Atomic Structure Calculations for Neutral Oxygen
Norah Alonizan; Rabia Qindeel; Nabil Ben Nessib
2016-01-01
Energy levels and oscillator strengths for neutral oxygen have been calculated using the Cowan (CW), SUPERSTRUCTURE (SS), and AUTOSTRUCTURE (AS) atomic structure codes. The results obtained with these atomic codes have been compared with MCHF calculations and experimental values from the National Institute of Standards and Technology (NIST) database.
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter
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....
Hyun-Kyung Chung; Per Jönsson; Alexander Kramida
2013-01-01
Atomic structure and transition probabilities are fundamental physical data required in many fields of science and technology. Atomic physics codes are freely available to other community users to generate atomic data for their interest, but the quality of these data is rarely verified. This special issue addresses estimation of uncertainties in atomic structure and transition probability calculations, and discusses methods and strategies to assess and ensure the quality of theoretical atomic...
Advances in Atomic Structure Calculations%原子结构计算的进展
Institute of Scientific and Technical Information of China (English)
Charlotte Froese Fischer
2007-01-01
Correlation and relativistic effects are both needed for accurate atomic structure calculations of energy levels and their atomic properties. For transition probabilities of radiative transitions between low-lying levels of an atom or ion, accurate wave functions for the outer region of are required. For lighter atoms, relativistic effects can be included through the Breit-Pauli approximation. This paper outlines the advances in the treatment of correlation and describes the current state of Breit-Pauli calculations for complex systems.
Lin, Lin
2012-01-01
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...
First-principles calculations atomic structure and elastic properties of Ti-Nb alloys
Timoshevskii, A N; Ivasishin, O M
2011-01-01
Elastic properties of Ti based \\beta-alloy were studied by the method of the model structure first principle calculations. Concentrational dependence of Young modulus for the binary \\beta-alloy Ti-Nb was discovered. It is shown that peculiarities visible at 15-18% concentrations can be related to the different Nb atoms distribution. Detailed comparison of the calculation results with the measurement results was done. Young modulus for the set of the ordered structures with different Nb atoms location, which simulate triple \\beta-alloys Ti-29.7%Zr-18.5%Nb and Ti-51.8%Zr-18.5%Nb have been calculated. The results of these calculations allowed us to suggest the concentration region for single-phase ternary \\beta-phase alloys possessing low values of Young's modulus.
Ansari, Reza; Ajori, Shahram; Malakpour, Sina
2016-04-01
The considerable demand for novel materials with specific properties has motivated the researchers to synthesize supramolecular nanostructures through different methods. Porous graphene is the first two-dimensional hydrocarbon synthesized quite recently. This investigation is aimed at studying the mechanical properties of atom-decorated (functionalized) porous graphene by employing density functional theory (DFT) calculation within both local density approximations (LDA) and generalized gradient approximations (GGA). The atoms are selected from period 3 of periodic table as well as Li and O atom from period 2. The results reveal that metallic atoms and noble gases are adsorbed physically on porous graphene and nonmetallic ones form chemical bonds with carbon atom in porous graphene structure. Also, it is shown that, in general, atom decoration reduces the values of mechanical properties such as Young's, bulk and shear moduli as well as Poisson's ratio, and this reduction is more considerable in the case of nonmetallic atoms (chemical adsorption), especially oxygen atoms, as compared to metallic atoms and noble gases (physical adsorption).
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.
Energy Technology Data Exchange (ETDEWEB)
Piskunov, Sergei, E-mail: piskunov@lu.l [Faculty of Computing, University of Latvia, 19 Raina blvd., Riga LV-1586 (Latvia); Faculty of Physics and Mathematics, University of Latvia, 8 Zellu Str., Riga LV-1002 (Latvia); Zvejnieks, Guntars; Zhukovskii, Yuri F. [Institute for Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia); Bellucci, Stefano [INFN-Laboratori Nazionali di Frascati, Via Enrico Fermi 40, I-00044, Frascati (Italy)
2011-03-31
In this study, we perform first principles simulations on both atomically smooth and nanostructured Ni(111) slabs. The latter contains periodically distributed nickel nanoclusters atop a thin metal film gradually growing from adatoms and serving as a promising catalyst. Applying the generalized gradient approximation within the formalism of the density functional theory we compare the atomic and electronic structures of Ni bulk, as well as both perfect and nanostructured (111) surfaces obtained using two different ab initio approaches: (i) the linear combination of atomic orbitals and (ii) the projector augmented plane waves. The most essential inter-atomic forces between the Ni adatoms upon the substrate have been found to be formed via: (i) attractive pair-wise interactions, (ii) repulsive triple-wise interactions within a triangle and (iii) attractive triple-wise interactions within a line between the nearest adatoms. The attractive interactions surmount the repulsive forces, hence resulting in the formation of stable clusters from Ni adatoms. The magnetic moment and the effective charge (within both Mulliken and Bader approaches) of the outer atoms in Ni nanoparticles increase as compared to those for the smooth Ni(111) surface. The calculated electronic charge redistribution in the Ni nanoclusters features them as possible adsorption centers with increasing catalytic activity, e.g., for further synthesis of carbon nanotubes.
Per Jönsson; Hyun-Kyung Chung
2013-01-01
There exist several codes in the atomic physics community to generate atomic structure and transition probabilities freely and readily distributed to researchers outside atomic physics community, in plasma, astrophysical or nuclear physics communities. Users take these atomic physics codes to generate the necessary atomic data or modify the codes for their own applications. However, there has been very little effort to validate and verify the data sets generated by non-expert users. [...
Lin, Lin; Yang, Chao; He, Lixin
2012-01-01
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 hundr...
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.
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
Jayatilaka, Dylan; Dittrich, Birger
2008-05-01
An approach is outlined for X-ray structure refinement using atomic density fragments obtained by Hirshfeld partitioning of quantum-mechanical density fragments. Results are presented for crystal structure refinements of urea and benzene using these 'Hirshfeld atoms'. Using this procedure, the quantum-mechanical non-spherical electron density is taken into account in the structural model based on the conformation found in the crystal. Contrary to current consensus in structure refinement, the anisotropic displacement parameters of H atoms can be reproduced from neutron diffraction measurements simply from a least-squares fit using the Hirshfeld atoms derived from the BLYP level of theory and including a simple point-charge model to treat the crystal environment.
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.
Landau, Arie; Kaprálová-Žďánská, Petra Ruth; Moiseyev, Nimrod
2015-01-01
Complex eigenvalues, resonances, play an important role in large variety of fields in physics and chemistry. For example, in cold molecular collision experiments and electron scattering experiments, autoionizing and pre-dissociative metastable resonances are generated. However, the computation of complex resonance eigenvalues is difficult, since it requires severe modifications of standard electronic structure codes and methods. Here we show how resonance eigenvalues, positions and widths, can be calculated using the standard, widely used, electronic-structure packages. Our method enables the calculations of the complex resonance eigenvalues by using analytical continuation procedures (such as Pad\\'{e}). The key point in our approach is the existence of narrow analytical passages from the real axis to the complex energy plane. In fact, the existence of these analytical passages relies on using finite basis sets. These passages become narrower as the basis set becomes more complete, whereas in the exact limit,...
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.
dftatom: A robust and general Schrödinger and Dirac solver for atomic structure calculations
Čertík, Ondřej; Pask, John E.; Vackář, Jiří
2013-07-01
Classification: 2.1. External routines: Numpy (http://www.numpy.org/) and Cython (http://cython.org/) Nature of problem: Solution of the Schrödinger, Dirac, and Kohn-Sham equations of Density Functional Theory for isolated atoms. Solution method: Radial integrations are carried out using a combination of asymptotic forms, Runge-Kutta, and implicit Adams methods. Eigenfunctions are determined by a combination of bisection and perturbation methods. An outward Poisson integration is employed to increase accuracy in the core region. Self-consistent field equations are solved by adaptive linear mixing. Restrictions: Spherical symmetry Unusual features: Radial integrators work for general potentials and meshes. No restriction to Coulombic or self-consistent potentials; no restriction to uniform or exponential meshes. Outward Poisson integration. Fallback to bisection for robustness. Running time: For uranium, non-relativistic density functional calculation execution time is around 0.6 s for 10-6 a.u. accuracy in total energy on an Intel Core i7 1.46 GHz processor.
Nazir, R. T.; Bari, M. A.; Bilal, M.; Sardar, S.; Nasim, M. H.; Salahuddin, M.
2017-02-01
We performed R-matrix calculations for photoionization cross sections of the two ground state configuration 3s23p5 (^2P^o3/2,1/2) levels and 12 excited states of Ni XII using relativistic Dirac Atomic R-matrix Codes (DARC) across the photon energy range between the ionizations thresholds of the corresponding states and well above the thresholds of the last level of the Ni XIII target ion. Generally, a good agreement is obtained between our results and the earlier theoretical photoionization cross sections. Moreover, we have used two independent fully relativistic GRASP and FAC codes to calculate fine-structure energy levels, wavelengths, oscillator strengths, transitions rates among the lowest 48 levels belonging to the configuration (3s23p4, 3s3p5, 3p6, 3s23p33d) in Ni XIII. Additionally, radiative lifetimes of all the excited states of Ni XIII are presented. Our results of the atomic structure of Ni XIII show good agreement with other theoretical and experimental results available in the literature. A good agreement is found between our calculated lifetimes and the experimental ones. Our present results are useful for plasma diagnostic of fusion and astrophysical plasmas.
Bierón, Jacek; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka
2009-01-01
The multiconfiguration Dirac-Hartree-Fock (MCDHF) model has been employed to calculate the expectation values for the hyperfine splittings of the 5d96s2 2D3/2 and 5d96s2 2D5/2 levels of atomic gold. One-, two-, and three-body electron correlation effects involving all 79 electrons have been included in a systematic manner. The approximation employed in this study is equivalent to a Complete Active Space (CAS) approach. Calculated electric field gradients, together with experimental values of the electric quadrupole hyperfine structure constants, allow us to extract a nuclear electric quadrupole moment Q(197Au)=521.5(5.0) mb.
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
Atomic Structure Theory Lectures on Atomic Physics
Johnson, Walter R
2007-01-01
Atomic Structure Theory is a textbook for students with a background in quantum mechanics. The text is designed to give hands-on experience with atomic structure calculations. Material covered includes angular momentum methods, the central field Schrödinger and Dirac equations, Hartree-Fock and Dirac-Hartree-Fock equations, multiplet structure, hyperfine structure, the isotope shift, dipole and multipole transitions, basic many-body perturbation theory, configuration interaction, and correlation corrections to matrix elements. Numerical methods for solving the Schrödinger and Dirac eigenvalue problems and the (Dirac)-Hartree-Fock equations are given as well. B-spline basis sets are used to carry out sums arising in higher-order many-body calculations. Illustrative problems are provided, together with solutions. FORTRAN programs implementing the numerical methods in the text are included.
Interaction between LiH molecule and Li atom from state-of-the-art electronic structure calculations
Skomorowski, Wojciech; Korona, Tatiana; Moszyński, Robert; Zuchowski, Piotr S \\; Hutson, Jeremy M
2010-01-01
State-of-the-art ab initio techniques have been applied to compute the potential energy surface for the lithium atom interacting with the lithium hydride molecule in the Born-Oppenheimer approximation. The interaction potential was obtained using a combination of the explicitly correlated unrestricted coupled-cluster method with single, double, and noniterative triple excitations [UCCSD(T)-F12] for the core-core and core-valence correlation and full configuration interaction for the valence-valence correlation. The potential energy surface has a global minimum 8743 cm^{-1} deep if the Li-H bond length is held fixed at the monomer equilibrium distance or 8825 cm^{-1} deep if it is allowed to vary. In order to evaluate the performance of the conventional CCSD(T) approach, calculations were carried out using correlation-consistent polarized valence X-tuple-zeta bases, with X ranging from 2 to 5. The contribution beyond the CCSD(T)-F12 model, obtained from full configuration interaction (FCI) calculations for the...
Modified embedded atom method calculations of interfaces
Energy Technology Data Exchange (ETDEWEB)
Baskes, M.I.
1996-05-01
The Embedded Atom Method (EAM) is a semi-empirical calculational method developed a decade ago to calculate the properties of metallic systems. By including many-body effects this method has proven to be quite accurate in predicting bulk and surface properties of metals and alloys. Recent modifications have extended this applicability to a large number of elements in the periodic table. For example the modified EAM (MEAM) is able to include the bond-bending forces necessary to explain the elastic properties of semiconductors. This manuscript will briefly review the MEAM and its application to the binary systems discussed below. Two specific examples of interface behavior will be highlighted to show the wide applicability of the method. In the first example a thin overlayer of nickel on silicon will be studied. Note that this example is representative of an important technological class of materials, a metal on a semiconductor. Both the structure of the Ni/Si interface and its mechanical properties will be presented. In the second example the system aluminum on sapphire will be examined. Again the class of materials is quite different, a metal on an ionic material. The calculated structure and energetics of a number of (111) Al layers on the (0001) surface of sapphire will be compared to recent experiments.
Electronic structure interpolation via atomic orbitals.
Chen, Mohan; Guo, G-C; He, Lixin
2011-08-17
We present an efficient scheme for accurate electronic structure interpolation based on systematically improvable optimized atomic orbitals. The atomic orbitals are generated by minimizing the spillage value between the atomic basis calculations and the converged plane wave basis calculations on some coarse k-point grid. They are then used to calculate the band structure of the full Brillouin zone using the linear combination of atomic orbitals algorithms. We find that usually 16-25 orbitals per atom can give an accuracy of about 10 meV compared to the full ab initio calculations, and the accuracy can be systematically improved by using more atomic orbitals. The scheme is easy to implement and robust, and works equally well for metallic systems and systems with complicated band structures. Furthermore, the atomic orbitals have much better transferability than Shirley's basis and Wannier functions, which is very useful for perturbation calculations.
Turkington, M. D.; Ballance, C. P.; Hibbert, A.; Ramsbottom, C. A.
2016-08-01
In this work we explore the validity of employing a modified version of the nonrelativistic structure code civ3 for heavy, highly charged systems, using Na-like tungsten as a simple benchmark. Consequently, we present radiative and subsequent collisional atomic data compared with corresponding results from a fully relativistic structure and collisional model. Our motivation for this line of study is to benchmark civ3 against the relativistic grasp0 structure code. This is an important study as civ3 wave functions in nonrelativistic R -matrix calculations are computationally less expensive than their Dirac counterparts. There are very few existing data for the W LXIV ion in the literature with which we can compare except for an incomplete set of energy levels available from the NIST database. The overall accuracy of the present results is thus determined by the comparison between the civ3 and grasp0 structure codes alongside collisional atomic data computed by the R -matrix Breit-Pauli and Dirac codes. It is found that the electron-impact collision strengths and effective collision strengths computed by these differing methods are in good general agreement for the majority of the transitions considered, across a broad range of electron temperatures.
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.
Energy Technology Data Exchange (ETDEWEB)
Piskunov, S. [Institute of Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga (Latvia); Kotomin, E.A. [Institute of Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga (Latvia) and Max-Planck-Institut fuer Festkoerperforschung, Heisenbergstrasse 1, 70569 Stuttgart (Germany)]. E-mail: kotomin@latnet.lv; Fuks, D. [Materials Engineering Department, Ben-Gurion University of the Negev, POB 653, Beer-Sheva (Israel); Dorfman, S. [Department of Physics, Technion- Israel Institute of Technology, Haifa 32000 (Israel)
2005-04-25
Understanding of the atomic and electronic structure of Ba{sub c}Sr{sub 1-c}TiO{sub 3} (BST) solid solutions is important for several applications including the non-volatile ferroelectric memories (dynamic random access memory, DRAM). We present results of ab initio calculations of several spatial arrangements of Ba{sub 0.5}Sr{sub 0.5}TiO{sub 3} solid solutions based on DFT-HF B3PW hybrid method. We calculate the atomic and electronic structure, the effective charges, interatomic bond populations, the electronic density distribution, and densities of states for three layered structures with the same composition. The suggested method reproduces experimental lattice parameters of both pure BaTiO{sub 3} and SrTiO{sub 3}. The calculated optical band gaps for the pure SrTiO{sub 3} and BaTiO{sub 3} are in a good agreement with experimental data, much better than those from the standard LDA or HF calculations. In the studied BST structures with the equiatomic composition (c = 0.5) the gap is reduced by ca. 0.2 eV. The electron density maps demonstrate the covalency effects in the Ti-O bonding. The electron density near the Sr atoms is stronger localized, as compared with the Ba ions.
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.
AJAC: Atomic data calculation tool in Python
Institute of Scientific and Technical Information of China (English)
Amani Tahat; Jordi Marti; Kaher Tahat; Ali Khwaldeh
2013-01-01
In this work,new features and extensions of a currently used online atomic database management system are reported.A multiplatform flexible computation package is added to the present system,to allow the calculation of various atomic radiative and collisional processes,based on simplifying the use of some existing atomic codes adopted from the literature.The interaction between users and data is facilitated by a rather extensive Python graphical user interface working online and could be installed in personal computers of different classes.In particular,this study gives an overview of the use of one model of the package models (i.e.,electron impact collisional excitation model).The accuracy of computing capability of the electron impact collisional excitation in the adopted model,which follows the distorted wave approximation approach,is enhanced by implementing the Dirac R-matrix approximation approach.The validity and utility of this approach are presented through a comparison of the current computed results with earlier available theoretical and experimental results.Finally,the source code is made available under the general public license and being distributed freely in the hope that it will be useful to a wide community of laboratory and astrophysical plasma diagnostics.
Ikuhara, Yuichi
2011-01-01
Grain boundaries and interfaces of crystals have peculiar electronic structures, caused by the disorder in periodicity, providing the functional properties, which cannot be observed in a perfect crystal. In the vicinity of the grain boundaries and interfaces, dopants or impurities are often segregated, and they play a crucial role in deciding the properties of a material. Spherical aberration (Cs)-corrected scanning transmission electron microscopy (STEM), allowing the formation of sub-angstrom-sized electron probes, can directly observe grain boundary-segregated dopants. On the other hand, ceramic materials are composed of light elements, and these light elements also play an important role in the properties of ceramic materials. Recently, annular bright-field (ABF)-STEM imaging has been proposed, which is now known to be a very powerful technique in producing images showing both light- and heavy-element columns simultaneously. In this review, the atomic structure determination of ceramic grain boundaries and direct observation of grain boundary-segregated dopants and light elements in ceramics were shown to combine with the theoretical calculations. Examples are demonstrated for well-defined grain boundaries in rare earth-doped Al(2)O(3) and ZnO ceramics, CeO(2) and SrTiO(3) grain boundary, lithium battery materials and metal hydride, which were characterized by Cs-corrected high-angle annular dark-field and ABF-STEM. It is concluded that the combination of STEM characterization and first-principles calculation is very useful in interpreting the structural information and in understanding the origin of the properties in various ceramics.
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...
A simplified approach to calculate atomic partition functions in plasmas
Energy Technology Data Exchange (ETDEWEB)
D' Ammando, Giuliano [Dipartimento di Chimica, Universita di Bari, Via Orabona 4, 70125 Bari (Italy); Colonna, Gianpiero [CNR-IMIP, Via Amendola 122/D, 70126 Bari (Italy); Capitelli, Mario [Dipartimento di Chimica, Universita di Bari, Via Orabona 4, 70125 Bari (Italy); CNR-IMIP, Via Amendola 122/D, 70126 Bari (Italy)
2013-03-15
A simplified method to calculate the electronic partition functions and the corresponding thermodynamic properties of atomic species is presented and applied to C(I) up to C(VI) ions. The method consists in reducing the complex structure of an atom to three lumped levels. The ground level of the lumped model describes the ground term of the real atom, while the second lumped level represents the low lying states and the last one groups all the other atomic levels. It is also shown that for the purpose of thermodynamic function calculation, the energy and the statistical weight of the upper lumped level, describing high-lying excited atomic states, can be satisfactorily approximated by an analytic hydrogenlike formula. The results of the simplified method are in good agreement with those obtained by direct summation over a complete set (i.e., including all possible terms and configurations below a given cutoff energy) of atomic energy levels. The method can be generalized to include more lumped levels in order to improve the accuracy.
Convergent variational calculation of positronium-hydrogen-atom scattering lengths
Adhikari, S K; Adhikari, Sadhan K.; Mandal, Puspajit
2001-01-01
We present a convergent variational basis-set calculational scheme for elastic scattering of positronium atom by hydrogen atom in S wave. Highly correlated trial functions with appropriate symmetry are needed for achieving convergence. We report convergent results for scattering lengths in atomic units for both singlet ($=3.49\\pm 0.20$) and triplet ($=2.46\\pm 0.10$) states.
Calculation of Al-Zn diagram from central atoms model
Institute of Scientific and Technical Information of China (English)
无
1999-01-01
A slightly modified central atoms model was proposed. The probabilities of various clusters with the central atoms and their nearest neighboring shells can be calculated neglecting the assumption of the param eter of energy in the central atoms model in proportion to the number of other atoms i (referred with the central atom). A parameter Pα is proposed in this model, which equals to reciprocal of activity coefficient of a component, therefore, the new model can be understood easily. By this model, the Al-Zn phase diagram and its thermodynamic properties were calculated, the results coincide with the experimental data.
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…
Atomic and Electronic Structures of Zr Atomic Chains
Institute of Scientific and Technical Information of China (English)
林益寿; 李爱玉; 朱梓忠
2004-01-01
The atomic, binding and electronic structures of very thin Zr chains are studied by the first-principles densityfunctional method. The present calculations reveal that zirconium can form planar chains in zigzag, dimer and ladder structures. The zigzag geometry has two minima. The most stable geometry is the zigzag one with a unit cell rather close to equilateral triangles with four nearest neighbours. The other stable zigzag structure has a wide bond angle and allows for two nearest neighbours. An intermediary structure has the ladder geometry and is formed by two strands. The dimer structure is also found to be more stable than the truly linear chain. All these planar geometries are more favourable energetically than the linear chain. We also show that by going from Zr bulk to a Zr chain, the characters of bonding do not change significantly.
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.
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.
Ab-initio Green's Functions Calculations of Atoms
Barbieri, C
2009-01-01
The Faddeev random phase approximation (FRPA) method is applied to calculate the ground state and ionization energies of simple atoms. First ionization energies agree with the experiment at the level of ~10 mH or less. Calculations with similar accuracy are expected to provide information required for developing the proposed quasiparticle-DFT method.
Institute of Scientific and Technical Information of China (English)
马堃; 褚园; 焦铮; 谢国秋
2013-01-01
以多电子原子精细结构哈密顿的球张量形式为基础,借助不可约张量理论,对铍原子1s22snp(n=2～6) 3p态精细结构(包括自旋-轨道相互作用、自旋-其它轨道相互作用和自旋-自旋相互作用)进行了具体地计算,并将计算结果与文献结果进行了比较,符合地较好.同时,计算了1s22snp(n=2～6)3p态精细结构参数A和B的值.%Based on the tensor expression of the fine-structure Hamiltonian for many-electron atoms,and with the help of irreducible tensor theory,the fine-structure energies (including spin-orbit interaction,spin-other-orbit interaction and the spin-spin interaction) of the 1s22snp3p state in beryllium atom have been calculated.The results are in close agreement with the experimental data.Meanwhile,parameters of the fine-structure have been calculated further.
A Variational Monte Carlo Approach to Atomic Structure
Davis, Stephen L.
2007-01-01
The practicality and usefulness of variational Monte Carlo calculations to atomic structure are demonstrated. It is found to succeed in quantitatively illustrating electron shielding, effective nuclear charge, l-dependence of the orbital energies, and singlet-tripetenergy splitting and ionization energy trends in atomic structure theory.
Autoionizing states of atoms calculated using generalized sturmians
DEFF Research Database (Denmark)
Avery, James Emil; Avery, John Scales
2005-01-01
The generalized Sturmian method is applied to autoionizing states of atoms and ions. If the Goscinskian basis sets allow for a sufficient amount of angular correletion, the calculated energies of doubly-excited (autoionizing) states are found to agree well with the few available experimental ener...
Update on nuclear structure effects in light muonic atoms
Hernandez, Oscar Javier; Dinur, Nir Nevo; Ji, Chen; Bacca, Sonia; Barnea, Nir
2016-12-01
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.
Update on nuclear structure effects in light muonic atoms
Hernandez, Oscar Javier; Ji, Chen; Bacca, Sonia; Barnea, Nir
2016-01-01
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.
Nuclear forces and ab initio calculations of atomic nuclei
Meißner, Ulf-G.
2014-01-01
Nuclear forces and the nuclear many-body problem have been some of Gerry Brown's main topics in his so productive life as a theoretical physicist. In this talk, I outline how Gerry's work laid the foundations of the modern theory of nuclear forces and ab initio calculations of atomic nuclei. I also present some recent developments obtained in the framework of nuclear lattice simulations.
Isogeometric analysis in electronic structure calculations
Cimrman, Robert; Kolman, Radek; Tůma, Miroslav; Vackář, Jiří
2016-01-01
In electronic structure calculations, various material properties can be obtained by means of computing the total energy of a system as well as derivatives of the total energy w.r.t. atomic positions. The derivatives, also known as Hellman-Feynman forces, require, because of practical computational reasons, the discretized charge density and wave functions having continuous second derivatives in the whole solution domain. We describe an application of isogeometric analysis (IGA), a spline modification of finite element method (FEM), to achieve the required continuity. The novelty of our approach is in employing the technique of B\\'ezier extraction to add the IGA capabilities to our FEM based code for ab-initio calculations of electronic states of non-periodic systems within the density-functional framework, built upon the open source finite element package SfePy. We compare FEM and IGA in benchmark problems and several numerical results are presented.
Semiempirical studies of atomic structure
Energy Technology Data Exchange (ETDEWEB)
Curtis, L.J.
1992-01-01
The energy level structure, transition probabilities, and general spectroscopic properties of highly-ionized many-electron systems are studied through the combined use of sensitive semiempirical data systematizations, selected precision experimental measurements, and specialized theoretical computations. Measurements are made primarily through the use of fast ion beam excitation methods, which are combined with available data from laser- and tokamak-produced plasmas, astrophysical sources, and conventional light sources. The experimental studies are strengthened through large scale ab initio calculations. Large blocks of data are predictively systematized and parameterized along isoelectric, homologous, isoionic, Rydberg, and yrast series, to provide a comprehensive and reliable data base.
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_\
Local Atomic Structure of Piperidyl Nd Dithiocarbamate
Institute of Scientific and Technical Information of China (English)
吴忠华; 李前树; 等
1999-01-01
The atomic structure of a novel rare earth complex consisting of Nd and the sulfur-containing ligand pipdtc (C5H10NCS2-) has been studied with extended x-ray absortpiton fine structure(EXAFS) and x-ray diffraction techniques.The complex of formula Nd(pipdtc)4N(CH3)4 crystallizaes in the monoclinic space group P21/n with the following lattice parameters,a=22.685(2),b=20.332(2),c=17.1270(10)A,β=100.570(10)°.Z=8,the calculated density is 1.47g/cm3,A new derivative method is used to remove the piost-edge absorption background including the multielectron excitation effect.The EXAFS results demonstrate that there are about eight S and four O atoms around Nd with the Nd-S bond length of 2.916A and the Nd-O bond length of 2.415A,respectively.This implies that the powder of this complex is not stable and is easy to oxidize in air.The possible change of structure before and after oxidation is discussed.
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...
Global nuclear-structure calculations
Energy Technology Data Exchange (ETDEWEB)
Moeller, P.; Nix, J.R.
1990-04-20
The revival of interest in nuclear ground-state octupole deformations that occurred in the 1980's was stimulated by observations in 1980 of particularly large deviations between calculated and experimental masses in the Ra region, in a global calculation of nuclear ground-state masses. By minimizing the total potential energy with respect to octupole shape degrees of freedom in addition to {epsilon}{sub 2} and {epsilon}{sub 4} used originally, a vastly improved agreement between calculated and experimental masses was obtained. To study the global behavior and interrelationships between other nuclear properties, we calculate nuclear ground-state masses, spins, pairing gaps and {Beta}-decay and half-lives and compare the results to experimental qualities. The calculations are based on the macroscopic-microscopic approach, with the microscopic contributions calculated in a folded-Yukawa single-particle potential.
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...
Introduction to Atomic Structure: Demonstrations and Labs.
Ciparick, Joseph D.
1988-01-01
Demonstrates a variety of electrical phenomena to help explain atomic structure. Topics include: establishing electrical properties, electrochemistry, and electrostatic charges. Recommends demonstration equipment needed and an explanation of each. (MVL)
Direct atomic structure determination by the inspection of structural phase.
Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne
2013-08-27
A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.
Quantum Structures of the Hydrogen Atom
Jeknic-Dugic, J; Francom, A; Arsenijevic, M
2012-01-01
Modern quantum theory introduces quantum structures (decompositions into subsystems) as a new discourse that is not fully comparable with the classical-physics counterpart. To this end, so-called Entanglement Relativity appears as a corollary of the universally valid quantum mechanics that can provide for a deeper and more elaborate description of the composite quantum systems. In this paper we employ this new concept to describe the hydrogen atom. We offer a consistent picture of the hydrogen atom as an open quantum system that naturally answers the following important questions: (a) how do the so called "quantum jumps" in atomic excitation and de-excitation occur? and (b) why does the classically and seemingly artificial "center-of-mass + relative degrees of freedom" structure appear as the primarily operable form in most of the experimental reality of atoms?
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.
Theoretical study of atomic oxygen on gold surface by Hückel theory and DFT calculations.
Sun, Keju; Kohyama, Masanori; Tanaka, Shingo; Takeda, Seiji
2012-09-27
It is fundamental to understand the behavior of atomic oxygen on gold surfaces so as to elucidate the mechanism of nano gold catalysts for low-temperature CO oxidation reactions since the atomic oxygen on gold system is an important intermediate involved in both the processes of O(2) dissociation and CO oxidation. We performed theoretical analysis of atomic oxygen adsorption on gold by using Hückel theory. It is found that formation of linear O-Au-O structure on Au surfaces greatly stabilizes the atomic oxygen adsorption due to stronger bond energy and bond order, which is confirmed subsequently by density functional theory (DFT) calculations. The linear O-Au-O structure may explain the surprising first order kinetics behavior of O(2) desorption from gold surfaces. This view of the linear O-Au-O structure as the natural adsorption status is quite different from the conventional view, which may lead to new understanding toward the reaction mechanism of low-temperature CO oxidation reaction on nano gold catalysts.
Bannikov, V. V.; Shein, I. R.; Ivanovskii, A. L.
2012-01-01
Using the first principles FLAPW-GGA method, comparative study of structural, electronic properties and of chemical bonding in four 1111-like chalcogenide oxides La MChO (LaCuSO, LaCuSeO, LaAgSO, and LaAgSeO) with ZrCuSiAs-type structure was performed. Our studies showed that: (i) replacements of d metal atoms (Cu ↔ Ag) and chalcogen atoms (S ↔ Se) lead to anisotropic deformations of the crystal structure; this effect is related to strong anisotropy of inter-atomic bonds; (ii) all of the examined chalcogenide oxides are semiconducting; the band gap decreases both at S → Se and Cu → Ag substitutions; and (iii) the bonding in La MChO phases can be classified as a high-anisotropic mixture of ionic and covalent contributions, where mixed covalent-ionic bonds take place inside [La 2O 2] and [ M2Ch2] blocks, whereas between the adjacent [La 2O 2]/[ M2Ch2] blocks, ionic bonds emerge owing to [La 2O 2] → [ M2Ch2] charge transfer. Since the near-Fermi bands of La MChO phases originate mainly from electronic states of [ M2Ch2] blocks, we speculate that chemical substitutions inside these blocks can result in striking differences in electronic properties of these systems; therefore, this approach can be promising for significant enlargement of the functional properties of these materials.
Calculation of strange star structure
Directory of Open Access Journals (Sweden)
GH Bordbar
2009-12-01
Full Text Available In this paper, we have considered that the strange-star consists of quark matter from its center to surface. For quark matter, we have used two models, the MIT bag model and string-flip like model. In the bag model, the energy of the system has been considered the kinetic energy of the particles of system in addition to a constant B. We have considered two states for B, one of them is constant and the other one is density dependent. The second state has been obtained from the recent Cern data from quark-geleon plasma formation. In string-flip like model, the energy of the particles of the system has been obtained from the Schrodinger equation, where the Hamiltonian has been considered the sum of kinetic and potential energies. The potential in Hamiltonian is the general potential which depends on density that is the block potential. In the String-flip like model, the block potential is linear or square functions of the relative distance between two quarks. We have also obtained the equation of state of quark matter for all considered cases. Finally, we have computed the structure of the quark star using our equations of state.
Energy Technology Data Exchange (ETDEWEB)
Farkas, D. [Department of Materials Science and Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (United States); Zhou, S.J. [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Vailhe, C.; Mutasa, B.; Panova, J. [Department of Materials Science and Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (United States)
1997-01-01
We performed embedded atom method calculations on surface energies and unstable stacking fault energies for a series of intermetallics for which interatomic potentials of the embedded atom type have recently been developed. These results were analyzed and applied to the prediction of relative ductility of these materials using the various current theories. Series of alloys with the B2 ordered structure were studied, and the results were compared to those in pure body-centered cubic (bcc) Fe. Ordered compounds with L1{sub 2} and L1{sub 0} structures based on the face-centered cubic (fcc) lattice were also studied. It was found that there is a correlation between the values of the antiphase boundary (APB) energies in B2 alloys and their unstackable stacking fault energies. Materials with higher APB energies tend to have higher unstable stacking fault energies, leading to an increased tendency to brittle fracture. {copyright} {ital 1997 Materials Research Society.}
Atomic vapor spectroscopy in integrated photonic structures
Ritter, Ralf; Pernice, Wolfram; Kübler, Harald; Pfau, Tilman; Löw, Robert
2015-01-01
We investigate an integrated optical chip immersed in atomic vapor providing several waveguide geometries for spectroscopy applications. The narrow-band transmission through a silicon nitride waveguide and interferometer is altered when the guided light is coupled to a vapor of rubidium atoms via the evanescent tail of the waveguide mode. We use grating couplers to couple between the waveguide mode and the radiating wave, which allow for addressing arbitrary coupling positions on the chip surface. The evanescent atom-light interaction can be numerically simulated and shows excellent agreement with our experimental data. This work demonstrates a next step towards miniaturization and integration of alkali atom spectroscopy and provides a platform for further fundamental studies of complex waveguide structures.
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.
Bannikov, V. V.; Ivanovskii, A. L.
2013-06-01
By means of the FLAPW-GGA approach, we have systematically studied the structural and electronic properties of tetragonal dichalcogenides KNi2Ch2 (Ch=S, Se, and Te). Our results show that replacements of chalcogens (S→Se→Te) lead to anisotropic deformations of the crystals structure, which are related to the strong anisotropic character of the inter-atomic bonds, where inside the [Ni2Ch2] blocks, mixed covalent-ionic-metallic bonds occur, whereas between the adjacent [Ni2Ch2] blocks and K atomic sheets, ionic bonds emerge. We found that in the sequence KNi2S2→KNi2Se2→KNi2Te2 (i) the overall band structure (where the near-Fermi valence bands are due mainly to the Ni states) is preserved, but the width of the common valence band and the widths of the separate sub-bands and the gaps decrease; (ii) the total DOSs at the Fermi level also decrease; and (iii) for the Fermi surfaces, the most appreciable changes are demonstrated by the hole-like sheets, when a necklace-like topology is formed for the 2D-like sheets and the volume of the closed pockets decreases. Some trends in structural and electronic parameters for ThCr2Si2-type layered dichalcogenides, KNi2Ch2, KFe2Ch2, KCo2Se2, are discussed.
Atomic Structure of Graphene Subnanometer Pores.
Robertson, Alex W; Lee, Gun-Do; He, Kuang; Gong, Chuncheng; Chen, Qu; Yoon, Euijoon; Kirkland, Angus I; Warner, Jamie H
2015-12-22
The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert.
Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework.
Berger, Daniel; Logsdail, Andrew J; Oberhofer, Harald; Farrow, Matthew R; Catlow, C Richard A; Sherwood, Paul; Sokol, Alexey A; Blum, Volker; Reuter, Karsten
2014-07-14
We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).
Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework
Berger, Daniel; Logsdail, Andrew J.; Oberhofer, Harald; Farrow, Matthew R.; Catlow, C. Richard A.; Sherwood, Paul; Sokol, Alexey A.; Blum, Volker; Reuter, Karsten
2014-07-01
We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).
Atomic and electronic structure of twin growth defects in magnetite.
Gilks, Daniel; Nedelkoski, Zlatko; Lari, Leonardo; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Kepaptsoglou, Demie; Ramasse, Quentin; Evans, Richard; McKenna, Keith; Lazarov, Vlado K
2016-02-15
We report the existence of a stable twin defect in Fe3O4 thin films. By using aberration corrected scanning transmission electron microscopy and spectroscopy the atomic structure of the twin boundary has been determined. The boundary is confined to the (111) growth plane and it is non-stoichiometric due to a missing Fe octahedral plane. By first principles calculations we show that the local atomic structural configuration of the twin boundary does not change the nature of the superexchange interactions between the two Fe sublattices across the twin grain boundary. Besides decreasing the half-metallic band gap at the boundary the altered atomic stacking at the boundary does not change the overall ferromagnetic (FM) coupling between the grains.
DEFF Research Database (Denmark)
Ruud, Kenneth; Helgaker, Trygve; Kobayashi, Rika;
1994-01-01
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...
Energy Technology Data Exchange (ETDEWEB)
Stone, N. J., E-mail: n.stone@physics.ox.ac.uk; Stone, J. R. [University of Oxford (United Kingdom); Jonsson, P. [Malmo University (Sweden)
2010-04-15
Calculations of hyperfine interaction strength and life-times of states in highly ionized atoms, using the GRASP atomic structure package, are reported. The calculations aim at providing calibration for Recoil-in-Vacuum nuclear excited state g-factor measurements. The method is outlined and results compared with experiment. Inclusion of decay of higher electronic states is discussed.
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...
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.
Comment on mesic-atom Auger-rate calculation
Altman, A.; Fried, Z.
1983-07-01
Auger rates for a mesic atom consisting of a lithium nucleus and two electrons are presented. It is shown that the results are sensitive to the screening of the initial and final state of the ejected electron by the spectator electron. These results are compared to transition rates one would obtain by following the procedure used by Burbridge and de Borde, which neglect screening of one electron by the others. Our results show a 40% reduction in transition rates.
Real-time feedback from iterative electronic structure calculations
Vaucher, Alain C; Reiher, Markus
2015-01-01
Real-time feedback from iterative electronic structure calculations requires to mediate between the inherently unpredictable execution times of the iterative algorithm employed and the necessity to provide data in fixed and short time intervals for real-time rendering. We introduce the concept of a mediator as a component able to deal with infrequent and unpredictable reference data to generate reliable feedback. In the context of real-time quantum chemistry, the mediator takes the form of a surrogate potential that has the same local shape as the first-principles potential and can be evaluated efficiently to deliver atomic forces as real-time feedback. The surrogate potential is updated continuously by electronic structure calculations and guarantees to provide a reliable response to the operator for any molecular structure. To demonstrate the application of iterative electronic structure methods in real-time reactivity exploration, we implement self-consistent semi-empirical methods as the data source and a...
Electronic-structure calculations of large cadmium chalcogenide nanoparticles
Energy Technology Data Exchange (ETDEWEB)
Frenzel, Johannes [Lehrstuhl fuer Theoretische Chemie, Ruhr-Universitaet Bochum (Germany); Joswig, Jan-Ole [Physikalische Chemie, Technische Universitaet Dresden (Germany)
2012-02-15
In this paper, we will review our studies of large cadmium chalcogenide nanoparticles and present some new results on cadmium telluride systems. All calculations have been performed using density-functional based methods. The studies deal with the structural properties of saturated and unsaturated nanoparticles where the surfactants generally are hydrogen atoms or thiol groups. We have focused on the investigation of the density of states, the Mulliken charges, the eigenvalue spectra, and the spatial distributions of the frontier orbitals. Optical excitation spectra of pure CdS and CdSe/CdS core-shell systems have been calculated using a linear-response formalism. The reviewed studies are compared to the state of the art of modeling large cadmium chalcogenide particles. Optical excitations in large saturated cadmium chalcogenide nanoparticles with several thousand atoms. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Large-scale quantum transport calculations for electronic devices with over ten thousand atoms
Lu, Wenchang; Lu, Yan; Xiao, Zhongcan; Hodak, Miro; Briggs, Emil; Bernholc, Jerry
The non-equilibrium Green's function method (NEGF) has been implemented in our massively parallel DFT software, the real space multigrid (RMG) code suite. Our implementation employs multi-level parallelization strategies and fully utilizes both multi-core CPUs and GPU accelerators. Since the cost of the calculations increases dramatically with the number of orbitals, an optimal basis set is crucial for including a large number of atoms in the ``active device'' part of the simulations. In our implementation, the localized orbitals are separately optimized for each principal layer of the device region, in order to obtain an accurate and optimal basis set. As a large example, we calculated the transmission characteristics of a Si nanowire p-n junction. The nanowire is along (110) direction in order to minimize the number dangling bonds that are saturated by H atoms. Its diameter is 3 nm. The length of 24 nm is necessary because of the long-range screening length in Si. Our calculations clearly show the I-V characteristics of a diode, i.e., the current increases exponentially with forward bias and is near zero with backward bias. Other examples will also be presented, including three-terminal transistors and large sensor structures.
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...... is primarily outside the atom or ion, with only a small amplitude inside....
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.
PAMOP: Petascale Atomic, Molecular and Optical Collision Calculations
McLaughlin, Brendan M; Pindzola, Michael S; Müller, Alfred
2015-01-01
Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schr\\"odinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. In this report, various examples are shown from our theoretical results compared with experimental results obtained from Synchrotron Radiation facilities where the Cray architecture at HLRS is playing an integral part in our computational projects.
Atomic Structure of Ultrathin Gold Nanowires.
Yu, Yi; Cui, Fan; Sun, Jianwei; Yang, Peidong
2016-05-11
Understanding of the atomic structure and stability of nanowires (NWs) is critical for their applications in nanotechnology, especially when the diameter of NWs reduces to ultrathin scale (1-2 nm). Here, using aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM), we report a detailed atomic structure study of the ultrathin Au NWs, which are synthesized using a silane-mediated approach. The NWs contain large amounts of generalized stacking fault defects. These defects evolve upon sustained electron exposure, and simultaneously the NWs undergo necking and breaking. Quantitative strain analysis reveals the key role of strain in the breakdown process. Besides, ligand-like morphology is observed at the surface of the NWs, indicating the possibility of using AC-HRTEM for surface ligand imaging. Moreover, the coalescence dynamic of ultrathin Au NWs is demonstrated by in situ observations. This work provides a comprehensive understanding of the structure of ultrathin metal NWs at atomic-scale and could have important implications for their applications.
Lattice location of dopant atoms: An -body model calculation
Indian Academy of Sciences (India)
N K Deepak
2010-03-01
The channelling and scattering yields of 1 MeV -particles in the $\\langle 1 0 0 \\rangle$, $\\langle 1 1 0 \\rangle and $\\langle 1 1 1 \\rangle$ directions of silicon implanted with bismuth and ytterbium have been simulated using -body model. 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 continuum model. These results at the best gave only the transverse displacement of the lattice site from the concerned channelling direction. Here we applied the superior -body model to study the yield from bismuth in silicon. The finding that bismuth atom occupies a position close to the silicon substitutional site is new. The transverse displacement of the suggested lattice site from the channelling direction is consistent with the experimental results. The above model is also applied to determine the location of ytterbium in silicon. The present values show good agreement with the experimental results.
Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations.
Monastyrskii, Liubomyr S; Boyko, Yaroslav V; Sokolovskii, Bogdan S; Potashnyk, Vasylyna Ya
2016-12-01
An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method-the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range.
Multigrid Methods in Electronic Structure Calculations
Briggs, E L; Bernholc, J
1996-01-01
We describe a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods provide effective convergence acceleration and preconditioning on all length scales, thereby permitting efficient calculations for ill-conditioned systems with long length scales or high energy cut-offs. We discuss specific implementations of multigrid and real-space algorithms for electronic structure calculations, including an efficient multigrid-accelerated solver for Kohn-Sham equations, compact yet accurate discretization schemes for the Kohn-Sham and Poisson equations, optimized pseudo\\-potentials for real-space calculations, efficacious computation of ionic forces, and a complex-wavefunction implementation for arbitrary sampling of the Brillioun zone. A particular strength of a real-space multigrid approach is its ready adaptability to massively parallel computer architectures, and we present an implementation for the Cray-T3D with essen...
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 in the Lan...
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.
Calculating the Finite-Speed-of-Light Effect in Atom Gravimeters with General Relativity
Tan, Yu-Jie
2016-01-01
This work mainly presents a relativistic analytical calculating method for the finite speed-of-light effect in atom gravimeters, which can simplify the deriva- tion and give a more complete expression for the associated correction.
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...
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.
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.
Direct observation of a long-lived single-atom catalyst chiseling atomic structures in graphene.
Wang, Wei Li; Santos, Elton J G; Jiang, Bin; Cubuk, Ekin Dogus; Ophus, Colin; Centeno, Alba; Pesquera, Amaia; Zurutuza, Amaia; Ciston, Jim; Westervelt, Robert; Kaxiras, Efthimios
2014-02-12
Fabricating stable functional devices at the atomic scale is an ultimate goal of nanotechnology. In biological processes, such high-precision operations are accomplished by enzymes. A counterpart molecular catalyst that binds to a solid-state substrate would be highly desirable. Here, we report the direct observation of single Si adatoms catalyzing the dissociation of carbon atoms from graphene in an aberration-corrected high-resolution transmission electron microscope (HRTEM). The single Si atom provides a catalytic wedge for energetic electrons to chisel off the graphene lattice, atom by atom, while the Si atom itself is not consumed. The products of the chiseling process are atomic-scale features including graphene pores and clean edges. Our experimental observations and first-principles calculations demonstrated the dynamics, stability, and selectivity of such a single-atom chisel, which opens up the possibility of fabricating certain stable molecular devices by precise modification of materials at the atomic scale.
Structure and atomic vibrations in bimetallic Ni13 - n Al n clusters
Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.
2015-04-01
The binding energy, equilibrium geometry, and vibration frequencies in bimetallic clusters Ni13 - n Al n ( n = 0-13) have been calculated using the embedded atom method potentials. It has been shown that the icosahedral structure is the most stable in monoatomic and bimetallic clusters. A tendency of Al atoms to segregate on the cluster surface has been revealed in agreement with the experimental data. The calculations of the atomic vibrations have shown the nonmonotonic dependence of the minimum and maximum vibration frequencies of cluster atoms on its composition and the coupling of their extreme values with the most stable atomic configuration. The increase in the number of Al atoms leads to the shift of the frequency spectrum and the substantial redistribution of the localization of vibrations on the cluster atoms.
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.
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...
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.
Song, Young-Sun; Kim, Jeongwoo; Jhi, Seung-Hoon
2017-03-01
We study the nature of atomic rearrangement during the phase-change processes in the superlattice of GeTe and Sb2Te3 by developing a new approach combining the first-principles calculations and a pair-potential model. We investigate the phase-change process in terms of energy changes from individual pairs or atoms by applying the pair (atom)-projection analysis to the intermediate structures between the initial and final states obtained from the climbing-image nudged elastic band method. Among the prototypical steps that can lead to the atomic layer rearrangement, we find that the required energy for the phase change is dominated by specific atoms responsible for the intrinsic energy barrier and the response to external pressure. Our approach of combining the first-principles methods and pair potential model with the projecting analysis can be a very efficient method in revealing the detailed atomic motions and the mechanism of fast atomic transition of the phase-change materials.
Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele
2013-11-14
We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.
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
Lattice QCD Calculation of Nucleon Structure
Energy Technology Data Exchange (ETDEWEB)
Liu, Keh-Fei; Draper, Terrence
2016-08-30
It is emphasized in the 2015 NSAC Long Range Plan [1] 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 rst-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 [2], axial-vector [3], NN [4], and scalar [5] form factors, the quark spin contribution [6] to the proton spin, the strangeness magnetic moment [7], the quark orbital angular momentum [8], the quark momentum fraction [9], and the quark and glue decomposition of the proton momentum and angular momentum [10]. These rst round of calculations were done with Wilson fermions in the `quenched' approximation where the dynamical e ects of the quarks in the sea are not taken into account in the Monte Carlo simulation to generate the background gauge con gurations. Beginning in 2000, we have started implementing the overlap fermion formulation into the spectroscopy and structure calculations [11, 12]. 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 [13], charm and strange quark masses, the charmonium spectrum and the Ds meson decay constant fDs [14], the strangeness and charmness [15], the
New method for calculating the Berry connection in atom-molecule systems
Institute of Scientific and Technical Information of China (English)
Cui Fu-Cheng; Wu Bao-Jun
2012-01-01
In the mean-field theory of atom molecule systems,where the bosonic atoms combine to form molecules,there is no usual U(1) symmetry,which presents an apparent hurdle for calculating the Berry connection in these systems.We develop a perturbation expansion method of Hannay's angle suitable for calculating the Berry curvature in the atom molecule systems.With this Berry curvature,the Berry connection can be computed naturally.We use a three-level atom-molecule system to illustrate our results.In particular,with this method,we compute the curvature for Hannay's angle analytically,and compare it to the Berry curvature obtained with the second-quantized model of the same system.An excellent agreement is found,indicating the validity of our method.
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.
Spin-splitting calculation for zincblende semiconductors using an atomic bond-orbital model.
Kao, Hsiu-Fen; Lo, Ikai; Chiang, Jih-Chen; Chen, Chun-Nan; Wang, Wan-Tsang; Hsu, Yu-Chi; Ren, Chung-Yuan; Lee, Meng-En; Wu, Chieh-Lung; Gau, Ming-Hong
2012-10-17
We develop a 16-band atomic bond-orbital model (16ABOM) to compute the spin splitting induced by bulk inversion asymmetry in zincblende materials. This model is derived from the linear combination of atomic-orbital (LCAO) scheme such that the characteristics of the real atomic orbitals can be preserved to calculate the spin splitting. The Hamiltonian of 16ABOM is based on a similarity transformation performed on the nearest-neighbor LCAO Hamiltonian with a second-order Taylor expansion k at the Γ point. The spin-splitting energies in bulk zincblende semiconductors, GaAs and InSb, are calculated, and the results agree with the LCAO and first-principles calculations. However, we find that the spin-orbit coupling between bonding and antibonding p-like states, evaluated by the 16ABOM, dominates the spin splitting of the lowest conduction bands in the zincblende materials.
Calculation of phonon spectrum for noble metals by modified analytic embedded atom method (MAEAM)
Institute of Scientific and Technical Information of China (English)
Zhang Xiao-Jun; Zhang Jian-Min; Xu Ke-Wei
2006-01-01
In the harmonic approximation, the atomic force constants are derived and the phonon dispersion curves along four major symmetry directions [00ζ], [0ζζ], [ζζζ] and [0ζ1] (or △, ∑, A and Z in group-theory notation) are calculated for four noble metals Cu, Ag, Au and Pt by combining the modified analytic embedded atom method (MAEAM) with the theory of lattice dynamics. A good agreement between calculations and measurements, especially for lower frequencies,shows that the MAEAM provides a reasonable description of lattice dynamics in noble metals.
Calculation of the ionization differential effective cross sections in fast ion-atom collisions
Kaminskij, A K
2002-01-01
The method of the calculations of the ionization effective cross sections d sigma/d OMEGA differential in the incident ion scattering angle is described in fast collisions of light ions and atoms. The calculated values of angular distributions of the ions Al, Mg (for the different values of charge and energy of ions) after their collisions with the Ne, Mg atoms being ionized are reported. The dependence of such angular distributions on the incident ion charge and energy and the initial state of ejected electron is investigated
Variational calculations of coupling of an incident helium atom to a slab of superfluid helium four
Energy Technology Data Exchange (ETDEWEB)
Campbell, C.E.; Halley, J.W.; Hoon, S. [and others
1995-04-01
In previous work on the interaction of single helium atoms with a slab of superfluid helium the authors found a large amplitude, dependent on the condensate fraction, for transmission with re-emission of a helium atom at the other side of the slab. Here they report a variational formulation of the problem which permits a time dependent calculation and which does not require any perturbation expansion. The variational principle involves a minimization of the expectation value of the square of the difference H-E. They will present preliminary results of a variational Monte Carlo calculation using a simple variational form for the wave function.
The effective atomic numbers of some biomolecules calculated by two methods: A comparative study
DEFF Research Database (Denmark)
Manohara, S.R.; Hanagodimath, S.M.; Gerward, Leif
2009-01-01
The effective atomic numbers Z(eff) of some fatty acids and amino acids have been calculated by two numerical methods, a direct method and an interpolation method, in the energy range of 1 keV-20 MeV. The notion of Z(eff) is given a new meaning by using a modern database of photon interaction cross...... constant and equal to the mean atomic number of the material. Wherever possible, the calculated values of Z(eff) are compared with experimental data....
Local atomic structure in cubic stabilized zirconia
Energy Technology Data Exchange (ETDEWEB)
Villella, P.; Conradson, S. D.; Espinosa-Faller, F. J.; Foltyn, S. R.; Sickafus, K. E.; Valdez, J. A.; Degueldre, C. A.
2001-09-01
X-ray-absorption fine structure measurements have been used to elucidate the local atomic structure of quaternary Zr, Y, Er, Ce/U cubic stabilized zirconia. These compounds display more complicated local environments than those reported for simpler binary systems. While the shortest cation-O distances are similar to those found in the binary cubic stabilized compounds, responding to the different sizes of the cations, we have identified large distortions in the first-shell oxygen distribution involving long, 2.8--3.2 {angstrom} cation-O distances that are similar to those found in the amorphous phase of zirconium. The cation-cation distributions are also found to be quite complicated (non-Gaussian) and element specific. The U-near neighbor distances are expanded relative to the Ce ions for which it substitutes, consistent with the larger size of the actinide, and the U-cation distribution is also more complicated. In terms of the effects of this substitution on the other cation sites, the local environment around Y is altered while the Zr and Er local environments remain unchanged. These results point out the importance of collective and correlated interactions between the different pairs of cations and the host lattice that are mediated by the local strain fields generated by the different cations. The presence of pair-specific couplings has not been commonly included in previous analyses and may have implications for the stabilization mechanisms of cubic zirconia.
Structural Features of Boron-Doped Si(113) Surfaces Simulated by ab initio Calculations
Institute of Scientific and Technical Information of China (English)
LIAO Long-Zhong; LIU Zheng-Hui; ZHANG Zhao-Hui
2008-01-01
Based on ab initio calculations, boron-doped Si(113) surfaces have been simulated and atomic structures of the surfaces have been proposed. It has been determined that surface features of empty and filled states that are separately localized at pentamers and adatoms indicates a low surface density of B atoms, while it is attributed to heavy doping of B atoms at the second layer that pentamers and adatoms are both present in an image of scanning tunnelling microscopy. B doping at the second layer should be balanced by adsorbed B or Si atoms beside the adatoms and inserted B interstitials below the adatoms.
Real-time feedback from iterative electronic structure calculations.
Vaucher, Alain C; Haag, Moritz P; Reiher, Markus
2016-04-05
Real-time feedback from iterative electronic structure calculations requires to mediate between the inherently unpredictable execution times of the iterative algorithm used and the necessity to provide data in fixed and short time intervals for real-time rendering. We introduce the concept of a mediator as a component able to deal with infrequent and unpredictable reference data to generate reliable feedback. In the context of real-time quantum chemistry, the mediator takes the form of a surrogate potential that has the same local shape as the first-principles potential and can be evaluated efficiently to deliver atomic forces as real-time feedback. The surrogate potential is updated continuously by electronic structure calculations and guarantees to provide a reliable response to the operator for any molecular structure. To demonstrate the application of iterative electronic structure methods in real-time reactivity exploration, we implement self-consistent semiempirical methods as the data source and apply the surrogate-potential mediator to deliver reliable real-time feedback.
Understanding the proton radius puzzle: Nuclear structure effects in light muonic atoms
Ji, Chen; Dinur, Nir Nevo; Bacca, Sonia; Barnea, Nir
2015-01-01
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.
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.
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.
Model operator approach to the Lamb shift calculations in relativistic many-electron atoms
Shabaev, V M; Yerokhin, V A
2013-01-01
A model operator approach to calculations of the QED corrections to energy levels in relativistic many-electron atomic systems is developed. The model Lamb shift operator is represented by a sum of local and nonlocal potentials which are defined using the results of ab initio calculations of the diagonal and nondiagonal matrix elements of the one-loop QED operator with H-like wave functions. The model operator can be easily included in any calculations based on the Dirac-Coulomb-Breit Hamiltonian. Efficiency of the method is demonstrated by comparison of the model QED operator results for the Lamb shifts in many-electron atoms and ions with exact QED calculations.
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.
Local atomic structures of single-component metallic glasses
Trady, Salma; Hasnaoui, Abdellatif; Mazroui, M.'hammed; Saadouni, Khalid
2016-10-01
In this study we examine the structural properties of single-component metallic glasses of aluminum. We use a molecular dynamics simulation based on semi-empirical many-body potential, derived from the embedded atom method (EAM). The radial distribution function (RDF), common neighbors analysis method (CNA), coordination number analysis (CN) and Voronoi tessellation are used to characterize the metal's local structure during the heating and cooling (quenching). The simulation results reveal that the melting temperature depends on the heating rate. In addition, atomic visualization shows that the structure of aluminum after fast quenching is in a glassy state, confirmed quantitatively by the splitting of the second peak of the radial distribution function, and by the appearance of icosahedral clusters observed via CNA technique. On the other hand, the Wendt-Abraham parameters are calculated to determine the glass transition temperature (Tg), which depends strongly on the cooling rate; it increases while the cooling rate increases. On the basis of CN analysis and Voronoi tessellation, we demonstrate that the transition from the Al liquid to glassy state is mainly due to the formation of distorted and perfect icosahedral clusters.
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).
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.
Using Density Functional Theory (DFT) for the Calculation of Atomization Energies
Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.
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...
Gao, Xiang; Han, Xiao-Ying; Li, Jia-Ming
2016-11-01
An extended atomic data base with sufficiently high precision in energy levels and transition/collision rates is required for satellite observation in astrophysics studies and energy development research in inertial confinement fusion and magnetic confinement fusion. We summarize in this paper a scenario for performing calculations leading to such large-scale atomic data with high precision based on the analytical continuation properties of the scattering matrices, connecting spectroscopy and collisions. Based on the scenario, we calculate directly the scattering matrices with spectroscopic accuracy, i.e. the accurate multi-channel quantum defect theory parameters in both bound and continuum energy regions based on the recently developed eigenchannel R-matrix approach. Applications of the related atomic processes are presented to demonstrate the advantages enjoyed by this approach, which is hoped to meet the requirements in the stages of precision physics for astrophysics and energy research.
Evaluation and Comparison of the Configuration Interaction Calculations for Complex Atoms
Directory of Open Access Journals (Sweden)
Charlotte Froese Fischer
2014-03-01
Full Text Available Configuration interaction (CI methods are the method of choice for the determination of wave functions for complex atomic systems from which a variety of atomic properties may be computed. When applied to highly ionized atoms, where few, if any, energy levels from observed wavelengths are available, the question arises as to how a calculation may be evaluated. Many different codes are available for such calculations. Agreement between the results from different codes in itself is not a check on accuracy, but may be due to a similarity in the computational procedures. This paper reviews basic theory, which, when applied in a systematic manner, can be the basis for the evaluation of accuracy. Results will be illustrated in the study of 4s24p5 (odd and 4s24p44d (even levels in W39+ and the transitions between them.
Field-theory calculation of the electric dipole moment of the neutron and paramagnetic atoms
Griffith, Joel; Blundell, Steven; Sapirstein, Jonathan
2013-04-01
Electric dipole moments (edms) of bound states that arise from the constituents having edms are studied with field-theoretic techniques. The systems treated are the neutron and a set of paramagnetic atoms. In the latter case it is well known that the atomic edm differs greatly from the electron edm when the internal electric fields of the atom are taken into account. In the nonrelativistic limit these fields lead to a complete suppression, but for heavy atoms large enhancement factors are present. A general bound-state field theory approach applicable to both the neutron and paramagnetic atoms is set up. It is applied first to the neutron, treating the quarks as moving freely in a confining spherical well. It is shown that the effect of internal electric fields is small in this case. The atomic problem is then revisited using field-theory techniques in place of the usual Hamiltonian methods, and the atomic enhancement factor is shown to be consistent with previous calculations. Possible application of bound-state techniques to other sources of the neutron edm is discussed.
DEFF Research Database (Denmark)
Ruud, K.; Helgaker, T.; Jørgensen, Poul
1994-01-01
We report a systematic investigation of the magnetizability of a series of small molecules. The use of London atomic orbitals ensures gauge invariance and a fast basis set convergence. Good agreement is obtained with experimental magnetizabilities, both isotropic and anisotropic. The calculations...
Perturbative calculation of the Sternheimer anti-shielding factor with Hartree-Fock atomic orbitals
2012-01-01
We report a calculation of the Sternheimer anti-shielding factor, \\gamma, by means of first order perturbation theory. In quality of basis functions, we use Hartree-Fock electronic orbitals, expanded on hydrogenic atomic states. The computed \\gamma(r) for Fe^{3+} and Cu^{1+} inner electronic cores are reported and compared with literature values, obtained from alternative methodologies.
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....
Quantum and Semiclassical Calculations of Cold Atom Collisions in Light Fields
Suominen, K A; Tuvi, I; Burnett, K; Julienne, P S
1998-01-01
We derive and apply an optical Bloch equation (OBE) model for describing collisions of ground and excited laser cooled alkali atoms in the presence of near-resonant light. Typically these collisions lead to loss of atoms from traps. We compare the results obtained with a quantum mechanical complex potential treatment, semiclassical Landau-Zener models with decay, and a quantum time-dependent Monte-Carlo wave packet (MCWP) calculation. We formulate the OBE method in both adiabatic and diabatic representations. We calculate the laser intensity dependence of collision probabilities and find that the adiabatic OBE results agree quantitatively with those of the MCWP calculation, and qualitatively with the semiclassical Landau-Zener model with delayed decay, but that the complex potential method or the traditional Landau-Zener model fail in the saturation limit.
Ultrathin film of nickel on the Cu (100) surface: Atomic structure and phonons
Energy Technology Data Exchange (ETDEWEB)
Borisova, Svetlana D., E-mail: svbor@ispms.tsc.ru, E-mail: rusina@ispms.tsc.ru, E-mail: rusina-g@mail.ru; Rusina, Galina G., E-mail: svbor@ispms.tsc.ru, E-mail: rusina@ispms.tsc.ru, E-mail: rusina-g@mail.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055, Russia and National Research Tomsk State University, Tomsk, 634050 (Russian Federation)
2014-11-14
We investigated the structural and vibrational properties of the Cu (100) surface covered with ultrathin (1-5 ML) Ni films using interaction potential from the embedded atom method. The surface relaxation, dispersion relation and polarization of vibrational modes are discussed. Our calculated structural parameters are in good agreement with experimental results. The obtained vibrational frequencies compare well with the available experimental data.
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): di...
STARK STRUCTURE OF THE RYDBERG STATES OF ALKALINE-EARTH ATOMS
Institute of Scientific and Technical Information of China (English)
郅妙婵; 戴长建; 李士本
2001-01-01
The Stark effects of the Rydberg states in the alkaline-earth atoms are studied theoretically. Using a method similar to the treatment of alkali atoms, the properties of the Stark states of Mg, Ca, Sr and Ba atoms in the regions far away from the perturbers are investigated. The Stark maps for Mg (n=16, M=0), Ca (n=10, M=0), Sr (n=12,M=0) and Ba (n=13, |M|=0,1) are presented. Topics such as the general methods of calculation, the treatment of fine structure, and the structure of level anti-crossings are discussed. The comparison between the theoretical and experimental Stark maps is satisfactory.
Ruiz-Serrano, Álvaro; Skylaris, Chris-Kriton
2013-08-07
A new method for finite-temperature density functional theory calculations which significantly increases the number of atoms that can be simulated in metallic systems is presented. A self-consistent, direct minimization technique is used to obtain the Helmholtz free energy of the electronic system, described in terms of a set of non-orthogonal, localized functions which are optimized in situ using a periodic-sinc basis set, equivalent to plane waves. Most parts of the calculation, including the demanding operation of building the Hamiltonian matrix, have a computational cost that scales linearly with the number of atoms in the system. Also, this approach ensures that the Hamiltonian matrix has a minimal size, which reduces the computational overhead due to diagonalization, a cubic-scaling operation that is still required. Large basis set accuracy is retained via the optimization of the localized functions. This method allows accurate simulations of entire metallic nanostructures, demonstrated with calculations on a supercell of bulk copper with 500 atoms and on gold nanoparticles with up to 2057 atoms.
Efficient Execution of Electronic Structure Calculations on SMP Clusters
Energy Technology Data Exchange (ETDEWEB)
Ustemirov, Nurzhan [Iowa State Univ., Ames, IA (United States)
2006-01-01
Applications augmented with adaptive capabilities are becoming common in parallel computing environments. For large-scale scientific applications, dynamic adjustments to a computationally-intensive part may lead to a large pay-off in facilitating efficient execution of the entire application while aiming at avoiding resource contention. Application-specific knowledge, often best revealed during the run-time, is required to initiate and time these adjustments. In particular, General Atomic and Molecular Electronic Structure System (GAMESS) is a program for ab initio quantum chemistry that places significant demands on the high-performance computing platforms. Certain electronic structure calculations are characterized by high consumption of a particular resource, such as CPU, main memory, or disk I/O. This may lead to resource contention among concurrent GAMESS jobs and other programs in the dynamically changing environment. Thus, it is desirable to improve GAMESS calculations by means of dynamic adaptations. In this thesis, we show how an application- or algorithm-specific knowledge may play a significant role in achieving this goal. The choice of implementation is facilitated by a module-driven middleware easily integrated with GAMESS that assesses resource consumption and invokes GAMESS adaptations to the system environment. We show that the throughput of GAMESS jobs may be improved greatly as a result of such adaptations.
Spectral fine structure of the atomic ground states based on full relativistic theory
Institute of Scientific and Technical Information of China (English)
Zhenghe Zhu; Yongjian Tang
2011-01-01
@@ We focus on the full relativistic quantum mechanical calculations from boron to fluorine atoms with electronic configuration of 1s22s22pn (n = 1, 2, 3, 4, and 5), where 1s22s2 is the closed shell and 2pn is the open shell. Their active electrons in the open shell occupy all the six spinors as far as possible.Therefore, we suggest a new rule called "maximum probability" for the full symmetry group relativistic theory. Furthermore, the spectral fine structure of the atomic ground states based on the full relativistic theory and their intervals of L-S splitting are all reasonable. It is impossible to calculate the L-S splitting through non-relativistic quantum mechanics. The relativistic effect of atomic mass is increased significantly by about 12 folds from boron atom to fluorine atom.%We focus on the full relativistic quantum mechanical calculations from boron to fluorine atoms with electronic configuration of 1s22s22pn (n = 1, 2, 3, 4, and 5), where 1s22s2 is the closed shell and 2pn is the open shell. Their active electrons in the open shell occupy all the six spinors as far as possible.Therefore, we suggest a new rule called "maximum probability" for the full symmetry group relativistic theory. Furthermore, the spectral fine structure of the atomic ground states based on the full relativistic theory and their intervals of L-S splitting are all reasonable. It is impossible to calculate the L-S splitting through non-relativistic quantum mechanics. The relativistic effect of atomic mass is increased significantly by about 12 folds from boron atom to fluorine atom.
Calculations of Self-diffusion Activation Energies for Alkaline Metals With Embedded Atom Method
Institute of Scientific and Technical Information of China (English)
欧阳义芳; 张邦维; 廖树帜
1994-01-01
Calculations were performed for the self-diffusion activation energies of monovacancy and both formation and binding energies of divacancies for alkaline metals Li, Na, K, Rb, Cs using the embedded atom method (EAM) model for bcc transition metals developed by the authors recently. The aim of the paper is to extend the application of the new model, to compare the calculated values for self-diffusion with the experimental data and those of previous calculations, and to discuss the intrinsic characteristic of self-diffusion in alkaline metals. The calculated monovacancy migration energies and activation energies are in excellent agreement with experimental data, and the calculated divacancy migration and activation energies are in good agreement with the experimental values available.
Computational method for general multicenter electronic structure calculations.
Batcho, P F
2000-06-01
Here a three-dimensional fully numerical (i.e., chemical basis-set free) method [P. F. Batcho, Phys. Rev. A 57, 6 (1998)], is formulated and applied to the calculation of the electronic structure of general multicenter Hamiltonian systems. The numerical method is presented and applied to the solution of Schrödinger-type operators, where a given number of nuclei point singularities is present in the potential field. The numerical method combines the rapid "exponential" convergence rates of modern spectral methods with the multiresolution flexibility of finite element methods, and can be viewed as an extension of the spectral element method. The approximation of cusps in the wave function and the formulation of multicenter nuclei singularities are efficiently dealt with by the combination of a coordinate transformation and a piecewise variational spectral approximation. The complete system can be efficiently inverted by established iterative methods for elliptical partial differential equations; an application of the method is presented for atomic, diatomic, and triatomic systems, and comparisons are made to the literature when possible. In particular, local density approximations are studied within the context of Kohn-Sham density functional theory, and are presented for selected subsets of atomic and diatomic molecules as well as the ozone molecule.
Embedded atom study of dislocation core structure in Fe
Energy Technology Data Exchange (ETDEWEB)
Farkas, D.; Rodriguez, P.L. (Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering Centro Atomico Bariloche (Argentina))
1994-04-01
The relaxed atomistic structure of dislocation cores in body centered cubic metals was investigated many years ago, using pair potentials. These studies are now classic and have been the basis for understanding mechanical behavior of these materials. They constitute the classic example of the importance of non-elastic core effect for the dislocations responsible for deformation, as described in several reviews written on the subject. Volume-dependent interatomic potentials were introduced in 1984. Despite the importance of the results obtained with pair potentials, no calculation of dislocation cores in pure bcc metals using volume-dependent interatomic potentials has yet been performed. The purpose of the present investigation is to compute the structures of 1/2[111] screw dislocation cores Fe. The objective is to compare these results with the structures obtained with pair potentials. The computation of Peierls stresses with pair potentials usually gives an overestimate of the actual Peierls stress. In the present work, they also use an improved boundary condition technique for the simulation of the dislocation cores can give more accurate Peierls stresses using manageable atomic block sizes. They also use a more recent graphical method for the representation of the core structures to obtain the information on the core structures and their relationship to the various crystallographic planes in the material and to analyze the shape of core in relation with the possible glide planes of the dislocation.
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.
Semiclassical Calculation of Recurrence Spectra of Rydberg Hydrogen Atom Near a Metal Surface
Institute of Scientific and Technical Information of China (English)
WANG De-Hua
2009-01-01
Using closed orbit theory, we give a clear physical picture description of the Rydberg hydrogen atom near a metal surface and calculate the Fourier transformed recurrence spectra of this system at different scaled energies below ionization threshold.The results show that with the increase of the scaled energy, the number of the closed orbit increases greatly.Some of the orbits are created by the bifurcation of the perpendicular orbit.This case is quite similar to the Rydberg atom in an electric field.When the scaled energy increases furthermore, chaotic orbits appear.This study provides a different perspective on the dynamical behavior of the Rydberg atom near a metal surface.
Institute of Scientific and Technical Information of China (English)
Wang De-Hua; Lin Sheng-Lu
2004-01-01
Closed orbit theory is a semiclassical technique for explaining the spectra of Rydberg atoms in external fields. By developing the closed orbit theory from two degrees of freedom to three non-separable degrees of freedom, we calculated the recurrence spectra of He Rydberg atom in perpendicular electric and magnetic fields. The closed orbits in the corresponding classical system have also been obtained. Fourier transformed spectra of He atoms have allowed direct comparison between the resonance peaks and the scaled action values of closed orbits, whereas the nonhydrogenic resonance can be explained in terms of the new orbits created by the core scattering. The semiclassical result is in good agreement with the quantum spectra, which suggests that our method is correct.
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.
Semiclassical Calculation of Recurrence Spectra of He Rydberg Atom in Strong External Fields
Institute of Scientific and Technical Information of China (English)
WANG De-Hua; DING Shi-Liang; LIN Sheng-Lu
2004-01-01
Using core-scattered closed-orbit theory and region-splitting iterative method, we calculated the scaled recurrence spectra of helium atom in parallel electric and magnetic fields. Closed orbits in the corresponding classical system have also been obtained. When we search the closed orbits, in order to remove the Coulomb singularity of the classical Hamiltonian motion equations, we implement the Kustaanheimo-Stiefel transformation, which transforms the system from a three-dimensional to a four-dimensional one. The Fourier transformed spectrum of helium atom has allowed direct comparison between peaks in such plot and the scaled action values of closed orbits. The results are compared with those of the hydrogen case, which shows that the core-scattered effects play an important role in the recurrence spectra of the multi-electron Rydberg atom.
Institute of Scientific and Technical Information of China (English)
XIAO Hai; LI Jun
2008-01-01
Benchmark calculations on the molar atomization enthalpy, geometry, and vibrational frequencies of uranium hexafluoride (UF6) have been performed by using relativistic density functional theory (DFT) with various levels of relativistic effects, different types of basis sets, and exchange-correlation functionals. Scalar relativistic effects are shown to be critical for the structural properties. The spin-orbit coupling effects are important for the calculated energies, but are much less important for other calculated ground-state properties of closed-shell UF6. We conclude through systematic investigations that ZORA- and RECP-based relativistic DFT methods are both appropriate for incorporating relativistic effects. Comparisons of different types of basis sets (Slater, Gaussian, and plane-wave types) and various levels of theoretical approximation of the exchange-correlation functionals were also made.
Calculation of Multiphoton Transition in Li Atoms via Chirped Microwave Pulse
Institute of Scientific and Technical Information of China (English)
JIA Guang-Rui; ZHANG Xian-Zhou; LIU Yu-Fang; YU Kun; ZHAO Yue-Jin
2011-01-01
The position and width of avoided crossings of Li atom energy levels in a static electric field is presented by using the B-spline basis set method combined with the model potential.Using the time-dependent multilevel approach,the population of Li atoms is transferred to the target state completely by one-photon,two-photon or a single multiphoton adiabatic rapid passage,which requires only a small frequency sweep.The calculation results agree well with the experiment and novel explanations are given to understand the experimental results.It is well known that adiabatic rapid passage (ARP) works perfectly in the population transfer of an atomic system.[1-3] Coherent population transfer via ARP in atoms through one-photon[2] or twophoton[4] transitions using chirped pulses has been demonstrated.If the frequency of an external field is swept through the resonance at a rate lower than the square of the Rabi frequency,the population can be transferred through many levels by sequential ARPs with approximately 100％ efficiency.%The position and width of avoided crossings of Li atom energy levels in a static electric field is presented by using the B-spline basis set method combined with the model potential Using the time-dependent multilevel approach, the population of Li atoms is transferred to the target state completely by one-photon, two-photon or a single multiphoton adiabatic rapid passage, which requires only a small frequency sweep. The calculation results agree well with the experiment and novel explanations are given to understand the experimental results.
Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures
Dowty, Eric; Clark, J.R.
1972-01-01
New crystal-structure refinements of Pca21 boracite, Mg3ClB7O13, and R??{lunate}c ericaite, Fe2.4Mg0.6ClB7O13, show that some boron and oxygen atoms are involved in the 'ferro' transitions as well as the metal and halogen atoms. The atomic displacements associated with the polarity changes are as large as 0.6A??. ?? 1972.
Directory of Open Access Journals (Sweden)
Yu.S. Nagornov
2016-03-01
Full Text Available 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 erythrocytes based on numerical modeling and data of atomic force microscopy of erythrocytes scan, which involves a comparison of the experimental data with the results of numerical calculation. The method is applied to the data of atomic force microscopy of erythrocytes of experimental animals - dwarf domestic pigs with different degrees of obstructive jaundice and normal. It is shown that with increasing severity of the disease and the concentration of bilirubin in the blood there is an infringement erythrocyte membranes, by an average increasing their volume and intracellular pressure.
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.
Electronic Structure of Helium Atom in a Quantum Dot
Saha, Jayanta K.; Bhattacharyya, S.; Mukherjee, T. K.
2016-03-01
Bound and resonance states of helium atom have been investigated inside a quantum dot by using explicitly correlated Hylleraas type basis set within the framework of stabilization method. To be specific, precise energy eigenvalues of bound 1sns (1Se) (n = 1-6) states and the resonance parameters i.e. positions and widths of 1Se states due to 2sns (n = 2-5) and 2pnp (n = 2-5) configurations of confined helium below N = 2 ionization threshold of He+ have been estimated. The two-parameter (Depth and Width) finite oscillator potential is used to represent the confining potential due to the quantum dot. It has been explicitly demonstrated that the electronic structural properties become sensitive functions of the dot size. It is observed from the calculations of ionization potential that the stability of an impurity ion within a quantum dot may be manipulated by varying the confinement parameters. A possibility of controlling the autoionization lifetime of doubly excited states of two-electron ions by tuning the width of the quantum cavity is also discussed here. TKM Gratefully Acknowledges Financial Support under Grant No. 37(3)/14/27/2014-BRNS from the Department of Atomic Energy, BRNS, Government of India. SB Acknowledges Financial Support under Grant No. PSW-160/14-15(ERO) from University Grants Commission, Government of India
X-alpha calculation of transition energies in multiply ionized atoms
Ringers, D. A.; Chen, M. H.
1974-01-01
It is shown that the accuracy of calculations can be improved if appropriate (different) values of alpha are used for each configuration. Alternatively, the Slater Transition state can be used, wherein a total energy difference is related to a difference in single electron eigenvalues. By a series expansion, the value of alpha for an excited configuration can be related to its value for the ground state configuration. The terms Delta alpha (delta Epsilon/delta alpha) exhibit a similar dependence on atomic number as the ground state values of alpha. Results of sample calculations are reported and compared with experiment.
Presentation of Atomic Structure in Turkish General Chemistry Textbooks
Niaz, Mansoor; Costu, Bayram
2009-01-01
Research in science education has recognized the importance of teaching atomic structure within a history and philosophy of science perspective. The objective of this study is to evaluate general chemistry textbooks published in Turkey based on the eight criteria developed in previous research. Criteria used referred to the atomic models of…
Structures of 38-atom gold-platinum nanoalloy clusters
Energy Technology Data Exchange (ETDEWEB)
Ong, Yee Pin; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)
2015-04-24
Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atoms are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.
Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui
2015-08-19
Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry.
Institute of Scientific and Technical Information of China (English)
杨忠志; 沈尔忠
1996-01-01
On the basis of a more precise expression of the atomic effective electronegativity deduced from the density functional theory and electronegativity equalization principle, a new scheme for calculating the group electronegativity and the atomic charges in a group is proposed and programed, and various parameters of electronegativity and hardness are given for some common atoms. Through calculation, analysis and comparison of more than one hundred groups, it is shown that the results from this scheme are reasonable and may be extended.
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.
Calculation of the fine structure of the level in Rydberg state of lithium
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
The level shift and level formula of lithium atom in Rydberg states are achieved by means of the calculation of polarization of the atomic core (including the contribution of dipole moment, quadrupole moment and octupole moment);meanwhile, the effect of relativity theory, the orbital angular momentum L and the spin angular momentum S coupling (LS coupling), and high order correction of the effective potential are considered. The some fine structures (N=5～12,L=4～9,J=L±1/2) and the corresponding level intervals in Rydberg states can be calculated by the above-mentioned level formula and compared with correlated experimental data.
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.
Atomic structure of graphene on SiO2.
Ishigami, Masa; Chen, J H; Cullen, W G; Fuhrer, M S; Williams, E D
2007-06-01
We employ scanning probe microscopy to reveal atomic structures and nanoscale morphology of graphene-based electronic devices (i.e., a graphene sheet supported by an insulating silicon dioxide substrate) for the first time. Atomic resolution scanning tunneling microscopy images reveal the presence of a strong spatially dependent perturbation, which breaks the hexagonal lattice symmetry of the graphitic lattice. Structural corrugations of the graphene sheet partially conform to the underlying silicon oxide substrate. These effects are obscured or modified on graphene devices processed with normal lithographic methods, as they are covered with a layer of photoresist residue. We enable our experiments by a novel cleaning process to produce atomically clean graphene sheets.
Atomic calculation for the atmospheres of strongly-magnetized neutron stars
Mori, K; Mori, Kaya; Hailey, Charles J.
2001-01-01
Complete modeling of radiative transfer in neutron star atmospheres is in progress, taking into account the anisotropy induced by magnetic fields, non-ideal effects and general relativity. As part of our modeling, we present a novel atomic calculation method producing an extensive atomic data set including energy values and oscillator strengths in the so-called Landau regime ($B > 4.7\\times10^9Z^2$ G). Conventional atmosphere models for B=0 are not applicable to typical field strengths of cooling neutron stars ($B \\sim10^{12}-10^{13}$ G), since an atom no longer keeps its spherical shape. The elemental composition and the configuration of the magnetic field in the atmosphere are presently unknown, so that atomic data must be produced for ground and excited states of several ions as a function of magnetic field. To accomplish this efficiently, we minimized the iterations in the Hartree equation and treated exchange terms and higher Landau states by perturbation methods. This method has the effect of reducing t...
Thorvaldsen, Andreas J.; Ruud, Kenneth; Rizzo, Antonio; Coriani, Sonia
2008-10-01
We present the first gauge-origin-independent, frequency-dependent calculations of the hypermagnetizability anisotropy, which determines the temperature-independent contribution to magnetic-field-induced linear birefringence, the so-called Cotton-Mouton effect. A density-matrix-based scheme for analytical calculations of frequency-dependent molecular properties for self-consistent field models has recently been developed, which is also valid with frequency- and field-dependent basis sets. Applying this scheme to Hartree-Fock wave functions and using London atomic orbitals in order to obtain gauge-origin-independent results, we have calculated the hypermagnetizability anisotropy. Our results show that the use of London orbitals leads to somewhat better basis-set convergence for the hypermagnetizability compared to conventional basis sets and that London orbitals are mandatory in order to obtain reliable magnetizability anisotropies.
Investigation of the diffusion of atomic fission products in UC by density functional calculations
Energy Technology Data Exchange (ETDEWEB)
Bévillon, Émile, E-mail: emile.bevillon@yahoo.fr [IRSN, SEMIC, DPAM, LETR, Centre de Cadarache, 13115 Saint Paul Lez Durance (France); Ducher, Roland; Barrachin, Marc; Dubourg, Roland [IRSN, SEMIC, DPAM, LETR, Centre de Cadarache, 13115 Saint Paul Lez Durance (France)
2013-03-15
Activation energies of U and C atoms self-diffusion in UC, as well as activation energies of hetero-diffusion of fission products (FPs) are investigated by first-principles calculations. According to a previous study which showed a likely U site occupation was favoured for all the FPs, their diffusion is restricted to the uranium sublattice of UC in the present study. In this framework, long-range displacements are only possible through a concerted mechanism with a surrounding uranium vacancy. Using the apparent formation energies of the uranium vacancy defect calculated in our previous study and the classical approach used in UO{sub 2} by Andersson et al., the activation energies of the main fission products in the various stoichiometric domains have been calculated. The results are compared to those obtained with the five frequency model applied to two representative fission products, Xe and Zr. Interestingly, despite strong differences of formalism, both models provided similar activation energies.
Investigation of the diffusion of atomic fission products in UC by density functional calculations
Bévillon, Émile; Ducher, Roland; Barrachin, Marc; Dubourg, Roland
2013-03-01
Activation energies of U and C atoms self-diffusion in UC, as well as activation energies of hetero-diffusion of fission products (FPs) are investigated by first-principles calculations. According to a previous study which showed a likely U site occupation was favoured for all the FPs, their diffusion is restricted to the uranium sublattice of UC in the present study. In this framework, long-range displacements are only possible through a concerted mechanism with a surrounding uranium vacancy. Using the apparent formation energies of the uranium vacancy defect calculated in our previous study and the classical approach used in UO2 by Andersson et al., the activation energies of the main fission products in the various stoichiometric domains have been calculated. The results are compared to those obtained with the five frequency model applied to two representative fission products, Xe and Zr. Interestingly, despite strong differences of formalism, both models provided similar activation energies.
Mapping energetics of atom probe evaporation events through first principles calculations.
Peralta, Joaquín; Broderick, Scott R; Rajan, Krishna
2013-09-01
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 L1₂-Al₃Sc 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 L1₂-Al₃Sc, 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.
Kalesaki, E.; Evers, W.H.; Vanmaekelbergh, D.; Delerue, C.
2013-01-01
The electronic structure of recently synthesized square superlattices with atomic coherence composed of PbSe, CdSe, or CdTe nanocrystals (NCs) attached along {100} facets is investigated using tight-binding calculations. In experimental realizations of these systems [W. H. Evers et al., Nano Lett. 1
Institute of Scientific and Technical Information of China (English)
WANG De-Hua; DING Shi-Liang
2003-01-01
Closed-orbit theory is a semiclassical technique for explaining the spectra of Rydberg atoms in external fields. Using the closed-orbit theory and classical perturbation theory, we calculate the scaled recurrence spectra of Lithium atom in magnetic field plus a weak perpendicular electric field. The results show when the crossed electric field is added, the recurrence spectra are weakened greatly. As the scaled electric field f increases, the peaks of the recurrence spectra lose strength. Some recurrences are very sensitive and fall off rapidly as f increases; others persist till much higher f . As the electric field is stronger, some of the peaks revive. This phenomenon, caused by the interference among the electron waves that return to the nucleus, can be computed from the azimuthal dependence of the classical closed orbits.
Institute of Scientific and Technical Information of China (English)
WANGDe-Hua; DINGShi-Liang
2003-01-01
Closed-orbit theory is a semiclassical technique for explaining the spectra of Rydberg atoms in external fields. Using the dosed-orblt theory and classical perturbation theory, we calculate the scaled recurrence spectra of Lithium atom in magnetic field plus a weak perpendicular electric field. The results show when the crossed electric field is added, the recurrence spectra are weakened greatly. As the scaled electric field f increases, the peaks of the recurrence spectra lose strength. Some recurrences are very sensitive and fall off rapidly as f increases, others persist till much higher f. As the electric field is stronger, some of the peaks revive. This phenomenon, caused by the interference among the electron waves that return to the nucleus, can be computed from the azimuthal dependence of the classical closed orbits.
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.
Toward the Atomic Structure of PrPSc.
Rodriguez, Jose A; Jiang, Lin; Eisenberg, David S
2017-01-17
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.
Guiltat, Mathilde; Brut, Marie; Vizzini, Sébastien; Hémeryck, Anne
2017-03-01
First principles calculations are conducted to investigate kinetic behavior of oxygen species at the surface of clean and defective Al(111) substrate. Oxygen island, aluminum vacancy, aluminum sub-vacancy, aluminum ad-atom and aluminum terraces defects are addressed. Adsorption of oxygen molecule is first performed on all these systems resulting in dissociated oxygen atoms in main cases. The obtained adsorbed configurations are then picked to study the behavior of atomic oxygen specie and get a detailed understanding on the effect of the local environment on the ability of the oxygen atom to diffuse on the surface. We pointed out that local environment impacts energetics of oxygen atom diffusion. Close packed oxygen island, sub-vacancy and ad-atoms favor oxygen atom stability and decrease mobility of oxygen atom on the surface, to be seen as surface area for further nucleation of oxygen island.
Rotational Spectrum and Carbon Atom Structure of Dihydroartemisinic Acid
Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks
2016-06-01
Dihydroartemisinic acid (DHAA, C15H24O2, five chiral centers) is a precursor in proposed low-cost synthetic routes to the antimalarial drug artemisinin. In one reaction process being considered in pharmaceutical production, DHAA is formed from an enantiopure sample of artemisinic acid through hydrogenation of the alkene. This reaction needs to properly set the stereochemistry of the asymmetric carbon for the synthesis to produce artemisinin. A recrystallization process can purify the diastereomer mixture of the hydrogenation reaction if the unwanted epimer is produced in less than 10% abundance. There is a need in the process analytical chemistry to rapidly (less than 1 min) measure the diastereomer excess and current solutions, such a HPLC, lack the needed measurement speed. The rotational spectrum of DHAA has been measured at 300:1 signal-to-noise ratio in a chirped-pulsed Fourier transform microwave spectrometer operating from 2-8 GHz using simple heating of the compound. The 13C isotope analysis provides a carbon atom structure that confirms the diastereomer. This structure is in excellent agreement with quantum chemistry calculations at the B2PLYPD3/ 6-311++G** level of theory. The DHAA spectrum is expected to be fully resolved from the unwanted diastereomer raising the potential for fast diastereomer excess measurement by rotational spectroscopy in the pharmaceutical production process.
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,…
Interface Structure and Atomic Bonding Characteristics in Silicon Nitride Ceramics
Energy Technology Data Exchange (ETDEWEB)
Ziegler, A; Idrobo, J C; Cinibulk, M K; Kisielowski, C; Browning, N D; Ritchie, R O
2004-10-12
This investigation examines the interface atomic structure and bonding characteristics in an advanced ceramic, obtaining new and unique experimental information that will help to understand and improve the properties of ceramics. Unique 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. It has been found that each rare-earth atom bonds to the interface at a different location, depending on atom size, electronic configuration and the presence of oxygen at the interface. This is the key factor to understanding the origin of the mechanical properties in these ceramics and will enable precise tailoring in the future to critically improve the materials performance in wide-ranging applications.
Calculation of the surface energy of fcc metals with modified embedded-atom method
Institute of Scientific and Technical Information of China (English)
Zhang Jian-Min; Ma Fei; Xu Ke-Wei
2004-01-01
The surface energies for 38 surfaces of fcc metals Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Rh and Ir have been calculated by using the modified embedded-atom method. The results show that, for Cu, Ag, Ni, Al, Pb and Ir, the average values of the surface energies are very close to the polycrystalline experimental data. For all fcc metals, as predicted, the close-packed (111) surface has the lowest surface energy. The surface energies for the other surfaces increase linearly with increasing angle between the surfaces (hkl) and (111). This can be used to estimate the relative values of the surface energy.
Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang
2016-09-21
Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts.
Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang
2016-01-01
Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts. PMID:27650485
Ab initio calculations of electronic structure of anatase TiO2
Institute of Scientific and Technical Information of China (English)
Chen Qiang; Cao Hong-Hong
2004-01-01
This paper presents the results of the self-consistent calculations on the electronic structure of anatase phase of TiO2. The calculations were performed using the full potential-linearized augmented plane wave method (FP-LAPW)in the framework of the density functional theory (DFT) with the generalized gradient approximation (GGA). The fully optimized structure, obtained by minimizing the total energy and atomic forces, is in good agreement with experiment.We also calculated the band structure and the density of states. In particular, the calculated band structure prefers an indirect transition between wlence and conduction bands of anatase TiO2, which may be helpful for clarifying the ambiguity in other theoretical works.
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.
Connolly Surface on an Atomic Structure via Voronoi Diagram of Atoms
Institute of Scientific and Technical Information of China (English)
Joonghyun Ryu; Rhohun Park; Deok-Soo Kim
2006-01-01
One of the most important geometric structures of a protein is the Connolly surface of protein since a Connolly surface plays an important role in protein folding, docking, interactions between proteins, amongst other things. This paper presents an algorithm for precisely and efficiently computing the Connolly surface of a protein using a proposed geometric construct called β-shape based on the Voronoi diagram of atoms in the protein. Given the Voronoi diagram of atoms based on the Euclidean distance from the atom surfaces, the proposed algorithm first computes a β-shape with an appropriate probe. Then, the Connolly surface is computed by employing the blending operation on the atomic complex of the protein by the given probe.
Borgardt, N. I.; Prihodko, A. S.; Seibt, M.
2016-12-01
The atomic structure of carbon materials is studied using the example of pyrocarbon and boronrich pyrocarbon by means of the method of reconstruction of the wave function in transmission electron microscopy. It is shown that the digital processing of the phase distributions of these functions allows us to find the average distance between the basal planes. Using the method of molecular dynamics for the formation of the test structures and obtaining for them the calculated phase distributions, the effect of depletion of the basal planes of the carbon atoms on the interplanar distance in the pyrocarbon materials is quantified.
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.
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.
Hydrogen atom in strong magnetic field: a high accurate calculation in spheroidal coordinates
Institute of Scientific and Technical Information of China (English)
LIU Qiang; KANG Shuai; ZHANG Xian-zhou; SHI Ting-yun
2006-01-01
A B-spline-type basis set method for the calculation of hydrogen atom in strong magnetic fields in the frame of spheroidal coordinates has been introduced.High accurate energy levels of hydrogen in the magnetic field,with strength ranging from 0 to 1000 a.u.,have been obtained.For the ground state,ls0,energies with at least 11 significant digits have been obtained.For the low-lying excited state,2p-1,energies with at least 9 significant digits are obtained.The method has also been applied to the calculation of hydrogen Rydberg states in laboratory magnetic fields.Energy spectra with at least 10 significant digits are presented.A comparison with other results in the literatures has been performed.Our results are comparable to the most accurate one up to date.A possible extension to the cases of parallel and crossed electric and magnetic fields have been discussed.
A fully relativistic approach for calculating atomic data for highly charged ions
Energy Technology Data Exchange (ETDEWEB)
Sampson, Douglas H. [Department of Astronomy and Astrophysics, Pennsylvania State University, University Park, PA 16802 (United States); Zhang Honglin [Applied Physics Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)], E-mail: zhang@lanl.gov; Fontes, Christopher J. [Applied Physics Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)], E-mail: cjf@lanl.gov
2009-07-15
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.
Energy Technology Data Exchange (ETDEWEB)
Bross, David H.; Parmar, Payal; Peterson, Kirk A., E-mail: kipeters@wsu.edu [Department of Chemistry, Washington State University, Pullman, Washington 99164-4630 (United States)
2015-11-14
The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set limit using new all-electron correlation consistent basis sets. The latter was carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons has been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. The final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV) and thus more reliable than the current experimental values of IP{sub 3} through IP{sub 6}.
A novel Gaussian-Sinc mixed basis set for electronic structure calculations
Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.
2015-08-01
A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree-Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the "localized" and "delocalized" regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the "delocalized" regions and the atom-centered Gaussian functions are used to represent the "localized" regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definable and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree-Fock energies for atoms up to neon, the diatomic systems H2, O2, and N2, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.
Roberts, B M; Flambaum, V V; Pospelov, M; Stadnik, Y V
2016-01-01
We revisit the WIMP-type dark matter scattering on electrons that results in atomic ionization, and can manifest itself in a variety of existing direct-detection experiments. Unlike the WIMP-nucleon scattering, where current experiments probe typical interaction strengths much smaller than the Fermi constant, the scattering on electrons requires a much stronger interaction to be detectable, which in turn requires new light force carriers. We account for such new forces explicitly, by introducing a mediator particle with scalar or vector couplings to dark matter and to electrons. We then perform state of the art numerical calculations of atomic ionization relevant to the existing experiments. Our goals are to consistently take into account the atomic physics aspect of the problem (e.g., the relativistic effects, which can be quite significant), and to scan the parameter space: the dark matter mass, the mediator mass, and the effective coupling strength, to see if there is any part of the parameter space that c...
Electronic structure calculations on helical conducting polymers.
Ripoll, Juan D; Serna, Andrei; Guerra, Doris; Restrepo, Albeiro
2010-10-21
We present a study of the electronic structure and derived properties of polyfurane (PFu), polypyrrol (PPy), and polythiophene (PTh). Two spatial arrangements are considered: trans chain (tc-PFu, tc-PPy, tc-PTh) and cis α-helical (α-PFu, α-PPy, α-PTh). Even at the small sizes considered here, helical conformations appear to be stable. Band gaps of pure, undoped oligomers fall into the semiconductor range. Density of states (DOS) analysis suggest dense valence and conduction bands. Bond length alternation analysis predicts almost complete delocalization of the π clouds in all spatial arrangements. Doping with electron donors or electron-withdrawing impurities reduces all band gaps close to the metallic regime in addition to increasing the DOS for the valence and conduction bands.
Ab-initio calculations of electronic structure and optical properties of TiAl alloy
Hussain, Altaf; Sikandar Hayat, Sardar; Choudhry, M. A.
2011-05-01
The electronic structures and optical properties of TiAl intermetallic alloy system are studied by the first-principle orthogonalized linear combination of atomic orbitals method. Results on the band structure, total and partial density of states, localization index, effective atomic charges, and optical conductivity are presented and discussed in detail. Total density of states spectra reveal that (near the Fermi level) the majority of the contribution is from Ti-3d states. The effective charge calculations show an average charge transfer of 0.52 electrons from Ti to Al in primitive cell calculations of TiAl alloy. On the other hand, calculations using supercell approach reveal an average charge transfer of 0.48 electrons from Ti to Al. The localization index calculations, of primitive cell as well as of supercell, show the presence of relatively localized states even above the Fermi level for this alloy. The calculated optical conductivity spectra of TiAl alloy are rich in structures, showing the highest peak at 5.73 eV for supercell calculations. Calculations of the imaginary part of the linear dielectric function show a prominent peak at 5.71 eV and a plateau in the range 1.1-3.5 eV.
Simulation of Rutherford backscattering spectrometry from arbitrary atom structures
Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.
2016-10-01
Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.
Structure and transport properties of atomic chains and molecules
DEFF Research Database (Denmark)
Strange, Mikkel
2008-01-01
to describe tip-suspended atomically thin chains between macroscopic size electrodes. It has been tested with the use of DFT calculations on metal chains for which good agreement with experiments was obtained. To ensure the correctness of the DFT based transport calculations presented here, and in more...... as the Siesta basis is enlarged. Overall, we find that a double zeta polarized atomic basis is generally sufficient, and in some cases necessary, to ensure quantitative agreement with the plane-wave calculation. In a detailed DFT study of the carbon monoxide molecule between Pt electrodes, a particularly stable...... with experiments is obtained. A study of CO in Au, Cu and Ni, reveals that the conductance for CO in the tilted bridge configuration for Ni is 0.5G0, in agreement with experiments [5]. For Au/CO and Cu/CO we find the effect of CO compared to the homogenous metal contacts is much smaller, in qualitative agreement...
Calculated electronic and magnetic structure of screw dislocations in alpha iron
Energy Technology Data Exchange (ETDEWEB)
Odbadrakh, K.; Rusanu, A.; Stocks, G. Malcolm; Samolyuk, G. D.; Eisenbach, M.; Wang, Yang; Nicholson, D. M.
2011-01-01
Local atomic magnetic moments in crystalline Fe are perturbed by the presence of dislocations. The effects are most pronounced near the dislocation core and decay slowly as the strain field of the dislocation decreases with distance. We have calculated local moments using the locally self-consistent multiple scattering (LSMS) method for a supercell containing a screw-dislocation quadrupole. Finite size effects are found to be significant indicating that dislocation cores affect the electronic structure and magnetic moments of neighboring dislocations. The influence of neighboring dislocations points to a need to study individual dislocations from first principles just as they appear amid surrounding atoms in large-scale classical force field simulations. An approach for the use of the LSMS to calculate local moments in subvolumes of large atomic configurations generated in the course of classical molecular dynamics simulation of dislocationdynamics is discussed.
Calculated electronic and magnetic structure of screw dislocations in alpha iron
Energy Technology Data Exchange (ETDEWEB)
Odbadrakh, Khorgolkhuu [ORNL; Rusanu, Aurelian [ORNL; Stocks, George Malcolm [ORNL; Samolyuk, German D [ORNL; Eisenbach, Markus [ORNL; Wang, Yang Nmn [ORNL; Nicholson, Don M [ORNL
2011-01-01
Local atomic magnetic moments in crystalline Fe are perturbed by the presence of dislocations. The effects are most pronounced near the dislocation core and decay slowly as the strain field of the dislocation decreases with distance. We have calculated local moments using the locally self-consistent multiple scattering (LSMS) method for a supercell containing a screw-dislocation quadrupole. Finite size effects are found to be significant indicating that dislocation cores affect the electronic structure and magnetic moments of neighboring dislocations. The influence of neighboring dislocations points to a need to study individual dislocations from first principles just as they appear amid surrounding atoms in large-scale classical force field simulations. An approach for the use of the LSMS to calculate local moments in subvolumes of large atomic configurations generated in the course of classical molecular dynamics simulation of dislocation dynamics is discussed. VC2011 American Institute of Physics. [doi:10.1063/1.3562217
Energy Technology Data Exchange (ETDEWEB)
Mehrabova, M. A., E-mail: Mehrabova@mail.ru; Madatov, R. S. [Azerbaijan National Academy of Sciences, Institute of Radiation Problems (Azerbaijan)
2011-08-15
The Green's functions theory and the bond-orbital model are used as a basis for calculations of the electron structure of local defects-specifically, vacancies and their compensated states in III-VI semiconductors. The energy levels in the band gap are established, and the changes induced in the electron densities in the GaS, GaSe, and InSe semiconductors by anion and cation vacancies and their compensated states are calculated. It is established that, if a vacancy is compensated by an atom of an element from the same subgroup with the same tetrahedral coordination and if the ionic radius of the compensating atom is smaller than that of the substituted atom, the local levels formed by the vacancy completely disappear. It is shown that this mechanism of compensation of vacancies provides a means not only for recovering the parameters of the crystal, but for improving the characteristics of the crystal as well.
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)
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
Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.
2017-01-01
Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.
Atomic structure of intracellular amorphous calcium phosphate deposits.
Betts, F; Blumenthal, N C; Posner, A S; Becker, G L; Lehninger, A L
1975-06-01
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.
Infrared image recognition based on structure sparse and atomic sparse parallel
Wu, Yalu; Li, Ruilong; Xu, Yi; Wang, Liping
2015-12-01
Use the redundancy of the super complete dictionary can capture the structural features of the image effectively, can achieving the effective representation of the image. However, the commonly used atomic sparse representation without regard the structure of the dictionary and the unrelated non-zero-term in the process of the computation, though structure sparse consider the structure feature of dictionary, the majority coefficients of the blocks maybe are non-zero, it may affect the identification efficiency. For the disadvantages of these two sparse expressions, a weighted parallel atomic sparse and sparse structure is proposed, and the recognition efficiency is improved by the adaptive computation of the optimal weights. The atomic sparse expression and structure sparse expression are respectively, and the optimal weights are calculated by the adaptive method. Methods are as follows: training by using the less part of the identification sample, the recognition rate is calculated by the increase of the certain step size and t the constraint between weight. The recognition rate as the Z axis, two weight values respectively as X, Y axis, the resulting points can be connected in a straight line in the 3 dimensional coordinate system, by solving the highest recognition rate, the optimal weights can be obtained. Through simulation experiments can be known, the optimal weights based on adaptive method are better in the recognition rate, weights obtained by adaptive computation of a few samples, suitable for parallel recognition calculation, can effectively improve the recognition rate of infrared images.
Calculated Electronic and Magnetic Structure of Screw Dislocations in Alpha Iron
Energy Technology Data Exchange (ETDEWEB)
Odbadrakh, Khorgolkhuu [ORNL; Rusanu, Aurelian [ORNL; Stocks, George Malcolm [ORNL; Samolyuk, German D [ORNL; Eisenbach, Markus [ORNL; Wang, Yang [Pittsburgh Supercomputing Center; Nicholson, Don M [ORNL
2011-01-01
Local atomic magnetic moments in crystalline Fe are perturbed by the presence of dislocations. The effects are most pronounced near the dislocation core and decay slowly as the strain field of the dislocation decreases with distance. We have calculated the local moments using the Locally Self-consistent Multiple Scattering (LSMS) method for an 1848 atom supercell containing a screw- dislocation quadrupole. The atomic positions were determined by relaxation with an embedded atom force field. Finite size effects are found to be significant for this small cell size indicating that dislocation cores affect the electronic structure and magnetic moments of neighboring dislocations. The influence of neighboring dislocations point to a need to study individual dislocations from first principles just as they appear amidst surrounding atoms in large scale classical force field simulations. An approach for the use of the LSMS to calculate local moments in sub-volumes of large atomic configurations generated in the course of classical MD simulation of dislocation dynamics is discussed.
Directory of Open Access Journals (Sweden)
Ouahrani T.
2013-03-01
Full Text Available ab initio calculations were performed for the cubic perovskites Borides XRh3B, (X=Dy, Ho, Er. In this work, we have used the augmented plane-wave plus local orbital method to compute the equilibrium structural parameters and electronic structure of densities of states, as well as for the first time, prediction of the thermo-elastic properties of these crystals are presented. The chemical bonding of these compounds has been investigated by using of topological analyses grounded in the theory of atoms in molecules (AIM. All of the electron density critical points in the unit cell were systematically calculated in order to calculate basins interaction of each atoms and give exact classification of the bonding character.
Bo, Xu; Huan-Sheng, Lu; Bo, Liu; Gang, Liu; Mu-Sheng, Wu; Chuying, Ouyang
2016-06-01
The adsorption and diffusion behaviors of alkali and alkaline-earth metal atoms on silicane and silicene are both investigated by using a first-principles method within the frame of density functional theory. Silicane is staler against the metal adatoms than silicene. Hydrogenation makes the adsorption energies of various metal atoms considered in our calculations on silicane significantly lower than those on silicene. Similar diffusion energy barriers of alkali metal atoms on silicane and silicene could be observed. However, the diffusion energy barriers of alkali-earth metal atoms on silicane are essentially lower than those on silicene due to the small structural distortion and weak interaction between metal atoms and silicane substrate. Combining the adsorption energy with the diffusion energy barriers, it is found that the clustering would occur when depositing metal atoms on perfect hydrogenated silicene with relative high coverage. In order to avoid forming a metal cluster, we need to remove the hydrogen atoms from the silicane substrate to achieve the defective silicane. Our results are helpful for understanding the interaction between metal atoms and silicene-based two-dimensional materials. Project supported by the Natural Science Foundation of Jiangxi Province, China (Grant Nos. 20152ACB21014, 20151BAB202006, and 20142BAB212002) and the Fund from the Jiangxi Provincial Educational Committee, China (Grant No. GJJ14254). Bo Xu is also supported by the Oversea Returned Project from the Ministry of Education, China.
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
Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L
2009-07-14
A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol.
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
Directory of Open Access Journals (Sweden)
Yajiang Hao
2015-07-01
Full Text Available We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin
2015-01-01
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
Campbellová, Anna; Ondráček, Martin; Pou, Pablo; Pérez, Rubén; Klapetek, Petr; Jelínek, Pavel
2011-07-22
A Si adatom on a Si(111)-(7 × 7) reconstructed surface is a typical atomic feature that can rather easily be imaged by a non-contact atomic force microscope (nc-AFM) and can be thus used to test the atomic resolution of the microscope. Based on our first principles density functional theory (DFT) calculations, we demonstrate that the structure of the termination of the AFM tip plays a decisive role in determining the appearance of the adatom image. We show how the AFM image changes depending on the tip-surface distance and the composition of the atomic apex at the end of the tip. We also demonstrate that contaminated tips may give rise to image patterns displaying so-called 'sub-atomic' features even in the attractive force regime.
Convergence of CI single center calculations of positron-atom interactions
Mitroy, J
2006-01-01
The Configuration Interaction (CI) method using orbitals centered on the nucleus has recently been applied to calculate the interactions of positrons interacting with atoms. Computational investigations of the convergence properties of binding energy, phase shift and annihilation rate with respect to the maximum angular momentum of the orbital basis for the e^+Cu and PsH bound states, and the e^+-H scattering system were completed. The annihilation rates converge very slowly with angular momentum, and moreover the convergence with radial basis dimension appears to be slower for high angular momentum. A number of methods of completing the partial wave sum are compared, an approach based on a Delta X_J = a/(J + 1/2)^n + b/(J + 1/2)^(n+1) form (with n = 4 for phase shift (or energy) and n = 2 for the annihilation rate) seems to be preferred on considerations of utility and underlying physical justification.
A computer code for calculations in the algebraic collective model of the atomic nucleus
Welsh, T A
2016-01-01
A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1,1) x SO(5) dynamical group. This, in particular, obviates the use of coefficients of fractional parentage. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [pi x q x pi]_0 and [pi x pi]_{LM}, where q_M are the model's quadrupole moments, and pi_N are corresponding conjugate momenta (-2>=M,N<=2). The code also provides ready access to SO(3)-reduced SO(5) Clebsch-Gordan coefficients through data files provided with the code.
The atomic structure and the properties of Ununbium (z=112) and Mercury (Z=80)
Institute of Scientific and Technical Information of China (English)
LI; JiGuang
2007-01-01
A super heavy element Uub (Z = 112) has been studied theoretically in conjunction with rela-tivistic effects and the effects of electron correlations. The atomic structure and the oscillator strengths of low-lying levels have been calculated, and the ground states have also been determined for the singly and doubly charged ions. The influence of relativity and correlation effects to the atomic properties of such a super heavy element has been investigated in detail. The results have been compared with the properties of an element Hg. Two energy levels at wave numbers 64470 and 94392 are suggested to be of good candidates for experimental observations.……
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...
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)
Magnetic Field and Force Calculations for ATLAS Asymmetrical Structure
Nessi, Marzio
2001-01-01
Magnetic field distortion in the assymetrical ATLAS structure are calculated. Magnetic forces in the system are estimated. 3D magnetic field simulation by the Opera3D code for symmetrical and asymmetrical systems is used.
Nanoscale Structuring of Surfaces by Using Atomic Layer Deposition.
Sobel, Nicolas; Hess, Christian
2015-12-01
Controlled structuring of surfaces is interesting for a wide variety of areas, including microelectronic device fabrication, optical devices, bio(sensing), (electro-, photo)catalysis, batteries, solar cells, fuel cells, and sorption. A unique feature of atomic layer deposition (ALD) is the possibility to form conformal uniform coatings on arbitrarily shaped materials with controlled atomic-scale thickness. In this Minireview, we discuss the potential of ALD for the nanoscale structuring of surfaces, highlighting its versatile application to structuring both planar substrates and powder materials. Recent progress in the application of ALD to porous substrates has even made the nanoscale structuring of high-surface-area materials now feasible, thereby enabling novel applications, such as those in the fields of catalysis and alternative energy.
Atomic structure and electronic properties of the two-dimensional (Au ,Al )/Si (111 )2 ×2 compound
Gruznev, D. V.; Bondarenko, L. V.; Matetskiy, A. V.; Tupchaya, A. Y.; Chukurov, E. N.; Hsing, C. R.; Wei, C. M.; Eremeev, S. V.; Zotov, A. V.; Saranin, A. A.
2015-12-01
A combination of scanning tunneling microscopy, angle-resolved photoelectron spectroscopy, ab initio random structure searching, and density functional theory electronic structure calculations was applied to elucidate the atomic arrangement and electron band structure of the (Au ,Al )/Si (111 )2 ×2 two-dimensional compound formed upon Al deposition onto the mixed 5 ×2 /√{3 }×√{3 } Au/Si(111) surface. It was found that the most stable 2 ×2 -(Au, Al) compound incorporates four Au atoms, three Al atoms, and two Si atoms per 2 ×2 unit cell. Its atomic arrangement can be visualized as an array of meandering Au atomic chains with two-thirds of the Al atoms incorporated into the chains and one-third of the Al atoms interconnecting the chains. The compound is metallic and its electronic properties can be controlled by appropriate Al dosing since energetic location of the bands varies by ˜0.5 eV during increasing of Al contents. The 2 ×2 -(Au, Al) structure appears to be lacking the C3 v symmetry typical for the hexagonal lattices. The consequence of the peculiar atomic structure of the two-dimensional alloy is spin splitting of the metallic states, which should lead to anisotropy of the current-induced in-plane spin polarization.
Ab initio calculations of the electronic structure and bonding characteristics of LaB6
Hossain, Faruque M.; Riley, Daniel P.; Murch, Graeme E.
2005-12-01
Lanthanum hexaboride ( LaB6 , NIST SRM-660a) is widely used as a standard reference material for calibrating the line position and line shape parameters of powder diffraction instruments. The accuracy of this calibration technique is highly dependent on how completely the reference material is characterized. Critical to x-ray diffraction, this understanding must include the valence of the La atomic position, which in turn will influence the x-ray form factor (f) and hence the diffracted intensities. The electronic structure and bonding properties of LaB6 have been investigated using ab initio plane-wave pseudopotential total energy calculations. The electronic properties and atomic bonding characteristics were analyzed by estimating the energy band structure and the density of states around the Fermi energy level. The calculated energy band structure is consistent with previously reported experimental findings; de Haas-van Alphen and two-dimensional angular correlation of electron-positron annihilation radiation. In addition, the bond strengths and types of atomic bonds in the LaB6 compound were estimated by analyzing the Mulliken charge density population. The calculated result revealed the coexistence of covalent, ionic, and metallic bonding in the LaB6 system and partially explains its high efficiency as a thermionic emitter.
Gao, Daqiang; Liu, Yonggang; Liu, Peitao; Si, Mingsu; Xue, Desheng
2016-10-01
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.
Calculation of Free-Atom Fractions in Hydrocarbon-Fueled Rocket Engine Plume
Verma, Satyajit
2006-01-01
Free atom fractions (Beta) of nine elements are calculated in the exhaust plume of CH4- oxygen and RP-1-oxygen fueled rocket engines using free energy minimization method. The Chemical Equilibrium and Applications (CEA) computer program developed by the Glenn Research Center, NASA is used for this purpose. Data on variation of Beta in both fuels as a function of temperature (1600 K - 3100 K) and oxygen to fuel ratios (1.75 to 2.25 by weight) is presented in both tabular and graphical forms. Recommendation is made for the Beta value for a tenth element, Palladium. The CEA computer code was also run to compare with experimentally determined Beta values reported in literature for some of these elements. A reasonable agreement, within a factor of three, between the calculated and reported values is observed. Values reported in this work will be used as a first approximation for pilot rocket engine testing studies at the Stennis Space Center for at least six elements Al, Ca, Cr, Cu, Fe and Ni - until experimental values are generated. The current estimates will be improved when more complete thermodynamic data on the remaining four elements Ag, Co, Mn and Pd are added to the database. A critique of the CEA code is also included.
The shells of atomic structure in metallic glasses
Pan, S. P.; Feng, S. D.; Qiao, J. W.; Dong, B. S.; Qin, J. Y.
2016-02-01
We proposed a scheme to describe the spatial correlation between two atoms in metallic glasses. Pair distribution function in a model iron was fully decomposed into several shells and can be presented as the spread of nearest neighbor correlation via distance. Moreover, angle distribution function can also be decomposed into groups. We demonstrate that there is close correlation between pair distribution function and angle distribution function for metallic glasses. We think that our results are very helpful understanding the atomic structure of metallic glasses.
Institute of Scientific and Technical Information of China (English)
刘洪毓
2007-01-01
Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what
Energetics of atomic scale structure changes in graphene.
Skowron, Stephen T; Lebedeva, Irina V; Popov, Andrey M; Bichoutskaia, Elena
2015-05-21
The presence of defects in graphene has an essential influence on its physical and chemical properties. The formation, behaviour and healing of defects are determined by energetic characteristics of atomic scale structure changes. In this article, we review recent studies devoted to atomic scale reactions during thermally activated and irradiation-induced processes in graphene. The formation energies of vacancies, adatoms and topological defects are discussed. Defect formation, healing and migration are quantified in terms of activation energies (barriers) for thermally activated processes and by threshold energies for processes occurring under electron irradiation. The energetics of defects in the graphene interior and at the edge is analysed. The effects of applied strain and a close proximity of the edge on the energetics of atomic scale reactions are overviewed. Particular attention is given to problems where further studies are required.
Directory of Open Access Journals (Sweden)
Seba Sara Varghese
2016-12-01
Full Text Available The structural, energetic, and electronic properties of single-layer graphene doped with boron and nitrogen atoms with varying doping concentrations and configurations have been investigated here via first-principles density functional theory calculations. It was found that the band gap increases with an increase in doping concentration, whereas the energetic stability of the doped systems decreases with an increase in doping concentration. It was observed that both the band gaps and the cohesive energies also depend on the atomic configurations considered for the substitutional dopants. Stability was found to be higher in N-doped graphene systems as compared to B-doped graphene systems. The electronic structures of B- and N-doped graphene systems were also found to be strongly influenced by the positioning of the dopant atoms in the graphene lattice. The systems with dopant atoms at alternate sublattices have been found to have the lowest cohesive energies and therefore form the most stable structures. These results indicate an ability to adjust the band gap as required using B and N atoms according to the choice of the supercell, i.e., the doping density and substitutional dopant sites, which could be useful in the design of graphene-based electronic and optical devices.
MODY - calculation of ordered structures by symmetry-adapted functions
Białas, Franciszek; Pytlik, Lucjan; Sikora, Wiesława
2016-01-01
In this paper we focus on the new version of computer program MODY for calculations of symmetryadapted functions based on the theory of groups and representations. The choice of such a functional frame of coordinates for description of ordered structures leads to a minimal number of parameters which must be used for presentation of such structures and investigations of their properties. The aim of this work is to find those parameters, which are coefficients of a linear combination of calculated functions, leading to construction of different types of structure ordering with a given symmetry. A spreadsheet script for simplification of this work has been created and attached to the program.
Abeln, Brant Anthony
The study of metastable electronic resonances, anion or neutral states of finite lifetime, in molecules is an important area of research where currently no theoretical technique is generally applicable. The role of theory is to calculate both the position and width, which is proportional to the inverse of the lifetime, of these resonances and how they vary with respect to nuclear geometry in order to generate potential energy surfaces. These surfaces are the basis of time-dependent models of the molecular dynamics where the system moves towards vibrational excitation or fragmentation. Three fundamental electronic processes that can be modeled this way are dissociative electronic attachment, vibrational excitation through electronic impact and autoionization. Currently, experimental investigation into these processes is being preformed on polyatomic molecules while theoreticians continue their fifty-year-old search for robust methods to calculate them. The separable insertion method, investigated in this thesis, seeks to tackle the problem of calculating metastable resonances by using existing quantum chemistry tools along with a grid-based method employing exterior complex scaling (ECS). Modern quantum chemistry methods are extremely efficient at calculating ground and (bound) excited electronic states of atoms and molecules by utilizing Gaussian basis functions. These functions provide both a numerically fast and analytic solution to the necessary two-electron, six-dimensional integrals required in structure calculations. However, these computer programs, based on analytic Gaussian basis sets, cannot construct solutions that are not square-integrable, such as resonance wavefunctions. ECS, on the other hand, can formally calculate resonance solutions by rotating the asymptotic electronic coordinates into the complex plane. The complex Siegert energies for resonances, Eres = ER - iGamma/2 where ER is the real-valued position of the resonance and Gamma is the width
Institute of Scientific and Technical Information of China (English)
LIN Sheng-Lu; ZHOU Hui; XU Xue-You; JIA Zheng-Mao; DENG Shan-Hong
2008-01-01
@@ By using a semiclassical method, we present theoretical computations of the ionization rate of Rydberg lithium atoms in parallel electric and magnetic fields with different scaled energies above the classical saddle point.The yielded irregular pulse trains of the escape electrons are recorded as a function of emission time, which allows for relating themselves to the terms of the recurrence periods of the photoabsorption.This fact turns to illustrate the dynamic mechanism how the electron pulses are stochastically generated.Comparing our computations with previous investigation results, we can deduce that the complicated chaos under consideration here consists of two kinds of self-similar fractal structures which correspond to the contributions of the applied magnetic field and the core scattering events.Furthermore, the effect of the magnetic field plays a major role in the profile of the autoionization rate curves, while the contribution of the core scattering is critical for specifying the positions of the pulse peaks.
Baker, S H; Roy, M; Gurman, S J; Binns, C
2009-05-06
It has been appreciated for some time that the novel properties of particles in the size range 1-10 nm are potentially exploitable in a range of applications. In order to ultimately produce commercial devices containing nanosized particles, it is necessary to develop controllable means of incorporating them into macroscopic samples. One way of doing this is to embed the nanoparticles in a matrix of a different material, by co-deposition for example, to form a nanocomposite film. The atomic structure of the embedded particles can be strongly influenced by the matrix. Since some of the key properties of materials, including magnetism, strongly depend on atomic structure, the ability to determine atomic structure in embedded nanoparticles is very important. This review focuses on nanoparticles, in particular magnetic nanoparticles, embedded in different metal matrices. Extended x-ray absorption fine structure (EXAFS) provides an excellent means of probing atomic structure in nanocomposite materials, and an overview of this technique is given. Its application in probing catalytic metal clusters is described briefly, before giving an account of the use of EXAFS in determining atomic structure in magnetic nanocomposite films. In particular, we focus on cluster-assembled films comprised of Fe and Co nanosized particles embedded in various metal matrices, and show how the crystal structure of the particles can be changed by appropriate choice of the matrix material. The work discussed here demonstrates that combining the results of structural and magnetic measurements, as well as theoretical calculations, can play a significant part in tailoring the properties of new magnetic cluster-assembled materials.
Institute of Scientific and Technical Information of China (English)
白玉林; 周晓林; 陈向荣; 芶清泉
2003-01-01
Local density approximation within the framework of the density functional theory is applied to calculate the scanning tunnelling microscopy(STM)images of Ar atoms adsorbed on a graphite sheet(Ar/graphite system).It is found that the optimal site of adsorbed Ar atom is at the top of the centre of the carbon hexagon and its equilibrium distance from the graphite surface is about 3.20A.We demonstrate that it is the hybridization of the C 2 p electronic states with the Ar 3 p and 4 s electronic states,which renders Ar atoms visible in the STM experiment.
Stable atomic structure of NiTi austenite
Energy Technology Data Exchange (ETDEWEB)
Zarkevich, Nikolai A [Ames Laboratory; Johnson, Duane D [Ames Laboratory
2014-08-01
Nitinol (NiTi), the most widely used shape-memory alloy, exhibits an austenite phase that has yet to be identified. The usually assumed austenitic structure is cubic B2, which has imaginary phonon modes, hence it is unstable. We suggest a stable austenitic structure that “on average” has B2 symmetry (observed by x-ray and neutron diffraction), but it exhibits finite atomic displacements from the ideal B2 sites. The proposed structure has a phonon spectrum that agrees with that from neutron scattering, has diffraction spectra in agreement with x-ray diffraction, and has an energy relative to the ground state that agrees with calorimetry data.
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.
Interfacial Atomic Structure of Twisted Few-Layer Graphene.
Ishikawa, Ryo; Lugg, Nathan R; Inoue, Kazutoshi; Sawada, Hidetaka; Taniguchi, Takashi; Shibata, Naoya; Ikuhara, Yuichi
2016-02-18
A twist in bi- or few-layer graphene breaks the local symmetry, introducing a number of intriguing physical properties such as opening new bandgaps. Therefore, determining the twisted atomic structure is critical to understanding and controlling the functional properties of graphene. Combining low-angle annular dark-field electron microscopy with image simulations, we directly determine the atomic structure of twisted few-layer graphene in terms of a moiré superstructure which is parameterized by a single twist angle and lattice constant. This method is shown to be a powerful tool for accurately determining the atomic structure of two-dimensional materials such as graphene, even in the presence of experimental errors. Using coincidence-site-lattice and displacement-shift-complete theories, we show that the in-plane translation state between layers is not a significant structure parameter, explaining why the present method is adequate not only for bilayer graphene but also a few-layered twisted graphene.
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.
Interfacial Atomic Structure of Twisted Few-Layer Graphene
Ishikawa, Ryo; Lugg, Nathan R.; Inoue, Kazutoshi; Sawada, Hidetaka; Taniguchi, Takashi; Shibata, Naoya; Ikuhara, Yuichi
2016-02-01
A twist in bi- or few-layer graphene breaks the local symmetry, introducing a number of intriguing physical properties such as opening new bandgaps. Therefore, determining the twisted atomic structure is critical to understanding and controlling the functional properties of graphene. Combining low-angle annular dark-field electron microscopy with image simulations, we directly determine the atomic structure of twisted few-layer graphene in terms of a moiré superstructure which is parameterized by a single twist angle and lattice constant. This method is shown to be a powerful tool for accurately determining the atomic structure of two-dimensional materials such as graphene, even in the presence of experimental errors. Using coincidence-site-lattice and displacement-shift-complete theories, we show that the in-plane translation state between layers is not a significant structure parameter, explaining why the present method is adequate not only for bilayer graphene but also a few-layered twisted graphene.
Structures and magnetic properties of Co-Zr-B magnets studied by first-principles calculations
Energy Technology Data Exchange (ETDEWEB)
Zhao, Xin; Ke, Liqin; Nguyen, Manh Cuong; Wang, Cai-Zhuang, E-mail: wangcz@ameslab.gov; Ho, Kai-Ming, E-mail: kmh@ameslab.gov [Ames Laboratory, U.S. DOE and Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011 (United States)
2015-06-28
The structures and magnetic properties of Co-Zr-B alloys near the composition of Co{sub 5}Zr with B at. % ≤6% were studied using adaptive genetic algorithm and first-principles calculations. The energy and magnetic moment contour maps as a function of chemical composition were constructed for the Co-Zr-B magnet alloys through extensive structure searches and calculations. We found that Co-Zr-B system exhibits the same structure motif as the “Co{sub 11}Zr{sub 2}” polymorphs, and such motif plays a key role in achieving strong magnetic anisotropy. Boron atoms were found to be able to substitute cobalt atoms or occupy the “interruption” sites. First-principles calculations showed that the magnetocrystalline anisotropy energies of the boron-doped alloys are close to that of the high-temperature rhombohedral Co{sub 5}Zr phase and larger than that of the low-temperature Co{sub 5.25}Zr phase. Our calculations provide useful guidelines for further experimental optimization of the magnetic performances of these alloys.
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)
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.
TUNABLE Band Structures of 2d Multi-Atom Archimedean-Like Phononic Crystals
Xu, Y. L.; Chen, C. Q.; Tian, X. G.
2012-06-01
Two dimensional multi-atom Archimedean-like phononic crystals (MAPCs) can be obtained by adding "atoms" at suitable positions in primitive cells of traditional simple lattices. Band structures of solid-solid and solid-air MAPCs are computed by the finite element method in conjunction with the Bloch theory. For the solid-solid system, our results show that the MAPCs can be suitably designed to split and shift band gaps of the corresponding traditional simple phononic crystal (i.e., with only one scatterer inside a primitive cell). For the solid-air system, the MAPCs have more and wider band gaps than the corresponding traditional simple phononic crystal. Numerical calculations for both solid-solid and solid-air MAPCs show that the band gap of traditional simple phononic crystal can be tuned by appropriately adding "atoms" into its primitive cell.
Institute of Scientific and Technical Information of China (English)
王金照; 陈民; 过增元
2002-01-01
Pair distribution functions and constant-volume heat capacities of liquid copper, silver and nickel have been calculated by molecular dynamics simulations with four different versions of the embedded-atom method (EAM) model, namely, the versions of Johnson, Mei, Cai and Pohlong. The simulated structural properties with the four potential models show reasonable agreement with experiments and have little difference with each other, while the calculated heat capacities with the different EAM versions show remarkable discrepancies. Detailed analyses of the energy of the liquid metallic system show that, to predict successfully the heat capacity, an EAM model should match the state equation first proposed by Rose.
Atomic structure of the amorphous nonstoichiometric silicon oxides and nitrides
Energy Technology Data Exchange (ETDEWEB)
Gritsenko, V A [Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)
2008-07-31
In addition to amorphous SiO{sub 2} and Si{sub 3}N{sub 4}, the two key dielectric film materials used in modern silicon devices, the fabrication technology of nonstoichiometric SiO{sub x}N{sub y}, SiN{sub x}, and SiO{sub x} compounds is currently under development. Varying the chemical composition of these compounds allows a wide range of control over their physical - specifically, optical and electrical - properties. The development of technology for synthesizing such films requires a detailed understanding of their atomic structure. Current views on the atomic structure of nonstoichiometric silicon nitrides and oxides are reviewed and summarized. (reviews of topical problems)
Atomic scale structure investigations of epitaxial Fe/Cr multilayers
Energy Technology Data Exchange (ETDEWEB)
Kąc, M., E-mail: malgorzata.kac@ifj.edu.pl [The Henryk Niewodniczański Institute of Nuclear Physics PAN, ul. Radzikowskiego 152, 31-342 Kraków (Poland); Morgiel, J. [Institute of Metallurgy and Materials Science PAN, 25 Reymonta St., 30-059 Kraków (Poland); Polit, A.; Zabila, Y.; Marszałek, M. [The Henryk Niewodniczański Institute of Nuclear Physics PAN, ul. Radzikowskiego 152, 31-342 Kraków (Poland)
2014-06-01
Fe/Cr multilayers were deposited by molecular beam epitaxy on the MgO(1 0 0) substrate. Structural properties of the samples were analyzed by low energy electron diffraction, high resolution transmission electron microscopy (HRTEM), as well as by X-ray reflectivity, conversion electron Mössbauer spectroscopy (CEMS) and Auger electron spectroscopy. Investigations revealed multilayered system built of well-ordered Fe and Cr thin films with (1 0 0) orientation. A high geometrical perfection of the system, i.e. planar form of interfaces and reproducible thickness of layers, was also proven. Fe/Cr interface roughness was determined to be 2–3 atomic layers. CEMS studies allowed to analyze at atomic scale the structure of buried Fe/Cr interfaces, as well as to distinguish origin of interface roughness. Roughnesses resulting from interface corrugations and from the Fe–Cr interdiffusion at interfaces were observed. Fe/Cr multilayers showed strong antiferromagnetic coupling of Fe layers.
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.
2014-10-01
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 × 106 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.
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.
A computer code for calculations in the algebraic collective model of the atomic nucleus
Welsh, T. A.; Rowe, D. J.
2016-03-01
A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1 , 1) × SO(5) dynamical group. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code enables a wide range of model Hamiltonians to be analysed. This range includes essentially all Hamiltonians that are rational functions of the model's quadrupole moments qˆM and are at most quadratic in the corresponding conjugate momenta πˆN (- 2 ≤ M , N ≤ 2). The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [ π ˆ ⊗ q ˆ ⊗ π ˆ ] 0 and [ π ˆ ⊗ π ˆ ] LM. The code is made efficient by use of an analytical expression for the needed SO(5)-reduced matrix elements, and use of SO(5) ⊃ SO(3) Clebsch-Gordan coefficients obtained from precomputed data files provided with the code.
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.
Band structure calculation of GaSe-based nanostructures using empirical pseudopotential method
Osadchy, A. V.; Volotovskiy, S. G.; Obraztsova, E. D.; Savin, V. V.; Golovashkin, D. L.
2016-08-01
In this paper we present the results of band structure computer simulation of GaSe- based nanostructures using the empirical pseudopotential method. Calculations were performed using a specially developed software that allows performing simulations using cluster computing. Application of this method significantly reduces the demands on computing resources compared to traditional approaches based on ab-initio techniques and provides receiving the adequate comparable results. The use of cluster computing allows to obtain information for structures that require an explicit account of a significant number of atoms, such as quantum dots and quantum pillars.
The crystal structure of samarosporin I at atomic resolution.
Gessmann, Renate; Axford, Danny; Evans, Gwyndaf; Brückner, Hans; Petratos, Kyriacos
2012-11-01
The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.
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).
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...
Semiclassical calculation of ionisation rate for Rydberg helium atoms in an electric field
Institute of Scientific and Technical Information of China (English)
Wang De-Hua
2011-01-01
The ionisation of Rydberg helium atoms in an electric field above the classical ionisation threshold has been examined using the semiclassical method, with particular emphasis on discussing the influence of the core scattering on the escape dynamics of electrons. The results show that the Rydberg helium atoms ionise by emitting a train of electron pulses. Unlike the case of the ionisation of Rydberg hydrogen atom in parallel electric and magnetic fields,where the pulses of the electron are caused by the external magnetic field, the pulse trains for Rydberg helium atoms are created through core scattering. Each peak in the ionisation rate corresponds to the contribution of one core-scattered combination trajectory. This fact further illustrates that the ionic core scattering leads to the chaotic property of the Rydberg helium atom in external fields. Our studies provide a simple explanation for the escape dynamics in the ionisation of nonhydrogenic atoms in external fields.
Institute of Scientific and Technical Information of China (English)
POPEL; P; S; KONSTANTINOVA; N; Yu
2010-01-01
The method of crucible rotating oscillation damping was employed to measure the kinematic viscosity of aluminum melt,and the curve of viscosity v versus temperature T from 935 to 1383 K was obtained.Besides,based on the calculation model of the evolution behavior of atomic clusters in liquid structure,the curve of atomic clusters size d versus temperature was obtained,and the calculated results are in good agreement with the experimental values.By analyzing experimental data,it was found that both the viscosity and the size of atomic clusters of aluminum melt are monodrome functions of temperature,and the relation between v(T) and d(T) is a linear function,i.e.,v = v 0 + K·d(T).This relation indirectly verifies the calculation model of the structural information of metal melt,which is of great significance for studying the relation between melt microstructure and macro-physical properties.
Poulain-Paul, Agnieszka; Nassour, Ayoub; Jelsch, Christian; Guillot, Benoit; Kubicki, Maciej; Lecomte, Claude
2012-11-01
Three models of charge-density distribution - Hansen-Coppens multipolar, virtual atom and kappa - of different complexities, different numbers of refined parameters, and with variable levels of restraints, were tested against theoretical and high-resolution X-ray diffraction structure factors for 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitrile. The influence of the model, refinement strategy, multipole level and treatment of the H atoms on the dipole moment was investigated. The dipole moment turned out to be very sensitive to the refinement strategy. Also, small changes in H-atom treatment can greatly influence the calculated magnitude and orientation of the dipole moment. The best results were obtained when H atoms were kept in positions determined by neutron diffraction and anisotropic displacement parameters (obtained by SHADE, in this case) were used. Also, constraints on kappa values of H atoms were found to be superior to the free refinement of these parameters. It is also shown that the over-parametrization of the multipolar model, although possibly leading to better residuals, in general gives worse dipole moments.
Megchiche, El Hocine; Amarouche, Mohand; Mijoule, Claude
2007-01-01
International audience; Within the framework of density functional theory using the projector augmented-wave (PAW) method, we present some energetic properties of atomic oxygen interstitials in crystalline Ni, i.e. the insertion and activation energies of the O diffusion. Concerning the activation energy, two pathways for the migration process are studied. The charge transfer process between atomic oxygen and nickel atoms is analysed in the interstitial sites. We find that the interstitial oc...
Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations.
Chain, Fernando E; Romano, Elida; Leyton, Patricio; Paipa, Carolina; Catalán, César A N; Fortuna, Mario; Brandán, Silvia Antonia
2015-01-01
In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G(∗) basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay's scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (μ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings.
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 ...
Calculation of surface acoustic waves in a multilayered piezoelectric structure
Institute of Scientific and Technical Information of China (English)
Zhang Zuwei; Wen Zhiyu; Hu Jing
2013-01-01
The propagation properties of the surface acoustic waves (SAWs) in a ZnO-SiO2-Si multilayered piezoelectric structure are calculated by using the recursive asymptotic method.The phase velocities and the electromechanical coupling coefficients for the Rayleigh wave and the Love wave in the different ZnO-SiO2-Si structures are calculated and analyzed.The Love mode wave is found to be predominantly generated since the c-axis of the ZnO film is generally perpendicular to the substrate.In order to prove the calculated results,a Love mode SAW device based on the ZnO-SiO2-Si multilayered structure is fabricated by micromachining,and its frequency responses are detected.The experimental results are found to be mainly consistent with the calculated ones,except for the slightly larger velocities induced by the residual stresses produced in the fabrication process of the films.The deviation of the experimental results from the calculated ones is reduced by thermal annealing.
Quasiparticle GW calculations within the GPAW electronic structure code
DEFF Research Database (Denmark)
Hüser, Falco
properties are to a large extent governed by the physics on the atomic scale, that means pure quantum mechanics. For many decades, Density Functional Theory has been the computational method of choice, since it provides a fairly easy and yet accurate way of determining electronic structures and related......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...... with respect to the system one wants to investigate by choosing a certain functional or by tuning parameters. A succesful alternative is the so-called GW approximation. It is mathematically precise and gives a physically well-founded description of the complicated electron interactions in terms of screening...
Snyder, David A; Grullon, Jennifer; Huang, Yuanpeng J; Tejero, Roberto; Montelione, Gaetano T
2014-02-01
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 (Snyder and 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.
Pfennig, Brian W.; Schaefer, Amy K.
2011-01-01
A general chemistry laboratory experiment is described that introduces students to instrumental analysis using gas chromatography-mass spectrometry (GC-MS), while simultaneously reinforcing the concepts of mass percent and the calculation of atomic mass. Working in small groups, students use the GC to separate and quantify the percent composition…
Ichino, Takatoshi; Cheng, Lan; Stanton, John F.
2016-06-01
The innovative application of the ion-trap technique by Wester and coworkers has yielded definitive experimental values of photodetachment cross sections for the atomic oxygen radical anion (Obullet -) [Hlavenka et al., J. Chem. Phys. 130, 061105 (2009)]. In the present study, equation-of-motion coupled-cluster (EOM-CC) calculations have been performed to derive theoretical values of photodetachment cross sections for the negative ions of atoms in the first two periods of the periodic table as well as of those which belong to the alkali metal and halogen groups. Two methods have been employed to derive the cross sections. One involves the Dyson orbitals obtained from EOM-CC calculations and plane wave functions for the detached electron in the transition dipole moment integrals. The other method utilizes the moment theory following EOM-CC calculations of transition dipole moments for a large number of pseudo-states. The cross sections so evaluated for Obullet - match the experimental values very well. Generally good agreement has been found between the theoretical and experimental values of the cross sections for the atoms in the first two periods, while the present calculations cast some doubt on reported experimental values for some atoms beyond the second period. Substantial relativistic effects on the cross section have been observed for heavy elements in the alkali metal and halogen groups.
Calculation of IR-spectra of structural fragments of lignins
Derkacheva, O. Yu.; Ishankhodzhaeva, M. M.
2016-12-01
To study structure of softwood lignins the experimental and theoretical IR-spectra in middle IR-diapason were analyzed. To interpret these data the quantum chemical calculations of IR-spectra of general dimmer fragments of softwood lignins by method of density functional theory (DFT/B3LYP) with 6-31G(d,p) as basis set were carried out. These calculations showed that frequencies of normal vibrations of fragment with β-alkyl-aryl linkage are close to the experimental values of the IR absorption bands of lignin, and infrared spectrum of this structure is similar to the experimental spectrum of lignin. The calculations with accounting for the solvent showed a strong increase in the intensity of the majority of the bands and the solvent effect on the frequencies of vibrations.
Structural uncertainty in air mass factor calculation for NO
Lorente Delgado, Alba; Folkert Boersma, K.; Yu, Huan; Dörner, Steffen; Hilboll, Andreas; Richter, Andreas; Liu, Mengyao; Lamsal, Lok N.; Barkley, Michael; Smedt, De Isabelle; Roozendael, Van Michel; Wang, Yang; Wagner, Thomas; Beirle, Steffen; Lin, Jin Tai; Krotkov, Nickolay; Stammes, Piet; Wang, Ping; Eskes, Henk J.; Krol, Maarten
2017-01-01
Air mass factor (AMF) calculation is the largest source of uncertainty in NO2 and HCHO satellite retrievals in situations with enhanced trace gas concentrations in the lower troposphere. Structural uncertainty arises when different retrieval methodologies are applied within the scientific community
Structural and electronic properties of perylene from first principles calculations.
Fedorov, I A; Zhuravlev, Y N; Berveno, V P
2013-03-07
The electronic structure of crystalline perylene has been investigated within the framework of density functional theory including van der Waals interactions. The computations of the lattice parameters and cohesive energy have good agreement with experimental values. We have also calculated the binding distance and energy of perylene dimers, using different schemes, which include van der Waals interactions.
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
2006-01-01
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 ty
Atomic Clocks and Variations of the FIne Structure Constant
Prestage, John D.; Tjoelker, Robert L.; Maleki, Lute
1995-01-01
We describe a new test for possible variations of the fine structure constant alpha by comparisons of rates between clocks based on hyperfine transitions in alkali atoms with different atomic number Z. H-maser, Cs, and Hg(+) clocks have a different dependence on alpha via relativistic contributions of order (Z-alpha)(sup 2). Recent H-maser vs Hg(+) clock comparison data improve laboratory limits on a time variation by 100-fold to give dot-alpha less than or equal to 3.7 x 10(exp -14)/yr. Future laser cooled clocks (Be(+), Rb, Cs, Hg(+), etc.), when compared, will yield the most sensitive of all tests for dot-alpha/alpha.
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.
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.
Viswanadhan, Vellarkad N; Rajesh, Hariharan; Balaji, Vitukudi N
2011-05-09
A new characterization of known drug, lead, and representative nondrug databases was performed taking into account several properties at the atomic and molecular levels. This characterization included atom type preferences, intrinsic structural diversity (Atom Type Diversity, ATD), and other well-known physicochemical properties, as an approach for rapid assessment of druglikeness for small molecule libraries. To characterize ATD, an elaborate united atom classification, UALOGP (United Atom Log P), with 148 atom types, was developed along with associated atomic physicochemical parameters. This classification also enabled an analysis of atom type and physicochemical property distributions (for calculated log P, molar refractivity, molecular weight, total atom count, and ATD) of drug, lead, and nondrug databases, a reassessment of the Ro5 (Rule of Five) and GVW (Ghose−Viswanadhan−Wendoloski) criteria, and development of new criteria and ranges more accurately reflecting the chemical space occupied by small molecule drugs. A relative druglikeness parameter was defined for atom types in drugs, identifying the most preferred types. The present work demonstrates that drug molecules are constitutionally more diverse relative to nondrugs, while being less diverse than leads.
Atomic structure of anthrax protective antigen pore elucidates toxin translocation.
Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong
2015-05-28
Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed.
Vapour phase growth and grain boundary structure of molybdenum disulphide atomic layers.
Najmaei, Sina; Liu, Zheng; Zhou, Wu; Zou, Xiaolong; Shi, Gang; Lei, Sidong; Yakobson, Boris I; Idrobo, Juan-Carlos; Ajayan, Pulickel M; Lou, Jun
2013-08-01
Single-layered molybdenum disulphide with a direct bandgap is a promising two-dimensional material that goes beyond graphene for the next generation of nanoelectronics. Here, we report the controlled vapour phase synthesis of molybdenum disulphide atomic layers and elucidate a fundamental mechanism for the nucleation, growth, and grain boundary formation in its crystalline monolayers. Furthermore, a nucleation-controlled strategy is established to systematically promote the formation of large-area, single- and few-layered films. Using high-resolution electron microscopy imaging, the atomic structure and morphology of the grains and their boundaries in the polycrystalline molybdenum disulphide atomic layers are examined, and the primary mechanisms for grain boundary formation are evaluated. Grain boundaries consisting of 5- and 7- member rings are directly observed with atomic resolution, and their energy landscape is investigated via first-principles calculations. The uniformity in thickness, large grain sizes, and excellent electrical performance signify the high quality and scalable synthesis of the molybdenum disulphide atomic layers.
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.
The first principle study on the atomic and electronic structure of GaN(101-bar 0) surface
Energy Technology Data Exchange (ETDEWEB)
Li Yonghua [Structure Research Laboratory, University of Science and Technology of China, Academia Sinica, Hefei 230026 (China); NSRL, University of Science and Technology of China, Hefei 230029 (China); Xu Pengshou [Structure Research Laboratory, University of Science and Technology of China, Academia Sinica, Hefei 230026 (China) and NSRL, University of Science and Technology of China, Hefei 230029 (China)]. E-mail: psxu@ustc.edu.cn; Pan Haibin [NSRL, University of Science and Technology of China, Hefei 230029 (China); Xu Faqiang [NSRL, University of Science and Technology of China, Hefei 230029 (China)
2005-06-15
In this paper, we have calculated the atomic and electronic structure of GaN(101-bar 0) surface using an augmented plane wave plus local orbital (APW+lo) method. It is found that the surface is characterized by a top-layer bond-length-contracting rotation relaxation. The surface Ga atom moves towards the substrate and tends to form a planar sp{sup 2}-like bonding. While the surface N atom tends to a p{sup 3}-like bonding. Surface relaxation induces the transformation from metallic to semiconducting characterization.
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.
Long-range correlation energy calculated from coupled atomic response functions
Ambrosetti, Alberto; DiStasio, Robert A; Tkatchenko, Alexandre
2013-01-01
An accurate determination of the electron correlation energy is essential for describing the structure, stability, and function in a wide variety of systems, ranging from gas-phase molecular assemblies to condensed matter and organic/inorganic interfaces. Even small errors in the correlation energy can have a large impact on the description of chemical and physical properties in the systems of interest. In this context, the development of efficient approaches for the accurate calculation of the long-range correlation energy (and hence dispersion) is the main challenge. In the last years a number of methods have been developed to augment density functional approximations via dispersion energy corrections, but most of these approaches ignore the intrinsic many-body nature of correlation effects, leading to inconsistent and sometimes even qualitatively incorrect predictions. Here we build upon the recent many-body dispersion (MBD) framework, which is intimately linked to the random-phase approximation for the co...
Minimal parameter implicit solvent model for ab initio electronic structure calculations
Dziedzic, Jacek; Skylaris, Chris-Kriton; Mostofi, Arash A; Payne, Mike C
2011-01-01
We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.
Atomic structure and electronic states of extended defects in silicon
Riedel, F; Schröter, W
2002-01-01
Defects in silicon like dislocations, grain boundaries, silicide precipitates, etc. are spatially extended and associated with a large number of electronic states in the band gap. Our knowledge on the relation between atomic structure and electronic states of these extended defects presently starts to grow by applying high-resolution electron microscopy (HRTEM) and deep level transient spectroscopy (DLTS) in combination with numerical simulations. While by means of HRTEM details of structure can be studied, DLTS has been shown to allow for a classification of extended defect states into bandlike and localized. Moreover, this method opens the perspective to distinguish between trap-like and recombination-like electrical activity. In this paper, we emphasize the particular role of nickel and copper silicide precipitates, since in their cases structural features could be successfully related to specific DLTS line characteristics. Rapid quenching from high diffusion temperatures prevents decoration of platelet-sh...
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.
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.
Directory of Open Access Journals (Sweden)
S. J Hashemifar
2015-01-01
Full Text Available In this paper, the structural, magnetic, and electronic properties of two- to nine-atom copper and silver clusters and their alloys with one palladium atom are investigated by using full-potential all-electron density functional computations. After calculating minimized energy of several structural isomers of every nanocluster, it is argued that the small size nanoclusters (up to size of 6, prefer planar structures, while by increasing size a 2D-3D structural transformation is observed. The structural transformation of pure and copper-palladium clusters occurs in the size of seven and that of silver-palladium cluster in happens at the size of six. The calculated second difference and dissociation energies confirm that the two- and eight- atom pure clusters and three- and seven- atom alloyed clusters are magic clusters. The electronic and magnetic properties of stable isomers are calculated and considered after applying many body based GW correction.
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.
Editorial . Quantum fluctuations and coherence in optical and atomic structures
Eschner, Jürgen; Gatti, Alessandra; Maître, Agnès; Morigi, Giovanna
2003-03-01
From simple interference fringes, over molecular wave packets, to nonlinear optical patterns - the fundamental interaction between light and matter leads to the formation of structures in many areas of atomic and optical physics. Sophisticated technology in experimental quantum optics, as well as modern computational tools available to theorists, have led to spectacular achievements in the investigation of quantum structures. This special issue is dedicated to recent developments in this area. It presents a selection of examples where quantum dynamics, fluctuations, and coherence generate structures in time or in space or where such structures are observed experimentally. The examples range from coherence phenomena in condensed matter, over atoms in optical structures, entanglement in light and matter, to quantum patterns in nonlinear optics and quantum imaging. The combination of such seemingly diverse subjects formed the basis of a successful European TMR network, "Quantum Structures" (visit http://cnqo.phys.strath.ac.uk/~gianluca/QSTRUCT/). This special issue partly re.ects the results and collaborations of the network, going however well beyond its scope by including contributions from a global community and from many related topics which were not addressed directly in the network. The aim of this issue is to present side by side these di.erent topics, all of which are loosely summarized under quantum structures, to highlight their common aspects, their di.erences, and the progress which resulted from the mutual exchange of results, methods, and knowledge. To guide the reader, we have organized the articles into subsections which follow a rough division into structures in material systems and structures in optical .elds. Nevertheless, in the following introduction we point out connections between the contributions which go beyond these usual criteria, thus highlighting the truly interdisciplinary nature of quantum structures. Much of the progress in atom optics
Electronic structure calculations of ESR parameters of melanin units.
Batagin-Neto, Augusto; Bronze-Uhle, Erika Soares; Graeff, Carlos Frederico de Oliveira
2015-03-21
Melanins represent an important class of natural pigments present in plants and animals that are currently considered to be promising materials for applications in optic and electronic devices. Despite their interesting properties, some of the basic features of melanins are not satisfactorily understood, including the origin of their intrinsic paramagnetism. A number of experiments have been performed to investigate the electron spin resonance (ESR) response of melanin derivatives, but until now, there has been no consensus regarding the real structure of the paramagnetic centers involved. In this work, we have employed electronic structure calculations to evaluate the ESR parameters of distinct melanin monomers and dimers in order to identify the possible structures associated with unpaired spins in this biopolymer. The g-factors and hyperfine constants of the cationic, anionic and radicalar structures were investigated. The results confirm the existence of at least two distinct paramagnetic centers in melanin structure, identifying the chemical species associated with them and their roles in electrical conductivity.
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.
Chaotic dynamics and fractal structures in experiments with cold atoms
Daza, Alvar; Georgeot, Bertrand; Guéry-Odelin, David; Wagemakers, Alexandre; Sanjuán, Miguel A. F.
2017-01-01
We use tools from nonlinear dynamics for the detailed analysis of cold-atom experiments. A powerful example is provided by the recent concept of basin entropy, which allows us to quantify the final-state unpredictability that results from the complexity of the phase-space geometry. We show here that this enables one to reliably infer the presence of fractal structures in phase space from direct measurements. We illustrate the method with numerical simulations in an experimental configuration made of two crossing laser guides that can be used as a matter-wave splitter.
Atomic structure prediction of nanostructures, clusters and surfaces
Ciobanu, Cristian V; Ho, Kai-Ming
2013-01-01
This work fills the gap for a comprehensive reference conveying the developments in global optimization of atomic structures using genetic algorithms. Over the last few decades, such algorithms based on mimicking the processes of natural evolution have made their way from computer science disciplines to solid states physics and chemistry, where they have demonstrated their versatility and predictive power for many materials. Following an introduction and historical perspective, the text moves on to provide an in-depth description of the algorithm before describing its applications to crystal s
Schwinger variational calculation of ionization of hydrogen atoms for large momentum transfers
Indian Academy of Sciences (India)
K Chakrabarti
2002-03-01
Schwinger variational principle is used here to study large momentum transfer cases of electron and positron impact ionization of atomic hydrogen from the ground state at intermediate and moderately high energies. The results appear somewhat better compared to other theories.
Institute of Scientific and Technical Information of China (English)
WEN QingBo; YU ShanSheng; ZHENG WeiTao
2009-01-01
Calculations have been made for single-walled zigzag (n, 0) carbon nanotubes containing substitutional boron impurity atoms using ab initio density functional theory. It is found that the formation energies of these nanotubes depend on the tube diameter, as do the electronic properties, and show periodic fea-ture that results from their different π bonding structures compared to those of perfect zigzag carbon nanotubes. When more boron atoms are incorporated into a single-walled zigzag carbon nanotube, the substitutional boron atoms tend to come together to form structure of BC3 nanodomains, and B-doped tubes have striking acceptor states above the top of the valence bands. For the structure of BC3, there are two kinds of configurations with different electronic structures.
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
Calculations have been made for single-walled zigzag(n,0) carbon nanotubes containing substitutional boron impurity atoms using ab initio density functional theory.It is found that the formation energies of these nanotubes depend on the tube diameter,as do the electronic properties,and show periodic fea-ture that results from their different π bonding structures compared to those of perfect zigzag carbon nanotubes.When more boron atoms are incorporated into a single-walled zigzag carbon nanotube,the substitutional boron atoms tend to come together to form structure of BC3 nanodomains,and B-doped tubes have striking acceptor states above the top of the valence bands.For the structure of BC3,there are two kinds of configurations with different electronic structures.
Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.
Colvin, Michael T; Silvers, Robert; Ni, Qing Zhe; Can, Thach V; Sergeyev, Ivan; Rosay, Melanie; Donovan, Kevin J; Michael, Brian; Wall, Joseph; Linse, Sara; Griffin, Robert G
2016-08-03
Amyloid-β (Aβ) is a 39-42 residue protein produced by the cleavage of the amyloid precursor protein (APP), which subsequently aggregates to form cross-β amyloid fibrils that are a hallmark of Alzheimer's disease (AD). The most prominent forms of Aβ are Aβ1-40 and Aβ1-42, which differ by two amino acids (I and A) at the C-terminus. However, Aβ42 is more neurotoxic and essential to the etiology of AD. Here, we present an atomic resolution structure of a monomorphic form of AβM01-42 amyloid fibrils derived from over 500 (13)C-(13)C, (13)C-(15)N distance and backbone angle structural constraints obtained from high field magic angle spinning NMR spectra. The structure (PDB ID: 5KK3 ) shows that the fibril core consists of a dimer of Aβ42 molecules, each containing four β-strands in a S-shaped amyloid fold, and arranged in a manner that generates two hydrophobic cores that are capped at the end of the chain by a salt bridge. The outer surface of the monomers presents hydrophilic side chains to the solvent. The interface between the monomers of the dimer shows clear contacts between M35 of one molecule and L17 and Q15 of the second. Intermolecular (13)C-(15)N constraints demonstrate that the amyloid fibrils are parallel in register. The RMSD of the backbone structure (Q15-A42) is 0.71 ± 0.12 Å and of all heavy atoms is 1.07 ± 0.08 Å. The structure provides a point of departure for the design of drugs that bind to the fibril surface and therefore interfere with secondary nucleation and for other therapeutic approaches to mitigate Aβ42 aggregation.
Calculation of band structure in (101)-biaxially strained Si
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
The structure model used for calculation was defined according to Vegard’s rule and Hooke’s law. Calculations were performed on the electronic structures of(101)-biaxially strained Si on relaxed Si1-X GeX alloy with Ge fraction ranging from X = 0 to 0.4 in steps of 0.1 by CASTEP approach. It was found that [±100] and [00±1] valleys(-4) splitting from the [0±10] valley(-2) constitute the conduction b0and(CB) edge,that valence band(VB) edge degeneracy is partially lifted and that the electron mass is un-altered under strain while the hole mass decreases in the [100] and [010] directions. In addition,the fitted dependences of CB splitting energy,VB splitting energy and indirect bandgap on X are all linear.
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 solve...... for the unknown normal velocities of the structure at the relatively large number of nodes in the numerical model. Efficiently the regularization technique smoothes the solution spatially, since a fast spatial variation is associated with high index singular values, which is filtered out or damped...... in the regularization. Hence, the effective number of degrees of freedom in the model is often much lower than the number of nodes in the model. The present paper deals with an alternative formulation possible for the subset of radiation problems in which a (structural) modal expansion is known for the structure...
Morphology and atomic-scale structure of single-layer WS2 nanoclusters.
Füchtbauer, Henrik G; Tuxen, Anders K; Moses, Poul G; Topsøe, Henrik; Besenbacher, Flemming; Lauritsen, Jeppe V
2013-10-14
Two-dimensional sheets of transition metal (Mo and W) sulfides are attracting strong attention due to the unique electronic and optical properties associated with the material in its single-layer form. The single-layer MoS2 and WS2 are already in widespread commercial use in catalytic applications as both hydrotreating and hydrocracking catalysts. Consequently, characterization of the morphology and atomic structure of such particles is of utmost importance for the understanding of the catalytic active phase. However, in comparison with the related MoS2 system only little is known about the fundamental properties of single-layer WS2 (tungstenite). Here, we use an interplay of atom-resolved Scanning Tunneling Microscopy (STM) studies of Au(111)-supported WS2 nanoparticles and calculated edge structures using Density Functional Theory (DFT) to reveal the equilibrium morphology and prevalent edge structures of single-layer WS2. The STM results reveal that the single layer S-W-S sheets adopt a triangular equilibrium shape under the sulfiding conditions of the synthesis, with fully sulfided edges. The predominant edge structures are determined to be the (101[combining macron]0) W-edge, but for the smallest nanoclusters also the (1[combining macron]010) S-edges become important. DFT calculations are used to construct phase diagrams of the WS2 edges, and describe their sulfur and hydrogen coordination under different conditions, and in this way shed light on the catalytic role of WS2 edges.
Ab initio calculations of yttrium nitride: structural and electronic properties
Energy Technology Data Exchange (ETDEWEB)
Zerroug, S.; Ali Sahraoui, F. [Universite Ferhat Abbas, Laboratoire d' Optoelectronique et Composants, Departement de Physique, Setif (Algeria); Bouarissa, N. [King Khalid University, Department of Physics, Faculty of Science, P.O. Box 9004, Abha (Saudi Arabia)
2009-11-15
Using first principles total energy calculations within the full-potential linearized augmented plane wave method, we have studied the structural and electronic properties of yttrium nitride (YN) in the three phases, namely wurtzite, caesium chloride and rocksalt structures. The calculations are performed at zero and under hydrostatic pressure. In agreement with previous findings, it is found that the favored phase for YN is the rocksalt-like structure. We predict that at zero pressure YN in the rocksalt structure is a semiconductor with an indirect bandgap of 0.8 eV. A phase transition from a rocksalt to a caesium chloride structure is found to occur at {proportional_to}134 GPa. Besides, a transition from an indirect ({gamma}-X) bandgap semiconductor to a direct (X-X) one is predicted at pressure of {proportional_to}84 GPa. For the electron effective mass of rocksalt YN, these are the first results, to our knowledge. The information derived from the present study may be useful for the use of YN as an active layer in electronic devices such as diodes and transistors. (orig.)
Constraints on proton structure from precision atomic physics measurements
Energy Technology Data Exchange (ETDEWEB)
Brodsky, S
2004-08-10
The ground-state hyperfine splittings in hydrogen and muonium are extremely well measured. The difference between them, after correcting for the different magnetic moments of the muon and proton and for reduced mass effects, is due solely to the structure of the proton - the large QED contributions for a pointlike nucleus essentially cancel. A major contribution to the rescaled hyperfine difference is proportional to the Zemach radius, a fundamental measure of the proton which can be computed as an integral over the product of the elastic electric and magnetic form factors of the proton. The remaining proton structure corrections, the polarization contribution from inelastic states in the spin-dependent virtual Compton amplitude and the proton size dependence of the relativistic recoil corrections, have small uncertainties. The resulting high precision determination of the Zemach radius (1.013 {+-} 0.016) fm from atomic physics provides an important constraint on fits to accelerator measurements of the proton electric and magnetic form factors. Conversely, the authors use the muonium data to extract an 'experimental' value for the QED corrections to the hyperfine splitting of hydrogenic atoms. There is a significant discrepancy between measurement and theory which is in the same direction as a corresponding discrepancy in positronium.
Energy Technology Data Exchange (ETDEWEB)
Bannikov, V.V. [Institute of Solid State Chemistry, Ural Branch, Russian Academy of Sciences, Pervomaiskaya Street, 91, Ekaterinburg 620990 (Russian Federation); Ivanovskii, A.L., E-mail: ivanovskii@ihim.uran.ru [Institute of Solid State Chemistry, Ural Branch, Russian Academy of Sciences, Pervomaiskaya Street, 91, Ekaterinburg 620990 (Russian Federation)
2013-06-01
By means of the FLAPW-GGA approach, we have systematically studied the structural and electronic properties of tetragonal dichalcogenides KNi{sub 2}Ch{sub 2} (Ch=S, Se, and Te). Our results show that replacements of chalcogens (S→Se→Te) lead to anisotropic deformations of the crystals structure, which are related to the strong anisotropic character of the inter-atomic bonds, where inside the [Ni{sub 2}Ch{sub 2}] blocks, mixed covalent–ionic–metallic bonds occur, whereas between the adjacent [Ni{sub 2}Ch{sub 2}] blocks and K atomic sheets, ionic bonds emerge. We found that in the sequence KNi{sub 2}S{sub 2}→KNi{sub 2}Se{sub 2}→KNi{sub 2}Te{sub 2} (i) the overall band structure (where the near-Fermi valence bands are due mainly to the Ni states) is preserved, but the width of the common valence band and the widths of the separate sub-bands and the gaps decrease; (ii) the total DOSs at the Fermi level also decrease; and (iii) for the Fermi surfaces, the most appreciable changes are demonstrated by the hole-like sheets, when a necklace-like topology is formed for the 2D-like sheets and the volume of the closed pockets decreases. Some trends in structural and electronic parameters for ThCr{sub 2}Si{sub 2}-type layered dichalcogenides, KNi{sub 2}Ch{sub 2}, KFe{sub 2}Ch{sub 2}, KCo{sub 2}Se{sub 2}, are discussed.
Afonso, Sabrina; Silva, Fabiano B.; Silva, Arnaldo F.; Scarminio, Ieda S.; Bruns, Roy E.
2017-02-01
FTIR spectra have been measured for 31 different five component - simplex centroid design solvent mixture extracts of shaded and sun-exposed Annonaceous leaves harvested in all four seasons. The spectral frequencies are characteristic of anonnaceous acetogenins known to be a major component of these leaves. Osbnd H stretching spectral bands in the 3100-3600 cm-1 region provide evidence of notable intensity changes for the shaded and sun-exposed leaves. Chemometric principal component analysis involving 264 spectra show that shaded samples tend to have more intense Osbnd H stretching bands than those grown in the sun. B3LYP density functional calculations indicate significant Osbnd H stretching band changes in this region owing to hydrogen bond formation. Weak Osbnd H intensity enhancements, around 40 km mol-1, occur when an Osbnd H group forms a hydrogen bond with the oxygen atom of an adjacent tetrahydrofuran ring oxygen atom. Much more intense enhancements, 400-500 km mol-1, are predicted to occur for acetogenins with two tetrahydrofuran rings for which the Osbnd H group hydrogen bonds with its fartherest removed tetrahydrofuran ring oxygen. Whereas weak or moderate H-bond stretching intensities are obtained for acetogenins with slightly bent carbon chain structures the strongest hydrogen bond intensities are calculated for molecules with a 45° V-type backbone structure. These important structural modifications as well as significant changes in bond lengths and angles owing to hydrogen bonding are detailed.
New crystal structure prediction of fully hydrogenated borophene by first principles calculations
Wang, Zhi-Qiang; Wang, Hui-Qiong; Feng, Yuan Ping; Zheng, Jin-Cheng
2016-01-01
We have studied the structure stability, band structures and mechanical properties of fully hydrogenated borophene (borophane) with different configurations by first principles calculations. Comparing with the Chair-like borophane (C-boropane) that has been reported in literature, we obtained four new conformers with much lower total-energy. The most stable one, Washboard-like borophane (W-borophane), has energy difference about 113.41 meV/atom lower than C-borophane. In W-borophane, B atoms are staggered by zigzag mode along the a direction, and staggered by up and down wrinkle mode along the b direction. Furthermore, we examined the dynamical stability of borophane conformers by calculating phonon dispersions. For the five conformers, no imaginary frequencies along the high-symmetry directions of the Brillouin zone were found, indicating that the five conformers are all dynamically stable. In addition, the band structures of the five conformers all show a Dirac cone along {\\Gamma}-Y or {\\Gamma}-X direction....
Constraints on proton structure from precision atomic physics measurements
Brodsky, S J; Hiller, J R; Hwang, D S
2004-01-01
The ground-state hyperfine splittings in hydrogen and muonium are extremely well measured. The difference between them, after correcting for the different magnetic moments of the muon and proton and for reduced mass effects, is due solely to the structure of the proton - the large QED contributions for a pointlike nucleus essentially cancel. A major contribution to the rescaled hyperfine difference is proportional to the Zemach radius, a fundamental measure of the proton which can be computed as an integral over the product of the elastic electric and magnetic form factors of the proton. The remaining proton structure corrections, the polarization contribution from inelastic states in the spin-dependent virtual Compton amplitude and the proton size dependence of the relativistic recoil corrections, have small uncertainties. The resulting high precision determination of the Zemach radius (1.013 +/- 0.016) fm from atomic physics provides an important constraint on fits to accelerator measurements of the proton ...
Atomic structure of amorphous shear bands in boron carbide.
Reddy, K Madhav; Liu, P; Hirata, A; Fujita, T; Chen, M W
2013-01-01
Amorphous shear bands are the main deformation and failure mode of super-hard boron carbide subjected to shock loading and high pressures at room temperature. Nevertheless, the formation mechanisms of the amorphous shear bands remain a long-standing scientific curiosity mainly because of the lack of experimental structure information of the disordered shear bands, comprising light elements of carbon and boron only. Here we report the atomic structure of the amorphous shear bands in boron carbide characterized by state-of-the-art aberration-corrected transmission electron microscopy. Distorted icosahedra, displaced from the crystalline matrix, were observed in nano-sized amorphous bands that produce dislocation-like local shear strains. These experimental results provide direct experimental evidence that the formation of amorphous shear bands in boron carbide results from the disassembly of the icosahedra, driven by shear stresses.
Priti; Dipti; Gangwar, R. K.; Srivastava, R.
2017-01-01
Electron impact excitation cross-sections and rate coefficients have been calculated using fully relativistic distorted wave theory for several fine-structure transitions from the ground as well as excited states of cesium atom in the wide range of incident electron energy. These processes play dominant role in low pressure hydrogen-cesium plasma, which is relevant to the negative ion based neutral beam injectors for the ITER project. As an application, the calculated detailed cross-sections are used to construct a reliable collisional radiative (CR) model to characterize the hydrogen-cesium plasma. Other processes such as radiative population transfer, electron impact ionization and mutual neutralization of Cs+ ion with negative hydrogen ion along with their reverse processes are also taken into account. The calculated cross-sections and the extracted plasma parameters from the present model are compared with the available experimental and theoretical results.
Wang, Hui; Li, Xu; Gao, Liang; Zhai, Jiao; Liu, Ru; Gao, Xueyun; Wang, Dongqi; Zhao, Lina
2016-06-02
Peptide coated gold nanoclusters (AuNCs) have a precise molecular formula and atomic structure, which are critical for their unique applications in targeting specific proteins either for protein analysis or drug design. To date, a study of the crystal structure of peptide coated AuNCs is absent primarily due to the difficulty of obtaining their crystalline phases in an experiment. Here we study a typical peptide coated AuNC (Au24Peptide8, Peptide = H2N-CCYKKKKQAGDV-COOH, Anal. Chem., 2015, 87, 2546) to figure out its atomic structure and electronic structure using a theoretical method for the first time. In this work, we identify the explicit configuration of the essential structure of Au24Peptide8, Au24(Cys-Cys)8, using density functional theory (DFT) computations and optical spectroscopic experiments, where Cys denotes cysteine without H bonded to S. As the first multidentate ligand binding AuNC, Au24(Cys-Cys)8 is characterized as a distorted Au13 core with Oh symmetry covered by two Au(Cys-Cys) and three Au3(Cys-Cys)2 staple motifs in its atomic structure. The most stable configuration of Au24(Cys-Cys)8 is confirmed by comparing its UV-vis absorption spectrum from time-dependent density-functional theory (TDDFT) calculations with optical absorption measurements, and these results are consistent with each other. Furthermore, we carry out frontier molecular orbital (FMO) calculations to elucidate that the electronic structure of Au24(Cys-Cys)8 is different from that of Au24(SR)20 as they have a different Au/S ratio, where SR represents alkylthiolate. Importantly, the different ligand coatings, Cys-Cys and SR, in Au24(Cys-Cys)8 and Au24(SR)20 cause the different Au/S ratios in the coated Au24. The reason is that the Au/S ratio is crucial in determining the size of the Au core of the ligand protected AuNC, and the size of the Au core corresponds to a specific electronic structure. By the adjustment of ligand coatings from alkylthiolate to peptide, the Au/S ratio
Megchiche, E H; Amarouche, M; Mijoule, C
2007-07-25
Within the framework of density functional theory using the projector augmented-wave (PAW) method, we present some energetic properties of atomic oxygen interstitials in crystalline Ni, i.e. the insertion and activation energies of the O diffusion. Concerning the activation energy, two pathways for the migration process are studied. The charge transfer process between atomic oxygen and nickel atoms is analysed in the interstitial sites. We find that the interstitial octahedral site (O site) is lower in energy than the tetrahedral site (T site). The most favourable pathway for the migration between two octahedral sites corresponds to an intermediate metastable state located in a tetrahedral site. Concerning the charge transfers we find that the atomic oxygen ionizes as O(-) and that the electron migrates essentially from the Ni nearest neighbours of atomic oxygen. In addition, the thermal expansion contribution through the dilatation of the solid is studied. When the thermal expansion is introduced, we show that the insertion process is stabilized and that the tetrahedral insertion energy becomes nearly equal to the octahedral ones. However, the activation energy decreases with the dilatation. Taking into account the thermal expansion effects, our results are consistent with the more reliable experimental data.
Energy Technology Data Exchange (ETDEWEB)
Babilas, Rafał, E-mail: rafal.babilas@polsl.pl
2015-09-15
The atomic structure of Fe{sub 70}Nb{sub 10}B{sub 20} alloy in “as-cast” state and after annealing was investigated using high-energy X-ray diffraction (XRD), Mössbauer spectroscopy (MS) and high resolution transmission electron microscopy (HRTEM). The HRTEM observations allowed to indicate some medium-range order (MRO) regions about 2 nm in size and formation of some kinds of short-range order (SRO) structures represented by atomic clusters with diameter ca. 0.5 nm. The Reverse Monte Carlo (RMC) method basing on the results of XRD measurements was used in modeling the atomic structure of Fe-based alloy. The structural model was described by peak values of partial pair correlation functions and coordination numbers determined by Mössbauer spectroscopy investigations. The three-dimensional configuration box of atoms was obtained from the RMC simulation and the representative Fe-centered clusters were taken from the calculated structure. According to the Gonser et al. approach, the measured spectra of alloy studied were decomposed into 5 subspectra representing average Fe–Fe coordination numbers. Basing on the results of disaccommodation of magnetic permeability, which is sensitive to the short order of the random packing of atoms, it was stated that an occurrence of free volume is not detected after nanocrystallization process. - Highlights: • Atomic cluster model of amorphous structure was proposed for studied glassy alloy. • Short range order (ca. 0.5 nm) regions interpreted as clusters were identified by HREM. • Clusters correspond to coordination numbers (N = 4,6,8,9) calculated by using Gonser approach. • Medium-range order (ca. 2 nm) could be referred to few atomic clusters. • SRO regions are able to grow up as nuclei of crystalline bcc Fe and iron borides. • Crystalline particles have spherical morphology with an average diameter of 20 nm.
Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR.
Shi, Chaowei; Fricke, Pascal; Lin, Lin; Chevelkov, Veniamin; Wegstroth, Melanie; Giller, Karin; Becker, Stefan; Thanbichler, Martin; Lange, Adam
2015-12-01
Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the species Caulobacter crescentus is not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR-derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.
Photonic Band Gap Structures with Periodically Arranged Atoms in a Two-Dimensional Photonic Crystal
Institute of Scientific and Technical Information of China (English)
LI Zhi-Yu; CHEN Fang; ZHOU Jian-Ying
2005-01-01
@@ Linear transmission, reflection and absorption spectra for a new two-dimensional photonic crystal with periodically arranged resonant atoms are examined. Numerical results show that a twin-gap structure with forbidden bands displaced from a non-doped bandgap structure can be produced as a result of atomic polarization. The absorption spectrum is also significantly altered compared to the single atom entity.
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...
Structure and analysis of atomic vibrations in clusters of Cu n ( n ≤ 20)
Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.
2013-02-01
The binding energy, equilibrium geometry, and vibration frequencies of free clusters Cu n (2 ≤ n ≤ 20) are calculated using the potentials of interatomic interactions found using the tight-binding approximation. The nonmonotonic dependence of the clusters' minimum vibration frequency on their sizes and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 is demonstrated. It is noted that this result agrees with the theoretical and experimental data on stable structures of small and medium metallic clusters.
You, Pei-Lin
2008-01-01
Using special capacitors our experiments discovered that the electric susceptibility Xe of K, Rb or Cs vapor varies in direct proportion to their density N, and inversely proportional to the absolute temperature T as polar molecules. Their capacitance(C) at different voltage (V) was measured. The C-V curve shows that the saturation polarization of K, Rb or Cs vapor has be observed when the field E more than ten to fiveth power V/m. The measurements show that the ground state K, Rb or Cs atom is polar atom with a large permanent electric dipole moment (EDM) of the order of eao (ao is Bohr radius) as excited state of hydrogen atom. But we can not calculate the EDM of an atom using Boltzmann constant. Because of the mechanism of polar atoms by which orientation polarization arises completely differs from polar molecules. The orientation polarization of polar molecule, such as HCl or H2O etc, is a molecule as a whole turned toward the direction of an external field. Unlike polar molecules, the orientation polariz...
Effects of atomic grain boundary structures on primary radiation damage in α-Fe
Energy Technology Data Exchange (ETDEWEB)
Esfandiarpour, A. [Department of Physics, Payame Noor University (PNU), P.O. BOX 19395-3697, Tehran (Iran, Islamic Republic of); Feghhi, S.A.H., E-mail: a.feghhi@gmail.com [Department of Radiation Application, Shahid Beheshti University G.C., Tehran (Iran, Islamic Republic of); Shokri, A.A. [Department of Physics, Payame Noor University (PNU), P.O. BOX 19395-3697, Tehran (Iran, Islamic Republic of)
2015-11-01
In this paper, we used five different grain boundary (GB) structures including two twists, two symmetric tilts and one asymmetric tilt for α-Fe, in order to study the influence of different GB structures on the production and time evolution of defects. Energetic behavior of point defects near GBs is investigated and analyzed using Molecular Static (MS) method to calculate and compare the “defect absorbency” of each structure. The primary radiation damage state near each GB structure is simulated using Molecular Dynamic (MD) method for 3 keV and 6 keV primary-knocked on atom (PKA) with velocity vector perpendicular to the GB plane at various distances in 300 K. We found that all five GB structures can decrease the defect number in bulk region, if cascade center locates on the GB plane (prefect overlap) and increase the vacancy number, if the overlap is imperfect. This depends on the energy of PKA and its distance from GB plane. Also, the results proved that the magnitude of the observed variations depends on the atomic structure of GB. Furthermore, the GBs that have stronger “interstitial absorbency” produce an excess concentration of vacancies in the bulk region, while the edge of the cascades overlaps with GB plane. This is the result of bigger “interstitial absorbency” of GBs in comparison with vacancies.
Energy Technology Data Exchange (ETDEWEB)
Miyasita, Mitiyasu, E-mail: miyasita.mitiyasu@gmail.com [Graduate School of Science and Engineering, Shinshu University, Ueda 386-8567 (Japan); Higuchi, Katsuhiko [Graduate School of Advanced Science of Matter, Hiroshima University, Higashi-Hiroshima 739-8527 (Japan); Higuchi, Masahiko [Department of Physics, Faculty of Science, Shinshu University, Matsumoto 390-8621 (Japan)
2012-07-15
We present an alternative scheme for calculating the unrestricted Hartree-Fock (HF) equation. The scheme is based on the variational method utilizing the sophisticated basis functions that include no adjustable parameters. The validity of the present scheme is confirmed by actual calculations of the boron and neon atoms. The total energy of the present scheme is lower than that of the conventional restrictive HF equation, but higher than that of the CI method. Also, the resultant wave function satisfies the electron-nucleus cusp condition.
Tirez, Kristof; Beutels, Filip; Brusten, Wilfried; Noten, Bart; De Brucker, Nicole
2002-11-01
The mercury mass fraction has been determined by atomic fluorescence spectrometry (AFS) in the framework of the project "Certification of a reference material (trace elements in fly ash) in replacement of BCR CRM 176". Calculation of the uncertainty budget, as described in this manuscript, emphasizes a practical and realistic approach to estimation of uncertainty components on the basis of statistical assumptions. GUM Workbench software was used, and resulted in a mercury mass fraction of 1.58+/-0.11 mg kg(-1) (with coverage factor k=2.2, 95% probability) related to dry mass, submitted in the certification exercise. The calculated total uncertainty budget applies to analogous samples analyzed by this procedure.
Energy Technology Data Exchange (ETDEWEB)
Yuan, H. K.; Chen, H., E-mail: chenh@swu.edu.cn; Tian, C. L.; Kuang, A. L.; Wang, J. Z. [School of Physical Science and Technology, Southwest University, Chongqing 400715 (China)
2014-04-21
Gadolinium-oxide clusters in various sizes and stoichiometries have been systematically studied by employing the density functional theory with the generalized gradient approximation. The clusters in bulk stoichiometry are relatively more stable and their binding energies increase with the increasing size. Stoichiometric (Gd{sub 2}O{sub 3}){sub n} clusters of n = 1–3 prefer cage-like structures, whereas the clusters of n = 4–30 prefer compact structures layered by wedge-like units and exhibit a rough feature toward the bulk-like arrangement with small disorders of atomic positions. The polyhedral-cages analogous to carbon-fullerenes are stable isomers yet not the minimum energy configurations. Their stabilities can be improved by embedding one oxygen atom or a suitable cage to form core-shell configurations. The mostly favored antiferromagnetic couplings between adjacent Gd atoms are nearly degenerated in energy with their ferromagnetic couplings, resulting in super-paramagnetic characters of gadolinium-oxide clusters. The Ruderman-Kittel-Kasuya-Yosida (RKKY)-type mechanism together with the superexchange-type mechanism plays cooperation role for the magnetic interactions in clusters. We present, as a function of n, calculated binding energies, ionization potential, electron affinity, and electronic dipole moment.
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)
Ying, Chun; Zhao, Erjun; Lin, Lin; Hou, Qingyu
2014-10-01
The structural determination, thermodynamic, mechanical, dynamic and electronic properties of 4d transitional metal diborides MB2 (M = Y-Ag) are systematically investigated by first-principles within the density functional theory (DFT). For each diboride, five structures are considered, i.e. AlB2-, ReB2-, OsB2-, MoB2- and WB2-type structures. The calculated lattice parameters are in good agreement with the previously theoretical and experimental studies. The formation enthalpy increases from YB2 to AgB2 in AlB2-type structure (similar to MoB2- and WB2-type). While the formation enthalpy decreases from YB2 to MoB2, reached minimum value to TcB2, and then increases gradually in ReB2-type structure (similar to OsB2-type), which is consistent with the results of the calculated density of states. The structural stability of these materials relates mainly on electronegative of metals, boron structure and bond characters. Among the considered structures, TcB2-ReB2 (TcB2-ReB2 represents TcB2 in ReB2-type structure, the same hereinafter) has the largest shear modulus (248 GPa), and is the hardest compound. The number of electrons transferred from metals to boron atoms and the calculated densities of states (DOS) indicate that each diboride is a complex mixture of metallic, ionic and covalent characteristics. Trends are discussed.
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.
Santos-Martins, Diogo; Fernandes, Pedro Alexandrino; Ramos, Maria João
2016-11-01
In the context of SAMPL5, we submitted blind predictions of the cyclohexane/water distribution coefficient (D) for a series of 53 drug-like molecules. Our method is purely empirical and based on the additive contribution of each solute atom to the free energy of solvation in water and in cyclohexane. The contribution of each atom depends on the atom type and on the exposed surface area. Comparatively to similar methods in the literature, we used a very small set of atomic parameters: only 10 for solvation in water and 1 for solvation in cyclohexane. As a result, the method is protected from overfitting and the error in the blind predictions could be reasonably estimated. Moreover, this approach is fast: it takes only 0.5 s to predict the distribution coefficient for all 53 SAMPL5 compounds, allowing its application in virtual screening campaigns. The performance of our approach (submission 49) is modest but satisfactory in view of its efficiency: the root mean square error (RMSE) was 3.3 log D units for the 53 compounds, while the RMSE of the best performing method (using COSMO-RS) was 2.1 (submission 16). Our method is implemented as a Python script available at https://github.com/diogomart/SAMPL5-DC-surface-empirical.
Construction of an E. Coli genome-scale atom mapping model for MFA calculations.
Ravikirthi, Prabhasa; Suthers, Patrick F; Maranas, Costas D
2011-06-01
Metabolic flux analysis (MFA) has so far been restricted to lumped networks lacking many important pathways, partly due to the difficulty in automatically generating isotope mapping matrices for genome-scale metabolic networks. Here we introduce a procedure that uses a compound matching algorithm based on the graph theoretical concept of pattern recognition along with relevant reaction information to automatically generate genome-scale atom mappings which trace the path of atoms from reactants to products for every reaction. The procedure is applied to the iAF1260 metabolic reconstruction of Escherichia coli yielding the genome-scale isotope mapping model imPR90068. This model maps 90,068 non-hydrogen atoms that span all 2,077 reactions present in iAF1260 (previous largest mapping model included 238 reactions). The expanded scope of the isotope mapping model allows the complete tracking of labeled atoms through pathways such as cofactor and prosthetic group biosynthesis and histidine metabolism. An EMU representation of imPR90068 is also constructed and made available.
Ren, Xiao-Yan; Niu, Chun-Yao; Chen, Wei-Guang; Tang, Ming-Sheng; Cho, Jun-Hyung
2016-07-21
Exploring the properties of noble metal atoms and nano- or subnano-clusters on the semiconductor surface is of great importance in many surface catalytic reactions, self-assembly processes, crystal growth, and thin film epitaxy. Here, the energetics and kinetic properties of a single Cu atom and previously reported Cu magic clusters on the Si(111)-(7 × 7) surface are re-examined by the state-of-the-art first-principles calculations based on density functional theory. First of all, the diffusion path and high diffusion rate of a Cu atom on the Si(111)-(7 × 7) surface are identified by mapping out the total potential energy surface of the Cu atom as a function of its positions on the surface, supporting previous experimental hypothesis that the apparent triangular light spots observed by scanning tunneling microscopy (STM) are resulted from a single Cu atom frequently hopping among adjacent adsorption sites. Furthermore, our findings confirm that in the low coverage of 0.15 monolayer (ML) the previously proposed hexagonal ring-like Cu6 cluster configuration assigned to the STM pattern is considerably unstable. Importantly, the most stable Cu6/Si(111) complex also possesses a distinct simulated STM pattern with the experimentally observed ones. Instead, an energetically preferred solid-centered Cu7 structure exhibits a reasonable agreement between the simulated STM patterns and the experimental images. Therefore, the present findings convincingly rule out the tentative six-atom model and provide new insights into the understanding of the well-defined Cu nanocluster arrays on the Si(111)-(7 × 7) surface.
Atomic structures of Zr-based metallic glasses
Institute of Scientific and Technical Information of China (English)
2008-01-01
The atomic structures of Zr-Ni and Zr-Ti-Al-Cu-Ni metallic glasses were investigated by using classical molecular dynamic (MD),reverse Monte Carlo (RMC),ab initio MD (AIMD) simulations and high resolution transmission electron microscopy (HRTEM) techniques. We focused on the short-range order (SRO) and medium-range order (MRO) in the glassy structure. It is shown that there are icosahedral,FCC-and BCC-type SROs in the Zr-based metallic glasses. A structural model,characterized by imperfect ordered packing (IOP),was proposed based on the MD simulation and confirmed by the HRTEM observation. Furthermore,the evolution from IOP to nanocrystal during the crystallization of metallic glasses was also ex-plored. It is found that the growth from IOP to nanocrystal proceeds through three distinct stages: the formation of quasi-ordered structure with one-dimensional (1D) periodicity,then 2D periodicity,and finally the formation of 3D nanocrystals. It is also noted that these three growth steps are crosslinked.
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.
The Atomic scale structure of liquid metal-electrolyte interfaces
Murphy, B. M.; Festersen, S.; Magnussen, O. M.
2016-07-01
Electrochemical interfaces between immiscible liquids have lately received renewed interest, both for gaining fundamental insight as well as for applications in nanomaterial synthesis. In this feature article we demonstrate that the atomic scale structure of these previously inaccessible interfaces nowadays can be explored by in situ synchrotron based X-ray scattering techniques. Exemplary studies of a prototypical electrochemical system - a liquid mercury electrode in pure NaCl solution - reveal that the liquid metal is terminated by a well-defined atomic layer. This layering decays on length scales of 0.5 nm into the Hg bulk and displays a potential and temperature dependent behaviour that can be explained by electrocapillary effects and contributions of the electronic charge distribution on the electrode. In similar studies of nanomaterial growth, performed for the electrochemical deposition of PbFBr, a complex nucleation and growth behaviour is found, involving a crystalline precursor layer prior to the 3D crystal growth. Operando X-ray scattering measurements provide detailed data on the processes of nanoscale film formation.
Energy Technology Data Exchange (ETDEWEB)
Davis, Barry M.; McCaffrey, John G., E-mail: john.mccaffrey@nuim.ie [Department of Chemistry, Maynooth University, National University of Ireland—Maynooth, County Kildare (Ireland)
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{sup 1}P←a{sup 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 (<130 cm{sup −1}). All of the M ⋅ RG diatomics have bond lengths considerably longer than those of the rare gas dimers, with the consequence that isolation of these metal 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 Sr{sub 2} while this transition is quenched in Ba{sub 2}. This behaviour is consistent with the absence of vibrational structure on the dimer absorption band in Ba{sub 2} 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.
Wang, Hui; Li, Xu; Gao, Liang; Zhai, Jiao; Liu, Ru; Gao, Xueyun; Wang, Dongqi; Zhao, Lina
2016-06-01
Peptide coated gold nanoclusters (AuNCs) have a precise molecular formula and atomic structure, which are critical for their unique applications in targeting specific proteins either for protein analysis or drug design. To date, a study of the crystal structure of peptide coated AuNCs is absent primarily due to the difficulty of obtaining their crystalline phases in an experiment. Here we study a typical peptide coated AuNC (Au24Peptide8, Peptide = H2N-CCYKKKKQAGDV-COOH, Anal. Chem., 2015, 87, 2546) to figure out its atomic structure and electronic structure using a theoretical method for the first time. In this work, we identify the explicit configuration of the essential structure of Au24Peptide8, Au24(Cys-Cys)8, using density functional theory (DFT) computations and optical spectroscopic experiments, where Cys denotes cysteine without H bonded to S. As the first multidentate ligand binding AuNC, Au24(Cys-Cys)8 is characterized as a distorted Au13 core with Oh symmetry covered by two Au(Cys-Cys) and three Au3(Cys-Cys)2 staple motifs in its atomic structure. The most stable configuration of Au24(Cys-Cys)8 is confirmed by comparing its UV-vis absorption spectrum from time-dependent density-functional theory (TDDFT) calculations with optical absorption measurements, and these results are consistent with each other. Furthermore, we carry out frontier molecular orbital (FMO) calculations to elucidate that the electronic structure of Au24(Cys-Cys)8 is different from that of Au24(SR)20 as they have a different Au/S ratio, where SR represents alkylthiolate. Importantly, the different ligand coatings, Cys-Cys and SR, in Au24(Cys-Cys)8 and Au24(SR)20 cause the different Au/S ratios in the coated Au24. The reason is that the Au/S ratio is crucial in determining the size of the Au core of the ligand protected AuNC, and the size of the Au core corresponds to a specific electronic structure. By the adjustment of ligand coatings from alkylthiolate to peptide, the Au/S ratio
Energy Technology Data Exchange (ETDEWEB)
Umicevic, A.; Belosevic-Cavor, J.; Koteski, V.; Cekic, B.; Ivanovski, V. [Inst. of Nuclear Sciences Vinca, Lab. for Nuclear and Plasma Physics, Belgrade (Yugoslavia)
2009-09-15
A detailed theoretical study of the structure and electric field gradients (EFG) of the Zr{sub 2}Ni compound is presented. Using all-electron augmented plane waves plus local orbitals formalism, the equilibrium volume, bulk modulus, and EFGs at both non-equivalent crystallographic positions, Zr and Ni, are calculated. The possible mechanism of formation of the EFGs at both sites are analyzed and discussed. We have also performed supercell calculations with Cd and Ta impurities. Through the comparison of theoretical and experimental EFGs in these cases, we elucidate the role played by the Cd and Ta probe atoms in the time-differential perturbed angular correlation measurements of this compound. (orig.)
Atomic Structure and Doping Response of Grain Boundary in Transition Metal Ni
Institute of Scientific and Technical Information of China (English)
王崇愚; 于涛
1994-01-01
Based on the coincidence site lattice model and by use of the molecular dynamics method, the relaxation calculations on the atomic structures of the grain boundaries of various generating functions (∑3,∑5,…, ∑19,…,∑33) in the transition metal Ni are performed. The features of atomic structures corresponding to the grain boundaries and the effects of the pre-parameter on the interface structures are given. To study the doping response relating to the properties of materials, the 23 tilt grain boundary is selected. Based on the interstice and vacancy mechanisms, the interface responses doping boron, nitrogen and phosphorus for the grain boundary are investigated. According to the criterion of the energy in molecular dynamics simulation, the most probable positions of doping impurities and effect of doping impurities on the interface structure are given, and the dependence of the fine structure on doping type and the order of the impurity amount are obtained. The analysis of the local energy for the
Heyrovska, Raji
2008-01-01
It has been shown recently that chemical bond lengths, in general, like those in the components of nucleic acids, caffeine related compounds, all essential amino acids, methane, benzene, graphene and fullerene are sums of the radii of adjacent atoms constituting the bond. Earlier, the crystal ionic distances in all alkali halides and lengths of many partially ionic bonds were also accounted for by the additivity of ionic as well as covalent radii. Here, the atomic structures of riboflavin and its reduced form are presented based on the additivity of the same set of atomic radii as for other biological molecules.
Siretanu, Igor; van den Ende, Dirk; Mugele, Frieder
2016-04-01
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 dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces.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 dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all
Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface.
Sun, Ce; Paulauskas, Tadas; Sen, Fatih G; Lian, Guoda; Wang, Jinguo; Buurma, Christopher; Chan, Maria K Y; Klie, Robert F; Kim, Moon J
2016-06-03
Extended defects are of considerable importance in determining the electronic properties of semiconductors, especially in photovoltaics (PVs), due to their effects on electron-hole recombination. We employ model systems to study the effects of dislocations in CdTe by constructing grain boundaries using wafer bonding. Atomic-resolution scanning transmission electron microscopy (STEM) of a [1-10]/(110) 4.8° tilt grain boundary reveals that the interface is composed of three distinct types of Lomer dislocations. Geometrical phase analysis is used to map strain fields, while STEM and density functional theory (DFT) modeling determine the atomic structure at the interface. The electronic structure of the dislocation cores calculated using DFT shows significant mid-gap states and different charge-channeling tendencies. Cl-doping is shown to reduce the midgap states, while maintaining the charge separation effects. This report offers novel avenues for exploring grain boundary effects in CdTe-based solar cells by fabricating controlled bicrystal interfaces and systematic atomic-scale analysis.
Energy Technology Data Exchange (ETDEWEB)
Belianinov, Alex, E-mail: belianinova@ornl.gov; Ganesh, Panchapakesan; Lin, Wenzhi; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V. [Oak Ridge National Laboratory, Institute for Functional Imaging of Materials, Center for Nanophase Material Science, Oak Ridge, Tennessee 37922 (United States); Sales, Brian C.; Sefat, Athena S. [Oak Ridge National Laboratory, Materials Science and Technology Division, Oak Ridge, Tennessee 37922 (United States)
2014-12-01
Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe{sub 1−x}Se{sub x} structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.
On the atomic structure of cocaine in solution.
Johnston, Andrew J; Busch, Sebastian; Pardo, Luis Carlos; Callear, Samantha K; Biggin, Philip C; McLain, Sylvia E
2016-01-14
Cocaine is an amphiphilic drug which has the ability to cross the blood-brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ∼5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Å of cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function.
QED shift calculations in relativistic many-electron atoms and ions
Tupitsyn, I I; Safronova, M S; Shabaev, V M; Dzuba, V A
2016-01-01
We incorporated quantum electrodynamics (QED) corrections into the broadly-applicable high-precision relativistic method that combines configuration interaction (CI) and linearized coupled-cluster approaches. With the addition of the QED, this CI+all-order method allows one to accurately predict properties of heavy ions of particular interest to the design of precision atomic clocks and tests of fundamental physics. To evaluate the accuracy of the QED contributions and test various QED models, we incorporated four different one-electron QED potentials. We demonstrated that all of them give consistent and reliable results. For the strongly bound electrons (i.e. inner electrons of heavy atoms, or valence electrons in highly-charged ions), the nonlocal potentials are more accurate, than the local one. Results are presented for cases of particular experimental interest.
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.
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...
Electronic Structure of KFe2Se2 from First-Principles Calculations
Institute of Scientific and Technical Information of China (English)
CAO Chao; DAI Jian-Hui
2011-01-01
@@ Electronic structures and magnetic properties for iron-selenide KFe2Se2 axe studied by first-principles calculations.The ground state is collinear antiferromagnetic with calculated 2.26μB magnetic moment on Fe atoms; and the J1 and J2 coupling strengths are calculated to be 0.038eV and 0.029eV.The states around EF are dominated by the Fe 3d orbitals which hybridize noticeably to the Se 4p orbitals.While the band structure of KFe2Se2 is similar to a heavily electron-doped BaFe2As2 or FeSe system,the Fermi surface of KFe2Se2 is much closer to the FeSe system since the electron sheets around M are symmetric with respect to x-y exchange.These features,as well as the absence of Fermi surface nesting,suggest that the parent KFe2Se2 could be regarded as an electron doped FeSe system with possible local moment magnetism.%Electronic structures and magnetic properties for iron-selenide KFe2Se2 are studied by first-principles calculations.The ground state is collinear antiferromagnetic with calculated 2.26μB magnetic moment on Fe atoms; and the J1 and J2 coupling strengths are calculated to be 0.038eV and 0.029eV.The states around EF are dominated by the Fe 3d orbitals which hybridize noticeably to the Se 4p orbitals.While the band structure of KFe2Se2 is similar to a heavily electron-doped BaFe2As2 or FeSe system, the Fermi surface of KFe2Se2 is much closer to the FeSe system since the electron sheets around M are symmetric with respect to x-y exchange.These features, as well as the absence of Fermi surface nesting, suggest that the parent KFe2Se2 could be regarded as an electron doped FeSe system with possible local moment magnetism.
Dostál, Jiří; Pecina, Adam; Hrušková-Heidingsfeldová, Olga; Marečková, Lucie; Pichová, Iva; Řezáčová, Pavlina; Lepšík, Martin; Brynda, Jiří
2015-12-01
The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized.
Energy Technology Data Exchange (ETDEWEB)
Bencs, László, E-mail: bencs.laszlo@wigner.mta.hu [Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Laczai, Nikoletta [Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Ajtony, Zsolt [Institute of Food Science, University of West Hungary, H-9200 Mosonmagyaróvár, Lucsony utca 15–17 (Hungary)
2015-07-01
A combination of former convective–diffusive vapor-transport models is described to extend the calculation scheme for sensitivity (characteristic mass — m{sub 0}) in graphite furnace atomic absorption spectrometry (GFAAS). This approach encompasses the influence of forced convection of the internal furnace gas (mini-flow) combined with concentration diffusion of the analyte atoms on the residence time in a spatially isothermal furnace, i.e., the standard design of the transversely heated graphite atomizer (THGA). A couple of relationships for the diffusional and convectional residence times were studied and compared, including in factors accounting for the effects of the sample/platform dimension and the dosing hole. These model approaches were subsequently applied for the particular cases of Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mg, Mn, Mo, Ni, Pb, Sb, Se, Sn, V and Zn analytes. For the verification of the accuracy of the calculations, the experimental m{sub 0} values were determined with the application of a standard THGA furnace, operating either under stopped, or mini-flow (50 cm{sup 3} min{sup −1}) of the internal sheath gas during atomization. The theoretical and experimental ratios of m{sub 0}(mini-flow)-to-m{sub 0}(stop-flow) were closely similar for each study analyte. Likewise, the calculated m{sub 0} data gave a fairly good agreement with the corresponding experimental m{sub 0} values for stopped and mini-flow conditions, i.e., it ranged between 0.62 and 1.8 with an average of 1.05 ± 0.27. This indicates the usability of the current model calculations for checking the operation of a given GFAAS instrument and the applied methodology. - Highlights: • A calculation scheme for convective–diffusive vapor loss in GFAAS is described. • Residence time (τ) formulas were compared for sensitivity (m{sub 0}) in a THGA furnace. • Effects of the sample/platform dimension and dosing hole on τ were assessed. • Theoretical m{sub 0} of 18 analytes were
Electronic structure calculations toward new potentially AChE inhibitors
de Paula, A. A. N.; Martins, J. B. L.; Gargano, R.; dos Santos, M. L.; Romeiro, L. A. S.
2007-10-01
The main purpose of this study was the use of natural non-isoprenoid phenolic lipid of cashew nut shell liquid from Anacardium occidentale as lead material for generating new potentially candidates of acetylcholinesterase inhibitors. Therefore, we studied the electronic structure of 15 molecules derivatives from the cardanol using the following groups: methyl, acetyl, N, N-dimethylcarbamoyl, N, N-dimethylamine, N, N-diethylamine, piperidine, pyrrolidine, and N-benzylamine. The calculations were performed at RHF level using 6-31G, 6-31G(d), 6-31+G(d) and 6-311G(d,p) basis functions. Among the proposed compounds we found that the structures with substitution by acetyl, N, N-dimethylcarbamoyl, N, N-dimethylamine, and pyrrolidine groups were better correlated to rivastigmine indicating possible activity.
2D Tl-Pb compounds on Ge(1 1 1) surface: atomic arrangement and electronic band structure.
Gruznev, D V; Bondarenko, L V; Tupchaya, A Y; Eremeev, S V; Mihalyuk, A N; Chou, J P; Wei, C M; Zotov, A V; Saranin, A A
2017-01-25
Structural transformations and evolution of the electron band structure in the (Tl, Pb)/Ge(1 1 1) system have been studied using low-energy electron diffraction, scanning tunneling microscopy, angle-resolved photoelectron spectroscopy and density functional theory calculations. The two 2D Tl-Pb compounds on Ge(1 1 1), [Formula: see text]-(Tl, Pb) and [Formula: see text]-(Tl, Pb), have been found and their composition, atomic arrangement and electron properties has been characterized. The (Tl, Pb)/Ge(1 1 1)[Formula: see text] compound is almost identical to the alike (Tl, Pb)/Si(1 1 1)[Formula: see text] system from the viewpoint of its atomic structure and electronic properties. They contain 1.0 ML of Tl atoms arranged into a honeycomb network of chained trimers and 1/3 ML of Pb atoms occupying the centers of the honeycomb units. The (Tl, Pb)/Ge(1 1 1)[Formula: see text] compound contains six Tl atoms and seven Pb atoms per [Formula: see text] unit cell (i.e. ∼0.67 ML Tl and ∼0.78 ML Pb). Its atomic structure can be visualized as consisting of Pb hexagons surrounded by Tl trimers. The (Tl, Pb)/Ge(1 1 1)[Formula: see text] and (Tl, Pb)/Ge(1 1 1)[Formula: see text] compounds are metallic and their band structures contain spin-split surface-state bands. By analogy with the (Tl, Pb)/Si(1 1 1)[Formula: see text], these (Tl, Pb)/Ge(1 1 1) compounds are believed to be promising objects for prospective studies of superconductivity in one-atom-layer systems.
2D Tl-Pb compounds on Ge(1 1 1) surface: atomic arrangement and electronic band structure
Gruznev, D. V.; Bondarenko, L. V.; Tupchaya, A. Y.; Eremeev, S. V.; Mihalyuk, A. N.; Chou, J. P.; Wei, C. M.; Zotov, A. V.; Saranin, A. A.
2017-01-01
Structural transformations and evolution of the electron band structure in the (Tl, Pb)/Ge(1 1 1) system have been studied using low-energy electron diffraction, scanning tunneling microscopy, angle-resolved photoelectron spectroscopy and density functional theory calculations. The two 2D Tl-Pb compounds on Ge(1 1 1), \\sqrt{3}× \\sqrt{3} -(Tl, Pb) and 3× 3 -(Tl, Pb), have been found and their composition, atomic arrangement and electron properties has been characterized. The (Tl, Pb)/Ge(1 1 1)\\sqrt{3}× \\sqrt{3} compound is almost identical to the alike (Tl, Pb)/Si(1 1 1)\\sqrt{3}× \\sqrt{3} system from the viewpoint of its atomic structure and electronic properties. They contain 1.0 ML of Tl atoms arranged into a honeycomb network of chained trimers and 1/3 ML of Pb atoms occupying the centers of the honeycomb units. The (Tl, Pb)/Ge(1 1 1)3× 3 compound contains six Tl atoms and seven Pb atoms per 3× 3 unit cell (i.e. ˜0.67 ML Tl and ˜0.78 ML Pb). Its atomic structure can be visualized as consisting of Pb hexagons surrounded by Tl trimers. The (Tl, Pb)/Ge(1 1 1)\\sqrt{3}× \\sqrt{3} and (Tl, Pb)/Ge(1 1 1)3× 3 compounds are metallic and their band structures contain spin-split surface-state bands. By analogy with the (Tl, Pb)/Si(1 1 1)\\sqrt{3}× \\sqrt{3} , these (Tl, Pb)/Ge(1 1 1) compounds are believed to be promising objects for prospective studies of superconductivity in one-atom-layer systems.
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.)
Computational aspects of sensitivity calculations in transient structural analysis
Greene, William H.; Haftka, Raphael T.
1988-01-01
A key step in the application of formal automated design techniques to structures under transient loading is the calculation of sensitivities of response quantities to the design parameters. This paper considers structures with general forms of damping acted on by general transient loading and addresses issues of computational errors and computational efficiency. The equations of motion are reduced using the traditional basis of vibration modes and then integrated using a highly accurate, explicit integration technique. A critical point constraint formulation is used to place constraints on the magnitude of each response quantity as a function of time. Three different techniques for calculating sensitivities of the critical point constraints are presented. The first two are based on the straightforward application of the forward and central difference operators, respectively. The third is based on explicit differentiation of the equations of motion. Condition errors, finite difference truncation errors, and modal convergence errors for the three techniques are compared by applying them to a simple five-span-beam problem. Sensitivity results are presented for two different transient loading conditions and for both damped and undamped cases.
Institute of Scientific and Technical Information of China (English)
Hou Yu-Jun; Cheng Xin-Lu; Chen Heng-Jie
2009-01-01
By correcting some primary parameters in the semi-classical Deutsch-Mark (DM) formula, this paper calculates the absolute single electron-impact ionization cross sections of atoms N, Cu, As, Se, Sn, Sb, Te, I and Pb from threshold to 10000 eV. The calculated cross sections are compared with available experimental data and other theoretical results. An excellent agreement was achieved between the calculated and measured cross sections for these atoms over a wide range of impact energies.
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.
Benhabilès, N; Gallet, X; Thomas-Soumarmon, A; Brasseur, R
1998-01-01
Among different ab initio approaches to calculate 3D-structures of proteins out of primary sequences, a few are using restricted dihedral spaces and empirical equations of energy as is OSIRIS. All those approaches were calibrated on a few proteins or fragments of proteins. To optimize the calculation over a larger diversity of structures, we need first to define for each sequence what are good conditions of calculations in order to choose a consensus procedure fitting most 3D-structures best. This requires objective classification of calculated 3D-structures. In this work, populations of avian and bovine pancreatic polypeptides (APP, BPP) and of calcium-binding protein (CaBP) are obtained by varying the rate of the angular dynamics of the second step of OSIRIS. Then, 3D-structures are clustered using a nonhierarchical method, SICLA, using rmsd as a distance parameter. A good clustering was obtained for four subpopulations of APP, BPP and CaBP. Each subpopulation was characterized by its barycenter, relative frequency and dispersion. For the three alpha-helix proteins, after the step 1 of OSIRIS, most secondary structures were correct but molecules have a few atomic contacts. Step 2, i.e., the angular dynamics, resolves those atomic contacts and clustering demonstrates that it generates subpopulations of topological conformers as the barycenter topologies show.
Ab initio random structure search for 13-atom clusters of fcc elements.
Chou, J P; Hsing, C R; Wei, C M; Cheng, C; Chang, C M
2013-03-27
The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd13 and Au13, we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au13, which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons.
Galvan, D H
2003-01-01
To get insight into the electronic properties of PrFe4P12 skutterudite, band electronic structure calculations, Total and Projected Density of States, Crystal Orbital Overlap Population and Mulliken Population Analysis were performed. The energy bands yield a semi metallic behavior with a direct gap (at gamma) of 0.02 eV. Total and Projected Density of States provided information of the contribution from each orbital of each atom to the total Density of States. Moreover, the bonding strength between some atoms within the unit cell was obtained. Mulliken Population analysis suggests ionic behavior for this compound.
ACRES: An Efficient Method for First-Principles Electronic Structure Calculations of Complex Systems
Energy Technology Data Exchange (ETDEWEB)
WAGHMARE,R.V.; KIM,HANCHUL; PARK,I.J.; MODINE,NORMAND A.; MARAGAKIS,P.; KAXIRAS,EFTHIMIOS
2000-08-29
The authors discuss their new implementation of the Adaptive Coordinate Real-space Electronic Structure (ACRES) method for studying the atomic and electronic structure of infinite periodic as well as finite systems, based on density functional theory. This improved version aims at making the method widely applicable and efficient, using high performance Fortran on parallel architectures. The scaling of various parts of an ACRES calculation is analyzed and compared to that of plane-wave based methods. The new developments that lead to enhanced performance, and their parallel implementation, are presented in detail. They illustrate the application of ACRES to the study of elemental crystalline solids, molecules and complex crystalline materials, such as blue bronze and zeolites.
A near atomic structure of the active human apoptosome
Cheng, Tat Cheung; Hong, Chuan; Akey, Ildikó V; Yuan, Shujun; Akey, Christopher W
2016-01-01
In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease. DOI: http://dx.doi.org/10.7554/eLife.17755.001
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.
The Dependence of All-Atom Statistical Potentials on Structural Training Database
Zhang, Chi; Liu, Song; Zhou, Hongyi; Zhou, Yaoqi
2004-01-01
An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, low-sequence-identity structural databases of 333 α-proteins and 271 β-proteins were built for examining the database dependence of three all-atom statistical energy functions. They are RAPDF (residue-specific all-atom conditional probability discriminatory function), atomic KBP ...
Skachkov, Dmitry; Krykunov, Mykhaylo; Kadantsev, Eugene; Ziegler, Tom
2010-05-11
We present here a method that can calculate NMR shielding tensors from first principles for systems with translational invariance. Our approach is based on Kohn-Sham density functional theory and gauge-including atomic orbitals. Our scheme determines the shielding tensor as the second derivative of the total electronic energy with respect to an external magnetic field and a nuclear magnetic moment. The induced current density due to a periodic perturbation from nuclear magnetic moments is obtained through numerical differentiation, whereas the influence of the responding perturbation in terms of the external magnetic field is evaluated analytically. The method is implemented into the periodic program BAND. It employs a Bloch basis set made up of Slater-type or numeric atomic orbitals and represents the Kohn-Sham potential fully without the use of effective core potentials. Results from calculations of NMR shielding constants based on the present approach are presented for isolated molecules as well as systems with one-, two- and three-dimensional periodicity. The reported values are compared to experiment and results from calculations on cluster models.
Siretanu, Igor; van den Ende, Dirk; Mugele, Frieder
2016-04-21
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 dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces.
Pawlak, Remy; Klinovaja, Jelena; Meier, Tobias; Kawai, Shigeki; Glatzel, Thilo; Loss, Daniel; Meyer, Ernst
2015-01-01
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 localization of MBSs is a key feature and 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 tunneling microscopy (STM) and atomic force microscopy (AFM). We demonstrate that the Fe chains are mono-atomic, structured in a linear fashion, and exhibit zero-bias conductance peaks at their ends which we interprete as signature for a Majorana bound state. Spatially resolved conductance maps of the atomic chains reveal that the MBSs are well localized at the chain ends (below 25 nm), with two localization lengths as predicted by theory. Our observation lends strong support to use MBSs in Fe chains as qubits for quantum computing devices.
Voronoi analysis of the short-range atomic structure in iron and iron-carbon melts
Sobolev, Andrey; Mirzoev, Alexander
2015-08-01
In this work, we simulated the atomic structure of liquid iron and iron-carbon alloys by means of ab initio molecular dynamics. Voronoi analysis was used to highlight changes in the close environments of Fe atoms as carbon concentration in the melt increases. We have found, that even high concentrations of carbon do not affect short-range atomic order of iron atoms — it remains effectively the same as in pure iron melts.
Institute of Scientific and Technical Information of China (English)
XIE Wen-Fang
2006-01-01
@@ Making use of the adiabatic hyperspherical approach, we report a calculation for the energy spectrum of the ground and low-excited states of the confined helium atom in a spherical parabolic well. We find that the energies of a spherical parabolic well are in good agreement with those of an impenetrable spherical box for the larger confined potential radius. However, the energy values of a spherical parabolic well are much lower than those of an impenetrable spherical box for small values of re. We also find that the confinement may cause accidental degeneracies between levels with different low-excited states and the inversion of the energy values.
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.
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.
Molecular Structure, Theoretical Calculation and Thermodynamic Properties of Tebuconazole
Institute of Scientific and Technical Information of China (English)
MA Haixia; SONG Jirong; HUANG Ting; LU Xingqiang; XU Kangzhen; SUN Xiaohong
2009-01-01
Single crystals of 5-(4-chlorophenyl)-2,2-dimethyl-3-(1,2,4-triazol-1-ylmethyl)-pentom-3-ol (tebuconazole) were obtained in toluene. The single-crystal X-ray diffraction studies showed that it crystallized in the monoclinic system, with space group P2(1)/c and crystal parameters of a= 1.1645(1) nm, b= 1.6768(2) nm, c= 1.7478(2) nm,β=92.055(2)°, Dc= 1.199 g/cm3, Z=4 and F(000)= 1312. Density functional theory (DFT) B3LYP was employed to optimize the structure and calculate the frequencies of tebuconazole. The calculated geometrical parameters are close to the corresponding experimental ones. The specific heat capacity of the title compound was determined with continuous Cp mode of a mircocalorimeter. In the determining temperature range from 283 to 353 K, the special heat capacity of the title compound presents good linear relation with temperature. Using the determined relation-ship of Cp with temperature T, thermodynamic functions (enthalpy, entropy and Gibbs free energy) of the title compound between 283 and 353 K, relative to the standard temperature 298.15 K, were derived through thermody-namic relationship.
Gradient type optimization methods for electronic structure calculations
Zhang, Xin; Wen, Zaiwen; Zhou, Aihui
2013-01-01
The density functional theory (DFT) in electronic structure calculations can be formulated as either a nonlinear eigenvalue or direct minimization problem. The most widely used approach for solving the former is the so-called self-consistent field (SCF) iteration. A common observation is that the convergence of SCF is not clear theoretically while approaches with convergence guarantee for solving the latter are often not competitive to SCF numerically. In this paper, we study gradient type methods for solving the direct minimization problem by constructing new iterations along the gradient on the Stiefel manifold. Global convergence (i.e., convergence to a stationary point from any initial solution) as well as local convergence rate follows from the standard theory for optimization on manifold directly. A major computational advantage is that the computation of linear eigenvalue problems is no longer needed. The main costs of our approaches arise from the assembling of the total energy functional and its grad...
DEFF Research Database (Denmark)
Johnsen, Kristinn; Yngvason, Jakob
1996-01-01
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...
Atomic structure of water/Au, Ag, Cu and Pt atomic junctions.
Li, Yu; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu
2017-02-08
Much progress has been made in understanding the transport properties of atomic-scale conductors. We prepared atomic-scale metal contacts of Cu, Ag, Au and Pt using a mechanically controllable break junction method at 10 K in a cryogenic vacuum. Water molecules were exposed to the metal atomic contacts and the effect of molecular adsorption was investigated by electronic conductance measurements. Statistical analysis of the electronic conductance showed that the water molecule(s) interacted with the surface of the inert Au contact and the reactive Cu ant Pt contacts, where molecular adsorption decreased the electronic conductance. A clear conductance signature of water adsorption was not apparent at the Ag contact. Detailed analysis of the conductance behaviour during a contact-stretching process indicated that metal atomic wires were formed for the Au and Pt contacts. The formation of an Au atomic wire consisting of low coordination number atoms leads to increased reactivity of the inert Au surface towards the adsorption of water.
Time-dependent second Born calculations for model atoms and molecules in strong laser fields
Balzer, K; Bonitz, M
2010-01-01
Using the finite-element discrete variable representation of the nonequilibrium Green's function (NEGF) we extend previous work [K.~Balzer et al., Phys. Rev. A \\textbf{81}, 022510 (2010)] to nonequilibrium situations and compute---from the two-time Schwinger-Keldysh-Kadanoff-Baym equations---the response of the helium atom and the heteronuclear molecule lithium hydride to laser fields in the uv and xuv regime. In particular, by comparing the one-electron density and the dipole moment to time-dependent Hartree-Fock results on one hand and the full solution of the time-dependent Schr\\"odinger equation on the other hand, we demonstrate that the time-dependent second Born approximation carries valuable information about electron-electron correlation effects. Also, we outline an efficient distributed memory concept which enables a parallel and well scalable algorithm for computing the NEGF in the two-time domain.
Energy Technology Data Exchange (ETDEWEB)
Shamim, Md; Harbola, Manoj K, E-mail: sami@iitk.ac.i, E-mail: mkh@iitk.ac.i [Department of Physics, Indian Institute of Technology, Kanpur 208 016 (India)
2010-11-14
Transition energies of a new class of excited states (two-gap systems) of various atoms are calculated in time-independent density functional formalism by using a recently proposed local density approximation exchange energy functional for excited states. It is shown that the excitation energies calculated with this functional compare well with those calculated with exact exchange theories.
Topography and Atomic Structure Investigations Of (100 Cleavage Surface of In4Se3 Layered Crystals
Directory of Open Access Journals (Sweden)
P.V. Galiy
2014-06-01
Full Text Available The atomic microstructure and crystallography of (100 surfaces of In4Se3 layered crystals obtained by cleavage in situ were studied by the methods of scanning tunneling and atomic force microscopies (STM, AFM and low energy electron diffraction (LEED for reflection. The obtained results indicate the existence of periodic corrugated structures on the cleavage surface. It is shown that (100 In4Se3 cleavage surface is structurally stable and doesn't undergo reconstruction in a wide temperature range of 77-295 K. The anisotropy of thermal expansion along the main crystallography directions in the (100 In4Se3 cleavage plane has been shown. The evaluation of the two-dimensional lattice constant in the cleavage (100 surface plane of orthorhombic In4Se3 layered crystal was done. The calculated values of the lattice constants in consequence of LEED study, such as b 11,475 Å and c 3,734 Å, coincide well with those obtained by the AFM and STM (b 13-14 Å and c 4 Å, and correlate, within the errors limits, with the corresponding values obtained by X-ray diffraction (b 12,308(1 Å and c 4,0810(5 Å. Besides, the obtained results of cleavage surface structure studies show the correctness of filtering application concerning topography images and indicate the adequacy of the model used for calculations of the cleavage (100 surfaces lattice constants of In4Se3 in accordance with the LEED results. The influence of the LEED experimental module structure on the results has been considered.
Calculated dipole moment and energy in collision of a hydrogen molecule and a hydrogen atom
Patch, R. W.
1973-01-01
Calculations were carried out using three Slater-type 1s orbitals in the orthogonalized valencebond theory of McWeeny. Each orbital exponent was optimized, the H2 internuclear distance was varied from 7.416 x 10 to the -11th power to 7.673 x 10 to the -11th power m (1.401 to 1.450 bohrs). The intermolecular distance was varied from 1 to 4 bohrs (0.5292 to 2.117 x 10 to the 10th power). Linear, scalene, and isosceles configurations were used. A weighted average of the interaction energies was taken for each intermolecular distance. Although energies are tabulated, the principal purpose was to calculate the electric dipole moment and its derivative with respect to H2 internuclear distance.
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.
Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas
2015-08-07
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.
Energy Technology Data Exchange (ETDEWEB)
Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas [Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn (Germany)
2015-08-07
methods 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.
Institute of Scientific and Technical Information of China (English)
Haijiang LIU; Shaoqing WANG; An DU; Caibei ZHANG
2004-01-01
The results of molecular dynamics calculations on the interfacial energies and atomic structures of Ag/Ni and Cu/Ni interaces are presented. Calculation on Ag/Ni interfaces with low-index planes shows that those containing the (111) plane have the lowest energies, which is in agreement with the experiments. Comparing surface energy with interracial energy, it is found the order of the interfacial energies of Ag/Ni and Cu/Ni containing the planes fall in the same order as solid-vapor surface energies of Ag, Cu and Ni. In this MD simulation, the relaxed atomic structure and dislocation network of (110)Ag||(110)Ni interface are coincident to HREM observations.
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.
Institute of Scientific and Technical Information of China (English)
何刚; 戎咏华; 徐祖耀
2000-01-01
The stacking fault energies of five fcc metals (Cu, Ag, Au, Ni and Al) with various quan-tivalences have been calculated by embedded-atom method (EAM). It indicated that the stacking fault energy is mainly determined by the metallic bond-energy and the lattice constant. Thus, monovalent fcc metals should have different stacking fault energies, contrary to Attree’s conclusion. The interaction energy between stacking faults one I 111 I layer apart in a fcc metal is found to be 1/40-1/250 of its self-energy, while it becomes zero when the two stacking faults are two layers apart. The twin energy is just half of the energy of intrinsic stacking fault energy without the consideration of lattice relaxation and the energy of a single intrinsic stacking fault is almost the same as that of extrinsic stacking fault, which are consistent with the results from the calculation of Lennard-Jones force between atoms, but differ from Attree’s result.
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.
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.
Ammar, H Y; Eid, Kh M
2013-10-01
The interactions of nitrogen dioxide molecule (NO2) on Au atom adsorbed on the surfaces of metal oxide MgO (100) on both anionic (O2-) and defect (F(s) and F(s)(+)-centers) sites have been studied using the Density Functional Theory (DFT) in combination with embedded cluster model. The adsorption energies of NO2 molecule (N-down as well as O-down) on O(-2), F(s) and F(s)(+)-sites were considered. Full optimization for the additive materials and partial optimization for MgO substrate surfaces have been done. The formation energies were evaluated for F(s) and F(s)(+) of MgO substrate surfaces. Some parameters, the Ionization Potential (IP) and electron Affinity (eA), for defect free and defect containing surfaces have been calculated. The interaction properties of NO2 have been analyzed in terms of the adsorption energy, the electron donation (basicity), the elongation of N-O bond length and the charge distribution by using Natural Bond Orbital (NBO) analysis. The adsorption properties were examined by calculation of the Density of State (DOS). The presence of the Au atom increases the surface chemistry of the anionic O(2-)-site of MgO substrate surfaces. On the other hand, the presence of the Au atom decreases the surface chemistry of the F(s) and F(s)(+)-sites of MgO substrate surfaces. Generally, the NO2 molecule is strongly adsorbed (chemisorption) on the MgO substrate surfaces containing F(s) and F(s)(+)-centers.
Institute of Scientific and Technical Information of China (English)
G(U)M(U)(S), Sedat; (O)ZDO(G)AN, Telhat
2004-01-01
Hartree-Fock-Roothaan (HFR) calculations for ground states of some atoms, i.e. He, Be, Ne, Ar, and Kr have been performed using minimal basis sets of Slater type orbitals (STOs) with integer and noninteger principal quantum numbers (integer n-STOs and noninteger n-STOs). The obtained total energies for these atoms using minimal basis sets of integer n-STOs are in good agreement with those in the previous literature. On the other hand, for the case of minimal basis sets of noninteger n-STOs, although the calculated total energies of these atoms agree well with the results in literature, some striking results have been obtained for atoms Ar and Kr. Our computational results for the energies of atoms Ar and Kr are slightly better than those in literature, by amount of 0.00222 and 0.000054 a.u., respectively. The improvement in the energies of atoms Ar and Kr may result from the efficient calculations of one-center two-electron integrals over noninteger n-STOs. For some atomic ions in their ground state,HFR calculations have been carried out using minimal basis sets of noninteger n-STOs. The obtained total energies for these atomic ions are substantially lower than those available in literature.
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.
Luo, M.; Shen, Y. H.; Yin, T. L.
2017-02-01
The magnetic properties of different transition-metal (TM) atoms (TM=Co, Cu, Mn, Fe, and Ni) adsorption on SiC monolayer are investigated using density functional theory (DFT). Magnetism appears in the cases of Co, Cu, Mn, and Fe. Among all the magnetic cases, the Co-adsorbed system has the most stable structure. Therefore, we further study the interaction in the two-Co-adsorbed system. Our results show that the interaction between two Co atoms is always FM and the p-d hybridization mechanism results in such ferromagnetic states. However, the FM interaction is obviously depressed by the increasing Co-Co distance, which could be well explained by the Zener-RKKY theory. Moreover, different magnetic behavior is observed in the two-Mn-adsorbed system and a long-range AFM state is showing. Such multiple magnetic properties may suggest promising applications of TM-adsorbed SiC monolayer in the future.
Brown, R. L.; Laufer, A. H.
1981-01-01
Activation energies are calculated by the bond-energy-bond-order (BEBO) and the bond-strength-bond-length (BSBL) methods for the reactions of C2H radicals with H2, CH4, and C2H6 and for the reactions of CN radicals with H2 and CH4. The BSBL technique accurately predicts the activation energies for these reactions while the BEBO method yields energies averaging 9 kcal higher than those observed. A possible reason for the disagreement is considered.
Synthesis, Crystal Structural Investigations, and DFT Calculations of Novel Thiosemicarbazones
Directory of Open Access Journals (Sweden)
Brian J. Anderson
2016-02-01
Full Text Available The crystal and molecular structures of three new thiosemicarbazones, 2-[1-(2-hydroxy-5-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide monohydrate (1, 2-[1-(2-hydroxy-5-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide (2 and 2-[1-(2-hydroxy-4-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide acetonitrile solvate (3, are reported and confirmed by single crystal X-ray diffraction, NMR and UV-vis spectroscopic data. Compound (1, C11H15N3O2S·H2O, crystallizes in the monoclinic with space group P21/c, with cell parameters a = 8.2304(3 Å, b = 16.2787(6 Å, c = 9.9708(4 Å, and β = 103.355(4°. Compound (2, C12H17N3O2S, crystallizes in the C2/c space group with cell parameters a = 23.3083(6 Å, b = 8.2956(2 Å, c = 13.5312(3 Å, β = 91.077(2°. Compound (3, C11H15N3O2S·C2H3N, crystallizes in the triclinic P-1 space group with cell constants a = 8.9384(7 Å, b = 9.5167(8 Å, c = 10.0574(8 Å, α = 110.773(7°, β = 92.413(6°, and γ = 90.654(7°. DFT B3LYP/6-31(G geometry optimized molecular orbital calculations were also performed and frontier molecular orbitals of each compound are displayed. The correlations between the calculated molecular orbital energies (eV for the surfaces of the frontier molecular orbitals to the electronic excitation transitions from the absorption spectra of each compound have been proposed. Additionally, similar correlations observed among three closely related compounds, (4, 2-[1-(2-hydroxy-4-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide, (5, 2-[1-(2-hydroxy-6-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide acetonitrile monosolvate and (6, 2-[1-(2-hydroxy-6-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide, examining structural differences from the substitution of the methoxy group from the phenyl ring (4, 5, or 6 position and the substitution of the terminal amine (methyl or ethyl to their frontier molecular orbital surfaces and from their Density Functional
Energy Technology Data Exchange (ETDEWEB)
Lobato, I; Rojas, J [Instituto Peruano de EnergIa Nuclear, Avenida Canada 1470, Lima 41 (Peru); Landauro, C V; Torres, J [Facultad de Ciencias Fisicas, Universidad Nacional Mayor de San Marcos, P.O. box 14-0149, Lima 14 (Peru)], E-mail: jrojast@unmsm.edu.pe
2009-02-04
The structural evolution and dynamics of silver nanodrops Ag{sub 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 x 10{sup 13} K s{sup -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 x 10{sup 12} K s{sup -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.
Lobato, I.; Rojas, J.; Landauro, C. V.; Torres, J.
2009-02-01
The structural evolution and dynamics of silver nanodrops Ag2869 (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 × 1013 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 × 1012 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.
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)
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.
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
Based on the theory of micro-inhomogeneity of liquid metal,a calculation model is established for the quantitative description of the structural information of metal melts.Only by thermophysical property parameters and basic structural parameters of solid metal,can this model produce the main information of melt structure,including the relative concentration of active atoms,size of atomic clusters and number of short-range order atoms.Based on this model,the main structural information of Al and Ni melts in the not high range above the liquidus is calculated,with results in good agreement with experimental values.Besides,analyzed is the influence of superheating temperature and atomic number on the melt structural information of the first (IA) and second main group (IIA) elements.With temperature increasing,melt structural information regularly changes for both IA and IIA elements.With the atomic number increasing,melt structural information of IA elements changes regularly,for the crystal structures of the IA elements are all of bcc lattice type.However,no notable regular change of melt structural information for IIA elements has been found,mainly because the lattice type of IIA elements is of hcp-fcc-bcc transition.The present work presents an effective way for better understanding metal melt structure and for forecasting the change of the physical property of metal melts.
Analysis of Nanometer Structure for Chromium Atoms in Gauss Standing Laser Wave
Institute of Scientific and Technical Information of China (English)
ZHANG Wen-Tao; ZHU Bao-Hua; XIONG Xian-Ming
2010-01-01
@@ The equation of motion of two-level chromium atoms in Gauss standing laser wave is discussed and the distribution of chromium atoms is given under different transverse velocity conditions.The results show that the focusing position of atoms will be affected by the transverse velocity of atoms.Based on the four-order Runge-Kutta method,the locus of chromium atoms in Gauss standing laser wave is simulated.The three-dimensional characteristics of nanometer structures are stimulated under perfect and emanative conditions.
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)
Helmich, Benjamin; Sierka, Marek
2012-01-15
An algorithm for similarity recognition of molecules and molecular clusters is presented which also establishes the optimum matching among atoms of different structures. In the first step of the algorithm, a set of molecules are coarsely superimposed by transforming them into a common reference coordinate system. The optimum atomic matching among structures is then found with the help of the Hungarian algorithm. For this, pairs of structures are represented as complete bipartite graphs with a weight function that uses intermolecular atomic distances. In the final step, a rotational superposition method is applied using the optimum atomic matching found. This yields the minimum root mean square deviation of intermolecular atomic distances with respect to arbitrary rotation and translation of the molecules. Combined with an effective similarity prescreening method, our algorithm shows robustness and an effective quadratic scaling of computational time with the number of atoms.
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.
Relativistic all-order calculations of Th, Th$^{+}$ and Th$^{2+}$ atomic properties
Safronova, M S; Clark, Charles W
2014-01-01
Excitation energies, term designations, and $g$-factors of Th, Th$^{+}$ and Th$^{2+}$ are determined using a relativistic hybrid configuration interaction (CI) + all-order approach that combines configuration interaction and linearized coupled-cluster methods. The results are compared with other theory and experiment where available. We find some "vanishing" $g$-factors, similar to those known in lanthanide spectra. Reduced matrix elements, oscillator strengths, transition rates, and lifetimes are determined for Th$^{2+}$. To estimate the uncertainties of our results, we compared our values with the available experimental lifetimes for higher $5f7p\\ ^3G_{4}$, $7s7p\\ ^3P_{0}$, $7s7p\\ ^3P_{1}$, and $6d7p\\ ^3F_{4}$ levels of Th$^{2+}$. These calculations provide a benchmark test of the CI+all-order method for heavy systems with several valence electrons and yield recommended values for transition rates and lifetimes of Th$^{2+}$.
Douberly, G E; Ricks, A M; Ticknor, B W; Duncan, M A
2008-02-07
The infrared photodissociation spectra (IRPD) in the 700 to 4000 cm(-1) region are reported for H+ (CO2)n clusters (n = 1-4) and their complexes with argon. Weakly bound Ar atoms are attached to each complex upon cluster formation in a pulsed electric discharge/supersonic expansion cluster source. An expanded IRPD spectrum of the H+ (CO2)Ar complex, previously reported in the 2600-3000 cm(-1) range [Dopfer, O.; Olkhov, R.V.; Roth, D.; Maier, J.P. Chem. Phys. Lett. 1998, 296, 585-591] reveals new vibrational resonances. For n = 2 to 4, the vibrational resonances involving the motion of the proton are observed in the 750 to 1500 cm(-1) region of the spectrum, and by comparison to the predictions of theory, the structure of the small clusters are revealed. The monomer species has a nonlinear structure, with the proton binding to the lone pair of an oxygen. In the dimer, this nonlinear configuration is preserved, with the two CO2 units in a trans configuration about the central proton. Upon formation of the trimer, the core CO2 dimer ion undergoes a rearrangement, producing a structure with near C2v symmetry, which is preserved upon successive CO2 solvation. While the higher frequency asymmetric CO2 stretch vibrations are unaffected by the presence of the weakly attached Ar atom, the dynamics of the shared proton motions are substantially altered, largely due to the reduction in symmetry of each complex. For n = 2 to 4, the perturbation due to Ar leads to blue shifts of proton stretching vibrations that involve motion of the proton mostly parallel to the O-H+-O axis of the core ion. Moreover, proton stretching motions perpendicular to this axis exhibit smaller shifts, largely to the red. Ab initio (MP2) calculations of the structures, complexation energies, and harmonic vibrational frequencies are also presented, which support the assignments of the experimental spectra.
Nagabalasubramanian, P B; Periandy, S; Karabacak, Mehmet; Govindarajan, M
2015-06-15
The solid phase FT-IR and FT-Raman spectra of 4-vinylcyclohexene (abbreviated as 4-VCH) have been recorded in the region 4000-100cm(-1). The optimized molecular geometry and vibrational frequencies of the fundamental modes of 4-VCH have been precisely assigned and analyzed with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method at 6-311++G(d,p) level basis set. The theoretical frequencies were properly scaled and compared with experimentally obtained FT-IR and FT-Raman spectra. Also, the effect due the substitution of vinyl group on the ring vibrational frequencies was analyzed and a detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated total energy distribution (TED). The time dependent DFT (TD-DFT) method was employed to predict its electronic properties, such as electronic transitions by UV-Visible analysis, HOMO and LUMO energies, molecular electrostatic potential (MEP) and various global reactivity and selectivity descriptors (chemical hardness, chemical potential, softness, electrophilicity index). Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Atomic charges obtained by Mulliken population analysis and NBO analysis are compared. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are also calculated.
Orbital-Free Density Functional Theory for Molecular Structure Calculations
Institute of Scientific and Technical Information of China (English)
Huajie Chen; Aihui Zhou
2008-01-01
We give here an overview of the orbital-free density functional theory that is used for modeling atoms and molecules. We review typical approximations to the kinetic energy, exchange-correlation corrections to the kinetic and Hartree energies, and constructions of the pseudopotentials. We discuss numerical discretizations for the orbital-free methods and include several numerical results for illustrations.
Sun, Y Y; Kim, Yong-Hyun; Lee, Kyuho; Zhang, S B
2008-10-21
Density functional theory (DFT) in the commonly used local density or generalized gradient approximation fails to describe van der Waals (vdW) interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential (LAP) approach, named DFT+LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD(T). Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database [P. Jurecka et al. Phys. Chem. Chem. Phys. 8, 1985 (2006)], which provides the interaction energies of CCSD(T) quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/mol. The DFT+LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.
Semiempirical studies of atomic structure. Progress report, 1 July 1991--1 October 1993
Energy Technology Data Exchange (ETDEWEB)
Curtis, L.J.
1993-10-01
Atomic structure/properties of highly ionized many-electron systems are studied using sensitive semiempirical data systematization, experiment, and theory. Measurements are made using fast ion beams, combined with data from laser- and tokamak-produced plasmas, astrophysical sources, and light sources. Results during this 3-y period are discussed under the following headings: Invited review article (decay rates in systems of negative ions to very heavy one-electron ions), fast ion beam lifetime measurements (Pt sequence, neutral carbon, Na sequence), multiplexed decay curve measurements, multiplexed decay curve measurements (lifetimes of alkali-like resonance transitions, spin-forbidden intercombination lines), lifetimes in Ne sequence, lifetimes for H and He sequences, data-based semiempirical formulations, calculations, and accelerator studies.
A DFT study of atomic structure and adhesion at the Fe(BCC)/Fe3O4 interfaces
Forti, M. D.; Alonso, P. R.; Gargano, P. H.; Balbuena, P. B.; Rubiolo, G. H.
2016-05-01
The adhesion at Fe/Fe3O4 interface is one of the critical pieces of information that is often lacking upon designing the protective magnetite layer on the inner surfaces of carbon steel piping or upon modeling the scale removal mechanism for optimization of industrial descaling of the wire or strip surface of carbon steel after hot rolling process. In this context, we have performed ab initio DFT calculations to determine the atomic structure, work of separation (γ), and bonding character of the Fe(001)/Fe3O4(001) interface. Three candidate interface geometries were considered, including Fe and FeO2 terminations of the oxide. The minimization of the forces resulted in substantial changes to the atomic structure of the metal and oxide layer at both side of the interface, and also of the subsurface layer of the oxide in the case of Fe-terminated oxide slab. Moreover, the relaxation of the geometry in one of the two considered Fe-terminated oxide interface leads to completely unstable interface structures. By applying several methods of analysis, we have thoroughly characterized the electronic structure and have determined that the dominant bonding mechanism is the metallic-ionic interaction between the iron atoms of both metal and oxide slabs. Our calculations predict γ ≈ 1.42 J/m2 regardless of the interfacial stoichiometry.
Structural properties of Al and TiAl3 metallic glasses — An embedded atom method study
Tahiri, M.; Trady, S.; Hasnaoui, A.; Mazroui, M.; Saadouni, K.; Sbiaai, K.
2016-06-01
In this paper, we investigated the structural properties of metallic glasses (MGs). We emphasized our study on monatomic Al and binary TiAl3 systems. The calculations are performed by using the molecular dynamics (MD) simulation based on semi-empirical many-body potentials derived from the embedded atom method. The structure is analyzed using the radial distribution function (RDF), the common neighbor analysis (CNA) and the coordination numbers (CNs). Our results demonstrated that it is possible to form MGs in both systems upon fast cooling from the liquid state. This is confirmed by the fact that the system energy and/or volume during the cooling stage decrease continuously with a slight change and by atomic scale analysis using the RDF, CNA and CN analyzing techniques. Furthermore, this specific study shows that under the same conditions, the icosahedral structures appeared in TiAl3 are more abundant than in pure Al. Implications of these findings are discussed.
Institute of Scientific and Technical Information of China (English)
杨忠志; 沈尔忠
1995-01-01
On the basis of electronegativity expressed in density functional theory and electronegativity equalization principle, a new scheme for calculating the atomic charges in a molecule has been proposed and designed, which gives a new scale of the atomic electronegativity and hardness in a certain molecular environment and takes the harmonic mean electronegativity as a reference value of the molecular electronegativity so that the multiple-regression and nonuniform parameters in the original method are avoided. This approach can be easily and widely applied to the calculation of atomic charges for a big molecule and quite good results of atomic charges in some illustrated molecules are obtained as compared with those from the ab initio STO-3G SCF calculations.
Structure of the electron momentum density of atomic systems
Energy Technology Data Exchange (ETDEWEB)
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.
Energy Technology Data Exchange (ETDEWEB)
Ilyasov, V.V., E-mail: viily@mail.ru; Pham, Khang D., E-mail: dinhkhang307@gmail.com; Holodova, O.M.; Ershov, I.V., E-mail: thijd@mail.ru
2015-10-01
We have performed ab initio simulation of oxygen atom adsorption on TiC(0 0 1) laser-reconstructed surface. Relaxed atomic structures of the O/Ti{sub x}C{sub y}(0 0 1) surface observed upon thermal impact have been studied. DFT calculations of their thermodynamic, electronic, and elastic properties have been carried out. For the first time we have established the bond length and adsorption energy for various reconstructions of the O/Ti{sub x}C{sub y}(0 0 1) surface atomic structure. We have examined the effects of the oxygen adatom upon the band and electron spectra of the O/TiC(0 0 1) surface in its various reconstructions. For the first time we have established a correlation between the energy level of flat bands (−5.4 eV and −5.8 eV) responsible for the doublet of singular peaks of partial densities of oxygen 2p electrons, and the adsorption energy of oxygen atom in non-stoichiometric O/TiC{sub y}(0 0 1) systems. Effective charges of titanium and carbon atoms surrounding the oxygen adatom in various reconstructions have been identified. We have established charge transfer from titanium atom to oxygen and carbon atoms determined by the reconstruction of local atomic and electron structures which correlate with atomic electronegativity values and chemisorption processes. Potential mechanisms for laser nanostructuring of titanium carbide surface have been suggested.
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.
Ding, Yi; Wang, Yanli
2016-08-17
Germanium monochalcogenides, i.e. GeS and GeSe sheets, are isoelectronic analogues of phosphorene, which have been synthesized in recent experiments (P. Ramasamy et al., J. Mater. Chem. C, 2016, 4, 479). Utilizing first-principles calculations, we have investigated their tunable electronic and magnetic properties via light non-metallic atom (B, C, N, O, Si, P, S) functionalization. We find that on these GeS and GeSe sheets O and S adatoms prefer to locate at the top site above the Ge atom, while the other ones like to occupy the anion site, which push the original S/Se atom to the hollow site instead. O and S adatoms slightly affect the semiconducting behaviour of the doped systems, while B, C, N, Si, P ones will drastically modify their band structures and induce versatile spintronic properties. Through the supercell calculations, B and C adatoms are found to induce a bipolar semiconducting behaviour in the decorated systems, while the N/P adatom will cause a spin-gapless-semiconducting/nearly-half-metallic feature in them. The B/C/N/Si/P-substituted GeS/GeSe sheet can be formed by removing the hollow-site S/Se atom from the adatom-decorated structures, which exhibit an opposite semiconducting/metallic behaviour to their phosphorene counterparts. A general odd-even rule is proposed for this phenomenon, which shows that an odd (even) number of valence electron difference between the substitution and host atoms would cause a metallic (semiconducting) feature in the substituted systems. Our study demonstrates that atom functionalization is an efficient way to tailor the properties of GeS and GeSe nanosheets, which have adaptable electronic properties for potential applications in nanoelectronics and spintronics.
Wang, Junmin; Guo, Shanlong; Ge, Yulong; Cheng, Yongjie; Yang, Baodong; He, Jun
2014-05-01
Magic wavelength optical-dipole trap (ODT) allows confinement of neutral atoms and cancellation of the position-dependent spatially inhomogeneous differential light shift for a desired atomic transition. The light shift of the 87Rb 5P3/2 state can be expediently tailored to be equal to that of the 87Rb 5S1/2 state by employing dicromatic (λ1 + λ2 (here λ2 = 2λ1 ˜ 1.5 µm)) linearly polarized ODT lasers. In our calculation, two sets of state-insensitive dichromatic (784.3 + 1568.6 nm and 806.4 + 1612.8 nm) are obtained for the 87Rb 5S1/2 (F = 2) - 5P3/2 (F‧ = 3) transition. Further, 784.3 + 1568.6 nm dicromatic laser system with a moderate output power has been realized experimentally by marrying efficient second-harmonic generation using a PPMgO:LN bulk crystal with a fibre-amplified 1.5 µm telecom laser.
Model creation and electronic structure calculation of amorphous hydrogenated boron carbide
Belhadj Larbi, Mohammed
Boron-rich solids are of great interest for many applications, particularly, amorphous hydrogenated boron carbide (a-BC:H) thin films are a leading candidate for numerous applications such as: heterostructure materials, neutron detectors, and photovoltaic energy conversion. Despite this importance, the local structural properties of these materials are not well-known, and very few theoretical studies for this family of disordered solids exist in the literature. In order to optimize this material for its potential applications the structure property relationships need to be discovered. We use a hybrid method in this endeavor---which is to the best of our knowledge the first in the literature---to model and calculate the electronic structure of amorphous hydrogenated boron carbide (a-BC:H). A combination of classical molecular dynamics using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and ab initio quantum mechanical simulations using the Vienna ab initio simulation package (VASP) have been conducted to create geometry optimized models that consist of a disordered hydrogenated twelve-vertex boron carbide icosahedra, with hydrogenated carbon cross-linkers. Then, the density functional theory (DFT) based orthogonalized linear combination of atomic orbitals (OLCAO) method was used to calculate the total and partial density of states (TDOS, PDOS), the complex dielectric function epsilon, and the radial pair distribution function (RPDF). The RPDF data stand as predictions that may be compared with future experimental electron or neutron diffraction data. The electronic structure simulations were not able to demonstrate a band gap of the same nature as that seen in prior experimental work, a general trend of the composition-properties relationship was established. The content of hydrogen and boron was found to be directly proportional to the decrease in the number of available states near the fermi energy, and inversely proportional to the
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
Kawai, Shigeki; Sadeghi, Ali; Xu, Feng; Feng, Xu; Peng, Lifen; Lifen, Peng; Pawlak, Rémy; Glatzel, Thilo; Willand, Alexander; Orita, Akihiro; Otera, Junzo; Goedecker, Stefan; Meyer, Ernst
2013-10-22
State-of-the art experimental techniques such as scanning tunneling microscopy have great difficulties in extracting detailed structural information about molecules adsorbed on surfaces. By combining atomic force microscopy and Kelvin probe force microscopy with ab initio calculations, we demonstrate that we can obtain a wealth of detailed structural information about the molecule itself and its environment. Studying an FFPB molecule on a gold surface, we are able to determine its exact location on the surface, the nature of its bonding properties with neighboring molecules that lead to the growth of one-dimensional strips, and the internal torsions and bendings of the molecule.
Energy Technology Data Exchange (ETDEWEB)
Yilmaz, Emel Maden; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)
2015-09-15
An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.
Johnston, Karen; Verho, Tuukka; Puska, Martti J
2010-01-01
Several dissociated and two non-dissociated adsorption structures of the phenol molecule on the Si(001)-(2 \\times 1) surface are studied using density functional theory with various exchange and correlation functionals. The relaxed structures and adsorption energies are obtained and it is found that the dissociated structures are energetically more favourable than the non-dissociated structures. However, the ground state energies alone do not determine which structure is obtained experimentally. To elucidate the situation core level shift spectra for Si 2p and C 1s states are simulated and compared with experimentally measured spectra. Several transition barriers were calculated in order to determine which adsorption structures are kinetically accessible. Based on these results we conclude that the molecule undergoes the dissociation of two hydrogen atoms on adsorption.
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.
Directory of Open Access Journals (Sweden)
Naichao Chen
2011-01-01
Full Text Available The focus of this paper is on the adsorption of unsaturated hydrocarbon molecules on β-SiC (111 surfaces during diamond film growth. The CHx and C2Hx molecules have been investigated to obtain a specific insight into absorbing diamond processes on the atomic scale. Structural and electronic properties of CHx and C2Hx adsorption on the Si- and C-terminated surfaces have been studied by first-principles calculations based on density functional theory (DFT. From the calculated energetics and geometries, we find that C2Hx adsorption on the Si-terminated surfaces has six possible surface reconstructions. For the C-terminated surface, there exist eight possible surface reconstructions. Five surface reconstructions, including CH2 adsorption on the Si- and C-terminated surface, CH–CH2 and CH=CH2 adsorption on the C-terminated surface, and C2H5 adsorption on the Si-terminated surface, have the largest hydrogen adsorption energies and more stability of surface reconstructions. Calculations demonstrate that the Si-terminated surface is energetically more favorable for fabricating CVD diamond coatings than the C-terminated surface.
Heyrovska, Raji
2008-01-01
Recently, the bond lengths of the molecular components of nucleic acids and of caffeine and related molecules were shown to be sums of the appropriate covalent radii of the adjacent atoms. Thus, each atom was shown to have its specific contribution to the bond length. This enabled establishing their atomic structures for the first time. In this work, the known bond lengths for amino acids and the peptide bond are similarly shown to be sums of the atomic covalent radii. Based on this result, the atomic structures of glycine, alanine and serine and their tripeptide have been presented.
Bramley, Matthew J.; Carrington, Tucker, Jr.
1993-12-01
We present a general variational method to calculate vibrational energy levels of polyatomic molecules without dynamical approximation. The method is based on a Lanczos algorithm, which does not require storage of the Hamiltonian matrix. The rate-determining step of each Lanczos iteration is the evaluation of the product of the matrix and a trial vector. We use simple product basis functions and write the Hamiltonian as a sum of factorizable terms. With n one-dimensional functions in each of f dimensions, the matrix-vector product requires no more than cnf+1 multiplications for a single term involving c coordinates. Choosing a (potential optimized) discrete variable representation (DVR) in each dimension, the potential energy matrix is diagonal. The rate-determining step is now the multiplication of a vector by the kinetic energy matrix and c is effectively (with rare exceptions) at most two. The nf+1 scaling holds for both diagonal and mixed second derivative operators. The method is directly applicable to any three-atom and any nonlinear four-atom molecule. We use a variety of coordinate systems (Jacobi, Radau, a hybrid of the two, and bond), for which the total number of factorizable terms in the exact kinetic energy operator is never large, to calculate very well-converged band origins of H2O up to 22 000 cm-1, of H+3 up to 18 000 cm-1, and of CH2O up to 5700 cm-1; and low-lying levels of H2O2. The results for CH2O are new, and those for H+3 clarify the causes of discrepancies in published work. The product basis results in very large matrices (up to 500 000×500 000 for four atoms), but the cost is within an order of magnitude of that of contracted-basis approaches using explicit diagonalization. While contracted basis approaches are molecule and Hamiltonian specific, it was possible to apply the DVR-Lanczos method to all the examples presented here with a single computer program. The principal advantage of our method is thus its generality, and in this
Institute of Scientific and Technical Information of China (English)
ZHAO Li-Ming; GU Ben-Yuan; ZHOU Yun-Song
2007-01-01
The spontaneous emission (SE) progress of polarized atoms in a stratified structure ofair-dielectric(D0)-metal(M)-dielectric(D1)-air can be controlled effectively by changing the thickness of the D1 layer and rotating the polarized direction of atoms. It is found that the normalized SE rate of atoms located inside the D0 layer crucially depends on the atomic position and the thickness of the D1 layer. When the atom is located near the D0-M interface, the normalized atomic SE rate as a function of the atomic position is abruptly onset for the thin D1 layer. However, with the increasing thickness of the D1 layer, the corresponding curve profile exhibits plateau and stays nearly unchanged. The substantial change of the SE rate stems from the excitation of the surface plasmon polaritons in metal-dielectric interface, and the feature crucially depends on the thickness of D1 layer. If atoms are positioned near the D0-air interface, the substantial variation of the normalized SE rate appears when rotating the polarized direction of atoms. These findings manifest that the atomic SE processes can be flexibly controlled by altering the thickness of the dielectric layer D1 or rotating the orientation of the polarization of atoms.
Songjun, Hou; Sunchao, Huang; Zhi, Zeng
2015-01-01
First principles calculations were performed to study the structural, elastic, and bonding properties of hcp ZrxTi1-x binary alloy. The special quasi- random structure (SQS) method is employed to mimic the random hcp ZrxTi1-x alloy. It is found that Bulk modulus, B, Young's modulus, E, and shear modulus, G, exhibit decreasing trends as increasing the amount of Zr. A ductile behavior ZrxTi1-x is predicted in the whole composition range. In terms of Mulliken charge analisis, we found that the element Ti behaves much more electronegative than Zr in hcp ZrxTi1-x alloy, and the charge transfer of an atom is approximately linear to the amount of other element atom surrounding it.
Chain-branching control of the atomic structure of alkanethiol-based gold-sulfur interfaces.
Wang, Yun; Chi, Qijin; Zhang, Jingdong; Hush, Noel S; Reimers, Jeffrey R; Ulstrup, Jens
2011-09-28
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): direct binding to the Au(111) surface without pitting, binding to adatoms above a regular surface with extensive pitting, and binding to adatoms with local surface vacancies and some pitting. Thermal motions are shown to produce some observed STM features, with a very tight energy balance controlling the observed structures. Variation of the degree of substitution on the α carbon is found to significantly change the relative energies for interaction of the different types of adatom structures with the surface, while the nature of the surface cell, controlled primarily by inter-adsorbate steric interactions, controls substrate reorganization energies and adsorbate distortion energies. Most significantly, by manipulating these features, chemical control of the adsorbate can produce stable interfaces with surface pitting eliminated, providing new perspectives for technological applications of SAMs.
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
Davis, Ian W; Leaver-Fay, Andrew; Chen, Vincent B; Block, Jeremy N; Kapral, Gary J; Wang, Xueyi; Murray, Laura W; Arendall, W Bryan; Snoeyink, Jack; Richardson, Jane S; Richardson, David C
2007-07-01
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.
Heat Transfer Principles in Thermal Calculation of Structures in Fire
Zhang, Chao; Usmani, Asif
2015-01-01
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 educa...
Tan, J; Wang, G; Liu, Z Y; Bednarčík, J; Gao, Y L; Zhai, Q J; Mattern, N; Eckert, J
2014-01-28
A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs.
Inhibition of LDL oxidation by flavonoids in relation to their structure and calculated enthalpy.
Vaya, Jacob; Mahmood, Saeed; Goldblum, Amiram; Aviram, Michael; Volkova, Nina; Shaalan, Amin; Musa, Ramadan; Tamir, Snait
2003-01-01
Twenty flavonoid compounds of five different subclasses were selected, and the relationship of their structure to the inhibition of low-density lipoprotein (LDL) oxidation in vitro was investigated. The most effective inhibitors, by either copper ion or 2,2'-azobis (2-amidino-propane) dihydrochloride (AAPH) induction, were flavonols and/or flavonoids with two adjacent hydroxyl groups at ring B. In the presence of the later catechol group, the contribution of the double bond and the carbonyl group at ring C was negligible. Isoflavonoids were more effective inhibitors than other flavonoid subclasses with similar structure. Substituting ring B with hydroxyl group(s) at 2' position resulted in a significantly higher inhibitory effect than by substituting ring A or ring B at other positions. The type of LDL inducer had no effect in flavonoids with catechol structure. Calculated heat of formation data (deltadeltaH(f)) revealed that the donation of a hydrogen atom from position 3 was the most likely result, followed by that of a hydroxyl from ring B. Position 3 was favored only in the presence of conjugated double bonds between ring A to ring B. This study makes it possible to assign the contribution of different functional groups among the flavonoid subclasses to in vitro inhibition of LDL oxidation.
Fine structure in a strong magnetic field: Paschen-Back effect reconsidered in Rydberg atoms
Liu, Wenyu; Gu, Sihong; Li, Baiwen
1996-05-01
Using a kind of potential model wave function for alkali metal atoms, we nonperturbatively study the effect of fine structure on the Rydberg spectra of Cs atom in a strong magnetic field. Our numerical results reveal spectral structure dramatically different from the well-established Paschen-Back effect, and we argue that the fine structure of the Rydberg Cs atom cannot be neglected even in a magnetic field as strong as several teslas. We also give an error estimate of our results and a word on possible experimental verification.
Adhikari, Jhashanath; Smith, Luis J.
2012-02-01
Inorganic niobates ACa2Nb3O10 (A= H and K) with layered structures are good photocatalytic materials due to their high surface areas accommodating a larger number of active sites and ease of processing through soft chemical techniques like exfoliation and restacking. Alkali metal phases can be ion-exchanged to the acid phase, which in turn can be easily exfoliated to individual nanosheets. The nanosheets can change their form to nanoscrolls with a curled geometry instead of a flat surface. During these morphological transformations, the local structure at the Nb-atom, H-atom and the interface may undergo rearrangement which is responsible for the alteration of properties of the materials. This presentation highlights the preliminary results on these structural modifications (interface variation, stacking of layers, lattice contraction and space group settings) and the possible positions of the proton. Our calculations show that the protons in the acid form are non-bridging and bonded to the same layer oxygen atoms unlike the K-atoms in its parent compound. The Electric field gradient (EFG) is a parameter very sensitive to the electron density around a quadrupolar nucleus ^2H and ^93Nb that can be detected using NMR. Changes in its magnitude/sign can be correlated to the change in the local environment (bond lengths and angles) around the sites of interest. EFG values from DFT calculations based on the proposed structural models will be used for the characterization of surface O-H bond lengths, H-bonding and Nb-O bond lengths and can be used to interpret NMR studies.
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.
Energy Technology Data Exchange (ETDEWEB)
Werwiński, M. [Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznań (Poland); Szajek, A. [Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznań (Poland); Centre for Advanced Materials and Smart Structures, Polish Academy of Sciences, Okólna 2, 50-950 Wrocław (Poland); Ślebarski, A. [Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland); Centre for Advanced Materials and Smart Structures, Polish Academy of Sciences, Okólna 2, 50-950 Wrocław (Poland); Kaczorowski, D., E-mail: D.Kaczorowski@int.pan.wroc.pl [Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P. O. Box 1410, 50-950 Wrocław (Poland); Centre for Advanced Materials and Smart Structures, Polish Academy of Sciences, Okólna 2, 50-950 Wrocław (Poland)
2015-10-25
The electronic structure of a heavy-fermion superconductor Ce{sub 2}PdIn{sub 8} was investigated by means of X-ray photoelectron spectroscopy (XPS) and ab initio density functional band structure calculations. The Ce 3d core-level XPS spectra point to stable trivalent configuration of Ce atoms that is also reproduced in the band structure calculations within the generalized gradient approximation GGA+U approach. Analysis of the 3d{sup 9}f{sup 2} weight in the 3d XPS spectra within the Gunnarsson-Schönhammer model suggests that the onsite hybridization energy between Ce 4f and the conduction band states, Δ{sub fs}, is ∼120 meV, which is about 30 meV larger than Δ{sub fs} in isostructural Ce{sub 2}TIn{sub 8} compounds with T = Co, Rh, and Ir. Taking into account a Coulomb repulsion U on both the Ce 4f and Pd 4d states in electronic band structure calculations, a satisfactory agreement was found between the calculated density of states (DOS) and the measured valence band XPS spectra. - Highlights: • XPS data validated strong electronic correlations in superconducting Ce{sub 2}PdIn{sub 8}. • DFT calculations reproduced XPS spectra measured for Ce{sub 2}PdIn{sub 8}. • Crucial role of Pd d electrons in the HF behavior of Ce{sub 2}PdIn{sub 8} was established.
Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite.
Chin, Yiing; Panduwinata, Dwi; Sintic, Maxine; Sum, Tze Jing; Hush, Noel S; Crossley, Maxwell J; Reimers, Jeffrey R
2011-01-20
The atomic structure of the chains of an alkyl porphyrin (5,10,15,20-tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for porphyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible. A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and, of the many possible atomic structures modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.
Realizing high magnetic moments in fcc Fe nanoparticles through atomic structure stretch.
Baker, S H; Roy, M; Thornton, S C; Binns, C
2012-05-02
We describe the realization of a high moment state in fcc Fe nanoparticles through a controlled change in their atomic structure. Embedding Fe nanoparticles in a Cu(1-x)Au(x) matrix causes their atomic structure to switch from bcc to fcc. Extended x-ray absorption fine structure (EXAFS) measurements show that the structure in both the matrix and the Fe nanoparticles expands as the amount of Au in the matrix is increased, with the data indicating a tetragonal stretch in the Fe nanoparticles. The samples were prepared directly from the gas phase by co-deposition, using a gas aggregation source and MBE-type sources respectively for the nanoparticle and matrix materials. The structure change in the Fe nanoparticles is accompanied by a sharp increase in atomic magnetic moment, ultimately to values of ~2.5 ± 0.3 μ(B)/atom .
Finite-Temperature Atomic Structure of 180^o Ferroelectric Domain Walls in PbTiO3
Angoshtari, Arzhang; Yavari, Arash
2010-01-01
In this letter we obtain the finite-temperature structure of 180^o domain walls in PbTiO3 using a quasi-harmonic lattice dynamics approach. We obtain the temperature dependence of the atomic structure of domain walls from 0K up to room temperature. We also show that both Pb-centered and Ti-centered 180^o domain walls are thicker at room temperature; domain wall thickness at T=300K is about three times larger than that of T=0K. Our calculations show that Ti-centered domain walls have a lower f...
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…
Niaz, Mansoor; Aguilera, Damarys; Maza, Arelys; Liendo, Gustavo
2002-01-01
Reports on a study aimed at facilitating freshman general chemistry students' understanding of atomic structure based on the work of Thomson, Rutherford, and Bohr. Hypothesizes that classroom discussions based on arguments/counterarguments of the heuristic principles on which these scientists based their atomic models can facilitate students'…
2010-01-01
The transition in structure and composition across the titanium carbide /nickel hybrid interface has been determined at near atomic resolution by...coupling high-resolution transmission electron microscopy with three-dimensional atom probe tomography. The titanium carbide phase adopts a rocksalt-type
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 ...
Low viscosity and high attenuation in MgSiO3 post-perovskite inferred from atomic-scale calculations
Goryaeva, Alexandra M.; Carrez, Philippe; Cordier, Patrick
2016-10-01
This work represents a numerical study of the thermal activation for dislocation glide of the [100](010) slip system in MgSiO3 post-perovskite (Mg-ppv) at 120 GPa. We propose an approach based on a one-dimensional line tension model in conjunction with atomic-scale calculations. In this model, the key parameters, namely, the line tension and the Peierls barrier, are obtained from density functional theory calculations. We find a Peierls stress σp = 2.1 GPa and a line tension Γ = 9.2 eV/Å, which lead to a kink-pair enthalpy (under zero stress) of 2.69 eV. These values confirm that this slip system bears a very low lattice friction because it vanishes for temperatures above approximately 500 K under mantle conditions. In the Earth’s mantle, high-pressure Mg-ppv silicate is thus expected to become as ductile as ferropericlase. These results confirm the hypothesis of a weak layer in the D″ layer where Mg-ppv is present. Easy glide along [100](010) suggests strong preferred orientations with (010) planes aligned. Highly mobile [100] dislocations are also likely to respond to stresses related to seismic waves, leading to energy dissipation and strong attenuation.
Molle, Alessandro; Bhuiyan, Md. Nurul Kabir; Tallarida, Grazia; Fanciulli, Marco
2006-08-01
The exposure of Ge(001) substrates to atomic oxygen was studied in situ to establish the stability of the germanium oxide. After preparing chemically clean and atomically flat Ge(001) surfaces, the Ge samples were exposed to atomic oxygen in a wide temperature range from room temperature to 400°C. The chemical composition of the so-formed oxides was studied by means of x-ray photoelectron spectroscopy, while the structure was observed by reflection high energy electron diffraction. At low substrate temperatures the atomic oxygen is efficiently chemisorbed and suboxides coexist with the dioxide, which in turn is remarkably promoted in the high temperature range.
Atomically resolved tomography to directly inform simulations for structure-property relationships
Moody, Michael P.; Ceguerra, Anna V.; Breen, Andrew J.; Cui, Xiang Yuan; Gault, Baptiste; Stephenson, Leigh T.; Marceau, Ross K. W.; Powles, Rebecca C.; Ringer, Simon P.
2014-11-01
Microscopy encompasses a wide variety of forms and scales. So too does the array of simulation techniques developed that correlate to and build upon microstructural information. Nevertheless, a true nexus between microscopy and atomistic simulations is lacking. Atom probe has emerged as a potential means of achieving this goal. Atom probe generates three-dimensional atomistic images in a format almost identical to many atomistic simulations. However, this data is imperfect, preventing input into computational algorithms to predict material properties. Here we describe a methodology to overcome these limitations, based on a hybrid data format, blending atom probe and predictive Monte Carlo simulations. We create atomically complete and lattice-bound models of material specimens. This hybrid data can then be used as direct input into density functional theory simulations to calculate local energetics and elastic properties. This research demonstrates the role that atom probe combined with theoretical approaches can play in modern materials engineering.
A Calculation Model for Corrosion Cracking in RC Structures
Institute of Scientific and Technical Information of China (English)
Xu Gang; Wei Jun; Zhang Keqiang; Zhou Xiwu
2007-01-01
A novel calculation model is proposed aiming at the problem of concrete cover cracking induced by reinforcement corrosion. In this article, the relationship between the corrosion depth of the bar and the thickness of the rust layer is established. By deducing the radial displacement expression of concrete, the formula for corrosion depth and corrosion pressure before cracking is proposed. The crack depth of cover in accordance with the maximum corrosion pressure is deduced; furthermore, the corrosion depth and corrosion pressure at the cracking time are obtained. Finally, the theoretical model is validated by several experiments, and the calculated values agree well with the experiment results.
Wetsel, Grover C., Jr.
1978-01-01
Calculates the energy-band structure of noninteracting electrons in a one-dimensional crystal using exact and approximate methods for a rectangular-well atomic potential. A comparison of the two solutions as a function of potential-well depth and ratio of lattice spacing to well width is presented. (Author/GA)
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
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.
Institute of Scientific and Technical Information of China (English)
张伟; 陈青云; 曾召益; 蔡灵仓
2015-01-01
We calculated the structural, elastic, and electronic properties of alkali metal Na atoms doped type-I silicon–clathrate compound (Na8Si46) under pressure using first-principles methods. The obtained dependencies of bond lengths and bond angles on pressure show heterogeneous behaviors which may bring out a structural transition. By using the elastic stability criteria from the calculated elastic constants, we confirm that the Na8Si46 is elastically unstable under high pressure. Some of the mechanical and thermal quantities include bulk modulus, shear modulus ,Young’s modulus, Debye temperature, sound velocity, melting point, and hardness, which are also derived from the elastic constants. The calculated total and partial electron densities of states of Na8Si46 indicate a weak interaction between the encapsulated Na atoms and the silicon framework. Moreover, the effect of pressure on its electronic structure is also investigated, which suggests that pressure is not a good choice to enhance the thermoelectricity performance of Na8Si46.
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.
Validation methods for low-resolution fitting of atomic structures to electron microscopy data
Xu, Xiao-Ping; Volkmann, Niels
2015-01-01
Fitting of atomic-resolution structures into reconstructions from electron cryo-microscopy is routinely used to understand the structure and function of macromolecular machines. Despite the fact that a plethora of fitting methods has been developed over recent years, standard protocols for quality assessment and validation of these fits have not been established. Here, we present the general concepts underlying current validation ideas as they relate to fitting of atomic-resolution models int...
Semiempirical Studies of Atomic Structure. Final Report for July 1, 2000 - June 30, 2003
Energy Technology Data Exchange (ETDEWEB)
Curtis, L. J.
2004-05-01
This project has developed a comprehensive and reliable base of accurate atomic structure data for complex many-electron systems. This has been achieved through the use of sensitive data-based parametric systematizations, precise experimental measurements, and supporting theoretical computations. The atomic properties studies involved primary data (wavelengths, frequency intervals, lifetimes, relative intensities, production rates, etc.) and derived structural parameters (energy levels, ionization potentials, line strengths, electric polarizabilities, branching fractions, excitation functions, etc).
Reconstructing Polyatomic Structures from Discrete X-Rays: NP-Completeness Proof for Three Atoms
Durr, Christoph; Chrobak, Marek
1999-01-01
We address a discrete tomography problem that arises in the study of the atomic structure of crystal lattices. A polyatomic structure T can be defined as an integer lattice in dimension D>=2, whose points may be occupied by $c$ distinct types of atoms. To ``analyze'' T, we conduct ell measurements that we call_discrete X-rays_. A discrete X-ray in direction xi determines the number of atoms of each type on each line parallel to xi. Given ell such non-parallel X-rays, we wish to reconstruct T....
Banerjee, Amartya S; Hu, Wei; Yang, Chao; Pask, John E
2016-01-01
The Discontinuous Galerkin (DG) electronic structure method employs an adaptive local basis set to solve the equations of density functional theory in a discontinuous Galerkin framework. The methodology is implemented in the Discontinuous Galerkin Density Functional Theory (DGDFT) code for large-scale parallel electronic structure calculations. In DGDFT, the basis is generated on-the-fly to capture the local material physics, and can systematically attain chemical accuracy with only a few tens of degrees of freedom per atom. Hence, DGDFT combines the key advantage of planewave basis sets in terms of systematic improvability with that of localized basis sets in reducing basis size. A central issue for large-scale calculations, however, is the computation of the electron density from the discretized Hamiltonian in an efficient and scalable manner. We show in this work how Chebyshev polynomial filtered subspace iteration (CheFSI) can be used to address this issue and push the envelope in large-scale materials si...
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.
Alternative similarity renormalization group generators in nuclear structure calculations
Dicaire, Nuiok M; Navratil, Petr
2014-01-01
The similarity renormalization group (SRG) has been successfully applied to soften interactions for ab initio nuclear calculations. In almost all practical applications in nuclear physics, an SRG generator with the kinetic energy operator is used. With this choice, a fast convergence of many-body calculations can be achieved, but at the same time substantial three-body interactions are induced even if one starts from a purely two-nucleon (NN) Hamiltonian. Three-nucleon (3N) interactions can be handled by modern many-body methods. However, it has been observed that when including initial chiral 3N forces in the Hamiltonian, the SRG transformations induce a non-negligible four-nucleon interaction that cannot be currently included in the calculations for technical reasons. Consequently, it is essential to investigate alternative SRG generators that might suppress the induction of many-body forces while at the same time might preserve the good convergence. In this work we test two alternative generators with oper...
Li, Zongbao; Wang, Xia; Xing, Xiaobo; Wang, Ying
2017-02-01
Using density functional theory, we calculated the geometries, band structures and densities of states of W-doped, N-doped, and W/N-codoped anatase TiO4 (001) and (101) surfaces, as well as while the formation energies, based on the overall reaction energy diagram. The calculated results reveal that, on the two surfaces, the absorption of W atoms are more stable than that of N atoms while a larger energy barrier blocks the transfer of W atoms from the surfaces to the body. For TiO2(001), the W-doping and the N/W-codoping lead to a visible lattice distortion while the recombination of photo-generated electron-holes pairs is reduced. A comprehensive analysis of the electronic structures show that the band-gap narrows and a new W-N bond appears, which obviously enhance the photocatalytic activity.
Valence electron structure of the（ZrTi）B2 solid solutions calculated by the three models
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
The Zr-rich(Zr0.8Ti0.2)B2 and the Ti-rich(Ti0.8Zr0.2)B2 solid solutions are formed when TiB2 and ZrB2 are hot-pressed.To forecast the properties of the two solid solutions,their valence electron structure was analyzed based on the empirical electron theory(EET) of solids and molecules.We used three different models,the average atom model,the average cell model and the real cell model,and compared with the calculation results from the three models.In the real cell model,the lattice constants of the solid solu-tions were supposed to be changed or unchanged.The results showed that different models could only result in slight change in the hybridization levels of the metal atoms in the two solid solutions and little difference between the calculation values.However,they can not change the variant trend of the va-lence electron structure nor the properties of the solid solutions.Thus,the three models and the methods are appropriate and the calculation results are reasonable and consistent.
Valence electron structure of the (ZrTi)B2 solid solutions calculated by the three models
Institute of Scientific and Technical Information of China (English)
LI JinPing; HAN JieCai; MENG SongHe; WANG BaoLin
2009-01-01
The Zr-rich (Zr0.8Ti0.2)B2 and the Ti-rich Zr0.8Ti0.2)B2 solid solutions are formed when TiB2 and ZrB2 are hot-pressed. To forecast the properties of the two solid solutions, their valence electron structure was analyzed based on the empirical electron theory (EET) of solids and molecules. We used three differen tmodels, the average atom model, the average cell model and the real cell model, and compared with the calculation results from the three models. In the real cell model, the lattice constants of the solid solu-tions were supposed to be changed or unchanged. The results showed that different models could only result in slight change in the hybridization levels of the metal atoms in the two solid solutions and little difference between the calculation values. However, they can not change the variant trend of the va-lence electron structure nor the properties of the solid solutions. Thus, the three models and the methods are appropriate and the calculation results are reasonable and consistent.
Institute of Scientific and Technical Information of China (English)
Ryota NAKANISHI; Koji SUEOKA; Seiji SHIBA; Makoto HINO; Koji MURAKAMI; Ken MURAOKA
2009-01-01
A study the with first principles calculation of the interfaces of the Ni layer or Cu layer on the Fe(100) surface formed with metal plating was performed. Ni or Cu atoms were shown to adopt the corresponding position to the bcc structure of the Fe(100) substrate. Other calculations showed that the interfaces of Ni (5 atomic layers)/Fe(100) (5 layers) or Cu (5 atomic layers)/Fe(100) (5 layers) had square lattices. The orientation relationship of Ni/Fe(100) interface corresponds to fcc-Ni(100)//bcc-Fe(100), Ni[011]//Fe[010], and Similar results were obtained for Cu/Fe(100) interfaces. This structure was supported by TEM analysis of plated Ni layer on Fe(100) surfaces. The adhesion strength of the Ni/Fe(100) interface evaluated by first principles calculation was higher than that of the Cu/Fe(100) interface. The experimental results of Hull cell iron plated with Ni or Cu supported the results of the calculation. These results indicate that the first principles calculation, which deals with the ideal interface at the atomic scale, has the potential to evaluate the adhesion strength of metallic material interfaces.
Energy Technology Data Exchange (ETDEWEB)
Pennycook, S.J.; Nellist, P.D. [Oak Ridge National Lab., TN (United States); Browning, N.D. [Illinois Univ., Chicago, IL (United States). Dept. of Physics
1996-08-01
The bulk properties of a large range of materials are controlled by the atomic structure and chemistry of grain boundaries, but how this occurs, at the fundamental atomic level, remains poorly understood. This is due largely to the many degrees of freedom associated with grain boundaries - five geometrical degrees of freedom along with a myriad of possibilities involving impurity segregation. Based on Z- contrast electron microscopy, a method have been developed for determining grain boundary atomic structure and chemistry directly from experimental data. The method utilizes the incoherent nature of the Z-contrast image; as there is no phase problem associated with an incoherent image, it represents a compositionally sensitive structure image which may be directly inverted to give atomic column positions. This method extracts the column locations to an accuracy of {+-}0.2 {Angstrom}, while preserving the intensity information. The procedure has been applied to SrTiO{sub 3} and YBCO.
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.
Elliott, S D; Dey, G; Maimaiti, Y
2017-02-07
Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.
Elliott, S. D.; Dey, G.; Maimaiti, Y.
2017-02-01
Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.
Barklem, P S
2001-01-01
With the exception of the sodium D-lines recent calculations of line broadening cross-sections for several multiplets of sodium by Leininger et al (2000) are in substantial disagreement with cross-sections interpolated from the tables of Anstee and O'Mara (1995) and Barklem and O'Mara (1997). The discrepancy is as large as a factor of three for the 3p-4d multiplet. The two theories are tested by using the results of each to synthesize lines in the solar spectrum. It is found that generally the data from the theory of Anstee, Barklem and O'Mara produce the best match to the observed solar spectrum. It is found, using a simple model for reflection of the optical electron by the potential barrier between the two atoms, that the reflection coefficient is too large for avoided crossings with the upper states of subordinate lines to contribute to line broadening, supporting the neglect of avoided ionic crossings by Anstee, Barklem and O'Mara for these lines. The large discrepancies between the two sets of calculati...
Lin, Yuyuan; Wu, Zili; Wen, Jianguo; Ding, Kunlun; Yang, Xiaoyun; Poeppelmeier, Kenneth R; Marks, Laurence D
2015-08-12
We report an aberration-corrected electron microscopy analysis of the adhesion and atomic structures of gold nanoparticle catalysts supported on ceria nanocubes and nanorods. Under oxidative conditions, the as-prepared gold nanoparticles on the ceria nanocubes have extended atom layers at the metal-support interface. In contrast, regular gold nanoparticles and rafts are present on the ceria nanorod supports. Under the reducing conditions of water-gas shift reaction, the extended gold atom layers and rafts vanish. In addition, the gold particles on the nanocubes change in morphology and increase in size while those on the nanorods are almost unchanged. The size, morphology, and atomic interface structures of gold strongly depend on the surface structures of ceria supports ((100) surface versus (111) surface) and the reaction environment (reductive versus oxidative). These findings provide insights into the deactivation mechanisms and the shape-dependent catalysis of oxide supported metal catalysts.
Impact of Atomic Structure on Absolute Energy Levels of Methylammonium Lead Iodide Perovskite
Choi, Joshua
2015-03-01
There has been a staggeringly rapid increase in the photovoltaic performance of methylammonium lead iodide (MAPbI3) perovskite - greater than 19 percent solar cell power conversion efficiency has been reported in less than five years since the first report in 2009. Despite the progress in device performance, structure-property relationships in MAPbI3 are still poorly understood. I will present our recent findings on the impact of changing the Pb-I bond length and Pb-I-Pb bond angle on the electronic structure of MAPbI3. By using the combination of temperature dependent X-ray scattering, ultraviolet photoelectron spectroscopy, absorbance and PL spectroscopy, we show that the energy levels of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) shift in the same direction as MAPbI3 goes through tetragonal-to-cubic structural phase transition wherein the rotational angle of PbI6 octahedra is the order parameter of the transition. Our experimental results are corroborated by density functional theory calculations which show that the lattice expansion and bond angle distortion cause different degree of orbital overlap between the Pb and I atoms and the anti-bonding orbital nature of both HOMO and LUMO results in the same direction of their shift. Moreover, through pair distribution function analysis of X-ray scattering, we discovered that the majority of MAPbI3 in thin film solar cell layer has highly disordered structure with a coherence range of only 1.4 nm. The nanostructuring correlates with a blueshift of the absorption onset and increases the photoluminescence. Our results underscore the importance of understanding the structure-property relationships in order to improve the device performance of metal-organic perovskites.
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.
Safronova, M S; Derevianko, S A
1999-01-01
Removal energies and hyperfine constants of the lowest four $ns, np_{1/2}$ and $np_{3/2}$ states in Na, K, Rb and Cs are calculated; removal energies of the n=7--10 states and hyperfine constants of the n=7 and 8 states in Fr are also calculated. The calculations are based on the relativistic single-double (SD) approximation in which single and double excitations of Dirac-Hartree-Fock (DHF) wave functions are included to all-orders in perturbation theory. Using SD wave functions, accurate values of removal energies, electric-dipole matrix elements and static polarizabilities are obtained, however, SD wave functions give poor values of magnetic-dipole hyperfine constants for heavy atoms. To obtain accurate values of hyperfine constants for heavy atoms, we include triple excitations partially in the wave functions. The present calculations provide the basis for reevaluating PNC amplitudes in Cs and Fr.
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.
Everyone Wants to Be a Model Teacher: Part III: Extensions to Atomic Structures and Bonding.
Schrader, C. L.
1985-01-01
Describes activities in which students: (1) propose creative atomic models that account for observed properties and predict additional experimental data; (2) calculate empirical formulas for 27 binary compounds; (3) propose a model to explain why certain elements have certain valences; and (4) arrange hypothetical elements into a periodic chart.…
Mota,F.B.; Rivelino, R.; Medeiros, P.V.C.; Mascarenhas, A.J.S.; de Castilho, C. M. C.
2014-01-01
p.23558-23563 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.
Close-coupling calculations of fine-structure excitation of Ne II due to H and electron collisions
Stancil, Phillip C.; Cumbee, Renata; Wang, Qianxia; Loch, Stuart; Pindzola, Michael; Schultz, David R.; Buenker, Robert; McLaughlin, Brendan; Ballance, Connor
2016-06-01
Fine-structure transitions within the ground term of ions and neutral atoms dominate the cooling in a variety of molecular regions and also provide important density and temperature diagnostics. While fine-structure rates due to electron collisions have been studied for many systems, data are generally sparse for elements larger than oxygen, at low temperatures, and for collisions due to heavy particles. We provide rate coefficients for H collisions for the first time. The calculations were performed using the quantum molecular-orbital close-coupling approach and the elastic approximation. The heavy-particle collisions use new potential energies for the lowest-lying NeH+ states computed with the MRDCI method. The focus of the electron-impact calculations is to provide fine-structure excitation rate coefficients down to 10 K. We compare with previous calculations at higher temperatures (Griffin et al. 2001), and use a range of calculations to provide an estimate of the uncertainty on our recommended rate coefficients. A brief discussion of astrophysical applications is also provided.Griffin, D.C., et al., 2001, J. Phys. B, 34, 4401This work partially supported by NASA grant No. NNX15AE47G.
Atomic structure and chemistry of human serum albumin
He, Xiao M.; Carter, Daniel C.
1992-01-01
The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.
van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira
2014-07-01
The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.
Matta, Chérif F
2010-04-30
This article compares molecular properties and atomic properties defined by the quantum theory of atoms in molecules (QTAIM) obtained from three underlying levels of theory: MP2(full), density functional theory (DFT) (B3LYP), and Hartree-Fock (H-F). The same basis set (6-311++G(d,p)) has been used throughout the study. The calculations and comparisons were applied to a set of 30 small molecules representing common fragments of biological molecules. The molecular properties investigated are the energies and the electrostatic moments (up to and including the quadrupoles), and the atomic properties include electron populations (and atomic charge), atomic dipolar and quadrupolar polarizations, atomic volumes, and corrected and raw atomic energies. The Cartesian distance between dipole vectors and the Frobenius distance between the quadrupole tensors calculated at the three levels of theory provide a measure of their correlation (or lack thereof). With the exception of energies (atomic and molecular), it is found that both DFT and H-F are in excellent agreement with MP2, especially with regards to the electrostatic mutipoles up to the quadrupoles, but DFT and MP2 agree better in almost all studied properties (with the exception of molecular geometries). QTAIM properties whether obtained from H-F, DFT(B3LYP), or MP2 calculations when used in the construction of empirical correlations with experiment such as quantitative structure-activity-(or property)-relationships (QSAR/QSPR) are equivalent (because the properties calculated at the three levels are very highly correlated among themselves with r(2) typically >0.95, and therefore preserving trends). These results suggest that the massive volume of results that were published in the older literature at the H-F level is valid especially when used to study trends or in QSAR or QSPR studies, and, as long as our test set of molecules is representative, there is no pressing need to re-evaluate them at other levels of theory
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.
Tupitsyn, I I; Shabaev, V M; Bondarev, A I; Deyneka, G B; Maltsev, I A; Hagmann, S; Plunien, G; Stoehlker, Th
2011-01-01
The previously developed technique for evaluation of charge-transfer and electron-excitation processes in low-energy heavy-ion collisions [I.I. Tupitsyn et al., Phys. Rev. A 82, 042701(2010)] is extended to collisions of ions with neutral atoms. The method employs the active electron approximation, in which only the active electron participates in the charge transfer and excitation processes while the passive electrons provide the screening DFT potential. The time-dependent Dirac wave function of the active electron is represented as a linear combination of atomic-like Dirac-Fock-Sturm orbitals, localized at the ions (atoms). The screening DFT potential is calculated using the overlapping densities of each ions (atoms), derived from the atomic orbitals of the passive electrons. The atomic orbitals are generated by solving numerically the one-center Dirac-Fock and Dirac-Fock-Sturm equations by means of a finite-difference approach with the potential taken as the sum of the exact reference ion (atom) Dirac-Fock...
Energy Technology Data Exchange (ETDEWEB)
Lopez-Bezanilla, Alejandro
2016-01-20
By means of a multi-scale first-principles approach, a description of the local electronic structure of 2D and narrow phosphorene sheets with various types of modifications is presented. Firtly, a rational argument based on the geometry of the pristine and modified P network, and supported by the Wannier functions formalism is introduced to describe a hybridization model of the P atomic orbitals. Ab initio calculations show that non-isoelectronic foreign atoms form quasi-bound states at varying energy levels and create different polarization states depending on the number of valence electrons between P and the doping atom. The quantum transport properties of modified phosphorene ribbons are further described with great accuracy. The distortions on the electronic bands induced by the external species lead to strong backscattering effects on the propagating charge carriers. Depending on the energy of the charge carrier and the type of doping, the conduction may range from the diffusive to the localized regime. Interstitial defects at vacant sites lead to homogeneous transport fingerprints across different types of doping atoms. We suggest that the relatively low values of charge mobility reported in experimental measurements may have its origin in the presence of defects.
He, Xin; Wang, Yuechao; Jiang, Hong; Zhao, Liang
2016-05-04
Asymmetric arrangement of metal atoms is crucial for understanding the chirality origin of chiral metal nanoclusters and facilitating the design and development of new chiral catalysts and chiroptical devices. Here, we describe the construction of four asymmetric gold and gold-silver clusters by chirality transfer from diimido ligands. The acquired metal clusters show strong circular dichroism (CD) response with large anisotropy factors of up to 6 × 10(-3), larger than the values of most reported chiral gold nanoclusters. Regardless of the same absolute configuration of the applied three diimido ligands, sigmoidal and reverse-sigmoidal arrangements of gold atoms both can be achieved, which resultantly produce an opposite Cotton effect within a specific absorption range. On the basis of the detailed structural characterization via X-ray crystallography and contrast experiments, the chirality contribution of the imido ligand, the asymmetrically arranged metal cluster, and the chiral arrangement of aromatic rings of phosphine ligands have been qualitatively evaluated. Time-dependent DFT calculations reveal that the chiroptical property of the acquired metal clusters is mainly influenced by the asymmetrically arranged metal atoms. Correlation of asymmetric arrangements of metal atoms in clusters with their chiroptical response provides a viable means of fabricating a designable chiral surface of metal nanoclusters and opens a broader prospect for chiral cluster application.
Ultrathin atomic vapor film transmission spectroscopy: analysis of Dicke narrowing structure
Institute of Scientific and Technical Information of China (English)
Yuanyuan Li; Yanpeng Zhang; Chenli Gan
2005-01-01
Transmission sub-Doppler spectroscopy with confined atomic vapor film between two dielectric walls is theoretically studied. Because of atoms flying from wall to wall, where they get de-excited, the atomfield interaction time is anisotropic so that the contribution of slow atoms is enhanced, a sub-Doppler transmission spectroscopy (Dicke narrowing effect) can be obtained when the thickness of the film is much small or comparable with the wavelength even at small angle oblique incidence. It is feasible to get a sub-Doppler structure in a new region (L ＜λ/4) in experiments.
Structures of Molecules at the Atomic Level: Caffeine and Related Compounds
Heyrovska, Raji
2008-01-01
Recent rsearches have shown that the lengths of the chemical bonds, whether completely or partially covalent or ionic, are sums of the radii of the adjacent atoms and/or ions. On investigating the bond length data for the molecular components of nucleic acids, all were found (for the first time) to be effectively the sums of the covalent radii of the adjacent atoms. This work shows that the bond lengths in caffeine and related molecules are likewise sums of the covalent radii of C, N, O and H. This has enabled arriving at the atomic structures of these molecules, also for the first time.
DEFF Research Database (Denmark)
Vanin, Marco; Gath, Jesper; Thygesen, Kristian Sommer;
2010-01-01
The stability of graphene nanoribbons in the presence of typical atmospheric molecules is systematically investigated by means of density-functional theory. We calculate the edge formation free energy of five different edge configurations passivated by H, H-2, O, O-2, N-2, CO, CO2, and H2O......, respectively. In addition to the well known hydrogen passivated armchair and zigzag edges, we find the edges saturated by oxygen atoms to be particularly stable under atmospheric conditions. Saturation of the zigzag edge by oxygen leads to the formation of metallic states strictly localized on the oxygen atoms...
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
Knee structure in double ionization of noble atoms in circularly polarized laser fields
Chen, Xiang; Wu, Yan; Zhang, Jingtao
2017-01-01
Nonsequential double ionization is characterized by a knee structure in the plot of double-ionization probability versus laser intensity. In circularly polarized (CP) laser fields, this structure has only been observed for Mg atoms. By choosing laser fields according to a scaling law, we exhibit the knee structure in CP laser fields for Ar and He atoms. The collision of the ionized electron with the core enhances the ionization of the second electron and forms the knee structure. The electron recollision is universal in CP laser fields, but the ionization probability in the knee region decreases as the wavelength of the driven field increases. For experimental observations, it is beneficial to use target atoms with small ionization potentials and laser fields with short wavelengths.
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.
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.
Kafka, Graeme R; Masters, Sarah L; Wann, Derek A; Robertson, Heather E; Rankin, David W H
2010-10-21
When refining structures using gas electron diffraction (GED) data, assumptions are often made in order to reduce the number of required geometrical parameters. Where these relate to light, peripheral atoms there is little effect on the refined heavy-atom structure, which is well defined by the GED data. However, this is not the case when heavier atoms are involved. We have determined the gas-phase structure of perfluoro(methylcyclohexane), C(6)F(11)CF(3), using three different refinement methods and have shown that our new method, which makes use of both MP2 and molecular mechanics (MM) calculations to restrain the peripheral-atom geometry, gives a realistic structure without the need for damaging constraints. Only the conformer with the CF(3) group in an equatorial position was considered, as ab initio calculations showed this to be 25 kJ mol(-1) lower in energy than the axial conformer. Refinements combining both high-level and low-level calculations to give constraints were superior both to those based only on molecular mechanics and to those in which assumptions about the geometry were imposed.
Near-Origin Structure of the Hooke's Atoms%Near-Origin Structure of the Hooke＇s Atoms
Institute of Scientific and Technical Information of China (English)
王雪梅
2012-01-01
The Hooke's atoms with two or more than two electrons give rise to an interesting quantum mechanical model with valuable practical applications. In this work, we study the electronic properties near the origin of the harmonic potential. It is seen that the spherically averaged density, ~, exhibits an interesting character -- it has only even order terms in its small r expansion. The spherical average of the Hartree potential, ~, and the spherical average of the Kohn-Sham exchange-correlation potential, 9~c, are also shown to have the same property -- all odd order terms in their expansions vanish. F~rthermore, the analysis and results extend also to the case of two-dimensional models. While only models interacting via. the Coulomb potential are primarily considered in the article, the results also extend to models interacting via. other potentials (viz. Van der Waals potential).
Calculation and Analysis of Internal Force in Arch Structure of Frozen Soil
Institute of Scientific and Technical Information of China (English)
YUE Feng-tian; ZHANG Yong; SHI Rong-jian
2005-01-01
Aimed at the frozen soil arch reinforcement form of upside shed used for the shield machine launching in tunneling the internal force of the structure was calculated with the aid of the structural mechanics theory. Considering the space characteristics of the structure,this calculating method is suitable for practical engineering.Moreover,the behavior of the freezing arch reinforcement structure was analyzed combined with an engineering case.
Damas, Aurélie; Chamoreau, Lise-Marie; Cooksy, Andrew L; Jutand, Anny; Amouri, Hani
2013-02-04
The synthesis and X-ray molecular structure of the first metal-stabilized o-dithiobenzoquinone [Cp*Ir-o-(η(4)-C(6)H(4)S(2))] (2) are described. The presence of the metal stabilizes this elusive intermediate by π coordination and increases the nucleophilic character of the sulfur atoms. Indeed, the π-bonded dithiolene complex 2 was found to react with the organometallic solvated species [Cp*M(acetone)(3)][OTf](2) (M = Rh, Ir) to give a unique class of binuclear dithiolene compounds [Cp*Ir(C(6)H(4)S(2))MCp*][OTf](2) [M = Rh (3), Ir (4)] in which the elusive dithiolene η-C(6)H(4)S(2) acts as a bridging ligand toward the two Cp*M moieties. The electrochemical behavior of all complexes was investigated and provided us with valuable information about their redox properties. Density functional theory (DFT) calculations on the π-bonded dithiobenzoquinone ligand and related bimetallic systems show that the presence of Cp*M at the arene system of the dithiolene ligand increases the stability compared to the known monomeric species [Cp*Ir-o-(C(6)H(4)S(2)-κ(2)-S,S)] and enables these complexes Cp*Ir(C(6)H(4)S(2))MCp*][OTf](2) (3 and 4) to act as electron reservoirs. Time-dependent DFT calculations also predict the qualitative trends in the experimental UV-vis spectra and indicate that the strongest transitions arise from ligand-metal charge transfer involving primarily the HOMO-1 and LUMO. All of these compounds were fully characterized and identified by single-crystal X-ray crystallography. These results illustrate the first examples describing the coordination chemistry of the elusive o-dithiobenzoquinone to yield bimetallic complexes with an o-benzodithiolene ligand. These compounds might have important applications in the area of molecular materials.
Getting CAD in shape: the atomic structure of human dihydroorotase domain.
Hermoso, Juan A
2014-02-04
CAD is a large multifunctional polypeptide that initiates and controls the de novo biosynthesis of pyrimidines in animals. In this issue of Structure, Grande-García and colleagues provide the first atomic information of this antitumoral target by reporting the crystal structure of the dihydroorotase domain of human CAD.
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…
Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio
2012-12-07
We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.
Advanced density matrix renormalization group method for nuclear structure calculations
Legeza, Ö; Poves, A; Dukelsky, J
2015-01-01
We present an efficient implementation of the Density Matrix Renormalization Group (DMRG) algorithm that includes an optimal ordering of the proton and neutron orbitals and an efficient expansion of the active space utilizing various concepts of quantum information theory. We first show how this new DMRG methodology could solve a previous $400$ KeV discrepancy in the ground state energy of $^{56}$Ni. We then report the first DMRG results in the $pf+g9/2$ shell model space for the ground $0^+$ and first $2^+$ states of $^{64}$Ge which are benchmarked with reference data obtained from Monte Carlo shell model. The corresponding correlation structure among the proton and neutron orbitals is determined in terms of the two-orbital mutual information. Based on such correlation graphs we propose several further algorithmic improvement possibilities that can be utilized in a new generation of tensor network based algorithms.
Advanced density matrix renormalization group method for nuclear structure calculations
Legeza, Ã.-.; Veis, L.; Poves, A.; Dukelsky, J.
2015-11-01
We present an efficient implementation of the Density Matrix Renormalization Group (DMRG) algorithm that includes an optimal ordering of the proton and neutron orbitals and an efficient expansion of the active space utilizing various concepts of quantum information theory. We first show how this new DMRG methodology could solve a previous 400 keV discrepancy in the ground state energy of 56Ni. We then report the first DMRG results in the p f +g 9 /2 shell model space for the ground 0+ and first 2+ states of 64Ge which are benchmarked with reference data obtained from a Monte Carlo shell model. The corresponding correlation structure among the proton and neutron orbitals is determined in terms of two-orbital mutual information. Based on such correlation graphs we propose several further algorithmic improvement possibilities that can be utilized in a new generation of tensor network based algorithms.
Informing saccharide structural NMR studies with density functional theory calculations.
Klepach, Thomas; Zhao, Hongqiu; Hu, Xiaosong; Zhang, Wenhui; Stenutz, Roland; Hadad, Matthew J; Carmichael, Ian; Serianni, Anthony S
2015-01-01
Density functional theory (DFT) is a powerful computational tool to enable structural interpretations of NMR spin-spin coupling constants ( J-couplings) in saccharides, including the abundant (1)H-(1)H ( JHH), (13)C-(1)H ( JCH), and (13)C-(13)C ( JCC) values that exist for coupling pathways comprised of 1-4 bonds. The multiple hydroxyl groups in saccharides, with their attendant lone-pair orbitals, exert significant effects on J-couplings that can be difficult to decipher and quantify without input from theory. Oxygen substituent effects are configurational and conformational in origin (e.g., axial/equatorial orientation of an OH group in an aldopyranosyl ring; C-O bond conformation involving an exocyclic OH group). DFT studies shed light on these effects, and if conducted properly, yield quantitative relationships between a specific J-coupling and one or more conformational elements in the target molecule. These relationships assist studies of saccharide structure and conformation in solution, which are often challenged by the presence of conformational averaging. Redundant J-couplings, defined as an ensemble of J-couplings sensitive to the same conformational element, are particularly helpful when the element is flexible in solution (i.e., samples multiple conformational states on the NMR time scale), provided that algorithms are available to convert redundant J-values into meaningful conformational models. If the latter conversion is achievable, the data can serve as a means of testing, validating, and refining theoretical methods like molecular dynamics (MD) simulations, which are currently relied upon heavily to assign conformational models of saccharides in solution despite a paucity of experimental data needed to independently validate the method.
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 to ...
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...
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.
Directory of Open Access Journals (Sweden)
R. Mathammal
2013-01-01
Full Text Available This work deals with the vibrational spectroscopy of O-Anisic acid (OAA and Anisic acid (AA. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT with standard B3LYP/6-31G** method and basis set combinations. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical force field. The infrared and Raman spectra were also predicted from the calculated intensities. The effects of carbonyl and methyl substitutions on the structure and vibrational frequencies have been investigated. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. The 13C and 1H NMR chemical shifts of the DFA and CA molecules were calculated using the gauge-invariant-atomic orbital (GIAO method in DMSO solution using IEF-PCM model and compared with experimental data.
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).
Structure of various K L1 x-ray satellite lines of heavy atoms
Polasik, Marek; Lewandowska-Robak, Maja
2004-11-01
Multiconfiguration Dirac-Fock calculations with the inclusion of the transverse (Breit) interaction and QED corrections have been carried out for Pd, Sn, Tb, Ta, Pb, and Th in order to obtain positions and intensities of various electric dipole, electric quadrupole, and magnetic dipole K x-ray diagram lines and of their KL1 satellites. Theoretically constructed stick spectra have been presented together with synthesized spectra (the sum of the Lorentzian natural line shapes) for each studied element. Taking into account the existence of an L -shell hole in the 2s or 2p subshell, the effect of additional L -shell ionization on the shapes and structure of the K x-ray spectra has been examined. It has been observed that generally with increasing atomic number Z the shapes of particular satellite line groups tend to become smoother and to differ less from the shapes of appropriate diagram lines. Relations between the values of energy shifts of various satellite lines for each element and the changes of these relations with Z have also been studied. Additionally, the relations between the intensities of different diagram lines for each element have been systematically analyzed, likewise the changes with Z of the role of particular diagram lines. This study can be helpful in reliable and quantitative interpretation of many experimental K x-ray spectra of Pd, Sn, Tb, Ta, Pb, and Th induced in collisions with various projectiles.
Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator.
Zhang, Zhe; Chen, Jue
2016-12-01
The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues. A single gate near the extracellular surface closes the channel. The regulatory domain, dephosphorylated, is located in the intracellular opening between the two nucleotide-binding domains (NBDs), preventing NBD dimerization and channel opening. The structure also reveals why many cystic-fibrosis-causing mutations would lead to defects either in folding, ion conduction, or gating and suggests new avenues for therapeutic intervention.
Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy
Directory of Open Access Journals (Sweden)
Nina A. Filenko
2012-01-01
Full Text Available Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their population was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.
Electron-Hole Counting Approach to Surface Atomic Structure
Chadi, D. J.
The observed reconstructions of III-V semiconductor surfaces are shown to be consistent with constraints imposed by a simple "electron-hole" counting rule proposed by Pashley. The rule ensures that the predicted surfaces are nonmetallic, nonpolar, and at least, metastable since the compensation of the "donor" electrons leaves no occupied states in the upper part of the band gap which can easily induce other reconstructions. Applications of the method to the problem of surface structure and passivation are examined.
Correlating atomic structure and transport in suspended graphene nanoribbons.
Qi, Zhengqing John; Rodríguez-Manzo, Julio A; Botello-Méndez, Andrés R; Hong, Sung Ju; Stach, Eric A; Park, Yung Woo; Charlier, Jean-Christophe; Drndić, Marija; Johnson, A T Charlie
2014-08-13
Graphene nanoribbons (GNRs) are promising candidates for next generation integrated circuit (IC) components; this fact motivates exploration of the relationship between crystallographic structure and transport of graphene patterned at IC-relevant length scales (edges after current annealing, presenting a pathway for the controlled fabrication of semiconducting GNRs with known edge geometry. Finally, we report on simulations of quantum transport in GNRs that are in qualitative agreement with the observations.
Directory of Open Access Journals (Sweden)
Eduardo A. Castro
2004-12-01
Full Text Available We report the results of a calculation of the normal boiling points of a representative set of 200 organic molecules through the application of QSPR theory. For this purpose we have used a particular set of flexible molecular descriptors, the so called Correlation Weighting of Atomic Orbitals with Extended Connectivity of Zero- and First-Order Graphs of Atomic Orbitals. Although in general the results show suitable behavior to predict this physical chemistry property, the existence of some deviant behaviors points to a need to complement this index with some other sort of molecular descriptors. Some possible extensions of this study are discussed.
Pimenov, Oleg A.; Belova, Natalya V.; Sliznev, Valery V.
2017-03-01
The molecular structure of tris-2,2,6,6-tetramethyl-heptane-3,5-dione thulium, or Tm(thd)3, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both the DFT(PBE0) calculations and the GED data collected at 400(8) K indicate that the molecules have D3 symmetry with a distorted antiprismatic TmO6 coordination geometry. According to GED refinements the twist angle θ, i.e. the angle of rotation of the upper O3 triangles relative to their position in regular prism is θ = 16.9(2.0)0. This value is close to both the equilibrium value obtained from the DFT calculations and to the thermal average value at the temperature of the GED experiment obtained by integration over the DFT potential energy surface. The bond distances (rh1) in the chelate ring are Tmsbnd O = 2.214(5) Å, Csbnd O = 1.278(4) Å, and Csbnd C = 1.404(3) Å. The DFT calculations yielded structure parameters in close agreement with those found experimentally. As an alternative to conventional Lewis model which was realized in NBO the topological analysis of ρ(r) in the frame of Bader's quantum theory of atoms in molecule (QTAIM) was performed.
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...
Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures
Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd
2016-05-01
Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous-crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.
Structured mirror array for two-dimensional collimation of a chromium beam in atom lithography
Institute of Scientific and Technical Information of China (English)
Zhang Wan-Jing; Ma Yan; Li Tong-Bao; Zhang Ping-Ping; Deng Xiao; Chen Sheng; Xiao Sheng-Wei
2013-01-01
Direct-write atom lithography,one of the potential nanofabrication techniques,is restricted by some difficulties in producing optical masks for the deposition of complex structures.In order to make further progress,a structured mirror array is developed to transversely collimate the chromium atomic beam in two dimensions.The best collimation is obtained when the laser red detunes by natural line-width of transition 7S3 → 7P40 of the chromium atom.The collimation ratio is 0.45 vertically (in x axis),and it is 0.55 horizontally (in y axis).The theoretical model is also simulated,and success of our structured mirror array is achieved.
Atomic resolution structure of serine protease proteinase K at ambient temperature
Masuda, Tetsuya; Suzuki, Mamoru; Inoue, Shigeyuki; Song, Changyong; Nakane, Takanori; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Mikami, Bunzo; Nureki, Osamu; Numata, Keiji; Iwata, So; Sugahara, Michihiro
2017-01-01
Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites. PMID:28361898