindCore protocol defines “expanded core atom sets” that match an expert’s intuition of which parts of the structure are sufficiently well-defined to use in assessing CASP model predictions. We also illustrate the impact of this analysis on the CASP GDT assessment scores. PMID:24327305
Lique, F; Kłos, J; Le Picard, S D
2017-10-02
Atomic sulfur and silicon are important constituents of the interstellar matter and are both used as tracers of the physical conditions in interstellar shocks and outflows. We present an investigation of the spin-orbit (de-)excitation of S((3)P) and Si((3)P) atoms induced by collisions with helium with the aim to improve the determination of atomic sulfur and silicon abundances in the interstellar medium from S and Si emission spectra. Quantum-mechanical calculations have been performed in order to determine rate coefficients for the fine-structure transitions in the 5-1000 K temperature range. The scattering calculations are based on new highly correlated ab initio potentials. The theoretical results show that the (de-)excitation of Si is much faster than that of S. The rate coefficients deduced from this study are in good agreement with previous experimental and theoretical findings despite some deviations at low temperatures. From the computation of critical densities defined as the ratios between Einstein coefficients and the sum of the relevant collisional de-excitation rate coefficients, we show that local thermodynamic equilibrium conditions are not fulfilled for analyzing S and Si emission spectra observed in the interstellar medium. Hence, the present rate coefficients will be extremely useful for the accurate determination of interstellar atomic sulfur and silicon abundances.
Atomic-resolution structures of prion AGAAAAGA amyloid fibrils
Zhang, Jiapu
2011-01-01
To the best of the author's knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, although many experimental studies have shown that this region has amyloid fibril forming properties and plays an important role in prion diseases. In view of this, the present study is devoted to address this problem from computational approaches such as local optimization steepest descent, conjugate gradient, discrete gradient and Newton methods, global optimization simulated annealing and genetic algorithms, canonical dual optimization theory, and structural bioinformatics. The optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils reported in this Chapter have a value to the scientific community in its drive to find treatments for prion diseases or at least be useful for the goals of medicinal chemistry.
Ordering of carbon atoms in boron carbide structure
Energy Technology Data Exchange (ETDEWEB)
Ponomarev, V. I., E-mail: i2212@yandex.ru; Kovalev, I. D.; Konovalikhin, S. V.; Vershinnikov, V. I. [Russian Academy of Sciences, Institute of Structural Macrokinetics and Materials Science (Russian Federation)
2013-05-15
Boron carbide crystals have been obtained in the entire compositional range according to the phase diagram by self-propagating high-temperature synthesis (SHS). Based on the results of X-ray diffraction investigations, the samples were characterized by the unit-cell metric and reflection half-width in the entire range of carbon concentrations. A significant spread in the boron carbide unit-cell parameters for the same carbon content is found in the data in the literature; this spread contradicts the structural concepts for covalent compounds. The SHS samples have not revealed any significant spread in the unit-cell parameters. Structural analysis suggests that the spread of parameters in the literary data is related to the unique process of ordering of carbon atoms in the boron carbide structure.
Refinement of Atomic Structures Against cryo-EM Maps.
Murshudov, G N
2016-01-01
This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models. © 2016 Elsevier Inc. All rights reserved.
Calculation of wakefields in 2D rectangular structures
Energy Technology Data Exchange (ETDEWEB)
Zagorodnov, I. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Bane, K.L.F.; Stupakov, G. [Stanford Univ., CA (United States). SLAC National Accelerator Lab.
2015-08-15
We consider the calculation of electromagnetic fields generated by an electron bunch passing through a vacuum chamber structure that, in general, consists of an entry pipe, followed by some kind of transition or cavity, and ending in an exit pipe. We limit our study to structures having rectangular cross-section, where the height can vary as function of longitudinal coordinate but the width and side walls remain fixed. For such structures, we derive a Fourier representation of the wake potentials through one-dimensional functions. A new numerical approach for calculating the wakes in such structures is proposed and implemented in the computer code ECHO(2D). The computation resource requirements for this approach are moderate and comparable to those for finding the wakes in 2D rotationally symmetric structures. Numerical examples obtained with the new numerical code are presented.
Calculation of wakefields in 2D rectangular structures
Directory of Open Access Journals (Sweden)
I. Zagorodnov
2015-10-01
Full Text Available We consider the calculation of electromagnetic fields generated by an electron bunch passing through a vacuum chamber structure that, in general, consists of an entry pipe, followed by some kind of transition or cavity, and ending in an exit pipe. We limit our study to structures having rectangular cross section, where the height can vary as function of longitudinal coordinate but the width and side walls remain fixed. For such structures, we derive a Fourier representation of the wake potentials through one-dimensional functions. A new numerical approach for calculating the wakes in such structures is proposed and implemented in the computer code echo(2d. The computation resource requirements for this approach are moderate and comparable to those for finding the wakes in 2D rotationally symmetric structures. Numerical examples obtained with the new numerical code are presented.
Atomic and Electronic Structure of Defects in Semiconductors.
1983-08-01
Ultramicroscopy, (1981) Vol 7, p. 59-64. 3. "Electron Energy Loss Spectroscopy as a probe of the Local Atomic Environment" O.L. Krivanek , M.M. Disko, J...Electron Energy-Loss Spectra, M.M. Disko, O.L. Krivanek and P. Rez, Phys. Rev. B15, #6, p. 4252 (1982). 8. "Electronic Structure of the Unreconstructed 30...and Preliminary Orientation Depencence Results" M. Disko, 0. Krivanek and J.C.H. Spence, Proc. EMSA, 1981. G.W. Bailey, Ed, Claitors Publishing Division
Understanding atomic-resolved STM images on TiO{sub 2}(110)-(1 x 1) surface by DFT calculations
Energy Technology Data Exchange (ETDEWEB)
Sanchez-Sanchez, C; Gonzalez, C; Mendez, J; De Andres, P L; MartIn-Gago, J A; Lopez, M F [Instituto Ciencia de Materiales de Madrid (CSIC), C/Sor Juana Ines de la Cruz 3, 28049-Madrid (Spain); Jelinek, P, E-mail: mflopez@icmm.csic.es [Institute of Physics, Czech Academy of Sciences, Cukrovarnicka 10, 162 53-Prague (Czech Republic)
2010-10-08
We present a combination of experimental STM images and DFT calculations to understand the atomic scale contrast of features found in high-resolution STM images. Simulating different plausible structural models for the tip, we have been able to reproduce various characteristics previously reported in experimental images on TiO{sub 2}(110)-(1 x 1) under controlled UHV conditions. Our results allow us to determine the influence of different chemical and morphological tip terminations on the atomic-resolution STM images of the TiO{sub 2}(110)-(1 x 1) surface. The commonest images have been properly explained using standard models for a W tip, either clean or with a single O atom located at the apex. Furthermore, a double transfer of oxygen atoms can account for different types of bizarre atomic-resolution features occasionally seen, and not conclusively interpreted before. Importantly, we discuss how typical point-defects are imaged on this surface by different tips, namely bridging O vacancies and adsorbed OH groups.
Bean, Jonathan J.; Saito, Mitsuhiro; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi; McKenna, Keith P.
2017-04-01
Polycrystalline metal oxides find diverse applications in areas such as nanoelectronics, photovoltaics and catalysis. Although grain boundary defects are ubiquitous their structure and electronic properties are very poorly understood since it is extremely challenging to probe the structure of buried interfaces directly. In this paper we combine novel plan-view high-resolution transmission electron microscopy and first principles calculations to provide atomic level understanding of the structure and properties of grain boundaries in the barrier layer of a magnetic tunnel junction. We show that the highly [001] textured MgO films contain numerous tilt grain boundaries. First principles calculations reveal how these grain boundaries are associated with locally reduced band gaps (by up to 3 eV). Using a simple model we show how shunting a proportion of the tunnelling current through grain boundaries imposes limits on the maximum magnetoresistance that can be achieved in devices.
Wu, Maokun; Yao, Xiaolong; Hao, Yuan; Dong, Hong; Cheng, Yahui; Liu, Hui; Lu, Feng; Wang, Weichao; Cho, Kyeongjae; Wang, Wei-Hua
2018-01-01
Utilizing first-principles calculations, the electronic structures, magnetic properties and band alignments of monolayer MoS2 doped by 3d transition metal atoms have been investigated. It is found that in V, Cr, Mn, Fe-doped monolayers, the nearest neighboring S atoms (SNN) are antiferromagnetically polarized with the doped atoms. While in Co, Ni, Cu, Zn-doped systems, the SNN are ferromagnetically coupled with the doped atoms. Moreover, the nearest neighboring Mo atoms also demonstrate spin polarization. Compared with pristine monolayer MoS2, little change is found for the band edges' positions in the doped systems. The Fermi level is located in the spin-polarized impurity bands, implying a half-metallic state. These results provide fundamental insights for doped monolayer MoS2 applying in spintronic, optoelectronic and electronic devices.
Lu, Shih-I.
2018-01-01
We use the discrete solvent reaction field model to evaluate the linear and second-order nonlinear optical susceptibilities of 3-methyl-4-nitropyridine-1-oxyde crystal. In this approach, crystal environment is created by supercell architecture. A self-consistent procedure is used to obtain charges and polarizabilities for environmental atoms. Impact of atomic polarizabilities on the properties of interest is highlighted. This approach is shown to give the second-order nonlinear optical susceptibilities within error bar of experiment as well as the linear optical susceptibilities in the same order as experiment. Similar quality of calculations are also applied to both 4-N,N-dimethylamino-3-acetamidonitrobenzene and 2-methyl-4-nitroaniline crystals.
Feshin, V. P.; Feshina, E. V.
2012-03-01
The results of ab initio calculations at the RHF/6-31G(d) and MP2/6-31G(d) levels of two stable structures of the 4-(trichlorgermyl)butan-2-one molecule with total optimization of their geometry have been represented. The structure with pentacoordinated Ge atom is energetically more advantageous as compared with that with tetracoordinated one. Using these results, the 35Cl nuclear quadrupole resonance (NQR) frequencies and asymmetry parameters of the electric field gradient (EFG) at the 35Cl nuclei in molecule with pentacoordinated Ge atom have been assessed, the frequencies satisfactorily agreeing with experimental data. Calculations at the RHF/6-31G(d) level have been performed also at various Ge⋯O distances. It has been demonstrated that convergence of the Ge and O coordination centers leads to the increase of positive charge at the Ge coordination center and of negative charge at the O coordination center, at that, electron density from the Ge atom shifts mainly to the axial Cl atom and from the C atom of carbonyl group - to its O atom. The electron density transfer from the O to Ge atom does not occur.
Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa.
Salih, Osman; He, Shaoda; Planamente, Sara; Stach, Lasse; MacDonald, James T; Manoli, Eleni; Scheres, Sjors H W; Filloux, Alain; Freemont, Paul S
2017-12-21
Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.
Structure of Nanocrystals by the atomic Pair Distribution Function technique
Petkov, Valeri
2003-03-01
Knowledge of the atomic-scale structure is an important prerequisite to understand and predict the properties of materials. In the case of crystals it is obtained from the positions and intensities of the Bragg peaks in the diffraction data. Materials constructed at the nanoscale, however, lack the long-range order and symmetry of perfect crystals. The result is that the diffraction patterns of nanocrystals are much more diffuse with few if any Bragg peaks. This poses a real challenge to the traditional techniques for structure determination. The challenge can be met by employing the so-called atomic Pair Distribution Function (PDF) technique. The basics of the PDF technique will be outlined and it advantages illustrated with results from recent studies of nanocrystalline WS_2, LiMoS_2, V_2O_5.nH_2O, GdAl2 nanomagnets, nanoporous silicates and Cs doped zeolites. Acknowledgements: Thanks are due to M. Kanatzidis, T. Pinnavaia, T. Vogt, S. Shastri, S.J.L. Billinge, D. Leslie-Pelecky and J. Dye for providing the samples and help with the experiments.
Celeste, Ricardo; Maringolo, Milena P; Comar, Moacyr; Viana, Rommel B; Guimarães, Amanda R; Haiduke, Roberto L A; da Silva, Albérico B F
2015-10-01
Accurate Gaussian basis sets for atoms from H to Ba were obtained by means of the generator coordinate Hartree-Fock (GCHF) method based on a polynomial expansion to discretize the Griffin-Wheeler-Hartree-Fock equations (GWHF). The discretization of the GWHF equations in this procedure is based on a mesh of points not equally distributed in contrast with the original GCHF method. The results of atomic Hartree-Fock energies demonstrate the capability of these polynomial expansions in designing compact and accurate basis sets to be used in molecular calculations and the maximum error found when compared to numerical values is only 0.788 mHartree for indium. Some test calculations with the B3LYP exchange-correlation functional for N2, F2, CO, NO, HF, and HCN show that total energies within 1.0 to 2.4 mHartree compared to the cc-pV5Z basis sets are attained with our contracted bases with a much smaller number of polarization functions (2p1d and 2d1f for hydrogen and heavier atoms, respectively). Other molecular calculations performed here are also in very good accordance with experimental and cc-pV5Z results. The most important point to be mentioned here is that our generator coordinate basis sets required only a tiny fraction of the computational time when compared to B3LYP/cc-pV5Z calculations.
ELECTRONIC-STRUCTURE OF THE LEAD MONOXIDES - BAND-STRUCTURE CALCULATIONS AND PHOTOELECTRON-SPECTRA
TERPSTRA, HJ; DEGROOT, RA; HAAS, C
1995-01-01
PbO is a layer compound which exists in two polymorphic forms, a red tetragonal (alpha) and a yellow orthorhombic (beta) modification. Ab initio band-structure calculations are presented for both phases. The calculated energy gaps are in agreement with optical data. The band-structure calculations
First-principle calculations of the structural, electronic ...
Indian Academy of Sciences (India)
For band structure calculations, in addition to WC-GGA approximation, both Engel–Vosko (EV-GGA) generalized gradient approximation and recently proposed modified Becke–Johnson (mBJ) potential approximation have been used. Our investigation on the effect of composition on lattice constant, bulk modulus and band ...
First-principle calculations of the structural, electronic ...
Indian Academy of Sciences (India)
correlation potential. For band structure calculations, in addition to WC-GGA approximation, both Engel–Vosko. (EV-GGA) generalized gradient approximation and recently proposed modified Becke–Johnson (mBJ) potential approximation have been used. Our investigation on the effect of composition on lattice constant, ...
Inverse boundary element calculations based on structural modes
DEFF Research Database (Denmark)
Juhl, Peter Møller
2007-01-01
The inverse problem of calculating the flexural velocity of a radiating structure of a general shape from measurements in the field is often solved by combining a Boundary Element Method with the Singular Value Decomposition and a regularization technique. In their standard form these methods sol...
Three real-space discretization techniques in electronic structure calculations
Torsti, T; Eirola, T; Enkovaara, J; Hakala, T; Havu, P; Havu, [No Value; Hoynalanmaa, T; Ignatius, J; Lyly, M; Makkonen, [No Value; Rantala, TT; Ruokolainen, J; Ruotsalainen, K; Rasanen, E; Saarikoski, H; Puska, MJ
A characteristic feature of the state-of-the-art of real-space methods in electronic structure calculations is the diversity of the techniques used in the discretization of the relevant partial differential equations. In this context, the main approaches include finite-difference methods, various
Calculation for Hull Strength Construction in Offshore Structures
African Journals Online (AJOL)
PROF. O. E. OSUAGWU
2013-09-01
Sep 1, 2013 ... Ship classification societies such as Det Norske Veritas, American Bureau of Shipping, and Lloyd's. Register have established standard calculation forms for hull loads, strength requirements, thickness of hull plating, reinforcing stiffeners, girders, and other structures. This paper therefore used the relevant ...
Correlation between muonic levels and nuclear structure in muonic atoms
Energy Technology Data Exchange (ETDEWEB)
Dong, J.M., E-mail: dongjm07@lzu.edu.cn [Research Center for Nuclear Science and Technology, Lanzhou University and Institute of Modern Physics of CAS, Lanzhou 730000 (China); Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Graduate University of Chinese Academy of Sciences, Beijing 100049 (China); School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); China Institute of Atomic Energy, P.O. Box 275(18), Beijing 102413 (China); Zuo, W., E-mail: zuowei@impcas.ac.cn [Research Center for Nuclear Science and Technology, Lanzhou University and Institute of Modern Physics of CAS, Lanzhou 730000 (China); Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Zhang, H.F. [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Scheid, W. [Institute for Theoretical Physics, Justus-Liebig-University, D-35392 Giessen (Germany); Gu, J.Z., E-mail: gujianzhong2000@yahoo.com.cn [China Institute of Atomic Energy, P.O. Box 275(18), Beijing 102413 (China); Wang, Y.Z. [China Institute of Atomic Energy, P.O. Box 275(18), Beijing 102413 (China)
2011-10-25
A method that deals with the nucleons and the muon unitedly is employed to investigate the muonic lead, with which the correlation between the muon and nucleus can be studied distinctly. A 'kink' appears in the muonic isotope shift at a neutron magic number where the nuclear shell structure plays a key role. This behavior may have very important implications for the experimentally probing the shell structure of the nuclei far away from the {beta}-stable line. We investigate the variations of the nuclear structure due to the interaction with the muon in the muonic atom and find that the nuclear structure remains basically unaltered. Therefore, the muon is a clean and reliable probe for studying the nuclear structure. In addition, a correction that the muon-induced slight change in the proton density distribution in turn shifts the muonic levels is investigated. This correction to muonic level is as important as the Lamb shift and high order vacuum polarization correction, but is larger than anomalous magnetic moment and electron shielding correction.
On Atoms-in-Molecules Energies from Kohn-Sham Calculations.
Tognetti, Vincent; Joubert, Laurent
2017-10-06
Herein, we discuss three methods to partition the total molecular energy into additive atomic contributions within the framework of Bader's atoms-in-molecules theory and in the particular context of Kohn-Sham density functional theory. The first method is derived from the virial theorem, whereas the two other schemes, termed "standard" and "model", are based on Pendás' interacting-quantum-atoms decomposition. The methods are then compared for a dataset of molecules of interest for direct application in organic chemistry and biochemistry. Finally, the relevance of the three methods for the prediction of intrinsic reactivity properties (e.g., electrophilicity) or for unravelling the nature of chemical bonding (e.g., in halogen bonds, beyond the pure electrostatic point of view), is examined and paves the way for their more systematic use for the in silico design of new reactants. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Chiral nucleon-nucleon forces in nuclear structure calculations
Directory of Open Access Journals (Sweden)
Coraggio L.
2016-01-01
Full Text Available Realistic nuclear potentials, derived within chiral perturbation theory, are a major breakthrough in modern nuclear structure theory, since they provide a direct link between nuclear physics and its underlying theory, namely the QCD. As a matter of fact, chiral potentials are tailored on the low-energy regime of nuclear structure physics, and chiral perturbation theory provides on the same footing two-nucleon forces as well as many-body ones. This feature fits well with modern advances in ab-initio methods and realistic shell-model. Here, we will review recent nuclear structure calculations, based on realistic chiral potentials, for both finite nuclei and infinite nuclear matter.
Mechanical deformation of atomic-scale metallic contacts: Structure and mechanisms
DEFF Research Database (Denmark)
Sørensen, Mads Reinholdt; Brandbyge, Mads; Jacobsen, Karsten Wedel
1998-01-01
We have simulated the mechanical deformation of atomic-scale metallic contacts under tensile strain using molecular dynamics and effective medium theory potentials. The evolution of the structure of the contacts and the underlying deformation mechanisms are described along with the calculated...... electronic conductance. Various defects such as intersecting stacking faults, local disorder, and vacancies are created during the deformation. Disordered regions act as weak spots that reduce the strength of the contacts. The disorder tends to anneal out again during the subsequent atomic rearrangements......, but vacancies can be permanently present. The transition states and energies for slip mechanisms have been determined using the nudged elastic band method, and we find a size-dependent crossover from a dislocation-mediated slip to a homogeneous slip when the contact diameter becomes less than a few nm. We show...
DEFF Research Database (Denmark)
Pawlowski, F; Jorgensen, P; Olsen, Jeppe
2002-01-01
A detailed study is carried out of the accuracy of molecular equilibrium geometries obtained from least-squares fits involving experimental rotational constants B(0) and sums of ab initio vibration-rotation interaction constants alpha(r)(B). The vibration-rotation interaction constants have been...... calculated for 18 single-configuration dominated molecules containing hydrogen and first-row atoms at various standard levels of ab initio theory. Comparisons with the experimental data and tests for the internal consistency of the calculations show that the equilibrium structures generated using Hartree......-Fock vibration-rotation interaction constants have an accuracy similar to that obtained by a direct minimization of the CCSD(T) energy. The most accurate vibration-rotation interaction constants are those calculated at the CCSD(T)/cc-pVQZ level. The equilibrium bond distances determined from these interaction...
On-the-Fly Machine Learning of Atomic Potential in Density Functional Theory Structure Optimization
Jacobsen, T. L.; Jørgensen, M. S.; Hammer, B.
2018-01-01
Machine learning (ML) is used to derive local stability information for density functional theory calculations of systems in relation to the recently discovered SnO2 (110 )-(4 ×1 ) reconstruction. The ML model is trained on (structure, total energy) relations collected during global minimum energy search runs with an evolutionary algorithm (EA). While being built, the ML model is used to guide the EA, thereby speeding up the overall rate by which the EA succeeds. Inspection of the local atomic potentials emerging from the model further shows chemically intuitive patterns.
Energy Technology Data Exchange (ETDEWEB)
Wang, Lin-Wang; Zhao, Zhengji; Meza, Juan; Wang, Lin-Wang
2008-07-11
We present a new linear scaling ab initio total energy electronic structure calculation method based on the divide-and-conquer strategy. This method is simple to implement, easily to parallelize, and produces very accurate results when compared with the direct ab initio method. The method has been tested using up to 8,000 processors, and has been used to calculate nanosystems up to 15,000 atoms.
Lattice location of dopant atoms: An N-body model calculation
Indian Academy of Sciences (India)
Abstract. The channelling and scattering yields of 1 MeV α-particles in the (100),. (110) and (111) directions of silicon implanted with bismuth and ytterbium have been simulated using N-body model. The close encounter yield from dopant atoms in silicon is determined from the flux density, using the Bontemps and ...
Lattice location of dopant atoms: An N-body model calculation
Indian Academy of Sciences (India)
2015-11-27
Nov 27, 2015 ... The close encounter yield from dopant atoms in silicon is determined from the flux density, using the Bontemps and Fontenille method. All previous works reported in literature so far have been done with computer programmes using a statistical analytical expression or by a binary collision model or a ...
Sun, Yongfu; Gao, Shan; Xie, Yi
2014-01-21
Atomically-thick two-dimensional crystals can provide promising opportunities to satisfy people's requirement of next-generation flexible and transparent nanodevices. However, the characterization of these low-dimensional structures and the understanding of their clear structure-property relationship encounter many great difficulties, owing to the lack of long-range order in the third dimensionality. In this review, we survey the recent progress in fine structure characterization by X-ray absorption fine structure spectroscopy and also overview electronic structure modulation by density-functional calculations in the ultrathin two-dimensional crystals. In addition, we highlight their structure-property relationship, transparent and flexible device construction as well as wide applications in photoelectrochemical water splitting, photodetectors, thermoelectric conversion, touchless moisture sensing, supercapacitors and lithium ion batteries. Finally, we outline the major challenges and opportunities that face the atomically-thick two-dimensional crystals. It is anticipated that the present review will deepen people's understanding of this field and hence contribute to guide the future design of high-efficiency energy-related devices.
Hu, Riming; Zhou, Xiaolong; Yu, Jie
2017-12-01
The interactions of Ag atom with different types of CuO(111) surface, including the perfect, oxygen-vacancy and precovered oxygen surfaces, have been systematically investigated using density functional theory (DFT) calculations to examine the effect of surface structures on Ag atom adsorption. The calculated results indicate that the Cu1-Cu1 bridge site and the oxygen-vacancy site are the active centres for atomic Ag adsorption on the perfect surface and the oxygen-vacancy surface respectively, while atomic Ag preferentially adsorbs at the Op site on the precovered oxygen surface. The activity of the CuO(111) surface for atomic Ag adsorption can be improved both on the perfect and oxygen-vacancy surfaces, while the activity of the CuO(111) surface for atomic Ag adsorption will be suppressed on precovered oxygen surfaces. Furthermore, the adsorption of NO on different CuO(111) surfaces with Ag adsorption was investigated, and the calculation results show that the adsorption of NO on an Ag-loaded CuO(111) surface is greater than that on the pure CuO(111) surface.
An atomic force microscopy investigation of cyanophage structure.
Kuznetsov, Yurii G; Chang, Sheng-Chieh; Credaroli, Arielle; Martiny, Jennifer; McPherson, Alexander
2012-12-01
Marine viruses have only relatively recently come to the attention of molecular biologists, and the extraordinary diversity of potential host organisms suggests a new wealth of genetic and structural forms. A promising technology for characterizing and describing the viruses structurally is atomic force microscopy (AFM). We provide examples here of some of the different architectures and novel structural features that emerge from even a very limited investigation, one focused on cyanophages, viruses that infect cyanobacteria (blue-green algae). These were isolated by phage selection of viruses collected from California coastal waters. We present AFM images of tailed, spherical, filamentous, rod shaped viruses, and others of eccentric form. Among the tailed phages numerous myoviruses were observed, some having long tail fibers, some other none, and some having no visible baseplate. Syphoviruses and a podovirus were also seen. We also describe a unique structural features found on some tailed marine phages that appear to have no terrestrial homolog. These are long, 450 nm, complex helical tail fibers terminating in a unique pattern of 3+1 globular units made up of about 20 small proteins. Copyright © 2012 Elsevier Ltd. All rights reserved.
de Carvalho, Hudson W P; Batista, Ana P L; Ramalho, Teodorico C; Pérez, Carlos A; Gobbi, Angelo Luiz
2009-09-15
In order to evaluate the interactions between Au/Cu atoms and clean Si(111) surface, we used synchrotron radiation grazing incidence X-ray fluorescence analysis and theoretical calculations. Optimized geometries and energies on different adsorption sites indicate that the binding energies at different adsorption sites are high, suggesting a strong interaction between metal atom and silicon surface. The Au atom showed higher interaction than Cu atom. The theoretical and experimental data showed good agreement.
Atomic and electronic structures of a-SiC:H from tight-binding molecular dynamics
Ivashchenko, V I; Shevchenko, V I; Ivashchenko, L A; Rusakov, G V
2003-01-01
The atomic and electronic properties of amorphous unhydrogenated (a-SiC) and hydrogenated (a-SiC:H) silicon carbides are studied using an sp sup 3 s sup * tight-binding force model with molecular dynamics simulations. The parameters of a repulsive pairwise potential are determined from ab initio pseudopotential calculations. Both carbides are generated from dilute vapours condensed from high temperature, with post-annealing at low temperature for a-SiC:H. A plausible model for the inter-atomic correlations and electronic states in a-SiC:H is suggested. According to this model, the formation of the amorphous network is weakly sensitive to the presence of hydrogen. Hydrogen passivates effectively only the weak bonds of threefold-coordinated atoms. Chemical ordering is very much affected by the cooling rate and the structure of the high-temperature vapour. The as-computed characteristics are in rather good agreement with the results for a-SiC and a-Si:H from ab initio calculations.
Heat Transfer Principles in Thermal Calculation of Structures in Fire.
Zhang, Chao; Usmani, Asif
2015-11-01
Structural fire engineering (SFE) is a relatively new interdisciplinary subject, which requires a comprehensive knowledge of heat transfer, fire dynamics and structural analysis. It is predominantly the community of structural engineers who currently carry out most of the structural fire engineering research and design work. The structural engineering curriculum in universities and colleges do not usually include courses in heat transfer and fire dynamics. In some institutions of higher education, there are graduate courses for fire resistant design which focus on the design approaches in codes. As a result, structural engineers who are responsible for structural fire safety and are competent to do their jobs by following the rules specified in prescriptive codes may find it difficult to move toward performance-based fire safety design which requires a deep understanding of both fire and heat. Fire safety engineers, on the other hand, are usually focused on fire development and smoke control, and may not be familiar with the heat transfer principles used in structural fire analysis, or structural failure analysis. This paper discusses the fundamental heat transfer principles in thermal calculation of structures in fire, which might serve as an educational guide for students, engineers and researchers. Insights on problems which are commonly ignored in performance based fire safety design are also presented.
Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure
Energy Technology Data Exchange (ETDEWEB)
Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be
2017-06-15
Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod. - Highlights: • Depth sectioning in HAADF STEM is combined with atom-counting. • This can be used to retrieve the 3D atomic structure. • The theoretical precision with atoms can be located is investigated. • An algorithm is introduced to reconstruct the morphology of a nanoparticle. • The method is applied to reconstruct a gold nanorod.
Atomic and electronic structure of MoS2 nanoparticles
DEFF Research Database (Denmark)
Bollinger, Mikkel; Jacobsen, Karsten Wedel; Nørskov, Jens Kehlet
2003-01-01
at the edges. The electronic structure of the edge states is studied and we discuss their influence on the chemical properties of the edges. In particular, we study the reactivity towards hydrogen and show that hydrogen may form stable chemical bonds with both the two low-Miller indexed edges of MoS2. A model...... for calculating Gibbs free energy of the edges in terms of the DFT energies is also presented. This model allows us to determine the stable edge structure in thermodynamic equilibrium under different conditions. We find that both the insulating and metallic edges may be stable depending on the temperature...
Interface Structure and Atomic Bonding Characteristics in Silicon Nitride Ceramics
National Research Council Canada - National Science Library
A. Ziegler; J. C. Idrobo; M. K. Cinibulk; C. Kisielowski; N. D. Browning; R. O. Ritchie
2004-01-01
Direct atomic resolution images have been obtained that illustrate how a range of rare-earth atoms bond to the interface between the intergranular phase and the matrix grains in an advanced silicon nitride ceramic...
Atomic structure of the adsorption of transition metals on silicon surfaces
Energy Technology Data Exchange (ETDEWEB)
Cocoletzi, G.H. [IF-BUAP, 72000 Puebla (Mexico); Takeuchi, N. [CCMC-UNAM, Ensenada, BCN (Mexico)
2007-07-01
Full text: Solid state devices are useful for their high sensitivity in a small volume. Applications of such devices as dose materials include semi-conducting dose-rate, and dose-reading measuring devices. Transition metals (TM) have electronic and atomic properties similar to those of rare earth elements when they are adsorbed on silicon surfaces. The interfaces of transition metals silicides with Si (111) have very small lattice mismatches, sharp interfaces, and low Schottky barrier, making them ideal in electronic devices, such as infrared detectors and rectifying contacts. In this work we shall describe our first principles total energy calculations to investigate structural properties of bulk ScSi and YSi, the two dimensional arrangement of ScSi{sub 2} and YSi{sub 2} on the Si(111) surface, and the growth of a few layers of ScSi{sub 1.7} and YSi{sub 1.7} on the Si(111) surface. Our calculated bulk structural parameters are in excellent agreement with experimental values. It will be shown that one monolayer of a TM on Si( l l 1) yields a two dimensional phase with (lxl) periodicity consisting of a layer of TM atoms on T4 sites and a Si bilayer on top. This double layer of Si atoms is very close to ideal Si(111)-(1x1) surface, but rotated 180 with respect to the rest of the crystal. More layers of TM silicide epitaxially grown on Si(l 11) result in a hexagonal structure similar to bulk ScSi2 and YSi2: graphite-like Si planes (with vacancies) intercalated with TM planes, and forming a ({radical}3x{radical}3) arrangement with a ScSi{sub 1.7} and YSi{sub 1.7} stoichiometry. The top Si layer does not contain vacancies and it does not present a graphite-like structure, but forms a bilayer arrangement as in bulk Si. (Author)
Structure and Thermodynamics of Metal Clusters on Atomically Smooth Substrates.
Eckhoff, M; Schebarchov, D; Wales, D J
2017-10-23
We analyze the structure of model NiN and CuN clusters (N = 55, 147) supported on a variety of atomically smooth van der Waals surfaces. The global minima are mapped in the space of two parameters: (i) the laterally averaged surface stickiness, γ, which controls the macroscopic wetting angle, and (ii) the surface microstructure, which produces more subtle but important templating via epitaxial stresses. We find that adjusting the substrate lattice (even at constant γ) can favor different crystal plane orientations in the cluster, stabilize hexagonal close-packed order, or induce various defects, such as stacking faults, twin boundaries, and five-fold disclinations. Thermodynamic analysis reveals substrate-dependent solid-solid transitions in cluster morphology, with tunable transition temperature and sometimes exhibiting re-entrant behavior. These results shed new light on the extent to which a supporting surface can be used to influence the equilibrium behavior of nanoparticles.
Are the program packages for molecular structure calculations really black boxes?
Directory of Open Access Journals (Sweden)
ANA MRAKOVIC
2007-12-01
Full Text Available In this communication it is shown that the widely held opinion that compact program packages for quantum–mechanical calculations of molecular structure can safely be used as black boxes is completely wrong. In order to illustrate this, the results of computations of equilibrium bond lengths, vibrational frequencies and dissociation energies for all homonuclear diatomic molecules involving the atoms from the first two rows of the Periodic Table, performed using the Gaussian program package are presented. It is demonstrated that the sensible use of the program requires a solid knowledge of quantum chemistry.
Davis, Barry M; McCaffrey, John G
2016-01-28
Isolation of the heavier alkaline earth metals Ba and Sr in the solid rare gases (RGs) Ar, Kr, and Xe is analysed with absorption spectroscopy and interpreted partly with the assistance of ab initio calculations of the diatomic M ⋅ RG ground state interaction potentials. The y(1)P ← a(1)S resonance transitions in the visible spectral region are used to compare the isolation conditions of these two metal atom systems and calcium. Complex absorption bands were recorded in all three metal atom systems even after extensive sample annealing. Coupled cluster calculations conducted on the ground states of the nine M ⋅ RG diatomics (M = Ca, Sr, and Ba; RG = Ar, Kr, and Xe) at the coupled cluster single, double, and non-iterative triple level of theory revealed long bond lengths (>5 Å) and shallow bound regions (atoms in a single substitutional site of the solid rare gas is unlikely, with the possible exception of Ca/Xe. The luminescence of metal dimer bands has been recorded for Ba and Sr revealing very different behaviours. Resonance fluorescence with a lifetime of 15 ns is observed for the lowest energy transition of Sr2 while this transition is quenched in Ba2. This behaviour is consistent with the absence of vibrational structure on the dimer absorption band in Ba2 indicating lifetime broadening arising from efficient relaxation to low-lying molecular states. More extensive 2D excitation-emission data recorded for the complex site structures present on the absorption bands of the atomic Ba and Sr systems will be presented in future publications.
Calculation of inelastic helium atom scattering from H2/ NaCl(001)
DEFF Research Database (Denmark)
Bruch, L.W.; Hansen, Flemming Yssing; Traeger, F.
2011-01-01
The one-phonon inelastic low energy helium atom scattering theory is adapted to cases where the target monolayer is a p(1 × 1) commensurate square lattice. Experimental data for para-H2/NaCl(001) are re-analyzed and the relative intensities of energy loss peaks in the range 6 to 9 meV are determi......The one-phonon inelastic low energy helium atom scattering theory is adapted to cases where the target monolayer is a p(1 × 1) commensurate square lattice. Experimental data for para-H2/NaCl(001) are re-analyzed and the relative intensities of energy loss peaks in the range 6 to 9 me...
Relativistic calculations of the non-resonant two-photon ionization of neutral atoms
Hofbrucker, Jiri; Fritzsche, Stephan
2016-01-01
The non-resonant two-photon one-electron ionization of neutral atoms is studied theoretically in the framework of relativistic second-order perturbation theory and independent particle approximation. In particular, the importance of relativistic and screening effects in the total two-photon ionization cross section is investigated. Detailed computations have been carried out for the K-shell ionization of neutral Ne, Ge, Xe, and U atoms. The relativistic effects significantly decrease the total cross section, for the case of U, for example, they reduce the total cross section by a factor of two. Moreover, we have found that the account for the screening effects of the remaining electrons leads to occurrence of an unexpected minimum in the total cross section at the total photon energies equal to the ionization threshold, for the case of Ne, for example, the cross section drops there by a factor of three.
Dopant distributions in n-MOSFET structure observed by atom probe tomography.
Inoue, K; Yano, F; Nishida, A; Takamizawa, H; Tsunomura, T; Nagai, Y; Hasegawa, M
2009-11-01
The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted.
Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.
2011-01-01
Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples. PMID:21997909
Calculation of hyperfine structure constants of small molecules using ...
Indian Academy of Sciences (India)
The Z-vector method in the relativistic coupled-cluster framework is employed to calculate the parallel and perpendicular components of the magnetic hyperfine structure constant of a few small alkaline earth hydrides (BeH, MgH, and CaH) and fluorides (MgF and CaF). We have compared our Z-vector results with the values ...
Strenalyuk, Tatyana; Samdal, Svein; Volden, Hans Vidar
2007-11-29
The molecular structures of phthalocyaninatozinc (HPc-Zn) and hexadecafluorophthalocyaninatozinc (FPc- Zn) are determined using the gas electron diffraction (GED) method and high-level density functional theory (DFT) quantum chemical calculations. Calculations at the B3LYP/6-311++G** level indicate that the equilibrium structures of HPc-Zn and FPc-Zn have D4h symmetry and yield structural parameters in good agreement with those obtained by GED at 480 and 523 degrees C respectively. The calculated force fields indicate that both molecules are flexible. Normal coordinate calculations on HPc-Zn yield five vibrational frequencies (one degenerate) in the range 22-100 cm(-1), and ten vibrational frequencies ranging from 13 to 100 cm(-1) (three degenerate) for FPc-Zn. The high-level force field calculations confirm most of the previous vibrational assignments, and some new ones are suggested. The out-of-plane vibration of the Zn atom in HPc-Zn was studied in detail optimizing models in which the distance from the Zn atom to the two symmetry equivalent diagonally opposed N atoms (h) was fixed. The calculations indicate that the vibrationally activated vertically displacement of the Zn atom is accompanied by distortion of the ligand from D4h to C2v symmetry. The average height, h, at the temperature of the GED experiment was calculated to be 14.5 pm. Small structural changes indicate that a full F substitution on the benzo-subunits do not significantly alter the geometry, however there are indications that the benzo-subunits may shrink slightly with perfluorination.
Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N
2009-05-01
Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.
Atomic simulations of twist grain boundary structures and deformation behaviors in aluminum
Directory of Open Access Journals (Sweden)
Qing Yin
2017-01-01
Full Text Available The structures and behaviors of grain boundaries (GBs have profound effects on the mechanical properties of polycrystalline materials. In this paper, twist GBs in aluminum were investigated with molecular dynamic simulations to reveal their atomic structures, energy and interactions with dislocations. One hundred twenty-six twist GBs were studied, and the energy of all these twist GBs were calculated. The result indicates that and twist GBs have lower energy than twist GBs because of their higher interplanar spacing. In addition, 12 types of twist GBs in aluminum were chosen to explore the deformation behaviors. Low angle twist GBs with high density of network structures can resist greater tension because mutually hindering behaviors between partial dislocations increase the twist GB strength.
Calculation of alloy solid-liquid interfacial free energies from atomic-scale simulations
Asta, M.; Hoyt, J. J.; Karma, A.
2002-09-01
Solid-liquid interfacial free energies and associated crystalline anisotropies are calculated for a model Ni-Cu alloy system based upon the analysis of equilibrium capillary fluctuations in molecular-dynamics simulations. Alloying of Ni by Cu leads to a reduction in the magnitude of the calculated interfacial free energy, while having only a minor effect on computed anisotropies. The present study demonstrates the viability of applying the fluctuation method to simulation-based calculations of solid-liquid interfacial free energies in alloys.
Thermoelectric Properties and Band Structure Calculations of Novel Boron Network Compounds
Mori, Takao; Nishimura, Toshiyuki; Grin, Yuri; Shishido, Toetsu; Nakajima, Kazuo
2009-03-01
Boron is an interesting element, tending to form atomic networks such as 2D atomic nets and clusters, with some analogy to carbon systems which have been more extensively studied. Boron has one less electron than carbon and thus is electron deficient when forming atomic networks, but this causes it to have a special affinity with the rare earth elements and as a result, many new compounds have recently been discovered [1]. Their potential as viable thermoelectric materials is attracting interest since they are high-temperature materials and possess intrinsic low thermal conductivity, with some compounds exhibiting Seebeck coefficients in excess of 200 μV/K above 1000 K. The thermoelectric properties and band structure calculations of novel borides such as RB44Si2, RB17CN, RB22C2N, RB28.5C4 will be presented. Features in the band structure near the Fermi level indicate large doping effects in these compounds. Various doping experiments were carried out resulting in large increases to the figure of merit. [1] T. Mori, ``Higher Borides,'' in: Handbook on the Physics and Chemistry of Rare Earths, Vol. 38, (North-Holland, Amsterdam, 2008) p. 105-173.
Iron phosphate glasses: Bulk properties and atomic scale structure
Energy Technology Data Exchange (ETDEWEB)
Joseph, Kitheri; Stennett, Martin C.; Hyatt, Neil C.; Asuvathraman, R.; Dube, Charu L.; Gandy, Amy S.; Govindan Kutty, K. V.; Jolley, Kenny; Vasudeva Rao, P. R.; Smith, Roger
2017-10-01
Bulk properties such as glass transition temperature, density and thermal expansion of iron phosphate glass compositions, with replacement of Cs by Ba, are investigated as a surrogate for the transmutation of 137Cs to 137Ba, relevant to the immobilisation of Cs in glass. These studies are required to establish the appropriate incorporation rate of 137Cs in iron phosphate glass. Density and glass transition temperature increases with the addition of BaO indicating the shrinkage and reticulation of the iron phosphate glass network. The average thermal expansion coefficient reduces from 19.8 × 10-6 K-1 to 13.4 × 10-6 K-1, when 25 wt. % of Cs2O was replaced by 25 wt. % of BaO in caesium loaded iron phosphate glass. In addition to the above bulk properties, the role of Ba as a network modifier in the structure of iron phosphate glass is examined using various spectroscopic techniques. The FeII content and average coordination number of iron in the glass network was estimated using Mössbauer spectroscopy. The FeII content in the un-doped iron phosphate glass and barium doped iron phosphate glasses was 20, 21 and 22 ± 1% respectively and the average Fe coordination varied from 5.3 ± 0.2 to 5.7 ± 0.2 with increasing Ba content. The atomic scale structure was further probed by Fe K-edge X-ray absorption spectroscopy. The average coordination number provided by extended X-ray absorption fine structure spectroscopy and X-ray absorption near edge structure was in good agreement with that given by the Mössbauer data.
Linear scaling 3D fragment method for large-scale electronic structure calculations
Energy Technology Data Exchange (ETDEWEB)
Wang, Lin-Wang; Wang, Lin-Wang; Lee, Byounghak; Shan, HongZhang; Zhao, Zhengji; Meza, Juan; Strohmaier, Erich; Bailey, David
2008-07-11
We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39% of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFT calculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N{sup 3}) methods, and the potential for petascale computation using the LS3DF method.
Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan
2017-08-30
A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.
Quasiparticle GW calculations within the GPAW electronic structure code
DEFF Research Database (Denmark)
Hüser, Falco
are explained in detail and many examples are given. This provides a full understanding of how the code works and how the outcome should be interpreted. Secondly, it gives an extensive discussion of calculated results for the electronic structure of 3-dimensional, 2-dimensional and finite systems and comparison......The GPAW electronic structure code, developed at the physics department at the Technical University of Denmark, is used today by researchers all over the world to model the structural, electronic, optical and chemical properties of materials. They address fundamental questions in material science...... and use their knowledge to design new materials for a vast range of applications. Todays hottest topics are, amongst many others, better materials for energy conversion (e.g. solar cells), energy storage (batteries) and catalysts for the removal of environmentally dangerous exhausts. The mentioned...
Donval, Gaël; Moreau, Philippe; Danet, Julien; Larbi, Séverine Jouanneau-Si; Bayle-Guillemaud, Pascale; Boucher, Florent
2017-01-04
Most of the recent developments in EELS modelling has been focused on getting a better agreement with measurements. Less work however has been dedicated to bringing EELS calculations to larger structures that can more realistically describe actual systems. The purpose of this paper is to present a hybrid approach well adapted to calculating the whole set of localised EELS core-loss edges (at the XAS level of theory) on larger systems using only standard tools, namely the WIEN2k and VASP codes. We illustrate the usefulness of this method by applying it to a set of amorphous silicon structures in order to explain the flattening of the silicon L 2,3 EELS edge peak at the onset. We show that the peak flattening is actually caused by the collective contribution of each of the atoms to the average spectrum, as opposed to a flattening occurring on each individual spectrum. This method allowed us to reduce the execution time by a factor of 3 compared to a usual-carefully optimised-WIEN2k calculation. It provided even greater speed-ups on more complex systems (interfaces, ∼300 atoms) that will be presented in a future paper. This method is suited to calculate all the localized edges of all the atoms of a structure in a single calculation for light atoms as long as the core-hole effects can be neglected.
BNC nanoshells: a novel structure for atomic storage
Silva, F. W. N.; Cruz-Silva, E.; Terrones, M.; Terrones, H.; Barros, E. B.
2017-11-01
Quantum molecular dynamics (QMD) and density functional theory are employed in this work in order to study the structural and electronic properties of carbon, boron nitride or hybrid BNC nanoshells. The studied nanoshells can be formed by stacking two zigzag graphene nanoribbons, two zigzag boron nitride nanoribbons or one zigzag graphene nanoribbon on a boron nitride nanoribbon. In all cases only one of the edges of the ribbon is passivated, while the other one is left unpassivated. Our QMD results show that these nanoribbons collapse just a few femtoseconds after the beginning of the simulation, forming a coalesced structure in the shape of a shell. Our band structure calculations revealed that this structures may be metallic or semiconductor, depending on its stoichiometry. Furthermore, a spin splitting for energies near the Fermi level is predicted for both the pure carbon and the hybrid BNC-nanoshell systems. We further show that when a transverse electric field is applied to these systems, the nanoshell structure tends to open up. This effect can lead to the application of these nanoshells for molecular storage. As a proof of concept, We investigate this storage effect for the H2 molecule.
Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA
Energy Technology Data Exchange (ETDEWEB)
Mareuil, Fabien [Institut Pasteur, Cellule d' Informatique pour la Biologie (France); Malliavin, Thérèse E.; Nilges, Michael; Bardiaux, Benjamin, E-mail: bardiaux@pasteur.fr [Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 (France)
2015-08-15
In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to significantly improve the quality and the accuracy of determined structures. In this paper, we propose two modifications of the ARIA protocol: (1) the softening of the force field together with adapted hydrogen radii, which is meaningful in the context of the log-harmonic potential with Bayesian weighting, (2) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints, based on the fitting of the structure to the input data sets. The new ARIA protocols were fine-tuned on a set of eight protein targets from the CASD–NMR initiative. As a result, the convergence problems previously observed for some targets was resolved and the obtained structures exhibited better quality. In addition, the new ARIA protocols were applied for the structure calculation of ten new CASD–NMR targets in a blind fashion, i.e. without knowing the actual solution. Even though optimisation of parameters and pre-filtering of unrefined NOE peak lists were necessary for half of the targets, ARIA consistently and reliably determined very precise and highly accurate structures for all cases. In the context of integrative structural biology, an increasing number of experimental methods are used that produce distance data for the determination of 3D structures of macromolecules, stressing the importance of methods that successfully make use of ambiguous and noisy distance data.
Fast-ion-beam laser probing of ion-source energy distributions and atomic structure
Energy Technology Data Exchange (ETDEWEB)
Holt, Richard A., E-mail: rholt@uwo.ca; Rosner, S. David [University of Western Ontario, Physics and Astronomy Department (Canada)
2013-04-15
Collinear fast-ion-beam laser spectroscopy is a very high resolution probe for measuring ion-beam energy distributions and atomic structure parameters of interest in nuclear physics, atomic physics, and astrophysics. We have used offline 10-keV beams of atomic ions and a CW laser system to study the behavior of a Penning ion source and to measure hyperfine structure, isotope shifts, atomic lifetimes, spontaneous-emission branching fractions, oscillator strengths, and absolute wavelengths of a variety of atomic species from the lanthanide and transition-metal groups.
A suggested periodic table up to Z≤ 172, based on Dirac-Fock calculations on atoms and ions.
Pyykkö, Pekka
2011-01-07
Extended Average Level (EAL) Dirac-Fock calculations on atoms and ions agree with earlier work in that a rough shell-filling order for the elements 119-172 is 8s Periodic Table develops further that of Fricke, Greiner and Waber [Theor. Chim. Acta 1971, 21, 235] by formally assigning the elements 121-164 to (nlj) slots on the basis of the electron configurations of their ions. Simple estimates are made for likely maximum oxidation states, i, of these elements M in their MX(i) compounds, such as i = 6 for UF(6). Particularly high i are predicted for the 6f elements.
Tackley, P. J.; Nakagawa, T.; Deschamps, F.; Connolly, J.
2011-12-01
Phase diagrams of materials in Earth's transition zone (TZ) are complex and composition-dependent and phase transitions have a first-order influence on mantle dynamics, yet simulations of mantle convection typically include only one or two major phase transitions in the olivine system. In our recent work [1,2], phase assemblages of mantle rocks calculated by free energy minimization for MORB and harzburgite compositions expressed as the ratios of 5 or 6 oxides (CaO-FeO-MgO-Al2O3- SiO2-Na2O) are used to calculate the material properties density, thermal expansivity, specific heat capacity, and seismic velocity as a function of temperature and pressure, which are then incorporated into a numerical thermo-chemical mantle convection model in a 2-D spherical annulus or 3-D spherical shell. The advantage of using such an approach is that thermodynamic parameters affecting dynamics and seismic velocities are included implicitly and self-consistently, obviating the need for ad hoc parameterizations. Here we focus on the resulting thermo-chemical structures in the transition zone and their seismic signature. A robust result is some compositional stratification around 660 km depth caused by the inversion of the MORB-harzburgite density difference between ~660-740 km depth [3], with MORB enrichment in the lower TZ and depletion just below the TZ. The extent of this is quite sensitive to variations in MORB composition of the order 1-2% oxide fraction, particularly FeO and Al2O3, which influence the magnitude and depth of this effect and the density difference. The detailed structure also has a strong lateral variation. We plot radial profiles from different parts of our models, characterizing typical structures and the range of structures, and compare to local seismological profiles as well as profiles from regional inversions [4]. [1] Nakagawa, T., P.J. Tackley, F. Deschamps & J.A.D. Connolly (2009) Geochem. Geophys. Geosyst. 10, doi:10.1029/2008GC002280. [2] Nakagawa, T., P
Effect of Doped Transition Metal Atoms on Structure and Nonlinear Optical Properties of Decaborane
Beigi, Motahareh Noormohammad; Shamlouei, Hamid Reza; Omidi, Masoome; Jalalvandi, Esmat
2017-11-01
In this study, electrical and nonlinear optical properties of decaborane (B10H14) were investigated using the density functional theory method when transition metal atoms (scandium, titanium and vanadium) were doped on the structure. Hydrogen and boron atoms in B10H14 were substituted by the transition metals. This doping process resulted in a drastic reduction in the energy gap of decaborane. First, the hyperpolarizability ( β 0) of B10H14 dramatically increased in the presence of titanium (Ti) in the place of hydrogen atoms. The highest value of β 0 (≈ 98,387.90 a.u.) was obtained for B10TiH13 (in the S3 position) and calculated to be 1700 times larger than the β 0 value for B10H14 (≈57.82 a.u.). Therefore, the Ti-doped systems showed a significantly larger non-linear optical (NLO) response than the other studied transition metals, suggesting that its system might be useful as a promising NLO material.
The Band Structure of Polymers: Its Calculation and Interpretation. Part 2. Calculation.
Duke, B. J.; O'Leary, Brian
1988-01-01
Details ab initio crystal orbital calculations using all-trans-polyethylene as a model. Describes calculations based on various forms of translational symmetry. Compares these calculations with ab initio molecular orbital calculations discussed in a preceding article. Discusses three major approximations made in the crystal case. (CW)
Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations
Energy Technology Data Exchange (ETDEWEB)
Wang, Lin-Wang; Lee, Byounghak; Shan, Hongzhang; Zhao, Zhengji; Meza, Juan; Strohmaier, Erich; Bailey, David H.
2008-07-01
We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39percent of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFTcalculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N3) methods, and the potential for petascale computation using the LS3DF method.
Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki
2015-06-01
Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.
Zhang, Chuanzhao; Kuang, Xiaoyu; Jin, Yuanyuan; Lu, Cheng; Zhou, Dawei; Li, Peifang; Bao, Gang; Hermann, Andreas
2015-12-09
We present results of an unbiased structure search for stable ruthenium silicide compounds with various stoichiometries, using a recently developed technique that combines particle swarm optimization algorithms with first-principles calculations. Two experimentally observed structures of ruthenium silicides, RuSi (space group P2(1)3) and Ru2Si3 (space group Pbcn), are successfully reproduced under ambient pressure conditions. In addition, a stable RuSi2 compound with β-FeSi2 structure type (space group Cmca) was found. The calculations of the formation enthalpy, elastic constants, and phonon dispersions demonstrate the Cmca-RuSi2 compound is energetically, mechanically, and dynamically stable. The analysis of electronic band structures and densities of state reveals that the Cmca-RuSi2 phase is a semiconductor with a direct band gap of 0.480 eV and is stabilized by strong covalent bonding between Ru and neighboring Si atoms. On the basis of the Mulliken overlap population analysis, the Vickers hardness of the Cmca structure RuSi2 is estimated to be 28.0 GPa, indicating its ultra-incompressible nature.
Sîretanu, Igor; van den Ende, Henricus T.M.; Mugele, Friedrich Gunther
2016-01-01
Atomic scale details of surface structure play a crucial role for solid–liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to
First-principles calculations of BC{sub 4}N nanostructures: stability and electronic structure
Energy Technology Data Exchange (ETDEWEB)
Freitas, A.; Azevedo, S. [Universidade Federal da Paraiba, CCEN, Departamento de Fisica, Joao Pessoa, PB (Brazil); Machado, M. [Universidade Federal de Pelotas, Departamento de Fisica, Pelotas, RS (Brazil); Kaschny, J.R. [Instituto Federal da Bahia-Campus Vitoria da Conquista, Vitoria da Conquista, BA (Brazil)
2012-07-15
In this work, we apply first-principles methods to investigate the stability and electronic structure of BC{sub 4}N nanostructures which were constructed from hexagonal graphite layers where substitutional nitrogen and boron atoms are placed at specific sites. These layers were rolled up to form zigzag and armchair nanotubes, with diameters varying from 7 to 12 A, or cut and bent to form nanocones, with 60 and 120 disclination angles. The calculation results indicate that the most stable structures are the ones which maximize the number of B-N and C-C bonds. It is found that the zigzag nanotubes are more stable than the armchair ones, where the strain energy decreases with increasing tube diameter D, following a 1/D {sup 2} law. The results show that the 60 disclination nanocones are the most stable ones. Additionally, the calculated electronic properties indicate a semiconducting behavior for all calculated structures, which is intermediate to the typical behaviors found for hexagonal boron nitride and graphene. (orig.)
Directory of Open Access Journals (Sweden)
FANG FANG JIAN
2010-09-01
Full Text Available The main aim of this study was to investigate the relationship between mIn tA new Ni(II complex of bisglycinato-bis[p-(hydroxylmethylpy-ridine] was synthesized and characterized by elemental analysis, IR, UV–Vis spectroscopy and X-ray single crystal diffraction analysis. The thermal stability of the title complex was also determined. The complex adopts a distorted octahedral geometry and possesses inversion symmetry with the Ni(II ion as the center of inversion. Density function theory (DFT calculations of the structure, electronic absorption spectra, electron structure and natural population analysis (NPA at the B3LYP/LANL2DZ level of theory were performed. The predicted geometric parameters and electronic spectra were compared with the experimental values and they supported each other. The NPA results indicate that the electronic transitions were mainly derived from the contribution of an intra-ligand (IL transition, a ligand-to-metal charge transfer (LMCT transition and a d-d transition. The electron structure calculations suggest that the central Ni(II ion uses its 4s and 3d orbitals to form covalent bonds with coordinated N and O atoms. The calculated bond orders are also consistent with the thermal decomposition results. Based on vibrational analysis, the thermodynamic properties of the title complex were predicted and the correlative equations between these thermodynamic properties and temperature are also reported.
Atomic structures of symmetric tilt grain boundaries in hexagonal close packed (hcp) crystals
Wang, J.; Beyerlein, I. J.
2012-03-01
Using molecular dynamics (MD) simulations, the dislocation structures of [1 \\bar {2} 1 0] symmetric tilt grain boundaries (STGBs) in hexagonal close packed (hcp) crystal structures are studied. STGBs over the entire range of possible rotation angles θ from 0° to 90° are found to have an ordered atomic structure. Formation energy calculations reveal four local minimum-energy boundaries that correspond to coherent grain boundaries (GBs). Deviations in tilt from the basal plane (θ = 0°, P_B(1) ) , prismatic plane (θ = 90°, P_B(6) ) , or one of these four minimum-energy boundaries, P_B(2) ,P_B(3) ,P_B(4) ,P_B(5) , result in the formation of a tilt wall (edge-type grain boundary dislocations, GBDs) superimposed on the nearest GB structure P_B(i) in θ-space. As θ deviates far from the rotation angle of one P_B(i) and draws closer to that of an adjacent P_B(j) , an abrupt transition in STGB base boundary structure and GBD Burgers vector occurs. For all θ, the sign and spacing of GBDs depend on θ, and their Burgers vector is either one or two times the interplanar spacing of PB. We present a simple model that generalizes the results to other c/a ratios. Subsequent MD simulations show that (1) the model forecasts the STGB structure to first-order and (2) STGBs with two distinct atomic structures can have remarkably different responses when interacting with basal lattice dislocations originating from the adjoining crystals.
Brachytherapy structural shielding calculations using Monte Carlo generated, monoenergetic data
Energy Technology Data Exchange (ETDEWEB)
Zourari, K.; Peppa, V.; Papagiannis, P., E-mail: ppapagi@phys.uoa.gr [Medical Physics Laboratory, Medical School, University of Athens, 75 Mikras Asias, 11527 Athens (Greece); Ballester, Facundo [Department of Atomic, Molecular and Nuclear Physics, University of Valencia, Burjassot 46100 (Spain); Siebert, Frank-André [Clinic of Radiotherapy, University Hospital of Schleswig-Holstein, Campus Kiel 24105 (Germany)
2014-04-15
: The data of this work allow for the accurate calculation of structural shielding thickness, taking into account the spectral variation with shield thickness, and broad beam conditions, in a realistic geometry. The simplicity of calculations also obviates the need for the use of crude transmission data estimates such as the half and tenth value layer indices. Although this study was primarily designed for brachytherapy, results might also be useful for radiology and nuclear medicine facility design, provided broad beam conditions apply.
Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas
2015-08-01
and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.
Atomic structure of machined semiconducting chips: An x-ray absorption spectroscopy study
Energy Technology Data Exchange (ETDEWEB)
Paesler, M.; Sayers, D.
1988-12-01
X-ray absorption spectroscopy (XAS) has been used to examine the atomic structure of chips of germanium that were produced by single point diamond machining. It is demonstrated that although the local (nearest neighbor) atomic structure is experimentally quite similar to that of single crystal specimens information from more distant atoms indicates the presence of considerable stress. An outline of the technique is given and the strength of XAS in studying the machining process is demonstrated.
Page 1 Electronic structure calculation of Cumn alloy 187 chosen ...
Indian Academy of Sciences (India)
Schwartz (1976). Since neutral atoms were put together to form the cluster, a net charge of zero electron was promoted to the Watson sphere. The atomic value of radius of Cu was assigned as its muffin-tin radius. The radius of Mn was obtained by subtracting the Cu radius from Cu-Mn bond length, so that the muffin-tin ...
Bhattacharjee, Rahul; Chattopadhyaya, Surya
2017-09-01
The effects of doping of Ca atom(s) on structural, electronic and optical properties of binary strontium chalcogenide semiconductor compounds have been investigated theoretically using DFT based FP-LAPW approach by modeling the rock-salt (B1) ternary alloys CaxSr1-xS, CaxSr1-xSe and CaxSr1-xTe at some specific concentrations 0 ≤ x ≤ 1 and studying their aforesaid properties. The exchange-correlation potentials for their structural properties have been computed using the Wu-Cohen generalized-gradient approximation (WC-GGA) scheme, while those for the electronic and optical properties have been computed using recently developed Tran-Blaha modified Becke-Johnson (TB-mBJ) scheme. In addition, we have computed the electronic and optical properties with the traditional BLYP and PBE-GGA schemes for comparison. The atomic and orbital origin of different electronic states in the band structure of each of the compounds have been identified from the respective density of states (DOS). Using the approach of Zunger and co-workers, the microscopic origin of band gap bowing has been discussed in term of volume deformation, charge exchange and structural relaxation. Bonding characteristics among the constituent atoms of each of the specimens have been discussed from their charge density contour plots. Optical properties of the binary compounds and ternary alloys have been investigated theoretically in terms of their respective dielectric function, refractive index, normal incidence reflectivity and optical conductivity. Several calculated results have been compared with available experimental and other theoretical data.
Energy Technology Data Exchange (ETDEWEB)
Segala, Maximiliano [Universidade Estadual do Rio Grande do Sul, Rua Oscar Matzembacher 475, 96760-000, Tapes, RS (Brazil); Chong, Delano P. [Department of Chemistry, 2036 Main Mall, University of British Columbia, Vancouver, B.C., V6T 1Z1 (Canada)], E-mail: chong@chem.ubc.ca
2009-04-15
In this paper, ionization energies of gas-phase atoms and molecules are calculated by energy-difference method and by approximate transition-state models with density functional theory (DFT). To determine the best functionals for ionization energies, we first study the H to Ar atoms. An approximation is used in which the electron density is first obtained from Kohn-Sham computations with an exchange-correlation potential V{sub xc} known as statistical average of orbital potentials (SAOP), after which the energy is computed from that density with 59 different exchange-correlation energy functionals E{sub xc}. For the 18 atoms, the best E{sub xc} functional providing an average absolute deviation (AAD) of only 0.110 eV is one known as the Krieger-Chen-Iafrate-Savin functional modified by Krieger, Chen, Iafrate, and Kurth, if one uses the spin-polarized spherical atom description. On the other hand, if one imposes the condition of integer-electrons, the best functional is the Becke 1997 functional modified by Wilson, Bradley, and Tozer, with an AAD of 0.107 eV, while several other functionals perform almost as well. For molecules, we can achieve an accuracy of AAD = 0.21 eV for valence VIPs of nonperhalo molecules with {delta}E(V{sub xc} = SAOP;PBE0) using integer-electron description. For perhalo molecules our best approach is {delta}E(V{sub xc} from either E{sub xc} or SAOP;mPW1PW) with full symmetry to obtain an AAD = 0.24 eV.
Accelerating VASP electronic structure calculations using graphic processing units
Hacene, Mohamed
2012-08-20
We present a way to improve the performance of the electronic structure Vienna Ab initio Simulation Package (VASP) program. We show that high-performance computers equipped with graphics processing units (GPUs) as accelerators may reduce drastically the computation time when offloading these sections to the graphic chips. The procedure consists of (i) profiling the performance of the code to isolate the time-consuming parts, (ii) rewriting these so that the algorithms become better-suited for the chosen graphic accelerator, and (iii) optimizing memory traffic between the host computer and the GPU accelerator. We chose to accelerate VASP with NVIDIA GPU using CUDA. We compare the GPU and original versions of VASP by evaluating the Davidson and RMM-DIIS algorithms on chemical systems of up to 1100 atoms. In these tests, the total time is reduced by a factor between 3 and 8 when running on n (CPU core + GPU) compared to n CPU cores only, without any accuracy loss. © 2012 Wiley Periodicals, Inc.
Structural evolution and atomic dynamics in Ni-Nb metallic glasses: A molecular dynamics study
Xu, T. D.; Wang, X. D.; Zhang, H.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.
2017-10-01
The composition and temperature dependence of static and dynamic structures in NixNb1-x (x = 50-70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu-Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni-Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni-Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.
Atomic structure and electrochemical potential of Li[sub 1+x]V[sub 3]O[sub 8
Energy Technology Data Exchange (ETDEWEB)
Benedek, R.; Thackeray, M.M. (Chemical Technology Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)); Yang, L.H. (Condensed Matter Physics Division, Lawrence Livermore National Laboratory, University of California, Livermore, California 94551 (United States))
1999-09-01
The atomic configurations and total energies of both monoclinic phases of Li[sub 1+x]V[sub 3]O[sub 8], a candidate electrode material in rechargeable Li batteries, are calculated as a function of [ital x] within local-density-functional theory, using the plane-wave pseudopotential method. The predicted structures at the most standard compositions, 1+x=1.2 and 1+x=4, agree closely with x-ray-diffraction measurements of atomic structure. As Li is inserted into the low-Li compound, Li(2) is half filled and then S[sub t](3) is half filled, where the Li sites are labeled as in de Picciotto [ital et al.] This is followed by the onset of a two-phase region. Calculations of the electrochemical potential as a function of lithiation are in excellent overall agreement with experiment. thinsp [copyright] [ital 1999] [ital The American Physical Society
Energy Technology Data Exchange (ETDEWEB)
Carlsund, C. (Manne Siegbahn Inst. of Physics, Stockholm (Sweden) Dept. of Theoretical Physics, Royal Inst. of Tech., Stockholm (Sweden)); Krylstedt, P. (Manne Siegbahn Inst. of Physics, Stockholm (Sweden) Dept. of Theoretical Physics, Royal Inst. of Tech., Stockholm (Sweden) Swedish National Defence Establishment, Stockholm (Sweden)); Elander, N. (Manne Siegbahn Inst. of Physics, Stockholm (Sweden)); Cowan, R.D. (Los Alamos National Lab., NM (USA))
1990-09-01
Our work on analytically continued scattering theory based on the Schroedinger equation is reviewed. We give a brief description of how resonances, here defined as partial wave S-matrix poles, can be calculated as complex eigenvalues to the complex scaled Schroedinger equation. A Mittag-Leffler type expansion is then introduced and it is shown how one can partition a scattering cross section into contributions from isolated S-matrix poles and a background. Computationally this method has proven to be considerably faster than conventional methods. A new, faster and more accurate integration method is used. Examples of detailed previous work as well as current research are given. (orig.).
Directory of Open Access Journals (Sweden)
Alberto Milani
2015-02-01
Full Text Available Graphene, nanotubes and other carbon nanostructures have shown potential as candidates for advanced technological applications due to the different coordination of carbon atoms and to the possibility of π-conjugation. In this context, atomic-scale wires comprised of sp-hybridized carbon atoms represent ideal 1D systems to potentially downscale devices to the atomic level. Carbon-atom wires (CAWs can be arranged in two possible structures: a sequence of double bonds (cumulenes, resulting in a 1D metal, or an alternating sequence of single–triple bonds (polyynes, expected to show semiconducting properties. The electronic and optical properties of CAWs can be finely tuned by controlling the wire length (i.e., the number of carbon atoms and the type of termination (e.g., atom, molecular group or nanostructure. Although linear, sp-hybridized carbon systems are still considered elusive and unstable materials, a number of nanostructures consisting of sp-carbon wires have been produced and characterized to date. In this short review, we present the main CAW synthesis techniques and stabilization strategies and we discuss the current status of the understanding of their structural, electronic and vibrational properties with particular attention to how these properties are related to one another. We focus on the use of vibrational spectroscopy to provide information on the structural and electronic properties of the system (e.g., determination of wire length. Moreover, by employing Raman spectroscopy and surface enhanced Raman scattering in combination with the support of first principles calculations, we show that a detailed understanding of the charge transfer between CAWs and metal nanoparticles may open the possibility to tune the electronic structure from alternating to equalized bonds.
Efremova, P. V.; Ped'ko, B. B.; Kuznecova, Yu. V.
2016-02-01
The structure of lithium niobate single crystals is studied by a complex technique that combines scanning electron microscopy and atomic force microscopy. By implementing the piezoresponse force method on an atomic force microscope, the domain structure of lithium niobate crystals, which was not revealed without electron beam irradiation, is visualized
Energy Technology Data Exchange (ETDEWEB)
Kupczyk-Subotkowska, L.; Saunders, W.H. Jr.; Shine, H.J.
1988-10-12
Kinetic isotope effects (KIE) were measured for the rearrangement at 220/degree/C of allyl ether (1) which was labeled successively at its oxygen atom ((/sup 18/O)-1), /alpha/-carbon atom ((/alpha/-/sup 14/C)-1), /gamma/-carbon atom ((/gamma/-/sup 14/C)-1), and ortho-carbon atom ((2-/sup 14/C)-1). The KIE were 1.0297 (/sup 18/O), 1.0306 (/alpha/-/sup 14/C), 1.0362 (/gamma/-/sup 14/C), and 1.0375 (2-/sup 14/C). KIE were determined from isotopic abundances in the product, o-allylphenol (2), which were measured by multiscan mass spectrometry (/sup 18/O) and scintillation counting (/sup 14/C). A model of the transition structure was then developed, whose bond orders gave calculated KIE in reasonably good agreement not only with the experimentally determined heavy-atom KIE but also with the deuterium KIE reported earlier by McMichael and Korver. A loose transition structure was thus found for the rearrangement of 1 into 2. In this transition structure the C/sub /alpha//-O bond is 50-60% broken while the C/sub /gamma//-C/sub ortho/ bond is only 10-20% complete. The results thus define this concerted, nonsynchronous rearrangement more explicitly than hitherto possible. 40 references, 8 tables.
Energy Technology Data Exchange (ETDEWEB)
Clade, P
2005-10-15
From a measurement of the recoil velocity of an atom absorbing a photon, it is possible to deduce a determination of the ratio h/m between the Planck constant and the mass of the atoms and then to deduce a value of the fine structure constant alpha. To do this measurement, we use the technique of Bloch oscillations, which allows us to transfer a large number of recoils to atoms. A velocity sensor, based on velocity selective Raman transition, enables us to measure the momentum transferred to the atoms. A measurement with a statistical uncertainty of 4.4 10{sup -9}, in conjunction with a careful study of systematic effects (5 10{sup -9}), has led us to a determination of alpha with an uncertainty of 6.7 10{sup -9}: {alpha}{sup -1}(Rb) = 137.03599878 (91). This uncertainty is similar to the uncertainty of the best determinations of alpha based on atom interferometry. (author)
Convergence of calculated dislocation core structures in hexagonal close packed titanium
Poschmann, Max; Asta, Mark; Chrzan, D. C.
2018-01-01
The core structure of -type screw dislocations in hexagonal close packed titanium is investigated computationally using periodic supercells with quadrupolar configurations in combination with density functional theory (DFT) and a modified embedded atom method (MEAM) classical potential. Two arrangements of the quadrupolar supercell configurations are examined, and within each arrangement two initial dislocation positions are compared. (Meta)stable pyramidal and prismatic dislocation core structures exist within both DFT and MEAM methods, and the relaxed structure from a given configuration resulting from our anisotropic elasticity theory solution depends only on the assumed initial dislocation positions. Within DFT we find the ground state core structure to be spread on the pyramidal plane. We find that it is necessary to include the semi-core 3p electrons as valence states in the DFT calculations in order to converge the ground state dislocation core configuration and difference in energy between structures. In terms of k-point sampling, it is found that at least a 1× 1× 15 k-point mesh is necessary to converge the dislocation core structure for a supercell one Burgers vector deep. Use of higher k-point densities or inclusion of additional semi-core electronic states as valence electrons results in the same core structure. With the MEAM potential considered in this work, we find the ground state core configuration to be spread predominantly on the prismatic plane, in contrast with the DFT results.
Self-Consistent Calculation of Atomic Adsorption on Metals in High Electric Fields
1991-05-17
this problem was recently performed by Gies and Gerhardts ( 3 ) and also by Schreier and Rebentrost(4). Including the crystal structure, Inglesfield has...Kohn, Phys. Rev.B 1, 4555 (1970); 3, 1215 (1971); 7, 3541 (1973). 3. P. Gies and R.R. Gerhardts , Phys. Rev. B 33, 982 (1981). 4. F. Schreier and F
Intracluster atomic and electronic structural heterogeneities in supported nanoscale metal catalysts
Elsen, A.; Jung, U.; Vila, F.; Li, Y.; Safonova, O.V.; Thomas, R.; Tromp, M.; Rehr, J.J.; Nuzzo, R.G.; Frenkel, A.I.
2015-01-01
This work reveals and quantifies the inherent intracluster heterogeneity in the atomic structure and charge distribution present in supported metal catalysts. The results demonstrate that these distributions are pronounced and strongly coupled to both structural and dynamic perturbations. They also
Lobato, I; Rojas, J; Landauro, C V; Torres, J
2009-02-04
The structural evolution and dynamics of silver nanodrops Ag(2869) (4.4 nm in diameter) under rapid cooling conditions have been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modelled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique are used to reveal the structural transition in the process of solidification. It is shown that Ag nanoparticles evolve into different nanostructures under different cooling processes. At a cooling rate of 1.5625 × 10(13) K s(-1) the nanoparticles preserve an amorphous-like structure containing a large amount of 1551 and 1541 pairs which correspond to icosahedral symmetry. For a lower cooling rate (1.5625 × 10(12) K s(-1)), the nanoparticles transform into a crystal-like structure consisting mainly of 1421 and 1422 pairs which correspond to the face centred cubic and hexagonal close packed structures, respectively. The variations of the electronic density of states for the differently cooled nanoparticles are small, but in correspondence with the structural changes.
Adaptations in Electronic Structure Calculations in Heterogeneous Environments
Energy Technology Data Exchange (ETDEWEB)
Talamudupula, Sai [Iowa State Univ., Ames, IA (United States)
2011-01-01
Modern quantum chemistry deals with electronic structure calculations of unprecedented complexity and accuracy. They demand full power of high-performance computing and must be in tune with the given architecture for superior e ciency. To make such applications resourceaware, it is desirable to enable their static and dynamic adaptations using some external software (middleware), which may monitor both system availability and application needs, rather than mix science with system-related calls inside the application. The present work investigates scienti c application interlinking with middleware based on the example of the computational chemistry package GAMESS and middleware NICAN. The existing synchronous model is limited by the possible delays due to the middleware processing time under the sustainable runtime system conditions. Proposed asynchronous and hybrid models aim at overcoming this limitation. When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting statically and dynamically its fragment scheduling policy based on the computing platform conditions. Signi cant execution time and throughput gains have been obtained due to such static adaptations when the compute nodes have very di erent core counts. Dynamic adaptations are based on the main memory availability at run time. NICAN prompts FMO to postpone scheduling certain fragments, if there is not enough memory for their immediate execution. Hence, FMO may be able to complete the calculations whereas without such adaptations it aborts.
Atomic Structures of Molecules Based on Additivity of Atomic and/or Ionic Radii
Raji Heyrovska; Sara Narayan
2009-01-01
The authors have shown in recent years that interatomic and interionic distances are sums of the radii of the adjacent atoms and/or ions. Many examples will be provided and it will be shown how the experimental bond lengths agree with the radii sums. The examples include inorganic compounds like alkali halides, metal hydrides, graphene, etc., organic like aliphatic and aromatic compounds and biochemical like nucleic acids, amino acids, caffeine-related compounds and vitamins.
Polydopamine and eumelanin molecular structures investigated with ab initio calculations.
Chen, Chun-Teh; Martin-Martinez, Francisco J; Jung, Gang Seob; Buehler, Markus J
2017-02-01
A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin. All probable early-polymerized 5,6-dihydroxyindole (DHI) oligomers, ranging from dimers to tetramers, have been systematically analyzed to find the most stable geometry connections as well as to propose a set of molecular models that represents the chemically diverse nature of PDA and eumelanin. Our results indicate that more planar oligomers have a tendency to be more stable. This finding is in good agreement with recent experimental observations, which suggested that PDA and eumelanin are composed of nearly planar oligomers that appear to be stacked together via π-π interactions to form graphite-like layered aggregates. We also show that there is a group of tetramers notably more stable than the others, implying that even though there is an inherent chemical diversity in PDA and eumelanin, the molecular structures of the majority of the species are quite repetitive. Our results also suggest that larger oligomers are less likely to form. This observation is also consistent with experimental measurements, supporting the existence of small oligomers instead of large polymers as main components of PDA and eumelanin. In summary, this work brings an insight into the controversial structure of PDA and eumelanin, explaining some of the most important structural features, and providing a set of molecular models for more accurate modeling of eumelanin-like materials.
The finite difference method in electronic structure calculations
Energy Technology Data Exchange (ETDEWEB)
Fattebert, Jean -Luc [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-11-21
Since the development of quantum mechanics, we know the equations describing the behavior of atoms and electrons at the microscopic level. The Schroedinger equation is however too difficult to solve for more than a few particles because of the high dimensional space of the solution - 3N for N particles. So various simplified models have been developed. Furthermore, the first simplification usually introduced is the Born-Oppenhaimer approximation in which atomic nuclei are treated as classical particles surrounded by quantum electrons.
Structure of the electron momentum density of atomic systems
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Romera, E.; Dehesa, J.S. [Granada Univ. (Spain). Dept. de Fisica Moderna; Koga, T. [Department of Applied Chemistry, Muroran Institute of Technology, Muroran, Hokkaido 050 (Japan)
1997-12-01
The present paper addresses the controversial problem on the nonmonotonic behavior of the spherically-averaged momentum density {gamma}(p) observed previously for some ground-state atoms based on the Roothaan-Hartree-Fock (RHF) wave functions of Clementi and Roetti. Highly accurate RHF wave functions of Koga et al. are used to study the existence of extrema in the momentum density {gamma}(p) of all the neutral atoms from hydrogen to xenon. Three groups of atoms are clearly identified according to the nonmonotonicity parameter {mu}, whose value is either equal to, larger, or smaller than unity. Additionally, it is found that the function p{sup -{alpha}} {gamma}(p) is (i) monotonically decreasing from the origin for {alpha}{>=}0.75, (ii) convex for {alpha}{>=}1.35, and (iii) logarithmically convex for {alpha}{>=}3.64 for all the neutral atoms with nuclear charges Z = 1-54. Finally, these monotonicity properties are applied to derive simple yet general inequalities which involve three momentum moments left angle p{sup t} right angle. These inequalities not only generalize similar inequalities reported so far but also allow us to correlate some fundamental atomic quantities, such as the electron-electron repulsion energy and the peak height of Compton profile, in a simple manner. (orig.) 40 refs.
QED Based Calculation of the Fine Structure Constant
Energy Technology Data Exchange (ETDEWEB)
Lestone, John Paul [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2016-10-13
Quantum electrodynamics is complex and its associated mathematics can appear overwhelming for those not trained in this field. Here, semi-classical approaches are used to obtain a more intuitive feel for what causes electrostatics, and the anomalous magnetic moment of the electron. These intuitive arguments lead to a possible answer to the question of the nature of charge. Virtual photons, with a reduced wavelength of λ, are assumed to interact with isolated electrons with a cross section of πλ^{2}. This interaction is assumed to generate time-reversed virtual photons that are capable of seeking out and interacting with other electrons. This exchange of virtual photons between particles is assumed to generate and define the strength of electromagnetism. With the inclusion of near-field effects the model presented here gives a fine structure constant of ~1/137 and an anomalous magnetic moment of the electron of ~0.00116. These calculations support the possibility that near-field corrections are the key to understanding the numerical value of the dimensionless fine structure constant.
Wright, Christopher James
Engineering the next generation of materials, especially nanomaterials, requires a detailed understanding of the material's underlying atomic structure. These structures give us better insight into structure-property relationships, allowing for property driven material design on the atomic level. Even more importantly, understanding structures in-situ will translate stimuli and responses on the macroscopic scale to changes on the nanoscale. Despite the importance of precise atomic structures for materials design, solving atomic structures is difficult both experimentally and computationally. Atomic pair distribution functions (PDFs) provide information on atomic structure, but the difficulty of extracting the PDF from x-ray total scattering measurements limits their use. Translating the PDF into an atomic structure requires the search of a very high dimensional space, the set of all potential atomic configurations. The large computational cost of running these simulations also limits the use of PDF as an atomistic probe. This work aims to address these issues by developing 1) novel statistical mechanical approaches to solving material structures, 2) fast simulation of x-ray total scattering and atomic pair distribution functions (PDFs), and 3) data processing procedures for experimental x-ray total scattering measurements. First, experimentally derived potential energy surfaces (PES) and the statistical mechanical ensembles used to search them are developed. Then the mathematical and computational framework for the PDF and its gradients will be discussed. The combined PDF-PES-ensemble system will be benchmarked against a series of nanoparticle structures to ascertain the efficiency and effectiveness of the system. Experimental data processing procedures, which maximize the usable data, will be presented. Finally, preliminary results from experimental x-ray total scattering measurements will be discussed. This work presents one of the most complete end
Femtosecond structural dynamics on the atomic length scale
Energy Technology Data Exchange (ETDEWEB)
Zhang, Dongfang
2014-03-15
This thesis reports on the development and application of two different but complementary ultrafast electron diffraction setups built at the Max Planck Research Department for Structural Dynamics. One is an ultra-compact femtosecond electron diffraction (FED) setup (Egun300), which is currently operational (with a maximum electron energy of 150 keV) and provides ultrashort (∝300 fs) and bright (∝10 e/μm{sup 2}) electron bunches. The other one, named as Relativistic Electron Gun for Atomic Exploration (REGAE) is a radio frequency driven 2 to 5 MeV FED setup built in collaboration with different groups from DESY. REGAE was developed as a facility that will provide high quality diffraction with sufficient coherence to even address structural protein dynamics and with electron pulses as short as 20 fs (FWHM). As one of the first students in Prof. R.J. Dwayne Miller's group, I led the femtosecond (fs) laser sub-group at REGAE being responsible for the construction of different key optical elements required to drive both of aforementioned FED systems. A third harmonic generation (THG) and a nonlinear optical parametric amplifier (NOPA) have been used for the photo-generation of ultrashort electron bursts as well as sample laser excitation. Different diagnostic tools have been constructed to monitor the performance of the fs optical system. A fast autocorrelator was developed to provide on the fly pulse duration correction. A transient-grating frequency-resolved optical gating (TG-FROG) was built to obtain detail information about the characteristics of fs optical pulse, i.e. phase and amplitude of its spectral components. In addition to these optical setups, I developed a fs optical pump-probe system, which supports broadband probe pulses. This setup was successfully applied to investigate the semiconductor-to-metal photoinduced phase transition in VO{sub 2} and the ultrafast photo-reduction mechanism of graphene oxide. In regard to FED setups, I have been
Evangelisti, Luca; Pate, Brooks
2017-06-01
A study of the minimally exciting topic of agreement between experimental and measured rotational constants of molecules was performed on a set of large molecules with 16-18 heavy atoms (carbon and oxygen). The molecules are: nootkatone (C_{15}H_{22}O), cedrol (C_{15}H_{26}O), ambroxide (C_{16}H_{28}O), sclareolide (C_{16}H_{22}O_{2}), and dihydroartemisinic acid (C_{15}H_{24}O_{2}). For this set of molecules we obtained 13C-subsitution structures for six molecules (this includes two conformers of nootkatone). A comparison of theoretical structures and experimental substitution structures was performed in the spirit of the recent work of Grimme and Steinmetz.[1] Our analysis focused the center-of-mass distance of the carbon atoms in the molecules. Four different computational methods were studied: standard DFT (B3LYP), dispersion corrected DFT (B3LYP-D3BJ), hybrid DFT with dispersion correction (B2PLYP-D3), and MP2. A significant difference in these theories is how they handle medium range correlation of electrons that produce dispersion forces. For larger molecules, these dispersion forces produce an overall contraction of the molecule around the center-of-mass. DFT poorly treats this effect and produces structures that are too expanded. MP2 calculations overestimate the correction and produce structures that are too compact. Both dispersion corrected DFT methods produce structures in excellent agreement with experiment. The analysis shows that the difference in computational methods can be described by a linear error in the center-of-mass distance. This makes it possible to correct poorer performing calculations with a single scale factor. We also reexamine the issue of the "Costain error" in substitution structures and show that it is significantly larger in these systems than in the smaller molecules used by Costain to establish the error limits. [1] Stefan Grimme and Marc Steinmetz, "Effects of London dispersion correction in density functional theory on
Green, Sheldon; Defrees, D. J.; Mclean, A. D.
1991-01-01
Theoretical computations of broadening parameters are reported for three microwave lines of H2O in a bath of He atoms. The potential-energy surfaces employed are corrected for basis-set superposition error, and their reliability is checked by repeating the calculations with a different basis set for orbital expansion. The results are presented in extensive tables and discussed in detail. The corrections applied are shown to have a significant impact on the accuracy of the room-temperature broadenings determined: 8.9 sq A for the 22.2-GHz line, 11.8 sq A for the 183,3-GHz line, and 10.0 sq A for the 380.2-GHz line, in good agreement with published experimental data. The importance of collisional broadening for the atmospheric transmission of radiation and for remote-sensing applications is indicated.
Watanabe, Shinta; Sawada, Yuki; Nakaya, Masato; Yoshino, Masahito; Nagasaki, Takanori; Kameyama, Tatsuya; Torimoto, Tsukasa; Inaba, Yusuke; Takahashi, Hideharu; Takeshita, Kenji; Onoe, Jun
2016-06-01
We have investigated the electronic structures and optical properties of Fe, Co, and Ni ferrocyanide nanoparticles using first-principles relativistic many-electron calculations. The overall features of the theoretical absorption spectra for Fe, Ni, and Co ferrocyanides calculated using a first-principles many-electron method well reproduced the experimental one. The origins of the experimental absorption spectra were clarified by performing a configuration analysis based on the many-electron wave functions. For Fe ferrocyanide, the experimental absorption peaks originated from not only the charge-transfer transitions from Fe2+ to Fe3+ but also the 3d-3d intra-transitions of Fe3+ ions. In addition, the spin crossover transition of Fe3+ predicted by the many-electron calculations was about 0.24 eV. For Co ferrocyanide, the experimental absorption peaks were mainly attributed to the 3d-3d intra-transitions of Fe2+ ions. In contrast to the Fe and Co ferrocyanides, Ni ferrocyanide showed that the absorption peaks originated from the 3d-3d intra-transitions of Ni3+ ions in a low-energy region, while from both the 3d-3d intra-transitions of Fe2+ ions and the charge-transfer transitions from Fe2+ to Ni3+ in a high-energy region. These results were quite different from those of density-functional theory (DFT) calculations. The discrepancy between the results of DFT calculations and those of many-electron calculations suggested that the intra- and inter-atomic transitions of transition metal ions are significantly affected by the many-body effects of strongly correlated 3d electrons.
Energy Technology Data Exchange (ETDEWEB)
Watanabe, Shinta, E-mail: s-watanabe@nucl.nagoya-u.ac.jp, E-mail: j-onoe@nucl.nagoya-u.ac.jp; Sawada, Yuki; Nakaya, Masato; Yoshino, Masahito; Nagasaki, Takanori; Onoe, Jun, E-mail: s-watanabe@nucl.nagoya-u.ac.jp, E-mail: j-onoe@nucl.nagoya-u.ac.jp [Department of Materials, Physics and Energy Engineering, Graduated School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Kameyama, Tatsuya; Torimoto, Tsukasa [Department of Crystalline Materials Science, Graduated School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Inaba, Yusuke; Takahashi, Hideharu; Takeshita, Kenji [Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, 2-12-1-N1-16 O-okayama, Meguro-ku, Tokyo 152-8550 (Japan)
2016-06-21
We have investigated the electronic structures and optical properties of Fe, Co, and Ni ferrocyanide nanoparticles using first-principles relativistic many-electron calculations. The overall features of the theoretical absorption spectra for Fe, Ni, and Co ferrocyanides calculated using a first-principles many-electron method well reproduced the experimental one. The origins of the experimental absorption spectra were clarified by performing a configuration analysis based on the many-electron wave functions. For Fe ferrocyanide, the experimental absorption peaks originated from not only the charge-transfer transitions from Fe{sup 2+} to Fe{sup 3+} but also the 3d-3d intra-transitions of Fe{sup 3+} ions. In addition, the spin crossover transition of Fe{sup 3+} predicted by the many-electron calculations was about 0.24 eV. For Co ferrocyanide, the experimental absorption peaks were mainly attributed to the 3d-3d intra-transitions of Fe{sup 2+} ions. In contrast to the Fe and Co ferrocyanides, Ni ferrocyanide showed that the absorption peaks originated from the 3d-3d intra-transitions of Ni{sup 3+} ions in a low-energy region, while from both the 3d-3d intra-transitions of Fe{sup 2+} ions and the charge-transfer transitions from Fe{sup 2+} to Ni{sup 3+} in a high-energy region. These results were quite different from those of density-functional theory (DFT) calculations. The discrepancy between the results of DFT calculations and those of many-electron calculations suggested that the intra- and inter-atomic transitions of transition metal ions are significantly affected by the many-body effects of strongly correlated 3d electrons.
Atomic and electronic structure of silicon nanocrystals embedded in a silica matrix
Energy Technology Data Exchange (ETDEWEB)
Nguyen, Ngoc Bich; Dufour, Christian [Centre de Recherche sur les Ions, les Materiaux et la Photonique, 6 boulevard Marechal Juin, 14050 Caen Cedex (France); Petit, Sebastien [Laboratoire de Cristallographie et Sciences des Materiaux, 6 boulevard Marechal Juin, 14050 Caen Cedex (France)
2008-11-12
The atomic structures and the optical and electronic properties of silicon nanocrystals (nc-Si) in a {beta} cristobalite matrix are studied using DFT calculations provided by the AIMPRO code. Five atomic models are considered (two nanocrystal diameters of 5.6 and 11 A with and without interface defects). After total relaxation, the mean Si-Si distances in nc-Si are found to be 6% higher than those in perfect bulk silicon. The optical and electronic properties are influenced by many parameters, among which are the nanograin density and size. The quantum confinement effect is demonstrated by the increase of energy gap when decreasing nanograin size. The energy gap of nc-Si is adjusted by using B3LYP functional calculations; the energy gap of 5.6 A nc-Si is found to be equal to 3.4 eV while that of 11 A nc-Si is equal to 3.1 eV. In the band structure, the levels due to nc-Si appear in the forbidden band of SiO{sub 2}. The electronic density of these levels is presented in 3D. A redshift is observed in the optical absorption spectrum as the nc-Si size increases, and the absorbance of nc-Si/SiO{sub 2} is proportional to the nanograin density. The system is more stable as the distance between nanograins increases. We have also studied two kinds of nc-Si/SiO{sub 2} interface defects (Si-O-Si and Si = O bonds). It is found that the Si-O-Si bridge bond leads to the most stable configuration. The presence of Si = O double bonds reduces the nc-Si energy gap and leads to a redshift in the absorption spectrum. The Si-O-Si bonds produce the inverse effect, i.e. an energy gap increase associated with a blueshift in the absorption spectrum.
The Atom in a Molecule: Implications for Molecular Structure and Properties
2016-05-23
Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry
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Singh, Janpreet; Singh, Satvinder; Tripathi, S. K., E-mail: surya@pu.ac.in, E-mail: surya-tr@yahoo.com [Department of Physics, Center of Advanced Study in Physics, Panjab University, Chandigarh-160 014 (India); Singh, Gurinder; Kaura, Aman [University Institute of Engineering and Technology, Hoshiarpur, Punjab (India)
2016-05-06
The atomic arrangements and chemical bonding of stable Ge{sub 4}Sb{sub 2}Te{sub 7} (GeTe rich), a phase-change material, have been investigated by means of ab initio total energy calculations. To study the atomic arrangement, GeTe block is considered into -TeSbTeSbTe- block and -Te-Te- layer in the stacking I and II respectively. The stacking I is energetically more stable than the stacking II. The reason for more stability of the stacking I has been explained. The chemical bonding has been studied with the electronic charge density distribution around the atomic bonds. The quantity of electronic charge loosed or gained by atoms has been calculated using the Bader charge analysis. The metallic character has been studied using band structures calculations. The band gap for the stacking I and II is 0.463 and 0.219 eV respectively.
Atomic and Electronic Structure of Polar Oxide Interfaces
Energy Technology Data Exchange (ETDEWEB)
Gajdardziska-Josifovska, Marija [University of Wisconsin Milwaukee
2014-01-17
In this project we developed fundamental understanding of atomic and electronic mechanisms for stabilization of polar oxide interfaces. An integrated experimental and theoretical methodology was used to develop knowledge on this important new class of ionic materials with limited dimensionality, with implications for multiple branches of the basic and applied energy sciences.
QUASI-LANDAU STRUCTURE OF DIAMAGNETIC HELIUM RYDBERG ATOMS
Vanderveldt, T.; Vassen, W.; Hogervorst, W.
1993-01-01
Diamagnetism in helium Rydberg atoms is studied near the ionisation threshold using constant scaled-energy laser spectroscopy. Quasi-Landau resonances in the Fouriertransform of the energy spectrum are explained using the classical periodic-orbit theory. Longlaser scans combined with a
NUMERICAL CALCULATIONS IN GEOMECHANICS APPLICABLE TO LINEAR STRUCTURES
Directory of Open Access Journals (Sweden)
Vlasov Aleksandr Nikolaevich
2012-10-01
Full Text Available The article covers the problem of applicability of finite-element and engineering methods to the development of a model of interaction between pipeline structures and the environment in the complex conditions with a view to the simulation and projection of exogenous geological processes, trustworthy assessment of their impacts on the pipeline, and the testing of varied calculation methodologies. Pipelining in the areas that have a severe continental climate and permafrost soils is accompanied by cryogenic and exogenous processes and developments. It may also involve the development of karst and/or thermokarst. The adverse effect of the natural environment is intensified by the anthropogenic impact produced onto the natural state of the area, causing destruction of forests and other vegetation, changing the ratio of soils in the course of the site planning, changing the conditions that impact the surface and underground waters, and causing the thawing of the bedding in the course of the energy carrier pumping, etc. The aforementioned consequences are not covered by effective regulatory documents. The latter constitute general and incomplete recommendations in this respect. The appropriate mathematical description of physical processes in complex heterogeneous environments is a separate task to be addressed. The failure to consider the above consequences has repeatedly caused both minor damages (denudation of the pipeline, insulation stripping and substantial accidents; the rectification of their consequences was utterly expensive. Pipelining produces a thermal impact on the environment; it may alter the mechanical properties of soils and de-frost the clay. The stress of the pipeline is one of the principal factors that determines its strength and safety. The pipeline stress exposure caused by loads and impacts (self-weight, internal pressure, etc. may be calculated in advance, and the accuracy of these calculations is sufficient for practical
Nancy Anna Anasthasiya, A.; Khaneja, Mamta; Jeyaprakash, B. G.
2017-10-01
Ammonia adsorption on graphene (G) and graphene oxide (GO) was investigated through density functional theory calculations. In the GO system, the obtained binding energy, band gap, charge transfer and electronic structure revealed that the epoxide (GO-O) and hydroxyl groups (GO-OH) in GO enhance the NH3 adsorption, which leads to the chemisorption of NH3 on GO. The dissociation of NH3 to NH2 and formation of OH was also observed when the O and H atoms were separated at 0.985 Å, 1.019 Å, 1.035 Å, and 1.044 Å for various GO systems. The maximum charge transfer value was found to be 0.054 |e| with the binding energy of 1.143 eV for GO with a single epoxide (GO-1O) group. The charge transfer from NH3 to G or GO and the bond formation in this study agree with the reported experimental results.
Electronic Structure Calculations and Adaptation Scheme in Multi-core Computing Environments
Energy Technology Data Exchange (ETDEWEB)
Seshagiri, Lakshminarasimhan; Sosonkina, Masha; Zhang, Zhao
2009-05-20
Multi-core processing environments have become the norm in the generic computing environment and are being considered for adding an extra dimension to the execution of any application. The T2 Niagara processor is a very unique environment where it consists of eight cores having a capability of running eight threads simultaneously in each of the cores. Applications like General Atomic and Molecular Electronic Structure (GAMESS), used for ab-initio molecular quantum chemistry calculations, can be good indicators of the performance of such machines and would be a guideline for both hardware designers and application programmers. In this paper we try to benchmark the GAMESS performance on a T2 Niagara processor for a couple of molecules. We also show the suitability of using a middleware based adaptation algorithm on GAMESS on such a multi-core environment.
Energy Technology Data Exchange (ETDEWEB)
Nascimento, Josenaide P. do; Santos, Lourivaldo S.; Carmo, Maria Carolina L. do; Brasil, Davi S.B.; Alves, Claudio N., E-mail: nahum@ufpa.b [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Inst. de Ciencias Exatas e Naturais; Santos, Regina Helena A.; Tozzo, Erica; Ferreira, Janaina G. [Universidade de Sao Paulo (IQSC/USP), Sao Carlos, SP (Brazil). Inst. de Quimica
2010-07-01
The synthesis and X-ray crystal diffraction structure of two analogues of neolignans, 2-(4-chlorophenyl)-1-phenylethanone (20) and 2-[(4-chlorophenyl)thio]-1-(3,4-dimethoxyphenyl) propan-1-one (12) is described. The compound 12 presents activity against intracellular Leishmania donovani and Leishmania amazonensis amastigotes that cause cutaneous and visceral leishmaniasis. In addition, the density functional theory (DFT) with the B3LYP hybrid functional was employed to calculate a set of molecular descriptors for nineteen synthetic analogues of neolignans with antileishmanial activities. Afterwards, the stepwise discriminant analysis was performed to investigate possible relationship between the molecular descriptors and biological activities. Through this analysis the compounds were classified into two groups active and inactive according to their degree of biological activities, and the more important properties were charges on some key atoms, electronic affinity and ClogP. (author)
Energy Technology Data Exchange (ETDEWEB)
Erhart, Paul [Applied Physics, Chalmers University of Technology, Gothenburg (Sweden); Lawrence Livermore National Laboratory, Livermore, California (United States); Aaberg, Daniel; Sadigh, Babak [Lawrence Livermore National Laboratory, Livermore, California (United States)
2012-07-01
Rare-earth based scintillators represent a challenging class of scintillator materials due to pronounced spin-orbit coupling and subtle interactions between d and f states that cannot be reproduced by standard electronic structure methods such as density functional theory. In this contribution we present a detailed investigation of the electronic band structure of LaBr{sub 3} using the quasi-p article self-consistent GW (scGW) method. This parameter-free approach is shown to yield an excellent description of the electronic structure of LaBr{sub 3}. Specifically we reproduce the correct level ordering and spacing of the 4f and 5d states, which are inverted with respect to the free La atom, the band gap as well as the spin-orbit splitting of La-derived states. We furthermore present electronic structure calculations using G{sub 0}W{sub 0} for the important scintillator material SrI{sub 2}. We explicitly take into account spin-orbit coupling at all levels of the theory. Our results demonstrate the applicability and reliability of the scGW approach for rare-earth halides. They furthermore provide an excellent starting point for investigating the electronic structure of rare-earth dopants such as Ce and Er.
Energy Technology Data Exchange (ETDEWEB)
Gupta, Bikash C; Konar, Shyamal [Department of Physics, Visva-Bharati, Santiniketan 731235 (India); Grein, C H; Sivananthan, S [Department of Physics, University of Illinois at Chicago, 845 W Taylor Street, Chicago, IL 60607-7059 (United States)
2009-09-16
Systematic theoretical investigations are carried out under the density functional formalism in an effort to understand the initial structural evolution due to the adsorption of ZnTe on As-exposed Si(211). Our calculations indicate that after the adsorption of Zn and Te on the As-exposed Si(211), the stable atomic structure qualitatively follows the ideal atomic structure of Si(211) with alteration of various bond lengths. Since the basic symmetry of the Si(211) is preserved after the adsorption of ZnTe, the deposition of ZnTe on the As terminated Si(211) prior to the deposition of CdTe and HgCdTe is useful for obtaining an ultimate quality layer of HgCdTe on Si(211). Some of our results are compared with the available experimental results, and they are found to agree with each other qualitatively.
Atomically Monodisperse Gold Nanoclusters Catalysts with Precise Core-Shell Structure
Directory of Open Access Journals (Sweden)
Yuhan Sun
2011-09-01
Full Text Available The emphasis of this review is atomically monodisperse Aun nanoclusters catalysts (n = number of metal atom in cluster that are ideally composed of an exact number of metal atoms. Aun which range in size from a dozen to a few hundred atoms are particularly promising for nanocatalysis due to their unique core-shell structure and non-metallic electronic properties. Aun nanoclusters catalysts have been demonstrated to exhibit excellent catalytic activity in hydrogenation and oxidation processes. Such unique properties of Aun significantly promote molecule activation by enhancing adsorption energy of reactant molecules on catalyst surface. The structural determination of Aun nanoclusters allows for a precise correlation of particle structure with catalytic properties and also permits the identification of catalytically active sites on the gold particle at an atomic level. By learning these fundamental principles, one would ultimately be able to design new types of highly active and highly selective gold nanocluster catalysts for a variety of catalytic processes.
An approach to first principles electronic structure calculation by symbolic-numeric computation
Directory of Open Access Journals (Sweden)
Akihito Kikuchi
2013-04-01
Full Text Available There is a wide variety of electronic structure calculation cooperating with symbolic computation. The main purpose of the latter is to play an auxiliary role (but not without importance to the former. In the field of quantum physics [1-9], researchers sometimes have to handle complicated mathematical expressions, whose derivation seems almost beyond human power. Thus one resorts to the intensive use of computers, namely, symbolic computation [10-16]. Examples of this can be seen in various topics: atomic energy levels, molecular dynamics, molecular energy and spectra, collision and scattering, lattice spin models and so on [16]. How to obtain molecular integrals analytically or how to manipulate complex formulas in many body interactions, is one such problem. In the former, when one uses special atomic basis for a specific purpose, to express the integrals by the combination of already known analytic functions, may sometimes be very difficult. In the latter, one must rearrange a number of creation and annihilation operators in a suitable order and calculate the analytical expectation value. It is usual that a quantitative and massive computation follows a symbolic one; for the convenience of the numerical computation, it is necessary to reduce a complicated analytic expression into a tractable and computable form. This is the main motive for the introduction of the symbolic computation as a forerunner of the numerical one and their collaboration has won considerable successes. The present work should be classified as one such trial. Meanwhile, the use of symbolic computation in the present work is not limited to indirect and auxiliary part to the numerical computation. The present work can be applicable to a direct and quantitative estimation of the electronic structure, skipping conventional computational methods.
Vora-ud, Athorn
2017-11-01
In this work, thermoelectric properties of Bi and Sb atoms substituted PbTe material were predicted by Mott theory through electronic structure calculation. This calculation has been carried by the first-principles DV-Xα molecular orbital method based on Hartree-Fock-Slater approximation. The Pb14Te13, Pb13SbTe13 and Pb13BiTe13 small clusters with a cubic rocksalt structure (Fm-3m; 225) were designed to be performed PbTe, Pb0.75Sb0.25Te and Pb0.75Bi0.25Te materials, respectively. The electronic structure showed that the high symmetry crystal structure, spin energy levels, partial spin density of states and electron charge density. The energy gap and Fermi level have been obtained from energy levels and density of state to be evaluated of electrical conductivity and Seebeck coefficient within Mott's theory predication.
Strenalyuk, Tatyana; Samdal, Svein; Volden, Hans Vidar
2008-10-09
The molecular structure of phthalocyaninatotin(II), Sn(II)Pc, is determined by density functional theory (DFT/B3LYP) calculations using various basis sets and gas-phase electron diffraction (GED). The quantum chemical calculations show that Sn(II)Pc has C4V symmetry, and this symmetry is consistent with the structure obtained by GED at 427 degrees C. GED locates the Sn atom at h(Sn) ) 112.8(48) pm above the plane defined by the four isoindole N atoms, and a N-Sn bond length of 226.0(10) pm is obtained. Calculation at the B3LYP/ccpVTZ/cc-pVTZ-PP(Sn) level of theory gives h(Sn) ) 114.2 pm and a N-Sn bond length of 229.4 pm. The phthalocyanine (Pc) macrocycle has a slightly nonplanar structure. Generally, the GED results are in good agreement with the X-ray structures and with the computed structure; however, the comparability between these three methods has been questioned. The N-Sn bond lengths determined by GED and X-ray are significantly shorter than those from the B3LYP predictions. Similar trends have been found for C-Sn bonds for conjugated organometallic tin compounds. Computed vibrational frequencies give five low frequencies in the range of 18-54 cm-1, which indicates a flexible molecule.
Raji Heyrovska
2011-01-01
The author has found in recent years that bond lengths are exact sums of the radii of adjacent atoms and or ions, where the ions have Golden ratio based radii. This work was prompted by the exciting observation last year of the Golden ratio in the magnetic properties of cobalt niobate. It is shown here that in cobalt and zinc niobates, cobalt, zinc and oxygen ions have Golden ratio based ionic radii, whereas in lead niobate, all atoms have covalent radii. Also, the angles at the single bond o...
Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness
Park, Eun Jung; Light, Gregory
2009-01-01
Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…
Directory of Open Access Journals (Sweden)
Liangliang Gou
2015-11-01
Full Text Available The study of crystal structures in shape memory alloys is of fundamental importance for understanding the shape memory effect. In order to investigate the mechanism of how Cu content affects martensite crystal structures of TiNiCu alloys, the present research examines the atomic displacement of Ti50Ni50−xCux (x = 0, 5, 12.5, 15, 18.75, 20, 25 shape memory alloys using density functional theory (DFT. By the introduction of Cu atoms into TiNi martensite crystal to replace Ni, the displacements of Ti and Ni/Cu atoms along the x-axis are obvious, but they are minimal along the y- and z-axes. It is found that along the x-axis, the two Ti atoms in the unit cell move in opposite directions, and the same occurred with the two Ni/Cu atoms. With increasing Cu content, the distance between the two Ni/Cu atoms increases while the Ti atoms draw closer along the x-axis, leading to a rotation of the (100 plane, which is responsible for the decrease in the monoclinic angle. It is also found that the displacements of both Ti atoms and Ni/Cu atoms along the x-axis are progressive, which results in a gradual change of monoclinic angle and a transition to B19 martensite crystal structure.
Coccia, Emanuele; Assaraf, Roland; Luppi, Eleonora; Toulouse, Julien
2017-07-01
We propose a method for obtaining effective lifetimes of scattering electronic states for avoiding the artificial confinement of the wave function due to the use of incomplete basis sets in time-dependent electronic-structure calculations of atoms and molecules. In this method, using a fitting procedure, the lifetimes are extracted from the spatial asymptotic decay of the approximate scattering wave functions obtained with a given basis set. The method is based on a rigorous analysis of the complex-energy solutions of the Schrödinger equation. It gives lifetimes adapted to any given basis set without using any empirical parameters. The method can be considered as an ab initio version of the heuristic lifetime model of Klinkusch et al. [J. Chem. Phys. 131, 114304 (2009)]. The method is validated on H and He atoms using Gaussian-type basis sets for the calculation of high-harmonic-generation spectra.
Chuluunbaatar, O.; Gusev, A. A.; Derbov, V. L.; Kaschiev, M. S.; Kouzakov, K. A.; Serov, V. V.; Samoylov, V. N.; Tupikova, T. V.; Vinitsky, S. I.
2006-07-01
We present theoretical calculations for the evolution of Zeeman states in a train of short electric half-cycle pulses (kicks). For the numerical solution of the corresponding time-dependent Schrodinger equation (TDSE) the high accuracy splitting scheme based on the unitary approximations of the evolution operator is developed. The finite element method is used for determining the spatial form of the solution. The efficiency and stability of the developed computational method is shown for 1D models in the cases of second-, forth-, and sixth-order accuracy with respect to the time step. Numerical calculations for the kicked hydrogen atom in the presence of magnetic field are performed using the scheme of the sixth-order accuracy with respect to a time step and both Galerkin and Kantorovich reductions of the problem with respect to the angular variables. For a particular choice of the electric- and magnetic-field parameters and the initial Zeeman state the corresponding results exhibit a two-state resonance picture.
Sarkadi, L
2015-01-01
The three-body dynamics of the ionization of the atomic hydrogen by 30 keV antiproton impact has been investigated by calculation of fully differential cross sections (FDCS) using the classical trajectory Monte Carlo (CTMC) method. The results of the calculations are compared with the predictions of quantum mechanical descriptions: The semi-classical time-dependent close-coupling theory, the fully quantal, time-independent close-coupling theory, and the continuum-distorted-wave-eikonal-initial-state model. In the analysis particular emphasis was put on the role of the nucleus-nucleus (NN) interaction played in the ionization process. For low-energy electron ejection CTMC predicts a large NN interaction effect on FDCS, in agreement with the quantum mechanical descriptions. By examining individual particle trajectories it was found that the relative motion between the electron and the nuclei is coupled very weakly with that between the nuclei, consequently the two motions can be treated independently. A simple ...
The electronic structure of LaO: Ligand field versus ab initio calculations
Schamps, Joël; Bencheikh, Mohammed; Barthelat, Jean-Claude; Field, Robert W.
1995-11-01
The potentially pathological example of LaO has been chosen to test the application of ligand field theory (LFT) to metal monoxides. The test consists of a comparison of closed-shell ligand LFT (CSLLFT) results (in which a 2+/2- ionic M2+O2- model is a priori postulated with a point-charge ligand) against ab initio multiconfiguration self-consistent-field-multireference configuration interaction (MCSCF-MRCI) results (in which no ionicity is assumed a priori and an internal structure is allowed for the ligand). Special care has been devoted to the determination of a La3+ pseudopotential and its associated atomic basis set in order to keep the ab initio model close to the LFT one, yet at the same time capable of clearly exhibiting the consequences and the importance of the restrictions imposed in the CSLLFT model. The ab initio calculations reveal that the effective (Mulliken) ionicity in LaO is not La2+O2- but quite close to La+O-. Despite this, the (2+/2-) ionic CSLLFT model leads to the correct orbital occupations in the ground state but this model cannot account for the significant covalency contribution via the nominal 2pσ and 2pπ oxygen orbitals. The CSLLFT calculations correctly reproduce the excitation energies of the four lowest-lying observed states of LaO: these states are calculated to within 2000 cm-1 and globally better than via ab initio calculations. However, the (2+/2-) ionic CSLLFT model is shown to ignore the existence of a manifold of low-lying quartet (and doublet) states of (1+/1-) ionicity that might be relevant for interpreting features of the spectrum. This result exemplifies the need for developing, beyond the first attempts made in this direction, a computationally manageable open-shell ligand theory for the frequently encountered case of predominantly ionic structures with an open-shell ligand.
Structure and transport properties of atomic chains and molecules
DEFF Research Database (Denmark)
Strange, Mikkel
2008-01-01
with the experimental findings [5]. The observed conductance properties of Metal/CO are shown to be determined by the local d-band at the Metal apex atoms. For carbon nanotubes it is shown that the conductance may be controlled by site selective adsorption of molecules. A model to explain this behavior is verified...... of atomically thin, suspended chains containing silver and oxygen atoms in an alternating sequence has been studied. The conductances of the chains exhibit weak even-odd oscillations around an anomalously low value of 0.1G0 (G0 = 2e2/h) in agreement with experiments [1] in the long chain limit. These unusual...... conductance properties are explained in terms of a resonating-chain model, which takes the reflection probability and phase-shift of a single bulk-chain interface as the only input. The stability of silver-oxygen chains was studied with a thermodynamic model. This model has been developed in this work...
Systematic model calculations of the hyperfine structure in light and heavy ions
Tomaselli, M; Nörtershäuser, W; Ewald, G; Sánchez, R; Fritzsche, S; Karshenboim, S G
2003-01-01
Systematic model calculations are performed for the magnetization distributions and the hyperfine structure (HFS) of light and heavy ions with a mass close to A ~ 6 208 235 to test the interplay of nuclear and atomic structure. A high-precision measurement of lithium-isotope shifts (IS) for suitable transition, combined with an accurate theoretical evaluation of the mass-shift contribution in the respective transition, can be used to determine the root-mean-square (rms) nuclear-charge radius of Li isotopes, particularly of the halo nucleus /sup 11/Li. An experiment of this type is currently underway at GSI in Darmstadt and ISOLDE at CERN. However, the field-shift contributions between the different isotopes can be evaluated using the results obtained for the charge radii, thus casting, with knowledge of the ratio of the HFS constants to the magnetic moments, new light on the IS theory. For heavy charged ions the calculated n- body magnetization distributions reproduce the HFS of hydrogen-like ions well if QED...
Electronic Structure Calculations of Hydrogen Storage in Lithium-Decorated Metal-Graphyne Framework.
Kumar, Sandeep; Dhilip Kumar, Thogluva Janardhanan
2017-08-30
Porous metal-graphyne framework (MGF) made up of graphyne linker decorated with lithium has been investigated for hydrogen storage. Applying density functional theory spin-polarized generalized gradient approximation with the Perdew-Burke-Ernzerhof functional containing Grimme's diffusion parameter with double numeric polarization basis set, the structural stability, and physicochemical properties have been analyzed. Each linker binds two Li atoms over the surface of the graphyne linker forming MGF-Li8 by Dewar coordination. On saturation with hydrogen, each Li atom physisorbs three H2 molecules resulting in MGF-Li8-H24. H2 and Li interact by charge polarization mechanism leading to elongation in average H-H bond length indicating physisorption. Sorption energy decreases gradually from ≈0.4 to 0.20 eV on H2 loading. Molecular dynamics simulations and computed sorption energy range indicate the high reversibility of H2 in the MGF-Li8 framework with the hydrogen storage capacity of 6.4 wt %. The calculated thermodynamic practical hydrogen storage at room temperature makes the Li-decorated MGF system a promising hydrogen storage material.
Energy Technology Data Exchange (ETDEWEB)
Yin, Zhu-Hua [College of Physics and Information Technology, Shaanxi Normal University, Xian, 710119, Shaanxi (China); Zhang, Jian-Min, E-mail: jmzhang@snnu.edu.cn [College of Physics and Information Technology, Shaanxi Normal University, Xian, 710119, Shaanxi (China); Xu, Ke-Wei [State Key Laboratory for Mechanical Behavior of Materials, Xian Jiaotong University, Xian, 710049, Shaanxi (China)
2016-11-01
The spin-polarized first-principles calculations are performed to study the structural, electronic and magnetic properties of a single and two identical transition metal (TM) atoms X (X = V, Cr, Mn, Fe, Co and Ni) doped ZnS dilute magnetic semiconductors (DMS). The single V-, Cr-, Fe- and Ni-doped ZnS systems exhibit the magnetic half-metallic (HM) characters, while Mn- and Co-doped ZnS systems display magnetic semiconducting characters. For two identical TM atoms doped ZnS systems, the two identical V, Cr and Ni atoms are in a ferromagnetic (FM) coupling under the double-exchange (DE) mechanism, leading V-, Cr- and Ni-doped ZnS systems to be HM with FM coupling. While two identical Mn- and Co-doped ZnS systems are semiconductors with antiferromagnetic (AFM) coupling consisting with the superexchange (SE) mechanism. Specifically, two identical Fe atoms display a competition between the SE and DE mechanisms. The Zn{sub 70}Fe{sub 2}S{sub 72} system is metal with AFM coupling at the nearest separation of two Fe atoms while HM with FM coupling at the farther separations of two Fe atoms. - Graphical abstract: The 3 × 2 × 3 supercell containing 72 formula units of zincblende ZnS. Red (Green) balls represent the S (Zn) atoms. One TM atom or two identical TM atoms X (X = V, Cr, Mn, Fe, Co or Ni) to substitute for one Zn atom at position 0 or two Zn atoms at positions 0 and i (i = 1, 2, 3 or 4). - Highlights: • A single V, Cr, Fe or Ni (Mn or Co) atoms doped ZnS are magnetic HM (magnetic semiconductor). • Two V, Cr or Ni (two Mn or Co) atoms doped ZnS are FM HM (AFM semiconductor). • Two Fe atoms doped ZnS are AFM metal (FM HM) at the nearest (farther) separations.
Malashevich, Andrei; Marshall, Matthew S J; Visani, Cristina; Disa, Ankit S; Xu, Haichao; Walker, Frederick J; Ahn, Charles H; Ismail-Beigi, Sohrab
2017-12-26
Coherent and epitaxial interfaces permit the realization of electric field driven devices controlled by atomic-scale structural and electronic effects at interfaces. Compared to conventional field effect devices where channel conductivity is modulated by carrier density modification, the propagation of atomic-scale distortions across an interface can control the atomic scale bonding, interatomic electron tunneling rates and thus the mobility of the channel material. We use first-principles theory to design an atomically abrupt epitaxial perovskite heterostructure involving an oxide ferroelectric (PbZr0.2Ti0.8O3) and conducting oxide channel (LaNiO3) where coupling of polar atomic motions to structural distortions can induce large, reversible changes in the channel mobility. We fabricate and characterize the heterostructure and measure record values, larger than 1000%, for the conductivity modulation. Our results describe how purely interfacial effects can be engineered to deliver unique electronic device properties and large responses to external fields.
de Grauw, C.J.; de Grauw, C.J.; Avogadro, A.; van den Heuvel, D.J.; van den Heuvel, D.J.; van der Werf, Kees; Otto, Cornelis; Kraan, Yvonne M.; van Hulst, N.F.; Greve, Jan
1998-01-01
Polytene chromosomes from Drosophila melanogaster, observed from squash preparations, and chromosomes from Chironomus thummi thummi, investigated under physiological conditions, are imaged using an Atomic Force Microscope. Various chromatin fiber structures can be observed with high detail in fixed
Dey, Tanusri; Praveena, Koduru Sri Shanthi; Pal, Sarbani; Mukherjee, Alok Kumar
2017-06-01
Three oxime ether derivatives, (E)-3-methoxy-4-(prop-2-ynyloxy)-benzaldehyde-O-prop-2-ynyl-oxime (C14H13NO3) (2), benzophenone-O-prop-2-ynyl-oxime (C16H13NO) (3) and (E)-2-chloro-6-methylquinoline-3-carbaldehyde-O-prop-2-ynyl-oxime (C14H11ClN2O) (4), have been synthesized and their crystal structures have been determined. The DFT optimized molecular geometries in 2-4 agree closely with those obtained from the crystallographic study. An interplay of intermolecular Csbnd H⋯O, Csbnd H⋯N, Csbnd H⋯Cl and Csbnd H···π(arene) hydrogen bonds and π···π interactions assembles molecules into a 2D columnar architecture in 2, a 1D molecular ribbon in 3 and a 3D framework in 4. Hirshfeld surface analysis showed that the structures of 2 and 3 are mainly characterized by H⋯H, H⋯C and H⋯O contacts but some contribution of H⋯N and H⋯Cl contacts is also observed in 4. Hydrogen-bond based interactions in 2-4 have been complemented by calculating molecular electrostatic potential (MEP) surfaces. The electronic structures of molecules reveal that the estimated band gap in 3, in which both aldehyde hydrogen atoms of formaldehyde-O-prop-2-ynyl-oxime (1) have been substituted by two benzene rings, is higher than that of 2 and 4 with only one aldehyde hydrogen atom replaced.
Fischer, Charlotte Froese
1986-06-01
The self-consistent field (SCF) and multiconfiguration (MC) Hartree-Fock (HF) methods are reviewed. The emphasis is on the specification, design and implementation of these methods as a part of an atomic structure software package, dealing with wavefunction determination. Numerical integration approaches will be used throughout. After outlining a class of MCHF problems, the derivation of the MCHF equations is reviewed and some theory developed on the variation of the energy functional with respect to a rotation of the orbital basis among orbitals of the same symmetry. Various procedures are proposed and evaluated for dealing with cases where the radial basis for a given total energy is not unique. A numerical MC SCF procedure is described using a top-down approach. The overall algorithm will be outlined first with numerical details provided later. Finally some test cases are proposed.
Structural influence on atomic hopping and electronic states of Pd-based bulk metallic glasses
Tang, X.-P.; Löffler, Jörg F.; Schwarz, R. B.; Johnson, William L.; Wu, Yue
2005-01-01
Atomic motion and electronic structures of Pd–Ni–Cu–P bulk metallic glasses were investigated using 31P nuclear magnetic resonance. The hopping rate of P atoms was determined by the stimulated echo technique. Significant hopping was observed in all alloys well below the glass transition temperature. Increasing the Cu content to above 25 at. % increases P hopping significantly, consistent with the previous finding that the openness of the structure increases with Cu content. In contrast, P h...
Hinuma, Yoyo; Hayashi, Hiroyuki; Kumagai, Yu; Tanaka, Isao; Oba, Fumiyasu
2017-09-01
High-throughput first-principles calculations based on density functional theory (DFT) are a powerful tool in data-oriented materials research. The choice of approximation to the exchange-correlation functional is crucial as it strongly affects the accuracy of DFT calculations. This study compares performance of seven approximations, six of which are based on Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) with and without Hubbard U and van der Waals corrections (PBE, PBE+U, PBED3, PBED3+U, PBEsol, and PBEsol+U), and the strongly constrained and appropriately normed (SCAN) meta-GGA on the energetics and crystal structure of elementary substances and binary oxides. For the latter, only those with closed-shell electronic structures are considered, examples of which include C u2O , A g2O , MgO, ZnO, CdO, SnO, PbO, A l2O3 , G a2O3 , I n2O3 , L a2O3 , B i2O3 , Si O2 , Sn O2 , Pb O2 , Ti O2 , Zr O2 , Hf O2 , V2O5 , N b2O5 , T a2O5 , Mo O3 , and W O3 . Prototype crystal structures are selected from the Inorganic Crystal Structure Database (ICSD) and cation substitution is used to make a set of existing and hypothetical oxides. Two indices are proposed to quantify the extent of lattice and internal coordinate relaxation during a calculation. The former is based on the second invariant and determinant of the transformation matrix of basis vectors from before relaxation to after relaxation, and the latter is derived from shifts of internal coordinates of atoms in the unit cell. PBED3, PBEsol, and SCAN reproduce experimental lattice parameters of elementary substances and oxides well with few outliers. Notably, PBEsol and SCAN predict the lattice parameters of low dimensional structures comparably well with PBED3, even though these two functionals do not explicitly treat van der Waals interactions. SCAN gives formation enthalpies and Gibbs free energies closest to experimental data, with mean errors (MEs) of 0.01 and -0.04 eV, respectively, and root
Amano, Ken-ich
2013-01-01
Recent frequency-modulated atomic force microscopy (FM-AFM) can measure three-dimensional force distribution between a probe and a sample surface in liquid. The force distribution is, in the present circumstances, assumed to be solvation structure on the sample surface, because the force distribution and solvation structure have somewhat similar shape. However, the force distribution is exactly not the solvation structure. If we would like to obtain the solvation structure by using the liquid AFM, a method for transforming the force distribution into the solvation structure is necessary. Therefore, in this letter, we present the transforming method in a brief style. We call this method as a solution for an inverse problem, because the solvation structure is obtained at first and the force distribution is obtained next in general calculation processes. The method is formulated (mainly) by statistical mechanics of liquid.
Litsarev, Mikhail S.
2013-02-01
A description of the DEPOSIT computer code is presented. The code is intended to calculate total and m-fold electron-loss cross-sections (m is the number of ionized electrons) and the energy T(b) deposited to the projectile (positive or negative ion) during a collision with a neutral atom at low and intermediate collision energies as a function of the impact parameter b. The deposited energy is calculated as a 3D integral over the projectile coordinate space in the classical energy-deposition model. Examples of the calculated deposited energies, ionization probabilities and electron-loss cross-sections are given as well as the description of the input and output data. Program summaryProgram title: DEPOSIT Catalogue identifier: AENP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 8726 No. of bytes in distributed program, including test data, etc.: 126650 Distribution format: tar.gz Programming language: C++. Computer: Any computer that can run C++ compiler. Operating system: Any operating system that can run C++. Has the code been vectorised or parallelized?: An MPI version is included in the distribution. Classification: 2.4, 2.6, 4.10, 4.11. Nature of problem: For a given impact parameter b to calculate the deposited energy T(b) as a 3D integral over a coordinate space, and ionization probabilities Pm(b). For a given energy to calculate the total and m-fold electron-loss cross-sections using T(b) values. Solution method: Direct calculation of the 3D integral T(b). The one-dimensional quadrature formula of the highest accuracy based upon the nodes of the Yacobi polynomials for the cosθ=x∈[-1,1] angular variable is applied. The Simpson rule for the φ∈[0,2π] angular variable is used. The Newton-Cotes pattern of the seventh order
Structure-Property Relationships in Atomic-Scale Junctions: Histograms and Beyond.
Hybertsen, Mark S; Venkataraman, Latha
2016-03-15
are pulled apart has given complementary information such as the stiffness and rupture force of the molecule-metal link bond. Overall, while the BJ technique does not produce a single molecule circuit for practical applications, it has proved remarkably versatile for fundamental studies. Measured data and analysis have been combined with atomic-scale theory and calculations, typically performed for representative junction structures, to provide fundamental physical understanding of structure-function relationships. This Account integrates across an extensive series of our specific nanoscale junction studies which were carried out with the STM- and AFM-BJ techniques and supported by theoretical analysis and density functional theory based calculations, with emphasis on the physical characteristics of the measurement process and the rich data sets that emerge. Several examples illustrate the impact of measured trends based on the most probable values for key characteristics (obtained from ensembles of order 1000-10 000 individual junctions) to build a solid picture of conductance phenomena as well as attributes of the link bond chemistry. The key forward-looking question posed here is the extent to which the full data sets represented by the individual trajectories can be analyzed to address structure-function questions at the level of individual junctions. Initial progress toward physical modeling of conductance of individual junctions indicates trends consistent with physical junction structures. Analysis of junction mechanics reveals a scaling procedure that collapses existing data onto a universal force-extension curve. This research directed to understanding the distribution of structures and physical characteristics addresses fundamental questions concerning the interplay between chemical control and stochastically driven diversity.
Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst
Zhu, Yihan
2012-08-28
The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex inhomogeneities. Here, we report an atomic structure study of an important MoVTeO complex metal oxide catalyst that is potentially useful for the industrially relevant propane-based BP/SOHIO process. We combined aberration-corrected scanning transmission electron microscopy with synchrotron powder X-ray crystallography to explore the structure at both nanoscopic and macroscopic scales. At the nanoscopic scale, this material exhibits structural and compositional order within nanosized "domains", while the domains show disordered distribution at the macroscopic scale. We proposed that the intradomain compositional ordering and the interdomain electric dipolar interaction synergistically induce the displacement of Te atoms in the Mo-V-O channels, which determines the geometry of the multifunctional metal oxo-active sites.
Amanullah, Mohamed Jamal Bin; Adam, Tijjani; Dhahi, Th S.; Mohammed, Mohammed; Hashim, U.; Noriman, N. Z.; Dahham, Omar S.
2017-09-01
Silicon is the most important material in semiconductor industry. As nano-devices shrink in size, the conventional understanding of electronic devices are no longer applicable as quantum effects start to play an important role for the behavior of the device. At the same time, when structures are approaching atomic scale, the precise fabrication by photo-lithographic techniques, for example, are not even applicable. Very often, the fabrication of regular structures rely on self-assembly is susceptible to fluctuations. Therefore, a deeper understanding to exploit the quantum behavior of nano-devices and precise control of building nano-structures are highly desired. Thus, genetic algorithm based on first principle analysis to optimize silicon nanowires electron and elastic properties is proposed. One nanometer (1nm) surface reconstruction by using genetic algorithm combined with ab-initio calculation is proposed. The SiNWs behavior to quasi-direct band gap transition with the decrease size and the band gap properties under different electrical voltage will be determined.
Structural Calculations of Drip Shield Exposed to Vibratory Ground Motion
Energy Technology Data Exchange (ETDEWEB)
S. Mastilovic
2003-06-16
The objective of this calculation is twofold. First, to determine whether or not separation of interlocking drip shield (DS) segments occurs during vibratory ground motion. Second, if DS separation does not occur, to estimate the area of the DS for which the residual 1st principal stress exceeds a certain limit. (The area of DS plate-1 and DS plate-2 [see Attachment I] where the residual 1st principal stress exceeds a certain limit will be, for brevity, referred to as ''the damaged area'' throughout this document; also, DS plate-1 and DS plate-2 will be referred to, for brevity, as ''DS plates'' henceforth.) The stress limit used throughout this document is defined as 50 percent of yield strength of the DS plate material, Titanium Grade 7 (Ti-7) (SB-265 R52400), at temperature of 150 C. A set of 15 calculations is performed at two different annual frequencies of occurrence (annual exceedance frequency): 10{sup -6} per year (1/yr) and 10{sup -7} 1/yr . (Note: Due to computational problems only five realizations at 10{sup -7} 1/yr are presented in this document.) Additionally, one calculation is performed at the annual frequency of occurrence of 5 {center_dot} 10{sup -4} 1/yr. The scope of this document is limited to reporting whether or not the DS separation occurs. If the DS separation does not occur the scope is limited to reporting the calculation results in terms of the damaged area. All these results are evaluated for the DS plates. This calculation is intended for use in support of the Total System Performance Assessment-License Application seismicity modeling. This calculation is associated with the DS design and was performed by the Waste Package Design group. AP-3.12Q, ''Design Calculations and Analyses'' (Ref. 1) is used to perform the calculation and develop the document. The DS is classified as Quality Level 1 (Ref. 5, p. 7). Therefore, this calculation is subject to the Quality Assurance
Energy Technology Data Exchange (ETDEWEB)
Wang, Lin-Wang
2006-12-01
Quantum mechanical ab initio calculation constitutes the biggest portion of the computer time in material science and chemical science simulations. As a computer center like NERSC, to better serve these communities, it will be very useful to have a prediction for the future trends of ab initio calculations in these areas. Such prediction can help us to decide what future computer architecture can be most useful for these communities, and what should be emphasized on in future supercomputer procurement. As the size of the computer and the size of the simulated physical systems increase, there is a renewed interest in using the real space grid method in electronic structure calculations. This is fueled by two factors. First, it is generally assumed that the real space grid method is more suitable for parallel computation for its limited communication requirement, compared with spectrum method where a global FFT is required. Second, as the size N of the calculated system increases together with the computer power, O(N) scaling approaches become more favorable than the traditional direct O(N{sup 3}) scaling methods. These O(N) methods are usually based on localized orbital in real space, which can be described more naturally by the real space basis. In this report, the author compares the real space methods versus the traditional plane wave (PW) spectrum methods, for their technical pros and cons, and the possible of future trends. For the real space method, the author focuses on the regular grid finite different (FD) method and the finite element (FE) method. These are the methods used mostly in material science simulation. As for chemical science, the predominant methods are still Gaussian basis method, and sometime the atomic orbital basis method. These two basis sets are localized in real space, and there is no indication that their roles in quantum chemical simulation will change anytime soon. The author focuses on the density functional theory (DFT), which is the
Dynamical Mean Field Theory and Electronic Structure Calculations
Chitra, R.; Kotliar, G.
1999-01-01
We formulate the dynamical mean field theory directly in the continuum. For a given definition of the local Green's function, we show the existence of a unique functional, whose stationary point gives the physical local Green's function of the solid. We present the diagrammatic rules to calculate it perturbatively in the interaction. Inspired by the success of dynamical mean field calculations for model Hamiltonian systems, we present approximations to the exact saddle point equations which m...
New density-independent interactions for nuclear structure calculations
Directory of Open Access Journals (Sweden)
Bennaceur K.
2014-03-01
Full Text Available We present a new two-body finite-range and momentum-dependent but density-independent effective interaction, which can be interpreted as a regularized zerorange force. We show that no three-body or density-dependent terms are needed for a correct description of saturation properties in infinite matter, that is, on the level of lowenergy density functional, the physical three-body effects can be efficiently absorbed in effective two-body terms. The new interaction gives a satisfying equation of state of nuclear matter and opens up extremely interesting perspectives for the mean-field and beyond-mean-field descriptions of atomic nuclei.
Ghatee, Mohammad Hadi; Bahrami, Maryam
2017-06-01
We investigate to contrasting structure, dynamic and thermophysical properties of quaternary ammonium and phosphonium ionic liquids (ILs) based on triethylalkylammonium [N222n]+ and triethylalkylphosphonium [P222n]+ cations (n = 5, 8, 12) and (bis(trifluoromethylsulfonyl)imide) anion [NTf2]- by quantum chemical calculations (QCC) and molecular dynamics (MD) simulations. QCCs conform to previous studies, showing that phosphonium cation alkyl chain rotational-energy-barrier is lower than ammonium cation. These molecular nature leads to no appreciable differences in their liquid density. However, their simulated transport properties (self-diffusion, conductivity, etc) are appreciably different. In particular, viscosity of phosphoniums are much lower than ammoniums. Ammoniums make nano-scale structural domains larger than phosphoniums. Employed analysis, vector re-orientational dynamics, ion-pair lifetime and nanostructure domain are in favor of faster dynamic for phosphoniums than ammoniums. [NTf2]- anion features a long lived pairing with ammoniums than phosphoniums. Overall, phosphoniums possess higher transference number, higher conductivity, and appreciably lower viscosity favorable for higher electrochemical performances.
Xu, Bing; Shi, Peipei; Huang, Tengfei; Wang, Xuefeng
2017-10-01
Reactions of laser-ablated cerium atoms with silane were investigated by matrix isolation infrared spectroscopy and theoretical calculations. The reaction products, Si(μ-H)3CeH, H3SiCeH, H2Si(μ-H)CeH and HSi(μ-H)2CeH were identified on the basis of the SiD4 isotopic substitutions and DFT frequency calculations. In the solid argon or krypton matrix, the inserted H3SiCeH molecule was observed as initial product on deposition, which rearranged to hydrogen bridge species Si(μ-H)3CeH on follow-up annealing through H2Si(μ-H)CeH and HSi(μ-H)2CeH species. The Sisbnd Hsbnd Ce hydrogen bridge was investigated by NBO and ELF analysis. Calculation suggested that in Si(μ-H)3CeH molecule Ce atom donated one electron to Si atom, resulting in electron-rich SiH3 subunit, which was confirmed by ESP and AIM analysis. The increased basicity of Sisbnd H bond facilitates the formation of hydrogen bridge bond between Si and Ce. For comparison only insertion H3CCeH structure was obtained from the reaction of Ce atoms with CH4.
Mondal, Abhisek; Datta, Saumen
2017-06-01
Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Atomic-structural synergy for catalytic CO oxidation over palladium-nickel nanoalloys.
Shan, Shiyao; Petkov, Valeri; Yang, Lefu; Luo, Jin; Joseph, Pharrah; Mayzel, Dina; Prasai, Binay; Wang, Lingyan; Engelhard, Mark; Zhong, Chuan-Jian
2014-05-14
Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly active and stable catalysts. However, the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium-nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable maximal catalytic activity at Pd:Ni ratio of ~50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies.
Ono, Tomoya; Kirkham, Christopher James; Saito, Shoichiro; Oshima, Yoshifumi
2017-09-01
Density functional theory calculations are carried out to investigate the atomic and electronic structures of the 4 H -SiC(0001 )/SiO2 interface. We find two characteristic interface atomic structures in scanning transmission electron microscopy images: One is an interface in which the density of atoms at the first interfacial SiC bilayer is greater than that in the SiC substrate, while the other is an interface where the density of atoms at the first interfacial SiC bilayer is lower. Density functional theory calculations reveal that the difference in the scanning transmission electron microscopy images is a reflection of the atomic structures of these two interfaces. In addition, it has been reported that the floating states, which appear at the conduction band edge of a 4 H -SiC(0001 )/SiO2 interface, affect the electronic structure of the interface and cause marked scattering of the electrons flowing along the interface [S. Iwase, C. J. Kirkham, and T. Ono, Phys. Rev. B 95, 041302(R) (2017), 10.1103/PhysRevB.95.041302]. Interestingly, we find that the floating states do not appear at the conduction band edge of one of the two interfaces. These results provide physical insights into understanding and controlling the electronic structure and carrier mobility of electronic devices using wide-band-gap semiconductors.
Structure and transport at grain boundaries in polycrystalline olivine: An atomic-scale perspective
Mantisi, Boris; Sator, Nicolas; Guillot, Bertrand
2017-12-01
Structure and transport properties at grain boundaries in polycrystalline olivine have been investigated at the atomic scale by molecular dynamics simulation (MD) using an empirical ionocovalent interaction potential. On the time scale of the simulation (a few tens of nanoseconds for a system size of ∼650,000 atoms) grain boundaries and grain interior were identified by mapping the atomic displacements along the simulation run. In the investigated temperature range (1300-1700 K) the mean thickness of the grain boundary phase is evaluated between 0.5 and 2 nm, a value which depends on temperature and grain size. The structure of the grain boundary phase is found to be disordered (amorphous-like) and is different from the one exhibited by the supercooled liquid. The self-diffusion coefficients of major elements in the intergranular region range from ∼10-13 to 10-10 m2/s between 1300 and 1700 K (with DSigb < DOgb < DFegb < DMggb) and are only one order of magnitude smaller than those evaluated in the supercooled melt. In using a newly derived expression for the bulk self-diffusion coefficient it is concluded that the latter one is driven by the grain boundary contribution as long as the grain size is smaller than a centimeter. In assuming that the electrical conduction at grain boundaries is purely ionic, the macroscopic grain boundary conductivity is found to be two orders of magnitude lower than in molten olivine, and one order of magnitude higher than the lattice conductivity. A consequence is that the conductivity of the olivine polycrystal is dominated by the grain interior contribution as soon as the grain size is larger than a micrometer or so. The grain boundary viscosity has been evaluated from the Green-Kubo relation expressing the viscosity as function of the stress tensor time correlation function. In spite of a slow convergence of the calculation by MD, the grain boundary viscosity was estimated about ∼105 Pa s at 1500 K, a value in agreement with
Local atomic and electronic structure of boron chemical doping in monolayer graphene.
Zhao, Liuyan; Levendorf, Mark; Goncher, Scott; Schiros, Theanne; Pálová, Lucia; Zabet-Khosousi, Amir; Rim, Kwang Taeg; Gutiérrez, Christopher; Nordlund, Dennis; Jaye, Cherno; Hybertsen, Mark; Reichman, David; Flynn, George W; Park, Jiwoong; Pasupathy, Abhay N
2013-10-09
We use scanning tunneling microscopy and X-ray spectroscopy to characterize the atomic and electronic structure of boron-doped and nitrogen-doped graphene created by chemical vapor deposition on copper substrates. Microscopic measurements show that boron, like nitrogen, incorporates into the carbon lattice primarily in the graphitic form and contributes ~0.5 carriers into the graphene sheet per dopant. Density functional theory calculations indicate that boron dopants interact strongly with the underlying copper substrate while nitrogen dopants do not. The local bonding differences between graphitic boron and nitrogen dopants lead to large scale differences in dopant distribution. The distribution of dopants is observed to be completely random in the case of boron, while nitrogen displays strong sublattice clustering. Structurally, nitrogen-doped graphene is relatively defect-free while boron-doped graphene films show a large number of Stone-Wales defects. These defects create local electronic resonances and cause electronic scattering, but do not electronically dope the graphene film.
Engel-Vosko GGA calculations of the structural, electronic and optical properties of LiYO2
Muhammad, Nisar; Khan, Afzal; Haidar Khan, Shah; Sajjaj Siraj, Muhammad; Shah, Syed Sarmad Ali; Murtaza, Ghulam
2017-09-01
Structural, electronic and optical properties of lithium yttrium oxide (LiYO2) are investigated using density functional theory (DFT). These calculations are based on full potential linearized augmented plane wave (FP-LAPW) method implemented by WIEN2k. The generalized gradient approximation (GGA) is used as an exchange correlation potential with Perdew-Burk-Ernzerhof (PBE) and Engel-Vosko (EV) as exchange correlation functional. The structural properties are calculated with PBE-GGA as it gives the equilibrium lattice constants very close to the experimental values. While, the band structure and optical properties are calculated with EV-GGA obtain much closer results to their experimental values. Our calculations confirm LiYO2 as large indirect band gap semiconductor having band gap of 5.23 eV exhibiting the characteristics of ultrawide band gap materials showing the properties like higher critical breakdown field, higher temperature operation and higher radiation tolerance. In this article, we report the density of states (DOS) in terms of contribution from s, p, and d-states of the constituent atoms, the band structure, the electronic structure, and the frequency-dependent optical properties of LiYO2. The optical properties presented in this article reveal LiYO2 a suitable candidate for the field of optoelectronic and optical devices.
Raji Heyrovska; Lakshmi Atchison; Sara Narayan
2010-01-01
Nanomaterials are currently of great importance in science, technology and commercial applications. Since these materials are atomic layer thick and are a few square nanometers of area, a knowledge of their precise atomic structures will help in the exact understanding of the properties at the nanoscale and in the fabrication and design of the nanomaterials for their many uses. Their known inter-atomic distances have been used here to obtain the exact atomic radii of the component atoms and t...
Mota, F de B; Rivelino, R; Medeiros, P V C; Mascarenhas, A J S; de Castilho, C M C
2014-11-21
First-principles calculations demonstrate that line/ribbon defects, resulting from a controlled dehydrogenation in graphane, lead to the formation of low-dimensional electron-rich tracks in a monolayer. The present simulations point out that hybrid graphane-graphene nanostructures exhibit important elements, greatly required for the fabrication of efficient electronic circuits at the atomic level.
First-principle calculations of structural, electronic, optical, elastic ...
Indian Academy of Sciences (India)
The predicted band gaps using the modified Becke–Johnson(mBJ) exchange approximation are in fairly good agreement with the experimental data. The optical constants such as the dielectric function, refractive index, and the extinction coefficient are calculated and analysed. The independent elastic parameters namely, ...
First-principle calculations of structural, electronic, optical, elastic ...
Indian Academy of Sciences (India)
S CHEDDADI
2017-11-28
Nov 28, 2017 ... The predicted band gaps using the modified Becke–Johnson. (mBJ) exchange approximation are in fairly good agreement with the experimental data. The optical constants such as the dielectric function, refractive index, and the extinction coefficient are calculated and analysed. The independent elastic ...
Ab initio calculation of the Structural, Mechanical and ...
African Journals Online (AJOL)
ADOWIE PERE
ABSTRACT: An ab initio plane-wave Pseudopotential calculations using the density functional theory (DFT) .... wave Pseudopotential PWPP method with the ..... Γ the longitudinal optical LO branch shows a sharp increasing amount of upward dispersion while the TO , a flat/horizontal dispersion it was also observed that the ...
Molecular-Field Calculation of the Magnetic Structure in Erbium
DEFF Research Database (Denmark)
Jensen, J.
1976-01-01
A molecular-field calculation of the magnetic configurations in Er is found to reproduce the neutron diffraction results of the three different magnetic phases and to give a reasonable fit to the magnetization data at 4.2K. The two-ion coupling is considered to be described by the inter...
Microscopic Nuclear Structure and Reaction Calculations in the FMD Approach
Neff, T.; Feldmeier, H.; Langanke, K.
We present here a first application of the Fermionic Molecular Dynamics (FMD) approach to low-energy nuclear reactions, namely the $^3$He($\\alpha$,$\\gamma$)$^7$Be radiative capture reaction. We divide the Hilbert space into an external region where the system is described as $^3$He and $^4$He clusters interacting only via the Coulomb interaction and an internal region where the nuclear interaction will polarize the clusters. Polarized configurations are obtained by a variation after parity and angular momentum projection procedure with respect to the parameters of all single particle states. A constraint on the radius of the intrinsic many-body state is employed to obtain polarized clusters at desired distances. The boundary conditions for bound and scattering states are implemented using the Bloch operator. The FMD calculations reproduce the correct energy for the centroid of the $3/2^-$ and $1/2^-$ bound states in $^7$Be. The charge radius of the ground state is in good agreement with recent experimental results. The FMD calculations also describe well the experimental phase shift data in the $1/2^+$, $3/2^+$ and $5/2^+$ channels that are important for the capture reaction at low energies. Using the bound and scattering many-body wave functions we calculate the radiative capture cross section. The calculated $S$ factor agrees very well, both in absolute normalization and energy dependence, with the recent experimental data from the Weizmann, LUNA, Seattle and ERNA experiments.
Calculation of hybrid joints used in modern aerospace structures
Directory of Open Access Journals (Sweden)
Marcel STERE
2011-12-01
Full Text Available The state – of - the art of aeronautical structures show that parts are manufactured and subsequently assembled with the use of fasteners and/ or bonding. Adhesive bonding is a key technology to low weight, high fatigue resistance, robustness and an attractive design for cost structures.The paper results resolve significant problems for two groups of end-users:1 for the aerospace design office: a robust procedure for the design of the hybrid joint structural components;2 for the aeronautical repair centres: a useful procedure for structural design and analysis with significant cost savings.
The structure of filled skutterudites and the local vibration behavior of the filling atom
Zhou, Xiaojuan; Zong, Peng-an; Chen, Xihong; Tao, Juzhou; Lin, He
2017-02-01
Both of atomic pair distribution function (PDF) and extended x-ray absorption fine structure (EXAFS) experiments have been carried out on unfilled and Yb-filled skutterudites YbxCo4Sb12 (x=0, 0.15, 0.2 and 0.25) samples. The structure refinements on PDF data confirm the large amplitude vibration of Yb atom and the dependence of Yb vibration amplitude on the filling content. Temperature dependent EXAFS experiment on filled skutterudites have been carried out at Yb LⅢ-edge in order to explore the local vibration behavior of filled atom. EXAFS experiments show that the Einstein temperature of the filled atom is very low (70.9 K) which agrees with the rattling behavior.
The structure of filled skutterudites and the local vibration behavior of the filling atom
Energy Technology Data Exchange (ETDEWEB)
Zhou, Xiaojuan [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Dongguan Institute of Neutron Science, Dongguan 523808 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zong, Peng-an [State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Chen, Xihong [Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Tao, Juzhou, E-mail: taoj@ihep.ac.cn [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Dongguan Institute of Neutron Science, Dongguan 523808 (China); Lin, He, E-mail: linhe@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201204 (China)
2017-02-15
Both of atomic pair distribution function (PDF) and extended x-ray absorption fine structure (EXAFS) experiments have been carried out on unfilled and Yb-filled skutterudites Yb{sub x}Co{sub 4}Sb{sub 12} (x=0, 0.15, 0.2 and 0.25) samples. The structure refinements on PDF data confirm the large amplitude vibration of Yb atom and the dependence of Yb vibration amplitude on the filling content. Temperature dependent EXAFS experiment on filled skutterudites have been carried out at Yb L{sub Ⅲ}-edge in order to explore the local vibration behavior of filled atom. EXAFS experiments show that the Einstein temperature of the filled atom is very low (70.9 K) which agrees with the rattling behavior.
Atomic-Scale Structure and Local Chemistry of CoFeB-MgO Magnetic Tunnel Junctions.
Wang, Zhongchang; Saito, Mitsuhiro; McKenna, Keith P; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi
2016-03-09
Magnetic tunnel junctions (MTJs) constitute a promising building block for future nonvolatile memories and logic circuits. Despite their pivotal role, spatially resolving and chemically identifying each individual stacking layer remains challenging due to spatially localized features that complicate characterizations limiting understanding of the physics of MTJs. Here, we combine advanced electron microscopy, spectroscopy, and first-principles calculations to obtain a direct structural and chemical imaging of the atomically confined layers in a CoFeB-MgO MTJ, and clarify atom diffusion and interface structures in the MTJ following annealing. The combined techniques demonstrate that B diffuses out of CoFeB electrodes into Ta interstitial sites rather than MgO after annealing, and CoFe bonds atomically to MgO grains with an epitaxial orientation relationship by forming Fe(Co)-O bonds, yet without incorporation of CoFe in MgO. These findings afford a comprehensive perspective on structure and chemistry of MTJs, helping to develop high-performance spintronic devices by atomistic design.
A Real-Time All-Atom Structural Search Engine for Proteins
Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.
2014-01-01
Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designabilit...
A real-time all-atom structural search engine for proteins.
Gabriel Gonzalez; Brett Hannigan; DeGrado, William F.
2014-01-01
Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designabilit...
DEFF Research Database (Denmark)
Long, A.; Rydberg, Patrik
2013-01-01
To enhance the discrimination rate for methods applying structural alerts and biotransformation rules in the prediction of toxicity and drug metabolism we have developed a set of novel fragment based atomic descriptors. These atomic descriptors encode the properties of the fragments separating...... an atom from the closest end of a branch or the molecule. The end of a branch and the end of a molecule, as well as the selection of the fragments, are made by an algorithm that uses only the distance matrix of the molecule. The novel descriptors are applied to a small set of biotransformation rules...
Atomic tritium as a surface nanoprobe in a structural investigation of molecular assemblies
Energy Technology Data Exchange (ETDEWEB)
Badun, G.A.; Lukashina, E.V.; Batuk, O.N.; Ksenofontov, A.L.; Fedoseev, V.M
2003-12-15
Possibilities of atomic tritium application as surface nanoprobe for structural investigations of adsorption layers on the liquid-air interface have been demonstrated. Frozen aqueous solutions of a series of amino acids and their mixtures and one well-known surface-active substance (cetyltrimethylammonium bromide, CTAB) were exposed to bombardment by tritium atoms generated on hot tungsten wire in a special vacuum device. This procedure resulted in substitution of hydrogen atoms by radioactive tritium in the thin surface layer of investigated samples. Curves of radioactivity changes depending on bombardment time and solution concentration for applied compounds were obtained and analyzed.
Gholibeigian, Hassan
2015-03-01
Iranian Philosopher, Mulla Sadra (1571-1640) in his theory of ``Substantial motion'' emphasized that ``the universe moves in its entity'', and ``the time is the fourth dimension of the universe'' This definition of space-time is proposed by him at three hundred years before Einstein. He argued that the time is magnitude of the motion (momentum) of the matter in its entity. In the other words, the time for each atom (body) is sum of the momentums of its involved fundamental particles. The momentum for each atom is different from the other atoms. In this methodology, by proposing some formulas, we can calculate the time for involved particles' momentum (time) for each atom in a second of the Eastern Time Zone (ETZ). Due to differences between these momentums during a second in ETZ, the time for each atom, will be different from the other atoms. This is the relativity in quantum physics. On the other hand, the God communicates with elementary particles via sub-particles (see my next paper) and transfers the packages (bit) of information and laws to them for processing and selection of their next step. Differences between packages like complexity and velocity of processing during the time, is the second variable in relativity of time for each atom which may be effective on the factor.
Energy Technology Data Exchange (ETDEWEB)
Kravtsova, Antonina N., E-mail: akravtsova@sfedu.ru [Research Center for Nanoscale Structure of Matter, Southern Federal University, Sorge str. 5, 344090 Rostov-on-Don (Russian Federation); Lomachenko, Kirill A. [Research Center for Nanoscale Structure of Matter, Southern Federal University, Sorge str. 5, 344090 Rostov-on-Don (Russian Federation); Department of Chemistry and NIS Centre of Excellence, University of Turin, Via P. Giuria 7, 10125 Turin (Italy); Soldatov, Alexander V., E-mail: soldatov@sfedu.ru [Research Center for Nanoscale Structure of Matter, Southern Federal University, Sorge str. 5, 344090 Rostov-on-Don (Russian Federation); Meyer, Jennifer; Niedner-Schatteburg, Gereon [Technische Universität Kaiserslautern, Fachbereich Chemie und Forschungszentrum OPTIMAS, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern (Germany); Peredkov, Sergey [Helmholtz-Zentrum Berlin für Materialien und Energie, Wilhelm-Conrad-Röntgen-Campus Adlershof, Elektronenspeicherring BESSY II, Albert-Einstein-Straße 15, Berlin (Germany); Eberhardt, Wolfgang [Technische Universität Berlin, IOAP, Straße des 17. Juni 135, 10623 Berlin (Germany); Neeb, Matthias, E-mail: matthias.neeb@helmholtz-berlin.de [Helmholtz-Zentrum Berlin für Materialien und Energie, Wilhelm-Conrad-Röntgen-Campus Adlershof, Elektronenspeicherring BESSY II, Albert-Einstein-Straße 15, Berlin (Germany)
2014-08-15
Highlights: • M{sub 4,5}-XANES spectra have been calculated for several structural models of free Nb{sub 13}{sup +} cluster. • Theoretical M{sub 4,5}-XANES have been compared with the experimental spectrum of free Nb{sub 13}{sup +}. • Icosahedral structure of Nb{sub 13}{sup +} shows better agreement with experiment than the “amorphous” one. • Distance between Nb atoms in the icosahedral cluster is distinctly reduced as compared to the bulk phase. - Abstract: The atomic and electronic structure of free niobium nanoclusters has been studied on the basis of X-ray absorption near-edge structure (XANES) spectroscopy and density functional theory. M{sub 4,5}-XANES spectra have been calculated for several structural models of the 13-atomic niobium cluster. The calculations have been done on the basis of both full multiple scattering theory within the muffin-tin approximation for a potential and full-potential finite difference method. The comparison of the experimental M{sub 4,5}-edge XANES spectrum (Peredkov et al., J. Electron Spectros. Relat. Phenomena 184 (2011) 113–118) with the simulated X-ray absorption spectra of Nb{sub 13}{sup +} hints to a highly-symmetric icosahedral structure of the cluster. An internuclear distance of 2.2 ± 0.1 Å between neighboring “surface” atoms of the icosahedron and 2.09 Å between the central “bulk” atom and “surface” atoms, respectively, has been found upon comparison of the experimental and theoretical XANES spectra.
Spek, Anthony L
2015-01-01
The completion of a crystal structure determination is often hampered by the presence of embedded solvent molecules or ions that are seriously disordered. Their contribution to the calculated structure factors in the least-squares refinement of a crystal structure has to be included in some way. Traditionally, an atomistic solvent disorder model is attempted. Such an approach is generally to be preferred, but it does not always lead to a satisfactory result and may even be impossible in cases where channels in the structure are filled with continuous electron density. This paper documents the SQUEEZE method as an alternative means of addressing the solvent disorder issue. It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015). Acta Cryst. C71. In the press] and other refinement programs that accept externally provided fixed contributions to the calculated structure factors. The PLATON SQUEEZE tool calculates the solvent contribution to the structure factors by back-Fourier transformation of the electron density found in the solvent-accessible region of a phase-optimized difference electron-density map. The actual least-squares structure refinement is delegated to, for example, SHELXL. The current versions of PLATON SQUEEZE and SHELXL now address several of the unnecessary complications with the earlier implementation of the SQUEEZE procedure that were a necessity because least-squares refinement with the now superseded SHELXL97 program did not allow for the input of fixed externally provided contributions to the structure-factor calculation. It is no longer necessary to subtract the solvent contribution temporarily from the observed intensities to be able to use SHELXL for the least-squares refinement, since that program now accepts the solvent contribution from an external file (.fab file) if the ABIN instruction is used. In addition, many twinned structures containing disordered solvents are now also
Grashchenko, A. S.; Kukushkin, S. A.; Osipov, A. V.; Feoktistov, N. A.
2017-07-01
This paper is dedicated to an exploration of the photoelectric properties of Si-SiC structures grown by the substitution method on silicon substrates of (001) orientation. For the samples with the synthesis times of 40, 60, 90, 120 and 900 s, magnitudes of the saturation currents are determined and the coefficients of efficiency are calculated. The obtained dependencies of the photoelectric characteristics on the synthesis time are explained using the theory of formation of dilatation dipoles during the synthesis by the method of atoms substitution.
Atomic oxygen fine-structure splittings with tunable far-infrared spectroscopy
Zink, Lyndon R.; Evenson, Kenneth M.; Matsushima, Fusakazu; Nelis, Thomas; Robinson, Ruth L.
1991-01-01
Fine-structure splittings of atomic oxygen (O-16) in the ground state have been accurately measured using a tunable far-infrared spectrometer. The 3P0-3pl splitting is 2,060,069.09 (10) MHz, and the 3Pl-3P2 splitting is 4,744,777.49 (16) MHz. These frequencies are important for measuring atomic oxygen concentration in earth's atmosphere and the interstellar medium.
Debela, T T; Wang, X D; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z
2014-02-05
Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt-Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.
Directory of Open Access Journals (Sweden)
M. V. Tchernycheva
2017-01-01
Full Text Available Subject of Research. The paper deals with development outcomes for creation method of one-electron wave functions of complex atoms, relatively simple, symmetrical for all atom electrons and free from hard computations. The accuracy and resource intensity of the approach are focused on systematic calculations of cross sections and rate constants of elementary processes of inelastic collisions of atoms or molecules with electrons (ionization, excitation, excitation transfer, and others. Method. The method is based on a set of two iterative processes. At the first iteration step the Schrödinger equation was solved numerically for the radial parts of the electron wave functions in the potential of the atomic core self-consistent field. At the second iteration step the new approximationfor the atomic core field is created that uses found solutions for all one-electron wave functions. The solution optimization for described multiparameter problem is achieved by the use of genetic algorithm. The suitability of the developed method was verified by comparing the calculation results with numerous data on the energies of atoms in the ground and excited states. Main Results. We have created the run-time version of the program for creation of sets of one-electron wave functions and calculation of the cross sections and constants of collisional transition rates in the first Born approximation. The priori available information about binding energies of the electrons for any many-particle system for creation of semi-empirical refined solutions for the one-electron wave functions can be considered at any step of this procedure. Practical Relevance. The proposed solution enables a simple and rapid preparation of input data for the numerical simulation of nonlocal gas discharge plasma. The approach is focused on the calculation of discharges in complex gas mixtures requiring inclusion in the model of a large number of elementary collisional and radiation
Schaller, Chris P.; Graham, Kate J.; Johnson, Brian J.; Jakubowski, Henry V.; McKenna, Anna G.; McIntee, Edward J.; Jones, T. Nicholas; Fazal, M. A.; Peterson, Alicia A.
2015-01-01
A one-semester, introductory chemistry course is described that develops a primarily qualitative understanding of structure-property relationships. Starting from an atoms-first approach, the course examines the properties and three-dimensional structure of metallic and ionic solids before expanding into a thorough investigation of molecules. In…
Role of anion doping on electronic structure and magnetism of GdN by first principles calculations
Zhang, Xuejing
2014-01-01
We have investigated the electronic structure and magnetism of anion doped GdN1-yXy (X = B, C, O, F, P, S and As) systems by first-principles calculations based on density functional theory. GdN 1-yXy systems doped by O, C, F, P, and S atoms are more stable than those doped by B and As atoms because of relatively high binding energies. The anion doping and the N defect states modify the density of states at the Fermi level, resulting in a decrease in spin polarization and a slight increase in the magnetic moment at the Gd and N sites. © 2014 The Royal Society of Chemistry.
Effects of the c-Si/a-SiO2 interfacial atomic structure on its band alignment: an ab initio study.
Zheng, Fan; Pham, Hieu H; Wang, Lin-Wang
2017-12-13
The crystalline-Si/amorphous-SiO2 (c-Si/a-SiO2) interface is an important system used in many applications, ranging from transistors to solar cells. The transition region of the c-Si/a-SiO2 interface plays a critical role in determining the band alignment between the two regions. However, the question of how this interface band offset is affected by the transition region thickness and its local atomic arrangement is yet to be fully investigated. Here, by controlling the parameters of the classical Monte Carlo bond switching algorithm, we have generated the atomic structures of the interfaces with various thicknesses, as well as containing Si at different oxidation states. A hybrid functional method, as shown by our calculations to reproduce the GW and experimental results for bulk Si and SiO2, was used to calculate the electronic structure of the heterojunction. This allowed us to study the correlation between the interface band characterization and its atomic structures. We found that although the systems with different thicknesses showed quite different atomic structures near the transition region, the calculated band offset tended to be the same, unaffected by the details of the interfacial structure. Our band offset calculation agrees well with the experimental measurements. This robustness of the interfacial electronic structure to its interfacial atomic details could be another reason for the success of the c-Si/a-SiO2 interface in Si-based electronic applications. Nevertheless, when a reactive force field is used to generate the a-SiO2 and c-Si/a-SiO2 interfaces, the band offset significantly deviates from the experimental values by about 1 eV.
Mathematical modeling and numerical calculation of composite structures
Golushko, S. K.
2017-10-01
The report is devoted to modeling the properties of composite materials. Two major approaches are considered: phenomenological and structural [1]. Within the framework of the first approach reinforced materials are modeled as homogeneous anisotropic medium with efficient physical and mechanical properties. In this case mechanical parameters of the material are determined basing on experimental data. In a structural approach, physical and mechanical parameters of the composite are expressed in terms of the parameters of its components and design of reinforcement that open up opportunities for improvement of the properties of composite structures. The mathematical relations describing the nonlinear elastic three-point bending of isotropic and reinforced beams with account of different strength and stiffness behavior in tension and compression are obtained. An algorithm for numerical solution of corresponding boundary-value problems is proposed and implemented. Results of numerical modeling have been compared to acquired data for polymer matrix and structural carbon fiber reinforced plastics.
Haaland, Arne; Martinsen, Kjell-Gunnar; Tafipolsky, Maxim A.; Volden, Hans Vidar; Rösler, Roland; Breunig, Hans Joachim
1997-09-01
Ab initio calculations at the MP2 level and gas electron-diffraction data of (CH 3) 2TeCl 2 show that the molecular structure is pseudo-trigonal bipyramidal with the two methyl groups occupying equatorial positions and the two Cl atoms axial positions. The bond distances are ( {GED}/{MP2 }): TeC = 213.2(5)/214.6 pm, TeCl = 250.4(3)/261.8 pm and the valence angles ∠ CTeC = {97(5)°}/{97.6°}; ∠ ClTeCl = {170(2)°}/{170.8°}.
Atomic Structure and Phase Transformations in Pu Alloys
Energy Technology Data Exchange (ETDEWEB)
Schwartz, A J; Cynn, H; Blobaum, K M; Wall, M A; Moore, K T; Evans, W J; Farber, D L; Jeffries, J R; Massalski, T B
2008-04-28
Plutonium and plutonium-based alloys containing Al or Ga exhibit numerous phases with crystal structures ranging from simple monoclinic to face-centered cubic. Only recently, however, has there been increased convergence in the actinides community on the details of the equilibrium form of the phase diagrams. Practically speaking, while the phase diagrams that represent the stability of the fcc {delta}-phase field at room temperature are generally applicable, it is also recognized that Pu and its alloys are never truly in thermodynamic equilibrium because of self-irradiation effects, primarily from the alpha decay of Pu isotopes. This article covers past and current research on several properties of Pu and Pu-(Al or Ga) alloys and their connections to the crystal structure and the microstructure. We review the consequences of radioactive decay, the recent advances in understanding the electronic structure, the current research on phase transformations and their relations to phase diagrams and phase stability, the nature of the isothermal martensitic {delta} {yields} {alpha}{prime} transformation, and the pressure-induced transformations in the {delta}-phase alloys. New data are also presented on the structures and phase transformations observed in these materials following the application of pressure, including the formation of transition phases.
Halo-like structures studied by atomic force microscopy
DEFF Research Database (Denmark)
Sørensen, Alexis Hammer; Kyhle, Anders; Hansen, L. Theil
1997-01-01
Nanometer-sized clusters of copper have been produced in a hollow cathode sputtering source and deposited on SiOx. Halo-like structures consisting of micrometer sized protrusions in the solicon oxide surface surrounded by thin rings of smaller particles are observed. The area in between seems...
Energy Technology Data Exchange (ETDEWEB)
Utsunomiya, S; Kushima, N; Katsura, K; Tanabe, S; Hayakawa, T; Sakai, H; Yamada, T; Takahashi, H; Abe, E; Wada, S; Aoyama, H [Niigata University, Niigata (Japan)
2016-06-15
Purpose: To establish a simple relation of backscatter dose enhancement around a high-Z dental alloy in head and neck radiation therapy to its average atomic number based on Monte Carlo calculations. Methods: The PHITS Monte Carlo code was used to calculate dose enhancement, which is quantified by the backscatter dose factor (BSDF). The accuracy of the beam modeling with PHITS was verified by comparing with basic measured data namely PDDs and dose profiles. In the simulation, a high-Z alloy of 1 cm cube was embedded into a tough water phantom irradiated by a 6-MV (nominal) X-ray beam of 10 cm × 10 cm field size of Novalis TX (Brainlab). The ten different materials of high-Z alloys (Al, Ti, Cu, Ag, Au-Pd-Ag, I, Ba, W, Au, Pb) were considered. The accuracy of calculated BSDF was verified by comparing with measured data by Gafchromic EBT3 films placed at from 0 to 10 mm away from a high-Z alloy (Au-Pd-Ag). We derived an approximate equation to determine the relation of BSDF and range of backscatter to average atomic number of high-Z alloy. Results: The calculated BSDF showed excellent agreement with measured one by Gafchromic EBT3 films at from 0 to 10 mm away from the high-Z alloy. We found the simple linear relation of BSDF and range of backscatter to average atomic number of dental alloys. The latter relation was proven by the fact that energy spectrum of backscatter electrons strongly depend on average atomic number. Conclusion: We found a simple relation of backscatter dose enhancement around high-Z alloys to its average atomic number based on Monte Carlo calculations. This work provides a simple and useful method to estimate backscatter dose enhancement from dental alloys and corresponding optimal thickness of dental spacer to prevent mucositis effectively.
Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P
2017-03-07
The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.
Directory of Open Access Journals (Sweden)
Michael G. Siskos
2017-03-01
Full Text Available The exact knowledge of hydrogen atomic positions of O–H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i density functional theory (DFT calculations after a structure has been determined by X-ray from single crystals or from powders; (ii 1H-NMR chemical shifts as constraints in DFT calculations, and (iii use of root-mean-square deviation between experimentally determined and DFT calculated 1H-NMR chemical shifts considering the great sensitivity of 1H-NMR shielding to hydrogen bonding properties.
Bengio, S
2003-01-01
This thesis work has been concerned with adsorption properties of silicon surfaces.The atomic and electronic structure of molecules and atoms adsorbed on Si has been investigated by means of photoemission experiments combined with synchrotron radiation.The quantitative atomic structure determination was held applying the photoelectron diffraction technique.This technique is sensible to the local structure of a reference atomic specie and has elemental and chemical-state specificity.This approach has been applied to three quite different systems with different degrees of complexity, Sb/Si(111) sq root 3x sq root 3R30 sup 0 , H sub 2 O/Si(100)2x1 and NH sub 3 /Si(111)7x7.Our results show that Sb which forms a ( sq root 3 sq root 3)R30 sup 0 phase produces a bulklike-terminated Si(111)1x1 substrate free of stacking faults.Regarding the atomic structure of its interface, this study strongly favours the T4-site milkstool model over the H3 one.An important aspect regarding the H sub 2 O/Si(100)(2x1) system was esta...
Energy Technology Data Exchange (ETDEWEB)
Han, Chang W. [Purdue Univ., West Lafayette, IN (United States); Iddir, Hakim [Argonne National Lab. (ANL), Argonne, IL (United States); Uzun, Alper [Koc Univ., Instanbul (Turkey); Curtiss, Larry A. [Argonne National Lab. (ANL), Argonne, IL (United States); Browning, Nigel D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gates, Bruce C. [Univ. of California, Davis, CA (United States); Ortalan, Volkan [Purdue Univ., West Lafayette, IN (United States)
2015-11-06
To address the challenge of fast, direct atomic-scale visualization of the diffusion of atoms and clusters on surfaces, we used aberration-corrected scanning transmission electron microscopy (STEM) with high scan speeds (as little as ~0.1 s per frame) to visualize the diffusion of (1) a heavy atom (Ir) on the surface of a support consisting of light atoms, MgO(100), and (2) an Ir_{3} cluster on MgO(110). Sequential Z-contrast images elucidate the diffusion mechanisms, including the hopping of Ir1 and the rotational migration of Ir_{3} as two Ir atoms remain anchored to the surface. Density functional theory (DFT) calculations provided estimates of the diffusion energy barriers and binding energies of the iridium species to the surfaces. The results show how the combination of fast-scan STEM and DFT calculations allow real-time visualization and fundamental understanding of surface diffusion phenomena pertaining to supported catalysts and other materials.
Large scale structural optimization of trimetallic Cu-Au-Pt clusters up to 147 atoms
Wu, Genhua; Sun, Yan; Wu, Xia; Chen, Run; Wang, Yan
2017-10-01
The stable structures of Cu-Au-Pt clusters up to 147 atoms are optimized by using an improved adaptive immune optimization algorithm (AIOA-IC method), in which several motifs, such as decahedron, icosahedron, face centered cubic, sixfold pancake, and Leary tetrahedron, are randomly selected as the inner cores of the starting structures. The structures of Cu8AunPt30-n (n = 1-29), Cu8AunPt47-n (n = 1-46), and partial 75-, 79-, 100-, and 147-atom clusters are analyzed. Cu12Au93Pt42 cluster has onion-like Mackay icosahedral motif. The segregation phenomena of Cu, Au and Pt in clusters are explained by the atomic radius, surface energy, and cohesive energy.
Soriano, L; Abbate, M; Pen, H; Prieto, P; Sanz, JM
We studied the electronic structure of TiN and VN by means of band structure calculations and spectroscopic techniques. The band structure calculations show that the bonding in these compounds is mostly covalent. The Fermi level intersects the transition metal 3d bands giving rise to the metallic
First principles calculations of structural, electronic and thermal ...
Indian Academy of Sciences (India)
Administrator
2013-07-28
Jul 28, 2013 ... full-potential linear augmented plane wave (FP-LAPW) method are investigated. The exchange–correlation energy ... The electronic band structure shows that the fundamental energy gap is direct (L–L) for all the compounds. Thermal ... voltaic energy converters (Zogg et al 1994). The semi- conductors PbS ...
Mossbauer analysis of the atomic and magnetic structure of alloys
Ovchinnikov, VV
2007-01-01
The monograph indicates the key problems that have to be solved for the further development of the Mössbauer methods for analysis of the nuclear and magnetic structure of alloys, and offer solution variants for some of these problems based on the generalised results of a wide range of theoretical and experimental investigations,including original work by the author of the book and his colleagues. Contents 1. Description of the nature of the Mössbauer effect 2. Interpretation of the ossbauer spectra of alloys 3.Electrical and magnetics hyperfine interactions of resonant nuclei in metals and
Interaction and dynamics of add-atoms with 2-dimensional structures
The interaction and dynamics of add-atoms with graphene, graphene-derivate structures and, later, MoSi$_2$, two-dimensional – single and few – atomic layers will be studied with the Perturbed Angular Correlation – PAC – technique. Graphene is also envisaged as new platform for growing semiconductor nanostructure devices, such as quantum dots and as a particularly powerful catalyst. Understanding nucleation of nanostructures and clusters on graphene and related phases in wet conditions as they are used in chemical methods in research and industry require complementary studies. These systems will therefore be studied systematically using radioactive probe atoms attaching via a transfer media (e.g., water in catalysis process) or being deposited with soft-landing techniques under vacuum and UHV conditions, as put in place at the ASPIC setup at ISOLDE. The hyperfine fields obtained under different environments are expected to reveal basic information on the rich atomic and physical mechanisms associated w...
Energy Technology Data Exchange (ETDEWEB)
Ayinol, M., E-mail: aydinolm@dicle.edu.tr [Dicle University, Faculty of Science, Department of Physics, Diyarbakir, 21280 Turkey (Turkey); Aydeniz, D., E-mail: daydeniz@hotmail.com [Artuklu University, At Rectorate of Artuklu University, Mardin (Turkey)
2016-03-25
L shell ionization cross section and L{sub i} subshells ionization cross sections of Rn, Ra, Th, U, Pu atoms calculated. For each of atoms, ten different electron impact energy values (E{sub o}) are used. Calculations carried out by using Lotz equation in Matlab. First, calculations done for non-relativistic case by using non-relativistic Lotz equation then repeated with relativistic Lotz equation. σ{sub L} total and σ{sub Li}(i = 1,2,3) subshells ionisation cross section values obtained for E{sub o} values in the energy range of E{sub Li}
Atomic shell structures observed in photoionization spectra of nickel and cobalt clusters
Energy Technology Data Exchange (ETDEWEB)
Vialle, J.L. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire; Pellarin, M. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire; Baguenard, B. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire; Lerme, J. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire; Broyer, M. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire
1995-12-31
Nickel and cobalt clusters have been studied by near threshold laser-photoionization and time-of-flight mass spectrometry. In the size domain from 50 up to 800 atoms, the mass distributions of the photoionized products look very similar for nickel and cobalt clusters. In both cases a regular structure is observed which is periodic on a N{sup 1/3} scale. It is found to be consistent with the filling of successive icosahedral shells of atoms. The recurring details of this structure agree with the so-called umbrellas model. (orig.)
Devaud, G; Furcinitti, P S; Fleming, J.C.; Lyon, M K; Douglas, K
1992-01-01
We have examined the structure of S-layers isolated from Sulfolobus acidocaldarius using atomic force microscopy (AFM) and transmission electron microscopy (TEM). From the AFM images, we were able to directly observe individual dimers of the crystal, defects in the crystal structure, and twin boundaries. We have identified two types of boundaries, one defined by a mirror plane and the other by a glide plane. This work shows that twin boundaries are highly structured regions that are directly ...
Azhar, N. S.; Taib, M. F. M.; Hassan, O. H.; Yahya, M. Z. A.; Ali, A. M. M.
2017-03-01
Crystal structures of α-Bi2O3 and β-Bi2O3 were calculated using Cambridge serial total energy package (CASTEP) based on the first-principles plane-wave ultrasoft pseudopotential method within local density approximation (LDA) and generalized gradient approximation (GGA) together with Perdew-Burke-Ernzerhof (GGA-PBE) and Perdew-Burke-Ernzerhof revised for solid (GGA-PBEsol). The structural parameter of α-Bi2O3 and β-Bi2O3 are in good agreement with previous experimental and theoretical data. All of the polymorphs were calculated for the total density of states (TDOS) and the partial density of states (PDOS) of Bi, O atoms. Density of states exhibits hybridization of Bi 6s and O 2p orbitals and the calculated charge density profiles exhibit the ionic character in the chemical bonding of this compound. The narrowed band gap (E g) and red-shift of light absorption edge are responsible for the photocatalytic activity of Bi2O3 for water splitting application. The optical properties such as optical absorption and electron energy loss function were calculated to show the best structure among these polymorphs for the photocatalytic water splitting application.
Energetic Materials and Atomic Force Microscopy: Structure and Kinetics
Energy Technology Data Exchange (ETDEWEB)
Weeks, B.L.; Weese, R.K.; Zaug, J.M.
2002-07-31
Understanding the structure and composition of energetic materials at the sub-micron level is imperative for the fundamental studies of hot-spot formation and structural composition of energetic materials. Using in situ high-temperature AFM we have observed the solid-solid phase transition of Octahydro-1,3,5,7,-tetrazocine, HMX, in real time. Massive surface reconstruction occurs during the 1st-order transition. The temperature induced increase in void space and surface roughness observed in the delta phase polymorph of HMX serve to increase the growth rate and volume of shock initiated hot spots and possibly reaction sensitivity. HMX exists in four solid phase polymorphs, labeled {alpha}, {beta}, {chi}, and {delta}. The phase conversion of the {beta} phase to the {delta} phase involves a major disruption of the crystal lattice. The energy required to bring about this change is a measurable quantity. Multiple thermal analysis techniques carried out simultaneously are preferable because the results are directly comparable. Thermal methods are dynamic techniques, where heating or cooling is applied to a sample, unless isothermal conditions are employed. Thermogravimetic Analysis, TGA, can be used to quantify decomposition components in a substance while Differential Thermal Analysis, DTA, can be used to measure the heat flow or the specific heat capacity, with respect to time and temperature. The advantage of TGA/DTA analysis is that the measurement of weight loss and heat flow are taken simultaneously and the observed events are directly related with respect to time and temperature. TGA/DTA experiments were performed to help us take a different look at the chemical nature of HMX and aid us in understanding the void formation process.
Robles, R.; Khanna, S. N.
2009-09-01
First principles electronic structure calculations on a free CrSi12 cluster, a (CrSi12)2 dimer, and CrSi12 clusters supported on Si(111) surfaces have been carried out within a gradient corrected density functional formalism using a supercell approach. The ground state of CrSi12 is a Cr centered hexagonal biprism of Si atoms in which the Cr spin moment is completely quenched. As two CrSi12 motifs are brought together, they form different composite units depending on initial direction of approach and, in most cases, the composite cluster is found to have a net spin moment. Cluster assemblies obtained by depositing CrSi12 motifs on a Si(111) surface exhibit similar finite spin moments for several initial directions of approach. An analysis of the electronic states shows that the origin of the magnetic moment lies in those Cr d -states that do not mix with silicon sp states. The studies suggest the possibility of forming silicon-based magnetic semiconductors through such assemblies.
Deformation-Induced Atomic Disordering and Reordering in Alloys with L12 Structure
Pantyukhova, O. D.; Starenchenko, S. V.; Solov'ev, A. N.; Solov'eva, Yu. V.; Starenchenko, V. A.
2017-10-01
The paper presents a mathematical model of thermal and strain hardening of alloys having L12 superstructure which allows calculating the atomic long-range order (LRO) parameter depending on the deformation degree under various temperature and loading conditions. The observed non-monotonic change in the atomic LRO parameter during plastic deformation occurs due to the two types of competitive processes. These processes are caused by the motion and accumulation of the deformation defects and their healing due to the migration of point defects of different nature. The competitiveness between these two types of processes leads to the periodical destruction and reconstruction of the atomic LRO parameter, while the equilibrium between them can stabilize it after which it continues to be stable despite the deformation.
Atomic and electronic structures of the (√(13)×√(13))R13.9° of silicene sheet on Ag(1 1 1)
Energy Technology Data Exchange (ETDEWEB)
Tchalala, Mohamed Rachid [Institut des Sciences Moléculaires d’Orsay, ISMO-CNRS, Bât. 210, Université Paris-Sud, F-91405 Orsay (France); Laboratoire de Chimie de Coordination et Catalyse, Département de Chimie, Faculté des Sciences-Semlalia, Université Cadi Ayyad, Marrakech 40001 (Morocco); Enriquez, Hanna [Institut des Sciences Moléculaires d’Orsay, ISMO-CNRS, Bât. 210, Université Paris-Sud, F-91405 Orsay (France); Yildirim, Handan; Kara, Abdelkader [Department of Physics, University of Central Florida, Orlando, FL 32816 (United States); Mayne, Andrew J.; Dujardin, Gérald [Institut des Sciences Moléculaires d’Orsay, ISMO-CNRS, Bât. 210, Université Paris-Sud, F-91405 Orsay (France); Ali, Mustapha Ait [Laboratoire de Chimie de Coordination et Catalyse, Département de Chimie, Faculté des Sciences-Semlalia, Université Cadi Ayyad, Marrakech 40001 (Morocco); Oughaddou, Hamid, E-mail: Hamid.Oughaddou@u-psud.fr [Institut des Sciences Moléculaires d’Orsay, ISMO-CNRS, Bât. 210, Université Paris-Sud, F-91405 Orsay (France); Département de Physique, Université de Cergy-Pontoise, F-95031 Cergy-Pontoise Cedex (France)
2014-06-01
Using scanning tunneling microscopy, low energy electron diffraction measurements, and ab initio calculations based on density functional theory, we present atomic models of the (√(13)×√(13))R13.9° silicene superstructure grown on Ag(1 1 1). The STM images reveal two co-existing atomic arrangements with two different orientations of the silicene sheet relative to the Ag(1 1 1) surface. DFT calculations with and without the inclusion of van der Waals interactions show corrugated Si atomic positions for both orientations implying a significant interaction with Ag(1 1 1) surface. The electronic structure of both silicene and Ag(1 1 1) surface are sufficiently affected that new interface states emerge close to the Fermi level.
Directory of Open Access Journals (Sweden)
Mingye Yang
2015-06-01
Full Text Available By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N4V 2 forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O2 dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N, the graphitic-N is more favorable to dissociate O2 molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.
Compound semiconductor alloys: From atomic-scale structure to bandgap bowing
Schnohr, C. S.
2015-09-01
Compound semiconductor alloys such as InxGa1-xAs, GaAsxP1-x, or CuInxGa1-xSe2 are increasingly employed in numerous electronic, optoelectronic, and photonic devices due to the possibility of tuning their properties over a wide parameter range simply by adjusting the alloy composition. Interestingly, the material properties are also determined by the atomic-scale structure of the alloys on the subnanometer scale. These local atomic arrangements exhibit a striking deviation from the average crystallographic structure featuring different element-specific bond lengths, pronounced bond angle relaxation and severe atomic displacements. The latter, in particular, have a strong influence on the bandgap energy and give rise to a significant contribution to the experimentally observed bandgap bowing. This article therefore reviews experimental and theoretical studies of the atomic-scale structure of III-V and II-VI zincblende alloys and I-III-VI2 chalcopyrite alloys and explains the characteristic findings in terms of bond length and bond angle relaxation. Different approaches to describe and predict the bandgap bowing are presented and the correlation with local structural parameters is discussed in detail. The article further highlights both similarities and differences between the cubic zincblende alloys and the more complex chalcopyrite alloys and demonstrates that similar effects can also be expected for other tetrahedrally coordinated semiconductors of the adamantine structural family.
Biswas, Katja
2017-09-01
A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating a thermal selection criterion, which makes it possible to reliably obtain low lying minima with just a small population size and is suitable for multimodal structural optimization. The method is tested on the structural optimization of amorphous graphene from unbiased atomic starting configurations. With just a population size of six systems, energetically very low structures are obtained. While each of the structures represents a distinctly different arrangement of the atoms, their properties, such as energy, distribution of rings, radial distribution function, coordination number, and distribution of bond angles, are very similar.
Zhou, Wu; Oxley, Mark P; Lupini, Andrew R; Krivanek, Ondrej L; Pennycook, Stephen J; Idrobo, Juan-Carlos
2012-12-01
We show that aberration-corrected scanning transmission electron microscopy operating at low accelerating voltages is able to analyze, simultaneously and with single atom resolution and sensitivity, the local atomic configuration, chemical identities, and optical response at point defect sites in monolayer graphene. Sequential fast-scan annular dark-field (ADF) imaging provides direct visualization of point defect diffusion within the graphene lattice, with all atoms clearly resolved and identified via quantitative image analysis. Summing multiple ADF frames of stationary defects produce images with minimized statistical noise and reduced distortions of atomic positions. Electron energy-loss spectrum imaging of single atoms allows the delocalization of inelastic scattering to be quantified, and full quantum mechanical calculations are able to describe the delocalization effect with good accuracy. These capabilities open new opportunities to probe the defect structure, defect dynamics, and local optical properties in 2D materials with single atom sensitivity.
Volkmann, Niels
2012-02-01
A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field. Copyright © 2011 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Du, Jincheng; Devanathan, Ramaswami; Corrales, Louis R.; Weber, William J.
2012-05-01
First-principles periodic density functional theory (DFT) calculations have been performed to understand the electronic structure, chemical bonding, phase transition, and physical properties of the mineral zircon (in the chemical composition of ZrSiO4) and its high pressure phase reidite. Temperature effect on phase transition and thermal–mechanical properties such as heat capacity and bulk modulus have been studied by combining the equation of states obtained from DFT calculations with the quasi-harmonic Debye model to take into account the entropy contribution to free energy. Local density approximation (LDA) and generalized gradient approximation (GGA) DFT functionals have been systematically compared in predicting the structure and property of this material. It is found that the LDA functional provides a better description of the equilibrium structure and bulk modulus, while GGA predicts a transition pressure closer to experimental values. Both functionals correctly predict the relative stability of the two phases, with GGA giving slightly larger energy differences. The calculated band structures show that both zircon and reidite have indirect bandgaps and the reidite phase has a narrower bandgap than the zircon phase. The electronic density of states and atomic charges analyses show that bonding in the high-pressure reidite phase has a stronger covalent character.
Energy Technology Data Exchange (ETDEWEB)
Du, Jincheng [University of North Texas; Devanathan, Ram [Pacific Northwest National Laboratory (PNNL); Corrales, L Rene [University of Arizona; Weber, William J [ORNL
2012-01-01
First principle periodic density functional theory (DFT) calculations have been performed to understand the electronic structure, chemical bonding, phase transition, and physical properties of the zircon (in the chemical composition of ZrSiO4) and its high pressure phase reidite. Temperature effect on phase transition and thermal-mechanical properties such as heat capacity and bulk modulus have been studied by combining the equation of states obtained from DFT calculations with the quasi-harmonic Debye model to take into account the entropy contribution to free energy. Local density approximation (LDA) and generalized gradient approximation (GGA) DFT functionals have been systematically compared in predicting the structure and property of this material. It is found that the LDA functional provides a better description of the equilibrium structure and bulk modulus, while GGA predicts a transition pressure closer to experimental values. Both functionals correctly predict the relative stability of the two phases, with GGA giving slightly larger energy differences. The calculated band structures show that both zircon and reidite have indirect bandgaps and the reidite phase has a narrower bandgap than the zircon phase. The atomic charges determined using the Bader method show that bonding in reidite has a stronger covalent character.
Comparison of measured and calculated temperatures for a Mach 8 hypersonic wing test structure
Quinn, R. D.; Fields, R. A.
1986-01-01
Structural temperatures were measured on a hypersonic wing test structure during a heating test that simulated a Mach 8 thermal environment. Measured data are compared to design calculations and temperature predictions obtained from a finite-difference thermal analysis.
The Band Structure of Polymers: Its Calculation and Interpretation. Part 3. Interpretation.
Duke, B. J.; O'Leary, Brian
1988-01-01
In this article, the third part of a series, the results of ab initio polymer calculations presented in part 2 are discussed. The electronic structure of polymers, symmetry properties of band structure, and generalizations are presented. (CW)
Mancera, L; Takeuchi, N
2003-01-01
We have studied the structural and electronic properties of YN in rock salt (sodium chloride), caesium chloride, zinc blende and wurtzite structures using first-principles total energy calculations. Rock salt is the calculated ground state structure with a = 4.93 A, B sub 0 = 157 GPa. The experimental lattice constant is a = 4.877 A. There is an additional local minimum in the wurtzite structure with total energy 0.28 eV/unit cell higher. At high pressure (approx 138 GPa), our calculations predict a phase transformation from a NaCl to a CsCl structure.
Using a matter wave model to study the structure of the electron inside an atom
Chang, Donald
In Bohr's atomic model, the atom was conceptually modeled as a miniature solar system. With the development of the Schrödinger equation, the wave function of the electron inside an atom becomes much better known. But the electron is still regarded as a pointed object; according to the Copenhagen Interpretation, the wave function is thought to describe only the probability of finding the electron. Such an interpretation, however, has raised some conceptual questions. For example, how can a point-like electron form a chemical bond between neighboring atoms? In an attempt to overcome this difficulty, we use a matter wave theory to model the structure of an electron inside the atom. This model is inspired by noticing the similarity between a free electron and a photon; both particles behave like a corpuscular object as well as a physical wave. Thus, we hypothesize that, like the photon, an electron is an excitation wave of a real physical field. Based on this hypothesis, we have derived a basic wave equation for the free electron. We show that, in the presence of an electrical potential, this basic wave equation can lead to the Schrödinger equation. This work implies that the solution of the Schrödinger equation actually represents the physical waves of the electron. Thus, the electron inside the atom should behave more like a topologically distributive wave than a pointed object. In this presentation, we will discuss the advantages and limitations of this model.
Energy Technology Data Exchange (ETDEWEB)
Grebennikov, V.I. [Institute of Metal Physics, UB RAS, 620066 Ekaterinburg (Russian Federation); Guy, D.E. [Physical-Technical Institute, Kirov st. 132, UB RAS, 426000 Izhevsk (Russian Federation)]. E-mail: lasas@fti.udm.ru; Ruts, Y.V. [Physical-Technical Institute, Kirov st. 132, UB RAS, 426000 Izhevsk (Russian Federation); Surnin, D.V. [Physical-Technical Institute, Kirov st. 132, UB RAS, 426000 Izhevsk (Russian Federation); Zheltysheva, O.R. [Physical-Technical Institute, Kirov st. 132, UB RAS, 426000 Izhevsk (Russian Federation)
2005-05-01
The problem of multipolarity of the atom core level ionization by electron impact in extended energy loss fine structure (EELFS) spectroscopy is studied. The intensities and amplitudes of electron transitions have been calculated in the OPW approximation. The experimental K EELFS spectra of Al, Si and L EELFS spectra of Fe, Co have been obtained. Corresponding calculations have been carried out in the monopole and dipole approximations. A comparison of theoretical and experimental spectra have been made. It is shown that a good agreement between the theoretical and experimental results points to the need for taking account of multipolarity of the electron transition processes in EELFS calculations.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Energy Technology Data Exchange (ETDEWEB)
Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Direct evidence of atomic-scale structural fluctuations in catalyst nanoparticles.
Lin, Pin Ann; Gomez-Ballesteros, Jose L; Burgos, Juan C; Balbuena, Perla B; Natarajan, Bharath; Sharma, Renu
2017-05-01
Rational catalyst design requires an atomic scale mechanistic understanding of the chemical pathways involved in the catalytic process. A heterogeneous catalyst typically works by adsorbing reactants onto its surface, where the energies for specific bonds to dissociate and/or combine with other species (to form desired intermediate or final products) are lower. Here, using the catalytic growth of single-walled carbon nanotubes (SWCNTs) as a prototype reaction, we show that the chemical pathway may in-fact involve the entire catalyst particle, and can proceed via the fluctuations in the formation and decomposition of metastable phases in the particle interior. We record in situ and at atomic resolution, the dynamic phase transformations occurring in a Cobalt catalyst nanoparticle during SWCNT growth, using a state-of-the-art environmental transmission electron microscope (ETEM). The fluctuations in catalyst carbon content are quantified by the automated, atomic-scale structural analysis of the time-resolved ETEM images and correlated with the SWCNT growth rate. We find the fluctuations in the carbon concentration in the catalyst nanoparticle and the fluctuations in nanotube growth rates to be of complementary character. These findings are successfully explained by reactive molecular dynamics (RMD) simulations that track the spatial and temporal evolution of the distribution of carbon atoms within and on the surface of the catalyst particle. We anticipate that our approach combining real-time, atomic-resolution image analysis and molecular dynamics simulations will facilitate catalyst design, improving reaction efficiencies and selectivity towards the growth of desired structure.
Atomic-scale structure of single-layer MoS2 nanoclusters
DEFF Research Database (Denmark)
Helveg, S.; Lauritsen, J. V.; Lægsgaard, E.
2000-01-01
We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide (MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2...
Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms
Directory of Open Access Journals (Sweden)
Oscar Martínez-Santiago
2016-05-01
Full Text Available This report examines the interpretation of the Graph Derivative Indices (GDIs from three different perspectives (i.e., in structural, steric and electronic terms. It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.
Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal
Directory of Open Access Journals (Sweden)
Tsunetomo Yamada
2016-07-01
Full Text Available The detailed atomic structure of the binary icosahedral (i ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP, both resulting from a close-packing of a large (Sc and a small (Zn atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K2/K1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason Debye–Waller factor, which explains the vanishing of `high-Qperp' reflections.
Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal
Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc
2016-01-01
The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of ‘high-Q perp’ reflections. PMID:27437112
Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms
Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.
2016-01-01
This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357
Studying the Consistency between and within the Student Mental Models for Atomic Structure
Zarkadis, Nikolaos; Papageorgiou, George; Stamovlasis, Dimitrios
2017-01-01
Science education research has revealed a number of student mental models for atomic structure, among which, the one based on Bohr's model seems to be the most dominant. The aim of the current study is to investigate the coherence of these models when students apply them for the explanation of a variety of situations. For this purpose, a set of…
Sunyono; Yuanita, L.; Ibrahim, M.
2015-01-01
The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…
High Resolution Measurements and Electronic Structure Calculations of a Diazanaphthalene
Gruet, Sébastien; Goubet, Manuel; Pirali, Olivier
2014-06-01
Polycyclic Aromatic Hydrocarbons (PAHs) have long been suspected to be the carriers of so called Unidentified Infrared Bands (UIBs). Most of the results published in the literature report rotationally unresolved spectra of pure carbon as well as heteroatom-containing PAHs species. To date for this class of molecules, the principal source of rotational informations is ruled by microwave (MW) spectroscopy while high resolution measurements reporting rotational structure of the infrared (IR) vibrational bands are very scarce. Recently, some high resolution techniques provided interesting new results to rotationally resolve the IR and far-IR bands of these large carbonated molecules of astrophysical interest. One of them is to use the bright synchrotron radiation as IR continuum source of a high resolution Fourier transform (FTIR) spectrometer. We report the very complementary analysis of the [1,6] naphthyridine (a N-bearing PAH) for which we recorded the microwave spectrum at the PhLAM laboratory (Lille) and the high resolution far-infrared spectrum on the AILES beamline at synchrotron facility SOLEIL. MW spectroscopy provided highly accurate rotational constants in the ground state to perform Ground State Combinations Differences (GSCD) allowing the analysis of the two most intense FT-FIR bands in the 50-900 wn range. Moreover, during this presentation the negative value of the inertial defect in the GS of the molecule will be discussed. A. Leger, J. L. Puget, Astron. Astrophys. 137, L5-L8 (1984) L. J. Allamandola et al. Astrophys. J. 290, L25-L28 (1985). Z. Kisiel et al. J. Mol. Spectrosc. 217, 115 (2003) S. Thorwirth et al. Astrophys. J. 662, 1309 (2007) D. McNaughton et al. J. Chem. Phys. 124, 154305 (2011). S. Albert et al. Faraday Discuss. 150, 71-99 (2011) B. E. Brumfield et al. Phys. Chem. Lett. 3, 1985-1988 (2012) O. Pirali et al. Phys. Chem. Chem. Phys. 15, 10141 (2013).
Energy Technology Data Exchange (ETDEWEB)
Klein, Dionne C.G., E-mail: dionne.c.g.klein@ntnu.no [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway); Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Latz, Eicke [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 (United States); Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn (Germany); Espevik, Terje [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Stokke, Bjorn T. [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway)
2010-05-15
Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.
Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study
Energy Technology Data Exchange (ETDEWEB)
Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z
2014-04-01
The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Flambaum, V. V.; Ginges, J. S. M.
2005-01-01
We derive an approximate expression for a "radiative potential" which can be used to calculate QED strong Coulomb field radiative corrections to energies and electric dipole (E1) transition amplitudes in many-electron atoms with an accuracy of a few percent. The expectation value of the radiative potential gives radiative corrections to the energies. Radiative corrections to E1 amplitudes can be expressed in terms of the radiative potential and its energy derivative (the low-energy theorem): ...
An effective introduction to structural crystallography using 1D Gaussian atoms
Smith, Emily; Evans, Gwyndaf; Foadi, James
2017-11-01
The most important quantitative aspects of computational structural crystallography can be introduced in a satisfactory way using 1D truncated and periodic Gaussian functions to represent the atoms in a crystal lattice. This paper describes in detail and demonstrates 1D structural crystallography starting with the definition of such truncated Gaussians. The availability of the computer programme CRONE makes possible the repetition of the examples provided in the paper as well as the creation of new ones.
Chemical structure of descriptors with an active hydrogen atom in certain bioregulators.
Kurchii, B A
1996-01-01
The chemical structure of descriptors (D) for some plant growth regulators (PGR), herbicides, pesticides and drugs is described. The presence of an active hydrogen atom in molecules is an essential factor determining biological activity of chemicals. The results obtained from the study of dependence existing between the structure of a certain substance and its biological activity may be used in designing of novel compounds which possess in biological activity.
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.
Xie, Jianming [San Diego, CA; Wang, Lei [San Diego, CA; Wu, Ning [Boston, MA; Schultz, Peter G [La Jolla, CA
2008-07-15
Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.
Electronic and atomic structure of the AlnHn+2 clusters
DEFF Research Database (Denmark)
Martinez, Jose Ignacio; Alonso, J.A.
2008-01-01
The electronic and atomic structure of the family of hydrogenated Al clusters AlnHn+2 with n=4-11 has been studied using the density functional theory with the generalized gradient approximation (GGA) for exchange and correlation. All these clusters have substantial gaps between the highest...... a polyhedron of n vertices and n H atoms form strong H-Al terminal bonds; one pair of electrons is involved in each of those bonds. The remaining n+1 electron pairs form a delocalized cloud over the surface of the Al cage. The clusters fulfilling the Wade-Mingos rule have wider HOMO-LUMO gaps...
A history of gap junction structure: hexagonal arrays to atomic resolution.
Grosely, Rosslyn; Sorgen, Paul L
2013-02-01
Gap junctions are specialized membrane structures that provide an intercellular pathway for the propagation and/or amplification of signaling cascades responsible for impulse propagation, cell growth, and development. Prior to the identification of the proteins that comprise gap junctions, elucidation of channel structure began with initial observations of a hexagonal nexus connecting apposed cellular membranes. Concomitant with technological advancements spanning over 50 years, atomic resolution structures are now available detailing channel architecture and the cytoplasmic domains that have helped to define mechanisms governing the regulation of gap junctions. Highlighted in this review are the seminal structural studies that have led to our current understanding of gap junction biology.
Su, Chia-Ping; Syu, Wei-Jhe; Hsiao, Chien-Nan; Lai, Ping-Shan; Chen, Chien-Chun
2017-08-01
To investigate dislocations or heterostructures across interfaces is now of great interest to condensed matter and materials scientists. With the advances in aberration-corrected electron optics, the scanning transmission electron microscope has demonstrated its excellent capability of characterizing atomic structures within nanomaterials, and well-resolved atomic-resolution images can be obtained through long-exposure data acquisition. However, the sample drifting, carbon contamination, and radiation damage hinder further analysis, such as deriving three-dimensional (3D) structures from a series of images. In this study, a method for obtaining atomic-resolution images with significantly reduced exposure time was developed, using which an original high-resolution image with approximately one tenth the electron dose can be obtained by combining a fast-scan high-magnification image and a slow-scan low-magnification image. The feasibility of obtaining 3D atomic structures using the proposed approach was demonstrated through multislice simulation. Finally, the feasibility and accuracy of image restoration were experimentally verified. This general method cannot only apply to electron microscopy but also benefit to image radiation-sensitive materials using various light sources.
Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H
2016-05-05
Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species.
Ho, Phuong T; Reddy, Vijay S
2017-10-27
The recent technological advances in electron microscopes, detectors, as well as image processing and reconstruction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structures on the methods of structure determination, resolution of the structures, and size of the virus particles revealed a rapid increase in the virus structures determined by cryo-EM at near atomic resolution since 2010. In addition, the data highlight the median resolution (∼3.0 Å) and size (∼310.0 Å in diameter) of the virus particles determined by X-ray crystallography while no such limits exist for cryo-EM structures, which have a median diameter of 508 Å. Notably, cryo-EM virus structures in the last four years have a median resolution of 3.9 Å. Taken together with minimal sample requirements, not needing diffraction quality crystals, and being able to achieve similar resolutions of the crystal structures makes cryo-EM the method of choice for current and future virus capsid structure determinations. Copyright © 2017 Elsevier Inc. All rights reserved.
Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian
2016-05-19
Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum.
Dislocations in AlGaN: Core Structure, Atom Segregation, and Optical Properties.
Massabuau, Fabien C-P; Rhode, Sneha L; Horton, Matthew K; O'Hanlon, Thomas J; Kovács, András; Zielinski, Marcin S; Kappers, Menno J; Dunin-Borkowski, Rafal E; Humphreys, Colin J; Oliver, Rachel A
2017-08-09
We conducted a comprehensive investigation of dislocations in Al0.46Ga0.54N. Using aberration-corrected scanning transmission electron microscopy and energy dispersive X-ray spectroscopy, the atomic structure and atom distribution at the dislocation core have been examined. We report that the core configuration of dislocations in AlGaN is consistent with that of other materials in the III-Nitride system. However, we observed that the dissociation of mixed-type dislocations is impeded by alloying GaN with AlN, which is confirmed by our experimental observation of Ga and Al atom segregation in the tensile and compressive parts of the dislocations, respectively. Investigation of the optical properties of the dislocations shows that the atom segregation at dislocations has no significant effect on the intensity recorded by cathodoluminescence in the vicinity of the dislocations. These results are in contrast with the case of dislocations in In0.09Ga0.91N where segregation of In and Ga atoms also occurs but results in carrier localization limiting non-radiative recombination at the dislocation. This study therefore sheds light on why InGaN-based devices are generally more resilient to dislocations than their AlGaN-based counterparts.
Local atomic structure and discommensurations in the charge density wave of CeTe3.
Kim, H J; Malliakas, C D; Tomić, A T; Tessmer, S H; Kanatzidis, M G; Billinge, S J L
2006-06-09
The local structure of in the incommensurate charge density wave (IC-CDW) state has been obtained using atomic pair distribution function analysis of x-ray diffraction data. Local atomic distortions in the Te nets due to the CDW are larger than observed crystallographically, resulting in distinct short and long Te-Te bonds. Observation of different distortion amplitudes in the local and average structures is explained by the discommensurated nature of the CDW, since the pair distribution function is sensitive to the local displacements within the commensurate regions, whereas the crystallographic result averages over many discommensurated domains. The result is supported by STM data. This is the first quantitative local structural study within the commensurate domains in an IC-CDW system.
Integrative, dynamic structural biology at atomic resolution--it's about time.
van den Bedem, Henry; Fraser, James S
2015-04-01
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and other techniques are helping us realize the dream of seeing--in atomic detail--how different parts of biomolecules shift between functional substates using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution.
Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time
van den Bedem, Henry; Fraser, James S.
2015-01-01
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836
Jha, Kshitij C; Zhu, He; Dhinojwala, Ali; Tsige, Mesfin
2014-11-04
Utilizing all-atom molecular dynamics (MD), we have analyzed the effect of tacticity and temperature on the surface structure of poly(methyl methacrylate) (PMMA) at the polymer-vacuum interface. We quantify these effects primarily through orientation, measured as the tilt with respect to the surface normal, and the surface number densities of the α-methyl, ester-methyl, carbonyl, and backbone methylene groups. Molecular structure on the surface is a complex interplay between orientation and number densities and is challenging to capture through sum frequency generation (SFG) spectroscopy alone. Independent quantification of the number density and orientation of chemical groups through all-atom MD presents a comprehensive model of stereoregular PMMA on the surface. SFG analysis presented in part I of this joint publication measures the orientation of molecules that are in agreement with MD results. We observe the ester-methyl groups as preferentially oriented, irrespective of tacticity, followed by the α-methyl and carbonyl groups. SFG spectroscopy also points to ester-methyl being dominant on the surface. The backbone methylene groups show a very broad angular distribution, centered along the surface plane. The surface number density ratios of ester-methyl to α-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to α-methyl. These subtle trends in the relative angular orientation and number densities that influence the variation of surface structure with tacticity are highlighted in this article. A more planar conformation of the syndiotactic PMMA along the surface (x-y plane) can be visualized through the trajectories from all-atom MD. Results from conformation tensor calculations for chains with any of their segments contributing to the surface validate the visual observation.
Atomic structures and gram scale synthesis of three tetrahedral quantum dots.
Beecher, Alexander N; Yang, Xiaohao; Palmer, Joshua H; LaGrassa, Alexandra L; Juhas, Pavol; Billinge, Simon J L; Owen, Jonathan S
2014-07-30
Luminescent semiconducting quantum dots (QDs) are central to emerging technologies that range from tissue imaging to solid-state lighting. However, existing samples are heterogeneous, which has prevented atomic-resolution determination of their structures and obscured the relationship between their atomic and electronic structures. Here we report the synthesis, isolation, and structural characterization of three cadmium selenide QDs with uniform compositions (Cd35Se20(X)30(L)30, Cd56Se35(X)42(L)42, Cd84Se56(X)56(L)56; X = O2CPh, L = H2N-C4H9). Their UV-absorption spectra show a lowest energy electronic transition that decreases in energy (3.54 eV, 3.26 eV, 3.04 eV) and sharpens as the size of the QD increases (fwhm = 207 meV, 145 meV, 115 meV). The photoluminescence spectra of all three QDs are broad with large Stokes shifts characteristic of trap-luminescence. Using a combination of single-crystal X-ray diffraction and atomic pair distribution function analysis, we determine the structures of their inorganic cores, revealing a series of pyramidal nanostuctures with cadmium terminated {111} facets. Theoretical and experimental studies on these materials will open the door to a deeper fundamental understanding of structure-property relationships in quantum-confined semiconductors.
Morphology and atomic structure of InGaN(0001) surfaces
Energy Technology Data Exchange (ETDEWEB)
Biermann, Amelie; Friedrich, Christian; Kneissl, Michael; Vogt, Patrick [TU Berlin (Germany). Institute of Solid State Physics EW6-1; Hoffmann, Veit [Ferdinand-Braun-Institut f. Hoechstfrequenztechnik, Berlin (Germany); Esser, Norbert [ISAS-Berlin (Germany); TU Berlin (Germany). Institute of Solid State Physics EW6-1
2010-07-01
Group III-nitrides offer a broad application spectrum in optoelectronic devices. Although the fabrication of high-quality devices requires the control of nanometer thick layers, there is only limited knowledge about the atomic structure of the surface. Here we present a study on the morphology and atomic structure of (0001) In{sub x}Ga{sub 1-x}N surfaces grown by MOVPE. Samples are prepared under UHV conditions by thermal annealing between 600 C and 800 C to achieve clean, decontaminated surfaces. Additionally thermally cracked ammonia and nitrogen plasma are used as nitrogen sources in order to vary surface stoichiometries and to prevent nitrogen depletion of the crystal. The chemical composition of the surface during preparation is determined by Auger Electron Spectroscopy. Clean (0001) In{sub x}Ga{sub 1-x}N surfaces were prepared at 760 C revealing no surface carbon and low residual oxygen compounds. Depending on the surface preparation, surface structures showing different surface symmetries such as (1 x 1), (1+1/6) or (2 x 2) were obtained as determined by LEED. The chemical composition remains similar for all structures. In order to get further information STM measurements of the atomic structure are presented.
Strain engineering of atomic and electronic structures of few-monolayer-thick GaN
Kolobov, A. V.; Fons, P.; Saito, Y.; Tominaga, J.; Hyot, B.; André, B.
2017-07-01
Two-dimensional (2D) semiconductors possess the potential to ultimately minimize the size of devices and concomitantly drastically reduce the corresponding energy consumption. In addition, materials in their atomic-scale limit often possess properties different from their bulk counterparts paving the way to conceptually novel devices. While graphene and 2D transition-metal dichalcogenides remain the most studied materials, significant interest also exists in the fabrication of atomically thin structures from traditionally 3D semiconductors such as GaN. While in the monolayer limit GaN possesses a graphenelike structure and an indirect band gap, it was recently demonstrated that few-layer GaN acquires a Haeckelite structure in the direction of growth with an effectively direct gap. In this work, we demonstrate the possibility of strain engineering of the atomic and electronic structure of few-monolayer-thick GaN structures, which opens new avenues for their practical application in flexible nanoelectronics and nano-optoelectronics. Our simulations further suggest that due to the weak van der Waals-like interaction between a substrate and an overlayer, the use of a MoS2 substrate may be a promising route to fabricate few-monolayer Haeckelite GaN experimentally.
Structural and Theoretical Evidence of the Depleted Proton Affinity of the N3-Atom in Acyclovir
Directory of Open Access Journals (Sweden)
Esther Vílchez-Rodríguez
2016-10-01
Full Text Available The hydronium salt (H3O2[Cu(N7–acv2(H2O2(SO42]·2H2O (1, acv = acyclovir has been synthesized and characterized by single-crystal X-ray diffraction and spectral methods. Solvated Cu(OH2 is a by-product of the synthesis. In the all-trans centrosymmetric complex anion, (a the Cu(II atom exhibits an elongated octahedral coordination; (b the metal-binding pattern of acyclovir (acv consists of a Cu–N7(acv bond plus an (aquaO–H···O6(acv interligand interaction; and (c trans-apical/distal sites are occupied by monodentate O-sulfate donor anions. Neutral acyclovir and aqua-proximal ligands occupy the basal positions, stabilizing the metal binding pattern of acv. Each hydronium(1+ ion builds three H-bonds with O–sulfate, O6(acv, and O–alcohol(acv from three neighboring complex anions. No O atoms of solvent water molecules are involved as acceptors. Theoretical calculations of molecular electrostatic potential surfaces and atomic charges also support that the O-alcohol of the N9(acv side chain is a better H-acceptor than the N3 or the O-ether atoms of acv.
Vardi-Kilshtain, Alexandra; Azuri, Asaf; Major, Dan Thomas
2012-02-05
A convenient approach to compute kinetic isotope effects (KIEs) in condensed phase chemical reactions is via path integrals (PIs). Usually, the primitive approximation is used in PI simulations, although such quantum simulations are computationally demanding. The efficiency of PI simulations may be greatly improved, if higher-order Trotter factorizations of the density matrix operator are used. In this study, we use a higher-order PI method, in conjunction with mass-perturbation, to compute heavy-atom KIE in the decarboxylation of orotic acid in explicit sulfolane solvent. The results are in good agreement with experiment and show that the mass-perturbation higher-order Trotter factorization provides a practical approach for computing condensed phase heavy-atom KIE. Copyright © 2011 Wiley Periodicals, Inc.
Calculation of the effect of tip geometry on noncontact atomic force microscopy using a qPlus sensor
Directory of Open Access Journals (Sweden)
Julian Stirling
2013-01-01
Full Text Available In qPlus atomic force microscopy the tip length can in principle approach the length of the cantilever. We present a detailed mathematical model of the effects this has on the dynamic properties of the qPlus sensor. The resulting, experimentally confirmed motion of the tip apex is shown to have a large lateral component, raising interesting questions for both calibration and force-spectroscopy measurements.
Baskakova, P. E.; Belyakov, Alexander V.; Colacot, Thomas; Krannich, L. K.; Haaland, Arne; Volden, Hans Vidar; Swang, Ole
1998-04-01
The molecular structures of E(NMe 2) 3, E P, As or Sb and Me CH 3, have been determined by gas electron diffraction (GED) and ab initio molecular orbital calculations at the {HF}/{6-31 G∗ } level. The equilibrium structures have Cs symmetry with two NMe 2 ligands oriented in such a manner that the direction of the electron lone pair on each N atom is orthogonal to the direction of the lone pair on the E atom, while the third ligand is oriented in such a manner that the lone pair on the N atom is antiparallel to the lone pair on E. The coordination of the antiparallel N atom is distinctly pyramidal (sum of the valence angles = 337° by GED) while the two orthogonal N atoms are nearly planar (sum of valence angles = 353° by GED). The bond distances from E to the antiparallel N atom is two to four pm longer than the bond distances to the orthogonal N atoms, and the valence angle >NEN spanned by the orthogonal N atoms is some 10° larger than the two angles spanned by the antiparallel and one orthogonal N atom. It is suggested that the equilibrium structures are stabilized by anomeric effects, i.e. delocalization of the lone pairs of the orthogonal N atoms into antibonding σ∗(E-N) orbitals.
Directory of Open Access Journals (Sweden)
Ali Hossein Kianfar
2017-12-01
Full Text Available In this research, structures of M(BAE (where M = VO(IV, Zn(II, Cu(II and Ni (II, BAE = bis(acetylacetoneethylenediimine, [Ni(BFE], [Ni(BBE] and [Ni(BCE] (where BFE = bis(1,1,1-triflouroacetylacetoneethylenediimine, BBE = bis(benzoylacetoneethylenediimine and BCE = bis(3-hloroacetylacetoneethylenediimine were determined by MP2 theoretical study. The thermodynamics of the tautomerism reactions was studied and the equilibrium constant of the reactions was calculated. The optimized molecular geometry and atomic charges were calculated using MP2 method with 6-31G(d basis set and compared with the reported X-ray data. Nickel and copper complexes have a planar structure while the zinc structure shows a distorted square-planar N2O2 coordination geometry. The vanadyl structure has a square-pyramide N2O3 coordination geometry. Also the bond lengths and the bond angles were studied and compared.
Xie, Hujun; Liu, Chengcheng; Yuan, Ying; Zhou, Tao; Fan, Ting; Lei, Qunfang; Fang, Wenjun
2016-01-21
The mechanisms for the oxidation of phenyl and hydride ligands of bis(pentamethylcyclopentadienyl)hafnium derivatives (Cp* = η(5)-C5Me5) by nitrous oxide via selective oxygen atom transfer reactions have been systematically studied by means of density functional theory (DFT) calculations. On the basis of the calculations, we investigated the original mechanism proposed by Hillhouse and co-workers for the activation of N2O. The calculations showed that the complex with an initial O-coordination of N2O to the coordinatively unsaturated Hf center is not a local minimum. Then we proposed a new reaction mechanism to investigate how N2O is activated and why N2O selectively oxidize phenyl and hydride ligands of . Frontier molecular orbital theory analysis indicates that N2O is activated by nucleophilic attack by the phenyl or hydride ligand. Present calculations provide new insights into the activation of N2O involving the direct oxygen atom transfer from nitrous oxide to metal-ligand bonds instead of the generally observed oxygen abstraction reaction to generate metal-oxo species.
Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.
Chae, Myong-Ho; Krull, Florian; Knapp, Ernst-Walter
2015-05-01
The DOcking decoy-based Optimized Potential (DOOP) energy function for protein structure prediction is based on empirical distance-dependent atom-pair interactions. To optimize the atom-pair interactions, native protein structures are decomposed into polypeptide chain segments that correspond to structural motives involving complete secondary structure elements. They constitute near native ligand-receptor systems (or just pairs). Thus, a total of 8609 ligand-receptor systems were prepared from 954 selected proteins. For each of these hypothetical ligand-receptor systems, 1000 evenly sampled docking decoys with 0-10 Å interface root-mean-square-deviation (iRMSD) were generated with a method used before for protein-protein docking. A neural network-based optimization method was applied to derive the optimized energy parameters using these decoys so that the energy function mimics the funnel-like energy landscape for the interaction between these hypothetical ligand-receptor systems. Thus, our method hierarchically models the overall funnel-like energy landscape of native protein structures. The resulting energy function was tested on several commonly used decoy sets for native protein structure recognition and compared with other statistical potentials. In combination with a torsion potential term which describes the local conformational preference, the atom-pair-based potential outperforms other reported statistical energy functions in correct ranking of native protein structures for a variety of decoy sets. This is especially the case for the most challenging ROSETTA decoy set, although it does not take into account side chain orientation-dependence explicitly. The DOOP energy function for protein structure prediction, the underlying database of protein structures with hypothetical ligand-receptor systems and their decoys are freely available at http://agknapp.chemie.fu-berlin.de/doop/. © 2015 Wiley Periodicals, Inc.
Tu, Qing; Lange, Björn; Parlak, Zehra; Lopes, Joao Marcelo J; Blum, Volker; Zauscher, Stefan
2016-07-26
Interfaces and subsurface layers are critical for the performance of devices made of 2D materials and heterostructures. Facile, nondestructive, and quantitative ways to characterize the structure of atomically thin, layered materials are thus essential to ensure control of the resultant properties. Here, we show that contact-resonance atomic force microscopy-which is exquisitely sensitive to stiffness changes that arise from even a single atomic layer of a van der Waals-adhered material-is a powerful experimental tool to address this challenge. A combined density functional theory and continuum modeling approach is introduced that yields sub-surface-sensitive, nanomechanical fingerprints associated with specific, well-defined structure models of individual surface domains. Where such models are known, this information can be correlated with experimentally obtained contact-resonance frequency maps to reveal the (sub)surface structure of different domains on the sample.
DEFF Research Database (Denmark)
Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob
2002-01-01
The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations......, the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...
Peterson, Karen I.; Pullman, David P.
2016-01-01
A laboratory project for the upper-division physical chemistry laboratory is described, and it combines IR and Raman spectroscopies with Gaussian electronic structure calculations to determine the structure of the oxalate anion in solid alkali oxalates and in aqueous solution. The oxalate anion has two limiting structures whose vibrational spectra…
Xu, Dong; Zhang, Yang
2011-11-16
Most protein structural prediction algorithms assemble structures as reduced models that represent amino acids by a reduced number of atoms to speed up the conformational search. Building accurate full-atom models from these reduced models is a necessary step toward a detailed function analysis. However, it is difficult to ensure that the atomic models retain the desired global topology while maintaining a sound local atomic geometry because the reduced models often have unphysical local distortions. To address this issue, we developed a new program, called ModRefiner, to construct and refine protein structures from Cα traces based on a two-step, atomic-level energy minimization. The main-chain structures are first constructed from initial Cα traces and the side-chain rotamers are then refined together with the backbone atoms with the use of a composite physics- and knowledge-based force field. We tested the method by performing an atomic structure refinement of 261 proteins with the initial models constructed from both ab initio and template-based structure assemblies. Compared with other state-of-art programs, ModRefiner shows improvements in both global and local structures, which have more accurate side-chain positions, better hydrogen-bonding networks, and fewer atomic overlaps. ModRefiner is freely available at http://zhanglab.ccmb.med.umich.edu/ModRefiner. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Protein structure prediction by all-atom free-energy refinement
Verma, Abhinav; Wenzel, Wolfgang
2007-01-01
Background The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01) that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure prediction purposes. We therefore investigate here a low-cost free-energy relaxation protocol for protein structure prediction that combines heuristic methods for model generation with all-atom free-energy relaxation in PFF01. Results We use PFF01 to rank and cluster the conformations for 32 proteins generated by ROSETTA. For 22/10 high-quality/low quality decoy sets we select near-native conformations with an average Cα root mean square deviation of 3.03 Å/6.04 Å. The protocol incorporates an inherent reliability indicator that succeeds for 78% of the decoy sets. In over 90% of these cases near-native conformations are selected from the decoy set. This success rate is rationalized by the quality of the decoys and the selectivity of the PFF01 forcefield, which ranks near-native conformations an average 3.06 standard deviations below that of the relaxed decoys (Z-score). Conclusion All-atom free-energy relaxation with PFF01 emerges as a powerful low-cost approach toward generic de-novo protein structure prediction. The approach can be applied to large all-atom decoy sets of any origin and requires no preexisting structural information to identify the native conformation. The study provides evidence that a large class of proteins may be foldable by PFF01. PMID:17371594
Atomic Structures of Minor Proteins VI and VII in the Human Adenovirus.
Dai, Xinghong; Wu, Lily; Sun, Ren; Zhou, Z Hong
2017-10-04
Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts towards more effective applications. Since 2010, atomic models of human Ad5 have been independently derived from photographic film cryoEM and X-ray crystallography, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII and IX. To clarify these discrepancies, here we have employed the technology of direct electron-counting to obtain a cryoEM structure of human Ad5 at 3.2 Å resolution. Our improved structure unambiguously confirmed our previous cryoEM models of proteins IIIa, VIII and IX and explained the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavities of hexons - the cleaved N-terminus of precursor protein VI (pVIn), the cleaved N-terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2--by extension that of genome-condensing pVII--to hexons is consistent with the previously proposed dsDNA genome-capsid co-assembly for adenoviruses, which resembles that of ssRNA viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid, as exemplified by tailed bacteriophages and herpesviruses. IMPORTANCE Adenovirus is a double-edged sword to humans - as a widespread pathogen and a bioengineering tool for anti-cancer and gene therapy. Atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models from conventional/film cryoEM and X-ray crystallography for important cement proteins IIIa, VIII, and IX have caused confusion. Using the cutting-edge cryoEM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our
Ab initio band structure calculations of the low-temperature phases of Ag2Se, Ag2Te and Ag3AuSe2
Fang, C.M.; Groot, R.A. de; Wiegers, G.A.
Ab initio band structure calculations were performed for the low-temperature modifications of the silver chalcogenides β-Ag2Se, β-Ag2Te and the ternary compound β-Ag3AuSe2 by the local spherical wave (LSW) method. Coordinates of the atoms of β-Ag2Se and β-Ag3AuSe2 were obtained from refinements
Energy Technology Data Exchange (ETDEWEB)
Rabbe, C.; Madic, C. [CEA-DCC-DRRV, Bagnols-sur-Ceze (France); Sella, C. [E.S.P.C.I., Paris (France). Lab. de Chimie Analytique; Godard, A. [INSA Rouen, Mont-Saint-Aignan (France)
1999-01-01
This report describes the second part of a theoretical approach aimed at establishing structure-activity relationships in a data base made of twenty-two monoamides (A) used as uranium (VI) nitrate extractants. It was found that predominant factors determining the extracting ability of a monoamide are of three kinds: (1) electron density of the coordinating atoms or groups, which should be as high as possible; (2) steric effects, which should be as low as possible; and (3) lipophilicity of the ligands, which should be above a minimum threshold value. In the first paper of this series, quantum chemistry calculations were reported to account for electronic properties of the ligands. This second paper reports molecular mechanics calculations made on UO{sub 2}(NO{sub 3}){sub 2}A{sub 2} complexes in order to determine the influence of steric effects on the formation of these compounds. Calculations of monoamide lipophilicity using Rekker`s method showed that all the molecules of the data base were lipophilic enough and, consequently, that this parameter was not significantly important for the extraction of uranyl nitrate by these monoamides. A quantitative relationship was established between the U(VI) distribution ratio and the two parameters, calculated by quantum chemistry and molecular mechanics methods.
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.
Jonikas, Magdalena A; Radmer, Randall J; Altman, Russ B
2009-12-15
The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87-3.31 A RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 A RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure. Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org/home/c2a. russ.altman@stanford.edu
Energy Technology Data Exchange (ETDEWEB)
Zhou, Zhaobo [Key Laboratory of Advanced Materials of Yunnan Province & Key Laboratory of Advanced Materials of Non-Ferrous and Precious Rare Metals Ministry of Education, Kunming University of Science and Technology, Kunming 650093 (China); Zhou, Xiaolong, E-mail: kmzxlong@163.com [Key Laboratory of Advanced Materials of Yunnan Province & Key Laboratory of Advanced Materials of Non-Ferrous and Precious Rare Metals Ministry of Education, Kunming University of Science and Technology, Kunming 650093 (China); Zhang, Kunhua [State Key Laboratory of Rare Precious Metals Comprehensive Utilization of New Technologies, Kunming Institute of Precious Metals, Kunming 650106 (China)
2016-12-15
First-principle calculations were performed to investigate the structural, phase stability, electronic, elastic properties and hardness of monoclinic structure IrN{sub 2} (m-IrN{sub 2}), orthorhombic structure IrN{sub 2} (o-IrN{sub 2}) and zinc blende structure IrN (ZB IrN). The results show us that only m-IrN{sub 2} is both thermodynamic and dynamic stability. The calculated band structure and density of states (DOS) curves indicate that o-IrN{sub 2} and ZB Ir-N compounds we calculated have metallic behavior while m-IrN{sub 2} has a small band gap of ~0.3 eV, and exist a common hybridization between Ir-5d and N-2p states, which forming covalent bonding between Ir and N atoms. The difference charge density reveals the electron transfer from Ir atom to N atom for three Ir-N compounds, which forming strong directional covalent bonds. Notable, a strong N-N bond appeared in m-IrN{sub 2} and o-IrN{sub 2}. The ratio of bulk to shear modulus (B/G) indicate that three Ir-N compounds we calculated are ductile, and ZB IrN possesses a better ductility than two types IrN{sub 2}. m-IrN{sub 2} has highest Debye temperature (736 K), illustrating it possesses strongest covalent bonding. The hardness of three Ir-N compounds were also calculated, and the results reveal that m-IrN{sub 2} (18.23 GPa) and o-IrN{sub 2} (18.02 GPa) are ultraincompressible while ZB IrN has a negative value, which may be attributed to phase transition at ca. 1.98 GPa.
First principle calculation of structure and lattice dynamics of Lu2Si2O7
Directory of Open Access Journals (Sweden)
Nazipov D.V.
2017-01-01
Full Text Available Ab initio calculations of crystal structure and Raman spectra has been performed for single crystal of lutetium pyrosilicate Lu2Si2O7. The types of fundamental vibrations, their frequencies and intensities in the Raman spectrum has been obtained for two polarizations. Calculations were made in the framework of density functional theory (DFT with hybrid functionals. The isotopic substitution was calculated for all inequivalent ions in cell. The results in a good agreement with experimental data.
Small angle neutron and X-ray studies of carbon structures with metal atoms
Lebedev, V. T.; Szhogina, A. A.; Bairamukov, V. Yu
2017-05-01
Encapsulation of metal atoms inside carbon single-wall cages or within multi-layer cells has been realized using molecular precursors and high temperature processes transforming them into desirable structures. Endohedral fullerenols Fe@C60(OH)X with 3d-metal (iron) have been studied by SANS in aqueous solutions where they form stable globular clusters with radii R C ∼ 10-12 nm and aggregation numbers N C ∼ 104. This self-assembly is a crucial feature of paramagnetic fullerenols as perspective contrast agents for Magneto-Resonance Imaging in medicine. Cellular carbon-metal structures have been created by the pyrolysis of diphthalocyanines of lanthanides and actinides. It was established that these ultra porous matrices consist of globular cells of molecular precursor size (∼ 1 nm) which are aggregated into superstructures. This provides retain of metal atoms inside matrices which may serve for safety storage of spent fuel of nuclear power plants.
EM-Fold: De novo atomic-detail protein structure determination from medium resolution density maps
Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L.; Meiler, Jens
2012-01-01
Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy (cryoEM) or X-ray crystallography. In these density maps the general arrangement of secondary structure elements is revealed while their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the secondary structure elements de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins the protocol consistently and reproducibly achieves models with RMSD values smaller than 3 Å. PMID:22405005
High-speed atomic force microscopy: Structure and dynamics of single proteins.
Casuso, Ignacio; Rico, Felix; Scheuring, Simon
2011-10-01
For surface analysis of biological molecules, atomic force microscopy (AFM) is an appealing technique combining data acquisition under physiological conditions, for example buffer solution, room temperature and ambient pressure, and high resolution. However, a key feature of life, dynamics, could not be assessed until recently because of the slowness of conventional AFM setups. Thus, for observing bio-molecular processes, the gain of image acquisition speed signifies a key progress. Here, we review the development and recent achievements using high-speed atomic force microscopy (HS-AFM). The HS-AFM is now the only technique to assess structure and dynamics of single molecules, revealing molecular motor action and diffusion dynamics. From this imaging data, watching molecules at work, novel and direct insights could be gained concerning the structure, dynamics and function relationship at the single bio-molecule level. Copyright © 2011 Elsevier Ltd. All rights reserved.
The shell structure effects in neutron cross section calculation by a ...
African Journals Online (AJOL)
The role of the shell structure properties of the nucleus in the calculation of neutron-induced reaction cross-section data based on nuclear reaction theory has been investigated. In this investigation, measured, evaluated and calculated (n.p) reaction cross-section data on la spherical nucleus (i.e. 112Sn) and a deformed ...
NMR Investigation of Atomic Structure and Dynamics of Bulk Metallic Glasses
2013-09-17
that, via Al-27 nuclear magnetic resonance (NMR) measurements, that atomic level structures characterized by electric-field-gradient tensors and the...only by the second-order quadrupole effect, and wide satellite transitions 1m m ( 1/ 2m ) broadened by the first-order quadrupole ...was used to determine the corresponding linewidths of the central and satellite transitions as noted by the dashed curves in Fig 3.1. In addition, the
2014-01-01
ABSTRACT Microbial cells sense and respond to their environment using their surface constituents. Therefore, understanding the assembly and biophysical properties of cell surface molecules is an important research topic. With its ability to observe living microbial cells at nanometer resolution and to manipulate single-cell surface molecules, atomic force microscopy (AFM) has emerged as a powerful tool in microbiology. Here, we survey major breakthroughs made in cell surface microbiology using AFM techniques, emphasizing the most recent structural and functional insights. PMID:25053785
Wang, Neng-Ping
2011-01-01
I present a method to calculate the ballistic transport properties of atomic-scale structures under bias. The electronic structure of the system is calculated using the Kohn-Sham scheme of density functional theory (DFT). The DFT eigenvectors are then transformed into a set of maximally localized Wannier functions (MLWFs) [N. Marzari and D. Vanderbilt, Phys. Rev. B 56 (1997) 12847]. The MLWFs are used as a minimal basis set to obtain the Hamitonian matrices of the scattering region and the adjacent leads, which are needed for transport calculation using the nonequilibrium Green's function formalism. The coupling of the scattering region to the semi-infinite leads is described by the self-energies of the leads. Using the nonequilibrium Green's function method, one calculates self-consistently the charge distribution of the system under bias and evaluates the transmission and current through the system. To solve the Poisson equation within the scheme of MLWFs I introduce a computationally efficient method. The method is applied to a molecular hydrogen contact in two transition metal monatomic wires (Cu and Pt). It is found that for Pt the I-V characteristics is approximately linear dependence, however, for Cu the I-V characteristics manifests a linear dependence at low bias voltages and exhibits apparent nonlinearity at higher bias voltages. I have also calculated the transmission in the zero bias voltage limit for a single CO molecule adsorbed on Cu and Pt monatomic wires. While a chemical scissor effect occurs for the Cu monatomic wire with an adsorbed CO molecule, it is absent for the Pt monatomic wire due to the contribution of d-orbitals at the Fermi energy.
Helal, Mustafa R; Yousef, Yaser A; Afaneh, Akef T
2002-07-30
HF, MP2, and B3LYP calculations with different basis sets have been used in the computation of the stabilization energies of C(3)H(7)X isomers, where X is F, Cl, and Br. The experimental stabilization energies of the structural isomers of C(3)H(7)Cl and C(3)H(7)Br have been reproduced via B3LYP calculations. However, the calculated stabilization energies of fluoropropane isomers from their reported enthalpies of formation have been reproduced in all methods of calculations in present work. The experimental relative stabilities of the gauche conformers of 1-fluoro-, 1-chloro-, and 1-bromopropanes have been also reproduced via some of the used calculations in the present work. The effect of the geminal interactions on X atomic charges and on the C-X and C-C bond lengths in halopropane isomers are also discussed. Copyright 2002 Wiley Periodicals, Inc.
On the emergence of molecular structure from atomic shape in the 1/r2 harmonium model.
Müller-Herold, Ulrich
2006-01-07
The formal similarity of the three-body Hamiltonians for helium and the hydrogen molecule ion is used to demonstrate the unfolding of a rotating dumbbell-like proton distribution from a (1s)2-type electron distribution by smooth variation of the particles' masses in the 1/r2 harmonium model. The 1/r2 harmonium is an exactly solvable modification of the harmonium model (also known as Hooke's law atom) where the attraction between different particles is harmonic and the repulsion between the two equal particles is given by a 1/r2 potential. The dumbbell-like molecular structure appears as an expression of increasing spatial correlation due to increasing mass. It gradually appears in the one-density distribution of the two equal particles if their mass exceeds a critical value depending on the mass of the third particle. For large mass of the equal particles, their one-density distribution approaches an asymptotic form derived from the Born-Oppenheimer treatment of H2+ in the 1/r2 harmonium model. Below the critical value, the one density is a spherical, Gaussian-type atomic density distribution with a maximum at the center of mass. The topological transition at the critical value separates molecular structure and atomic shape as two qualitatively different manifestations of spatial structure.
A quantitative comparison of dura mater tissue structures measured with atomic force microscopy.
Sikora, Andrzej; Kedzia, Alicja
2012-01-01
The growth of a human embryo is a very sophisticated process. Understanding the way it proceeds is a key factor in pathology preventing and treating diseases. Therefore one needs to use advanced to tools and methods to investigate various aspects of the anatomy and physiology of humans during the first months of growth. This work is focused on the structure of dura mater tissue, one of the membranes protecting the brain, which can be responsible for a number of health issues if it develops abnormally. The aim of the work was to observe dura mater tissue structure with atomic force microscopy and to provide a quantitative method of discrimination of both the periosteal and meningeal layers in a 6-month-old human embryo. The measurements were performed with atomic force microscopy, in air, using tapping mode. The sample was stored in formaldehyde and dried prior to the measurements. The results obtained permitted observation of the structure of the tissue, in particular the presence of collagen fibers. By applying various image analysis tools, quantitative descriptions of both layers were created in order to distinguish them. The experiment proved that atomic force microscopy can be a useful tool in the investigation of the development process of the dura mater tissue in terms of the appearance of differences related to various functions of the periosteal and meningeal layers.
Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan
2014-09-01
Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
Interfacial engineering of two-dimensional nano-structured materials by atomic layer deposition
Energy Technology Data Exchange (ETDEWEB)
Zhuiykov, Serge, E-mail: serge.zhuiykov@ugent.be [Ghent University Global Campus, Department of Applied Analytical & Physical Chemistry, Faculty of Bioscience Engineering, 119 Songdomunhwa-ro, Yeonsu-Gu, Incheon 406-840 (Korea, Republic of); Kawaguchi, Toshikazu [Global Station for Food, Land and Water Resources, Global Institution for Collaborative Research and Education, Hokkaido University, N10W5 Kita-ku, Sapporo, Hokkaido 060-0810 (Japan); Graduate School of Environmental Science, Hokkaido University, N10W5 Kita-ku, Sapporo, Hokkaido 060-0810 (Japan); Hai, Zhenyin; Karbalaei Akbari, Mohammad; Heynderickx, Philippe M. [Ghent University Global Campus, Department of Applied Analytical & Physical Chemistry, Faculty of Bioscience Engineering, 119 Songdomunhwa-ro, Yeonsu-Gu, Incheon 406-840 (Korea, Republic of)
2017-01-15
Highlights: • Advantages of atomic layer deposition technology (ALD) for two-dimensional nano-crystals. • Conformation of ALD technique and chemistry of precursors. • ALD of semiconductor oxide thin films. • Ultra-thin (∼1.47 nm thick) ALD-developed tungsten oxide nano-crystals on large area. - Abstract: Atomic Layer Deposition (ALD) is an enabling technology which provides coating and material features with significant advantages compared to other existing techniques for depositing precise nanometer-thin two-dimensional (2D) nanostructures. It is a cyclic process which relies on sequential self-terminating reactions between gas phase precursor molecules and a solid surface. ALD is especially advantageous when the film quality or thickness is critical, offering ultra-high aspect ratios. ALD provides digital thickness control to the atomic level by depositing film one atomic layer at a time, as well as pinhole-free films even over a very large and complex areas. Digital control extends to sandwiches, hetero-structures, nano-laminates, metal oxides, graded index layers and doping, and it is perfect for conformal coating and challenging 2D electrodes for various functional devices. The technique’s capabilities are presented on the example of ALD-developed ultra-thin 2D tungsten oxide (WO{sub 3}) over the large area of standard 4” Si substrates. The discussed advantages of ALD enable and endorse the employment of this technique for the development of hetero-nanostructure 2D semiconductors with unique properties.
Structure stability and magnetism in graphene impurity complexes with embedded V and Nb atoms
Energy Technology Data Exchange (ETDEWEB)
Thakur, Jyoti [Department of Physics, University College, Kurukshetra University, Kurukshetra 136119, Haryana (India); Kashyap, Manish K., E-mail: manishdft@gmail.com [Department of Physics, Kurukshetra University, Kurukshetra 136119, Haryana (India); Ames Laboratory, U.S. Department of Energy, Iowa State University, Ames, IA 50011-3020 (United States); Taya, Ankur; Rani, Priti [Department of Physics, Kurukshetra University, Kurukshetra 136119, Haryana (India); Saini, Hardev S. [Department of Physics, Guru Jambheshwar University of Science & Technology, Hisar 125001, Haryana (India); Reshak, A.H. [New Technologies – Research Centre, University of West Bohemia, Univerzitni 8, 306 14 Pilsen (Czech Republic); School of Material Engineering, University Malaysia Perlis, 01007 Kangar, Perlis (Malaysia)
2017-07-01
Highlights: • V/Nb embedding in graphene containing monovacancies/divacancies is presented. • Spin polarization near/equal to 100% ensures use of studied nanosystems in spin filter devices. • Bandstructures are analyzed to identify shifting of Dirac cone of graphene. - Abstract: The appearance of vacancy defects could produce appropriate magnetic moment in graphene and the sensitivity to absorb atoms/molecules also increases with this. In this direction, a DFT study of embedding V and Nb atom in graphene containing monovacancies (MV) and divacancies (DV) is reported. Complete/almost complete spin polarization is detected for V/Nb embedding. The origin of magnetism has been identified via interaction of 3d-states of embedded atom with C-p states present in the vicinity of embedded site. The band structures have been analyzed to counter the observed semiconducting nature of graphene in minority spin on embedding V/Nb atom. The isosurface analysis also confirms the induced magnetism of present nanosystems. The present results reveal that these nanosystems have the potential for futuristic applications like spintronics and energy resources.
Energy Technology Data Exchange (ETDEWEB)
Tucker, Jon R.; Magyar, Rudolph J.
2012-02-01
High explosives are an important class of energetic materials used in many weapons applications. Even with modern computers, the simulation of the dynamic chemical reactions and energy release is exceedingly challenging. While the scale of the detonation process may be macroscopic, the dynamic bond breaking responsible for the explosive release of energy is fundamentally quantum mechanical. Thus, any method that does not adequately describe bonding is destined to lack predictive capability on some level. Performing quantum mechanics calculations on systems with more than dozens of atoms is a gargantuan task, and severe approximation schemes must be employed in practical calculations. We have developed and tested a divide and conquer (DnC) scheme to obtain total energies, forces, and harmonic frequencies within semi-empirical quantum mechanics. The method is intended as an approximate but faster solution to the full problem and is possible due to the sparsity of the density matrix in many applications. The resulting total energy calculation scales linearly as the number of subsystems, and the method provides a path-forward to quantum mechanical simulations of millions of atoms.
Sharma, R.; Zygelman, B.; von Esse, F.; Dalgarno, A.
1994-08-01
Using a recent calculation of the cross sections for fine structure changing collisions during an encounter between two oxygen atoms in the ground electronic state, we determine the population of the fine structure levels of oxygen as a function of altitude for four model atmospheres representing conditions at 0 deg longitude, 45 deg latitude, at midday and midnight, and high and low solar and geomagnetic activity. We include the effect of electron impacts. The fine structure levels are shown to be in local thermodynamic equilibrium (LTE) at the local neutral atom translational temperature for altitudes up to 350 km and 400 km for midnight and midday, respectively, at low activity, and up to at least 600 km at high activity. At higher altitudes spotaneous emission causes deviation from LTE and overpopulates the lowest (J = 2) level at the expense of the other two levels.
Kreissl, M; Stephens, T; Ziebeck, K R A
2003-01-01
The effect of atomic order on the martensitic phase transition and magnetic properties of stoichiometric Ni sub 2 MnGa has been investigated in a sample quenched from 1000 deg C. Magnetization, resistivity and x-ray diffraction measurements indicate that the structural phase transition occurs at approx 103 K, substantially lower than the value reported for samples quenched from 800 deg C and ordered in the Heusler L2 sub 1 structure. A small reduction in the ferromagnetic moment was also observed, although the Curie temperature remained largely unaffected. The electronic Sommerfeld coefficient obtained from heat capacity measurements is enhanced but smaller than that observed for the 800 deg C quenched sample. The results are consistent with band structure calculations and the electronic changes brought about by atomic disorder.
Energy Technology Data Exchange (ETDEWEB)
Sob, M.; Turek, I. [Akademie Ved Ceske Republiky, Brno (Czech Republic). Ustav Fyzikalni Metalurgie; Vitek, V. [Pennsylvania Univ., Philadelphia, PA (United States). Dept. of Materials Science and Engineering
1997-10-01
A quantum-mechanical approach for determining the electronic structure and atomic configuration of extended defects in metals is described and importance of theoretical methods for interpretation of positron annihilation spectroscopy data is stressed. As an example, atomic configuration of the {Sigma} = 5(210)/[001] tilt grain boundary in tungsten is determined and local densities of states at atoms in defect region are discussed. (author). 19 refs, 3 figs.
Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin
Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong
2004-04-01
We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.
Structure of nanocrystalline Ti3C2 MXene using atomic pair distribution function.
Shi, Chenyang; Beidaghi, Majid; Naguib, Michael; Mashtalir, Olha; Gogotsi, Yury; Billinge, Simon J L
2014-03-28
The structures of nanocrystalline pristine, potassium hydroxide and sodium acetate intercalated new two-dimensional materials Ti3C2 MXenes were studied using the x-ray atomic pair distribution function technique. Pristine MXene has a hexagonal structure with a=b=3.0505(5) Å, c=19.86(2) Å (S.G. P63/mmc No. 194). Both hydroxyl and fluoride terminating species are present. The intercalation of K+ or Na+ ions expands the Ti3C2 layers perpendicular to the planes but shrinks the in-plane a and b lattice parameters.
Energy Technology Data Exchange (ETDEWEB)
Alario, F.; Deves, J.M.
1993-05-21
The invention describes a composite catalyst which contains: a MFI structure zeolite containing, at least, an element chosen among alkaline or alkaline-earth metals, with a structure made of Silicon, Aluminium and / or Gallium; a matrix; platinum metals and additive metal chosen among Stain, Germanium, Indium, Copper, Iron, Molybdenum, Gallium, Thallium, Gold, Silver, Ruthenium, Chrome, Tungsten and Lead at least; an halogen chosen among Fluorine, Chlorine, Bromine and Iodine at least; Gallium and Zinc possibly; alkaline or alkaline-earth metal in the matrix preferentially. The invention describes also the use of this catalyst for aromatization reactions of hydrocarbons containing 5 to 12 carbon atoms per molecule.
Probing the atomic structure of amorphous Ta2O5 coatings
Bassiri, R.; Borisenko, K. B.; Cockayne, D. J. H.; Hough, J.; MacLaren, I.; Rowan, S.
2011-01-01
Low optical and mechanical loss Ta2O5 amorphous coatings have a growing number of applications in precision optical measurements systems. Transmission electron microscopy is a promising way to probe the atomic structure of these coatings in an effort to better understand the causes of the observed mechanical and optical losses. Analysis of the experimental reduced density functions using a combination of reverse Monte Carlo refinements and density functional theory molecular dynamics simulations reveals that the structure of amorphous Ta2O5 consists of clusters with increased contribution from a Ta2O2 ring fragment.
Adebayo, Adedayo S; Xuezeng, Zhao; Weijie, Wang
2013-06-01
Step height is defined as the vertical spacing between two plane-parallel planes comprising an elevation or an indentation and the substrate. In atomic force microscopy (AFM), there are many algorithms for determining feature dimensions such as step height and width. One common problem of many algorithms is the difficulty for users to accurately determine the corner positions needed to properly implement the said algorithms. A new algorithm based on ISO 5436-1 is proposed that determines the necessary corner positions along with two examples illustrating the implementation of this algorithm. We propose calling this new method the determinant method. Since the corner positions are automatically decided, feature dimensions such as step height of an AFM image are easily determined. Comparative experiments carried out to compare the step height measurement using this algorithm and the SPIP software from Image Metrology show encouraging results.
Energy Technology Data Exchange (ETDEWEB)
Guy, D., E-mail: ftiran@mail.r [Physical-Technical Institute, UB RAS, Kirov St., Bld.132, 426000 Izhevsk (Russian Federation); Bakieva, O. [Physical-Technical Institute, UB RAS, Kirov St., Bld.132, 426000 Izhevsk (Russian Federation); Grebennikov, V. [Institute of Metal Physics, UB RAS, GSP-170, S. Kovalevskaya St., Bld. 18, 620219 Ekaterinburg (Russian Federation); Surnin, D. [Physical-Technical Institute, UB RAS, Kirov St., Bld.132, 426000 Izhevsk (Russian Federation); Ruts, Y. [Physical-Technical Institute, UB RAS, Kirov St., Bld.132, 426000 Izhevsk (Russian Federation); Institute of Metal Physics, UB RAS, GSP-170, S. Kovalevskaya St., Bld. 18, 620219 Ekaterinburg (Russian Federation)
2010-12-15
In this paper we present a theoretical description of the extended energy loss fine structure (EELFS) formation, and derive simple analytical formulas for the EELFS spectra calculation. Methods of calculating the amplitude and intensity of electron transitions of different multipolarity on excitation of an atomic core level by an electron impact are proposed, and the corresponding test calculations are carried out. The M{sub 2,3} EELFS spectra of pure 3d-metals (Fe, Ni, Cu) and stoichiometric oxide films (Fe{sub 2}O{sub 3}, NiO and CuO), as well as the K EELFS spectra of oxygen, obtained with a JEOL JAMP-10 Scanning Auger microprobe are presented. A technique of extracting the normalized oscillating parts from experimental EELFS data, based on the use of the calculated electron transition intensities is suggested. The atomic pair correlation functions of the investigated objects are obtained from the experimental EELFS data with allowance for multipolarity of the processes of excitation of the atomic core level by electron impact. The experimental results agree well with the known crystallographic data (partial interatomic distances, coordination numbers and Debye-Waller factors).
Fine- and hyperfine structure investigations of even configuration system of atomic terbium
Stefanska, D.; Elantkowska, M.; Ruczkowski, J.; Furmann, B.
2017-03-01
In this work a parametric study of the fine structure (fs) and the hyperfine structure (hfs) for the even-parity configurations of atomic terbium (Tb I) is presented, based in considerable part on the new experimental results. Measurements on 134 spectral lines were performed by laser induced fluorescence (LIF) in a hollow cathode discharge lamp; on this basis, the hyperfine structure constants A and B were determined for 52 even-parity levels belonging to the configurations 4f85d6s2, 4f85d26s or 4f96s6p; in all the cases those levels were involved in the transitions investigated as the lower levels. For 40 levels the hfs was examined for the first time, and for the remaining 12 levels the new measurements supplement our earlier results. As a by-product, also preliminary values of the hfs constants for 84 odd-parity levels were determined (the investigations of the odd-parity levels system in the terbium atom are still in progress). This huge amount of new experimental data, supplemented by our earlier published results, were considered for the fine and hyperfine structure analysis. A multi-configuration fit of 7 configurations was performed, taking into account second-order of perturbation theory, including the effects of closed shell-open shell excitations. Predicted values of the level energies, as well as of magnetic dipole and electric quadrupole hyperfine structure constants A and B, are quoted in cases when no experimental values are available. By combining our experimental data with our own semi-empirical procedure it was possible to identify correctly the lower and upper level of the line 544.1440 nm measured by Childs with the use of the atomic-beam laser-rf double-resonance technique (Childs, J Opt Soc Am B 9;1992:191-6).
A real-time all-atom structural search engine for proteins.
Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F
2014-07-01
Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).
Calculation of the sound transmission between dwellings by partitions and flanking structures
Gerretsen, E.
1979-01-01
A calculation model is presented for the sound transmission between dwellings by partitions and by flanking structures, based on the application of classical theory. The most important data needed are the sound reduction index for direct transmission of the different structures and the vibration
Calculation of condition indices for road structures using a deduct points method
CSIR Research Space (South Africa)
Roux, MP
2016-07-01
Full Text Available ) and relevancy (R) rating. The DER-rating method has been included in the Draft TMH19 Manual for the Visual Assessment of Road Structures. The D, E, and R ratings are used to calculate condition indices for road structures. The method used is a deduct...
Structure of the neopentane monolayer adsorbed on MgO(0 0 1): experiments and calculations
Trabelsi, M.; Saı̈di, S.; Chefi, C.; Picaud, S.; Hoang, P. N. M.; Coulomb, J. P.
2004-02-01
The monolayer of C(CH 3) 4 molecules adsorbed upon a highly homogeneous MgO powder surface has been studied by means of neutron diffraction techniques at the temperature 210 K. The structure of the monolayer presents a strong commensurability c(2 × 4) with the MgO(0 0 1) surface. The results of potential calculations support the proposed structure.
DEFF Research Database (Denmark)
Christensen, N. Egede; Feuerbacher, B.
1974-01-01
The electronic energy-band structure of tungsten has been calculated by means of the relativistic-augmented-plane-wave method. A series of mutually related potentials are constructed by varying the electronic configuration and the amount of Slater exchange included. The best band structure...
Etindele, A. J.; Maezono, R.; Melingui Melono, R. L.; Motapon, O.
2017-10-01
The influence of encapsulated atoms in the structural and dynamical properties of C60 in A@C60 complexes is studied in the framework of the Density Functional Theory using Density of states and the theoretical Electron Energy Loss Spectroscopy. It is shown that C60 preserves its spherical geometry no matter the equilibrium position of the encapsulated atom. The Infrared and Raman spectra of the H@C60, He@C60 and Ne@C60 complexes are found not to differ significantly from that of C60 whereas those for Li@C60 and Na@C60 exhibit more peaks. The analysis shows that the changes on the cage properties come from inside it.
Electronic structure of atomic-plane doped superlattice in GaAs
Zehe, A.; de la Cruz Estenoz, D.
A special atomic-plane doped superlattice is proposed and studied, where both donors and acceptors are incorporated during MBE growth simultaneously into sheets spaced equidistantly by intrinsic regions of the growing semiconductor material. The donor-acceptor Pair (DAP)-distribution function displays characteristics features of the proposed pair-doped delta-superlattice (PD-δiδi-SL) which allow for their experimental verification by luminescence measurements. With excess doping of one type a narrow V-shaped potential is formed about the atomic planes generating a multiquantum-well structure. In the present paper the size quantization in V-shaped potential wells is studied, and exact analytic expressions for wavefunctions and energy levels are given as function of determining measures of potential well and superlattices. The sawtooth doping superlattice is a special case in our calculus.
Golod, V. M.; Sufiiarov, V. Sh
2017-04-01
Gas atomization is a high-performance process for manufacturing superfine metal powders. Formation of the powder particles takes place primarily through the fragmentation of alloy melt flow with high-pressure inert gas, which leads to the formation of non-uniform sized micron-scale particles and subsequent their rapid solidification due to heat exchange with gas environment. The article presents results of computer modeling of crystallization process, simulation and experimental studies of the cellular-dendrite structure formation and microsegregation in different size particles. It presents results of adaptation of the approach for local nonequilibrium solidification to conditions of crystallization at gas atomization, detected border values of the particle size at which it is possible a manifestation of diffusionless crystallization.
Romanyuk, O.; Supplie, O.; Susi, T.; May, M. M.; Hannappel, T.
2016-10-01
The atomic and electronic band structures of GaP/Si(001) heterointerfaces were investigated by ab initio density functional theory calculations. Relative total energies of abrupt interfaces and mixed interfaces with Si substitutional sites within a few GaP layers were derived. It was found that Si diffusion into GaP layers above the first interface layer is energetically unfavorable. An interface with Si/Ga substitution sites in the first layer above the Si substrate is energetically the most stable one in thermodynamic equilibrium. The electronic band structure of the epitaxial GaP/Si(001) heterostructure terminated by the (2 ×2 ) surface reconstruction consists of surface and interface electronic states in the common band gap of two semiconductors. The dispersion of the states is anisotropic and differs for the abrupt Si-Ga, Si-P, and mixed interfaces. Ga 2 p , P 2 p , and Si 2 p core-level binding-energy shifts were computed for the abrupt and the lowest-energy heterointerface structures. Negative and positive core-level shifts due to heterovalent bonds at the interface are predicted for the abrupt Si-Ga and Si-P interfaces, respectively. The distinct features in the heterointerface electronic structure and in the core-level shifts open new perspectives in the experimental characterization of buried polar-on-nonpolar semiconductor heterointerfaces.
Głowacki, Leszek
2015-12-01
Relativistic configuration-interaction calculations using hydrogenlike or Dirac-Fock spin orbitals of the transition from the ground state to some n p1 /2 , n p3 /2 low-lying excited states for the alkali metals are presented. In these calculations each virtual spin orbital corresponds to a unique noninteger atomic number determined iteratively using the virtual-particle model. The virtual-particle model based on "condensed-space" idea is here adopted to many electron systems consisting of a single valence electron and the core. The transition energy and the oscillator strength values were computed for sodium, potassium, rubidium, cesium, and francium. Both hydrogenlike and Dirac-Fock basis functions have been used in the computations for comparison.
Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.
Das, Rhiju
2013-01-01
Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. Current approaches, such as the protein local optimization protocol or kinematic inversion closure (KIC) Monte Carlo, involve stages that coarse-grain proteins, simplifying modeling but precluding a systematic search of all-atom configurations. This article introduces an alternative modeling strategy based on a 'stepwise ansatz', recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA) protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include cis-Pro touch turns, loops that pass through tunnels of other side-chains, and loops of lengths up to 24 residues. Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth 'RNA-puzzle' competition. These results establish all-atom enumeration as an unusually
Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.
Directory of Open Access Journals (Sweden)
Rhiju Das
Full Text Available Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. Current approaches, such as the protein local optimization protocol or kinematic inversion closure (KIC Monte Carlo, involve stages that coarse-grain proteins, simplifying modeling but precluding a systematic search of all-atom configurations. This article introduces an alternative modeling strategy based on a 'stepwise ansatz', recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include cis-Pro touch turns, loops that pass through tunnels of other side-chains, and loops of lengths up to 24 residues. Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth 'RNA-puzzle' competition. These results establish all-atom enumeration as
Wigner’s phase-space function and atomic structure: II. Ground states for closed-shell atoms
DEFF Research Database (Denmark)
Springborg, Michael; Dahl, Jens Peder
1987-01-01
display and analyze the function for the closed-shell atoms helium, beryllium, neon, argon, and zinc in the Hartree-Fock approximation. The quantum-mechanical exact results are compared with those obtained with the approximate Thomas-Fermi description of electron densities in phase space....
Temperature Dependent Local Atomic Structure of LuFe2O4
Liu, S.; Zhang, H.; Ghose, S.; Cheong, S.-W.; Emge, T.; Chen, Y.-S.; Tyson, T.
The LuFe2O4 system has be studied intensively as a novel material with charge ordered driven ferroelectricity. However, the existence and origin of electric polarization and it coupling to the magnetic structure are open questions still to be addressed. Distinctly differing experiments yield different results. In this work, structural measurements on multiple length scales have been conducted over a broad range of temperatures. We have studied the correlation between the structural distortion and the electronic/magnetic properties in single-crystalline LuFe2O4 by using X-ray diffraction (XRD), temperature and orientation dependent Raman spectroscopy, temperature dependent X-ray pair distribution function (PDF) measurements and DFT modeling. The nature of the observed local atomic and electronic structural changes will be discussed and compared with previous work. This work is supported by DOE Grant DE-FG02-07ER46402.
DEFF Research Database (Denmark)
Valentin, Jan B.; Andreetta, Christian; Boomsma, Wouter
2014-01-01
We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length...... scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy...... terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive...
Iyer, Abhishek Hariharan; Krishna Deepak, R N V; Sankararamakrishnan, Ramasubbu
2018-01-25
Protein structures are stabilized by different types of hydrogen bonds. However, unlike the DNA double helical structure, the N-H···N type of hydrogen bonds is relatively rare in proteins. N-H···N hydrogen bonds formed by imidazole groups of two histidine residues have not been investigated. We have systematically analyzed 5333 high-resolution protein structures with resolution 1.8 Å or better and identified 285 histidine pairs in which the nitrogen atoms of the imidazole side chains can potentially participate in N-H···N hydrogen bonds. The histidine pairs were further divided into two groups, neutral-neutral and protonated-neutral, depending on the protonation state of the donor histidine. Quantum chemical calculations were performed on imidazole groups adopting the same geometry observed in the protein structures. Average interaction energies between the interacting imidazole groups are -6.45 and -22.5 kcal/mol for neutral-neutral and protonated-neutral, respectively. Hydrogen bond interaction between the imidazole moieties is further confirmed by natural bond orbital analyses of the model compounds. Histidine residues involved in N-H···N hydrogen bonds are relatively more buried and have low B-factor values in the protein structures. N-H···N hydrogen bond formed by a pair of buried histidine residues can significantly contribute to the structural stability of proteins.