WorldWideScience

Sample records for atomic structure

  1. Teach us atom structure

    International Nuclear Information System (INIS)

    This book is written to teach atom structure in very easy way. It is divided into nine chapters, which indicates what is the components of matter? when we divide matter continuously, it becomes atom, what did atom look like? particles comprised of matter is not only atom, discover of particles comprised of atom, symbol of element, various radiation, form alchemy to nuclear transmutation, shape of atom is evolving. It also has various pictures in each chapters to explain easily.

  2. Teach us atom structure

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Suh Yeon

    2006-08-15

    This book is written to teach atom structure in very easy way. It is divided into nine chapters, which indicates what is the components of matter? when we divide matter continuously, it becomes atom, what did atom look like? particles comprised of matter is not only atom, discover of particles comprised of atom, symbol of element, various radiation, form alchemy to nuclear transmutation, shape of atom is evolving. It also has various pictures in each chapters to explain easily.

  3. Atomic and molecular structure

    International Nuclear Information System (INIS)

    This book is a textbook for an introductory course of atomic physics for students of chemistry. After an introduction to the mathematical and physical foundations the quantum mechanical theory of atoms is described starting from simple examples of quantum mechanics. Then the atomic structure and the chemical bending are extensively discussed. This book is also suited for physicists who are especially interested in the atomic structure and the theory of chemical reactions. (HSI)

  4. Atomic Structure Theory Lectures on Atomic Physics

    CERN Document Server

    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.

  5. Fisher Information and Atomic Structure

    CERN Document Server

    Chatzisavvas, K Ch; Panos, C P; Moustakidis, Ch C

    2013-01-01

    We present a comparative study of several information and statistical complexity measures in order to examine a possible correlation with certain experimental properties of atomic structure. Comparisons are also carryed out quantitatively using Pearson correlation coefficient. In particular, we show that Fisher information in momentum space is very sensitive to shell effects, and is directly associated with some of the most characteristic atomic properties, such as atomic radius, ionization energy, electronegativity, and atomic dipole polarizability. Finally we present a relation that emerges between Fisher information and the second moment of the probability distribution in momentum space i.e. an energy functional of interest in (e,2e) experiments.

  6. Relativistic calculations of atomic structure

    OpenAIRE

    Fricke, Burkhard

    1984-01-01

    A review of relativistic atomic structure calculations is given with a emphasis on the Multiconfigurational-Dirac-Fock method. Its problems and deficiencies are discussed together with the contributions which go beyond the Dirac-Fock procedure.

  7. Arithmetic aspects of atomic structures

    International Nuclear Information System (INIS)

    The purpose of this presentation is to give an updated account of some on-going work related to the theory of large atoms in the context of large-Z asymptotics, which began over the last decade or so. The goal of that work is to produce a refined version of the Thomas-Fermi theory that accounts for observed physical features such as electronic orbitals or an atomic shell structure. This presents similarities with issues in quantum chaos. (orig.)

  8. Universal bosonic tetramers of dimer-atom-atom structure

    OpenAIRE

    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.

  9. SUPERSTRUCTURE - AN ATOMIC STRUCTURE CODE

    OpenAIRE

    Eissner, W.

    1991-01-01

    We summarize the properties of the atomic structure code SUPERSTRUCTURE, which yields bound state energies in LS coupling and intermediate coupling as well as associated radiative data. Other data that can be computed include term coupling coefficients and radiative data with allowance for cascading. Results are given, mainly for members of the Be isoelectronic sequence, to demonstrate the power and range of the code. Other examples deal with "forbidden" transitions in N-like and He-like ions.

  10. BOOK REVIEW: Computational Atomic Structure

    Science.gov (United States)

    Post, Douglass E.

    1998-02-01

    The primary purpose of `Computational Atomic Structure' is to give a potential user of the Multi-Configuration Hartree-Fock (MCHF) Atomic Structure Package an outline of the physics and computational methods in the package, guidance on how to use the package, and information on how to interpret and use the computational results. The book is successful in all three aspects. In addition, the book provides a good overview and review of the physics of atomic structure that would be useful to the plasma physicist interested in refreshing his knowledge of atomic structure and quantum mechanics. While most of the subjects are covered in greater detail in other sources, the book is reasonably self-contained, and, in most cases, the reader can understand the basic material without recourse to other sources. The MCHF package is the standard package for computing atomic structure and wavefunctions for single or multielectron ions and atoms. It is available from a number of ftp sites. When the code was originally written in FORTRAN 77, it could only be run on large mainframes. With the advances in computer technology, the suite of codes can now be compiled and run on present day workstations and personal computers and is thus available for use by any physicist, even those with extremely modest computing resources. Sample calculations in interactive mode are included in the book to illustrate the input needed for the code, what types of results and information the code can produce, and whether the user has installed the code correctly. The user can also specify the calculational level, from simple Hartree-Fock to multiconfiguration Hartree-Fock. The MCHF method begins by finding approximate wavefunctions for the bound states of an atomic system. This involves minimizing the energy of the bound state using a variational technique. Once the wavefunctions have been determined, other atomic properties, such as the transition rates, can be determined. The book begins with an

  11. Atomic structure and electron correlations

    International Nuclear Information System (INIS)

    Synchrotron experiments combined with theoretical calculations have already given much information on atomic structure and the effects of electron correlations, and this combination of theory and experiment is expected to yield much new information in coming years. In the calculations of photoabsorption cross sections, it is almost always necessary to include electron correlations in both initial and final states to obtain good agreement with experiment. The main theoretical approaches which include effects of electron correlations have been R-matrix theory, random phase approximation with exchange (RPAE), relativistic random phase approximation with exchange, and many-body perturbation theory

  12. Electronic structure interpolation via atomic orbitals

    OpenAIRE

    Chen, Mohan; Guo, G-C; HE, LIXIN

    2010-01-01

    We present an efficient scheme for accurate electronic structure interpolations based on the 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 (LCAO) algorithms. We find that usually 1...

  13. Electronic structure interpolation via atomic orbitals

    Energy Technology Data Exchange (ETDEWEB)

    Chen Mohan; Guo, G-C; He Lixin, E-mail: helx@ustc.edu.cn [Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, 230026 (China)

    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.

  14. LOCAL ATOMIC STRUCTURE OF AMORPHOUS METALS

    OpenAIRE

    Egami, T.; Maed, K.; Srolovitz, D.; Vitek, V.

    1980-01-01

    The local parameters are introduced to describe the local atomic structure of amorphous metals. They define the structural defects which facilitate the explanation of various properties, including the volume change by annealing.

  15. Atomic Structure Calculations for Neutral Oxygen

    OpenAIRE

    Alonizan, Norah; Qindeel, Rabia; Ben Nessib, Nabil

    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.

  16. Introduction to Atomic Structure: Demonstrations and Labs.

    Science.gov (United States)

    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)

  17. Semiempirical studies of atomic structure

    International Nuclear Information System (INIS)

    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

  18. Semiempirical studies of atomic structure

    International Nuclear Information System (INIS)

    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. Typical examples are the following: lifetime measurements in the neon isoelectronic sequence; multiplexed decay curve measurements of Li-like Si XII; and isoelectronic specification of intershell resonance and intercombination decay rates using measured transition probabilities and spectroscopically determined singlet-mixing amplitudes

  19. Atomic vapor spectroscopy in integrated photonic structures

    CERN Document Server

    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.

  20. Atomic vapor spectroscopy in integrated photonic structures

    Energy Technology Data Exchange (ETDEWEB)

    Ritter, Ralf; Kübler, Harald; Pfau, Tilman; Löw, Robert, E-mail: r.loew@physik.uni-stuttgart.de [5. Physikalisches Institut and Center for Integrated Quantum Science and Technology, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); Gruhler, Nico; Pernice, Wolfram [Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen (Germany)

    2015-07-27

    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.

  1. Atomic Structure of Ultrathin Gold Nanowires.

    Science.gov (United States)

    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. PMID:27071038

  2. METHODS OF CALCULATING THE ELECTRONIC AND ATOMIC STRUCTURES OF INTERFACES

    OpenAIRE

    Sutton, A

    1985-01-01

    Methods of calculating the electronic and atomic structures of interfaces are described. An introduction to pseudopotentials and LCAO methods is given. Methods of calculating the electronic structure of an interface with a given atomic structure are considered. The feasibility of total energy calculations, in which the atomic and electronic structures are calculated simultaneously, is discussed.

  3. Atomic Structure of Benzene Which Accounts for Resonance Energy

    OpenAIRE

    Heyrovska, Raji

    2008-01-01

    Benzene is a hexagonal molecule of six carbon atoms, each of which is bound to six hydrogen atoms. The equality of all six CC bond lengths, despite the alternating double and single bonds, and the surplus (resonance) energy, led to the suggestion of two resonanting structures. Here, the new atomic structure shows that the bond length equality is due to three carbon atoms with double bond radii bound to three other carbon atoms with resonance bond radii (as in graphene). Consequently, there ar...

  4. Description of an atomic structure software package

    International Nuclear Information System (INIS)

    The MCHF method has been shown to be effective for the study of correlation and for croblems where relativistic effects are small. It has been applied to some difficult cases where a perturber is embedded in a Rydberg series and mixing depends critically on correlation. Relativistic corrections may be included through the Breit-Pauli approximation. This approach has been used recently in a study of the Boron sequence where the fine structure splitting obtained from multiconfiguration Dirac-Hartree-Fock calculations was not in good agreement with observation and a correction process was needed. It has also been used to study forbidden transitions in the Carbon, Nitrogen, and Oxygen sequence. Thus the MCHF (or MCHF+BP) method is a versatile method for the study of atomic structure for a large class of problems. The present software package is based on this method

  5. Atoms

    International Nuclear Information System (INIS)

    Completed by recent contributions on various topics (atoms and the Brownian motion, the career of Jean Perrin, the evolution of atomic physics since Jean Perrin, relationship between scientific atomism and philosophical atomism), this book is a reprint of a book published at the beginning of the twentieth century in which the author addressed the relationship between atomic theory and chemistry (molecules, atoms, the Avogadro hypothesis, molecule structures, solutes, upper limits of molecular quantities), molecular agitation (molecule velocity, molecule rotation or vibration, molecular free range), the Brownian motion and emulsions (history and general features, statistical equilibrium of emulsions), the laws of the Brownian motion (Einstein's theory, experimental control), fluctuations (the theory of Smoluchowski), light and quanta (black body, extension of quantum theory), the electricity atom, the atom genesis and destruction (transmutations, atom counting)

  6. Evolution of atomic structure during nanoparticle formation

    Directory of Open Access Journals (Sweden)

    Christoffer Tyrsted

    2014-05-01

    Full Text Available Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ, all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structure is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries.

  7. Structure and properties of atomic nanoclusters

    CERN Document Server

    Alonso, Julio A

    2011-01-01

    Atomic clusters are aggregates of atoms containing a few to several thousand atoms. Due to the small size of these pieces of matter, the properties of atomic clusters in general are different from those of the corresponding material in the macroscopic bulk phase. This monograph presents the main developments of atomic clusters and the current status of the field. The book treats different types of clusters with very different properties: clusters in which the atoms or molecules are tied by weak van der Waals interactions, metallic clusters, clusters of ionic materials, and network clusters mad

  8. Structurally uniform and atomically precise carbon nanostructures

    Science.gov (United States)

    Segawa, Yasutomo; Ito, Hideto; Itami, Kenichiro

    2016-01-01

    Nanometre-sized carbon materials consisting of benzene units oriented in unique geometric patterns, hereafter named nanocarbons, conduct electricity, absorb and emit light, and exhibit interesting magnetic properties. Spherical fullerene C60, cylindrical carbon nanotubes and sheet-like graphene are representative forms of nanocarbons, and theoretical simulations have predicted several exotic 3D nanocarbon structures. At present, synthetic routes to nanocarbons mainly lead to mixtures of molecules with a range of different structures and properties, which cannot be easily separated or refined into pure forms. Some researchers believe that it is impossible to synthesize these materials in a precise manner. Obtaining ‘pure’ nanocarbons is a great challenge in the field of nanocarbon science, and the construction of structurally uniform nanocarbons, ideally as single molecules, is crucial for the development of functional materials in nanotechnology, electronics, optics and biomedical applications. This Review highlights the organic chemistry approach — more specifically, bottom-up construction with atomic precision — that is currently the most promising strategy towards this end.

  9. 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.

  10. Atomic probes of surface structure and dynamics

    International Nuclear Information System (INIS)

    Progress for the period Sept. 15, 1992 to Sept. 14, 1993 is discussed. Semiclassical methods that will allow much faster and more accurate three-dimensional atom--surface scattering calculations, both elastic and inelastic, are being developed. The scattering of He atoms from buckyballs is being investigated as a test problem. Somewhat more detail is given on studies of He atom scattering from defective Pt surfaces. Molecular dynamics simulations of He+ and Ar+ ion sputtering of Pt surfaces are also being done. He atom scattering from Xe overlayers on metal surfaces and the thermalized dissociation of H2 on Cu(110) are being studied. (R.W.R.) 64 refs

  11. Atomic Structure of Benzene Which Accounts for Resonance Energy

    CERN Document Server

    Heyrovska, Raji

    2008-01-01

    Benzene is a hexagonal molecule of six carbon atoms, each of which is bound to six hydrogen atoms. The equality of all six CC bond lengths, despite the alternating double and single bonds, and the surplus (resonance) energy, led to the suggestion of two resonanting structures. Here, the new atomic structure shows that the bond length equality is due to three carbon atoms with double bond radii bound to three other carbon atoms with resonance bond radii (as in graphene). Consequently, there are two kinds of CH bonds of slightly different lengths. The bond energies account for the resonance energy.

  12. Atomic and magnetic structure of manganites

    International Nuclear Information System (INIS)

    Complete text of publication follows. Perovskite manganites A1-xA'xMnO3 (A=La, Pr, ..., A' = Ca, Sr,...) have become a hot problem for neutron scattering during last three years. A long story of their neutron diffraction studies, started by a classical work of Wollan and Koehler [1] on La1-xCaxMnO3 and continued by a detailed investigation of Pr1-xCaxMnO3 by Jirak et al. [2], finalised with a burst-like interest in the middle of ninetieths which was provoked by rediscovering of CMR-effect in these compounds. In last three years numerous studies have been performed in all neutron scattering centres, which helped physicists to understand the main features of CMR materials. The most important of them are the strong correlation between transport properties and changes in atomic (charge/orbital ordering) and magnetic (FM/AFM ordering) structure and their dependence on the doping level, the mean A-site canon radius and its variance, as well as cation off-stoichiometry in the compound. Neutron scattering helped also to understand the important role of a local disorder and unusually strong electron-phonon coupling for the properties of manganites. (author) [1] E.O. Wollan and W.C. Koehler, Phys. Rev. 100 (1995) 545. [2] Z. Jirak, S. Krupicka, Z. Simsa, M. Dlouha and S. Vratislav, J. Magn. Magn. Mater. 53 (1985) 153

  13. Theoretical development of atomic structure: Past, present and future

    International Nuclear Information System (INIS)

    Theoretical development of atomic structure is briefly discussed. The role of correlation, relativity, quantum electrodynamic (QED), finite nuclear size (FNS) and parity nonconservation (PNC) in high precision theoretical investigation of properties of atomic and ionic systems is demonstrated. At present, we do not have a comprehensive and practical atomic structure theory which accounts all these physical effects on an equal footing. Suggestions are made for future directions. (author). 108 refs, 5 figs, 9 tabs

  14. A Variational Monte Carlo Approach to Atomic Structure

    Science.gov (United States)

    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.

  15. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

    Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    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....

  16. Stability and structure of atomic chains on Si(111)

    OpenAIRE

    Battaglia, Corsin; Aebi, Philipp; Erwin, Steven C.

    2008-01-01

    We study the stability and structure of self-assembled atomic chains on Si(111) induced by monovalent, divalent and trivalent adsorbates, using first-principles total-energy calculations and scanning tunneling microscopy. We find that only structures containing exclusively silicon honeycomb or silicon Seiwatz chains are thermodynamically stable, while mixed configurations, with both honeycomb and Seiwatz chains, may be kinetically stable. The stability and structure of these atomic chains can...

  17. Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures

    Science.gov (United States)

    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.

  18. Kinetic-energy density functional: Atoms and shell structure

    International Nuclear Information System (INIS)

    We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. copyright 1996 The American Physical Society

  19. Single structured light beam as an atomic cloud splitter

    International Nuclear Information System (INIS)

    We propose a scheme to split a cloud of cold noninteracting neutral atoms based on their dipole interaction with a single structured light beam which exhibits parabolic cylindrical symmetry. Using semiclassical numerical simulations, we establish a direct relationship between the general properties of the light beam and the relevant geometric and kinematic properties acquired by the atomic cloud as it passes through the beam.

  20. Presentation of Atomic Structure in Turkish General Chemistry Textbooks

    Science.gov (United States)

    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…

  1. 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.

  2. Structures of 38-atom gold-platinum nanoalloy clusters

    International Nuclear Information System (INIS)

    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, AunPt38−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

  3. Update on nuclear structure effects in light muonic atoms

    CERN Document Server

    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.

  4. Interfacial Atomic Structure of Twisted Few-Layer Graphene

    OpenAIRE

    Ryo Ishikawa; Nathan R. Lugg; Kazutoshi Inoue; Hidetaka Sawada; Takashi Taniguchi; Naoya Shibata; Yuichi Ikuhara

    2016-01-01

    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 parameterize...

  5. Crystal structure solution from experimentally determined atomic pair distribution functions

    OpenAIRE

    Juhas, Pavol; Granlund, Luke; Gujarathi, Saurabh R.; Duxbury, Phillip M.; Billinge, Simon J. L.

    2010-01-01

    The paper describes an extension of the Liga algorithm for structure solution from atomic pair distribution function (PDF), to handle periodic crystal structures with multiple elements in the unit cell. The procedure is performed in 2 separate steps - at first the Liga algorithm is used to find unit cell sites consistent with pair distances extracted from the experimental PDF. In the second step the assignment of atom species over cell sites is solved by minimizing the overlap of their empiri...

  6. Atomic fine structure in a space of constant curvature

    Energy Technology Data Exchange (ETDEWEB)

    Bessis, N.; Bessis, G.; Shamseddine, R. (Lyon-1 Univ., 69 - Villeurbanne (France))

    1982-10-01

    As a contribution to a tentative formulation of atomic physics in a curved space, the determination of atomic fine structure energies in a space of constant curvature is investigated. Starting from the Dirac equation in a curved space-time, the analogue of the Pauli equation in a general coordinate system is derived. The theoretical curvature induced shifts and splittings of the fine structure energy levels are put in evidence and examined for the particular case of the hydrogenic n=2 levels.

  7. Atomic fine structure in a space of constant curvature

    International Nuclear Information System (INIS)

    As a contribution to a tentative formulation of atomic physics in a curved space, the determination of atomic fine structure energies in a space of constant curvature is investigated. Starting from the Dirac equation in a curved space-time, the analogue of the Pauli equation in a general coordinate system is derived. The theoretical curvature induced shifts and splittings of the fine structure energy levels are put in evidence and examined for the particular case of the hydrogenic n=2 levels. (author)

  8. Generalized atomic displacements in crystallographie structure analysis

    International Nuclear Information System (INIS)

    An attempt is made to summarize both theoretical and experimental aspects of generalized atomic displacement parameters (ADP's) in crystalline matter. Generalized displacement parameters are used to describe the weakening of Bragg intensities via the anharmonic (static or thermal) Debye-Waller factor (DWF) and its real-space counterpart, the generalized atomic probability density function (p.d.f.). The lattice dynamical base of the harmonic and anharmonic thermal DWF is discussed. It is pointed out that the static DWF frequently contains higher-order terms. The mathematical case for an experimental determination of generalized ADP's is given. The most popular current formulations (one-particle potential and statistical approaches) are reviewed and their individual limitations are discussed. Likewise the demands put on the quality and extent of experimental data are assessed. Some aids to the interpretation of generalized ADP's established by crystallographic least-squares procedures are given and a Monte-Carlo method for the calculation of errors in p.d.f. maps is presented. Finally, some prospects for future work are outlined and a more frequent comparison of theoretical calculations and experimental determinations of generalized ADP's is advocated. (orig.)

  9. Max Auwaerter Price lecture: building and probing atomic structures

    International Nuclear Information System (INIS)

    Full text: The control of the geometric, electronic, and magnetic properties of atomic-scale nanostructures is a prerequisite for the understanding and fabrication of new materials and devices. Two routes lead towards this goal: Atomic manipulation of single atoms and molecules by scanning probe microscopy, or patterning using self-assembly. Atomic manipulation has been performed since almost 20 years, but it has been difficult to answer the simple question: how much force does it take to manipulate atoms and molecules on surfaces? To address this question, we used a combined atomic force and scanning tunneling microscope to simultaneously measure the force and the current between an adsorbate and a tip during atomic manipulation. We found that the force it takes to move an atom depends crucially on the binding between adsorbate and surface. Our results indicate that for moving metal atoms on metal surfaces, the lateral force component plays the dominant role. Measuring the forces during manipulation yielded the full potential energy landscape of the tip-sample interaction. Surprisingly, the potential energy barriers are comparable to diffusion barriers, which are obtained in the absence of a probe tip. Furthermore, we used the scanning tunneling microscope to assemble magnetic structures on a thin insulator. We found, that the spin of the atom is influenced by the magnetocrystalline anisotropy of the supporting surface which lifts the spin degeneracy of the ground state and enables the identification of individual atoms. The ground state of atoms with half-integer spin remains always degenerated at zero field due to Kramers theorem. We found that if these states differ by an orbital momentum of m = ±1 the localized spin is screened by the surrounding conducting electrons of the non-magnetic host and form a many-electron spin-singlet at sufficiently low temperature. (author)

  10. Unraveling the atomic structure of ultrafine iron clusters

    KAUST Repository

    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.

  11. Direct experimental determination of the atomic structure at internal interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Browning, N.D. [Oak Ridge National Lab., TN (United States)]|[Illinois Univ., Chicago, IL (United States); Pennycook, S.J. [Oak Ridge National Lab., TN (United States)

    1995-07-01

    A crucial first step in understanding the effect that internal interfaces have on the properties of materials is the ability to determine the atomic structure at the interface. As interfaces can contain atomic disorder, dislocations, segregated impurities and interphases, sensitivity to all of these features is essential for complete experimental characterization. By combining Z-contrast imaging and electron energy loss spectroscopy (EELS) in a dedicated scanning transmission electron microscope (STEM), the ability to probe the structure, bonding and composition at interfaces with the necessary atomic resolution has been obtained. Experimental conditions can be controlled to provide, simultaneously, both incoherent imaging and spectroscopy. This enables interface structures observed in the image to be interpreted intuitively and the bonding in a specified atomic column to be probed directly by EELS. The bonding and structure information can then be correlated using bond-valence sum analysis to produce structural models. This technique is demonstrated for 25{degrees}, 36{degrees} and 67{degrees} symmetric and 45{degrees} and 25{degrees} asymmetric [001] tilt grain boundaries in SrTiO{sub 3} The structures of both types of boundary were found to contain partially occupied columns in the boundary plane. From these experimental results, a series of structural units were identified which could be combined, using continuity of gain boundary structure principles, to construct all [001] tilt boundaries in SrTiO{sub 3}. Using these models, the ability of this technique to address the issues of vacancies and dopant segregation at grain boundaries in electroceramics is discussed.

  12. Atomic quantum systems in optical micro-structures

    International Nuclear Information System (INIS)

    Full text: We combine state-of-the-art technology in micro-optics with the quantum optical techniques of laser cooling, laser trapping, and quantum control to open a new gateway for quantum information processing and matter wave optics with atomic systems. We use micro-fabricated optical systems to create light fields that allow us to trap and guide neutral atoms as a result of the optical dipole force experienced by the atoms. The realization of arrays of laser traps that can serve as registers for atomic quantum bits and as integrated waveguide structures for atom optics and atom interferometry has been achieved. This approach opens the possibility to scale, parallelize, and miniaturize systems for quantum information processing and atom optics. Currently we investigate the production of quantum-degenerate systems in pure optical trapping geometries and the coherent manipulation (1-qubit rotations, Ramsey-oscillations, spin-echo experiments) of internal qubit states for atoms trapped in arrays of dipole traps (author)

  13. 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.

  14. Understanding Atomic Structure: Is There a More Direct and Compelling Connection between Atomic Line Spectra and the Quantization of an Atom's Energy?

    Science.gov (United States)

    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,…

  15. Atomic structure of grain boundaries in iron modeled using the atomic density function

    OpenAIRE

    Kapikranian, O.; Zapolsky, H; Domain, Ch.; Patte, R.; Pareige, C.; Radiguet, B.; Pareige, P.

    2013-01-01

    A model based on the continuous atomic density function (ADF) approach is applied to predict the atomic structure of grain boundaries (GBs) in iron. Symmetrical [100] and [110] tilt GBs in bcc iron are modeled with the ADF method and relaxed afterwards in molecular dynamics (MD) simulations. The shape of the GB energy curve obtained in the ADF model reproduces well the peculiarities of the angles of 70.53 deg. [$\\Sigma$ 3(112)] and 129.52 deg. [$\\Sigma$ 11(332)] for [110] tilt GBs. The result...

  16. Theoretical atomic physics code development I: CATS: Cowan Atomic Structure Code

    International Nuclear Information System (INIS)

    An adaptation of R.D. Cowan's Atomic Structure program, CATS, has been developed as part of the Theoretical Atomic Physics (TAPS) code development effort at Los Alamos. CATS has been designed to be easy to run and to produce data files that can interface with other programs easily. The CATS produced data files currently include wave functions, energy levels, oscillator strengths, plane-wave-Born electron-ion collision strengths, photoionization cross sections, and a variety of other quantities. This paper describes the use of CATS. 10 refs

  17. 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...

  18. Workshop on foundations of the relativistic theory of atomic structure

    International Nuclear Information System (INIS)

    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

  19. Nanoscale Structuring of Surfaces by Using Atomic Layer Deposition.

    Science.gov (United States)

    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. PMID:26538495

  20. Atomic Structure and Properties of Extended Defects in Silicon

    Energy Technology Data Exchange (ETDEWEB)

    Buczko, R.; Chisholm, M.F.; Kaplan, T.; Maiti, A.; Mostoller, M.; Pantelides, S.T.; Pennycook, S.J.

    1998-10-15

    The Z-contrast technique represents a new approach to high-resolution electron microscopy allowing for the first time incoherent imaging of materials on the atomic scale. The key advantages of the technique, an intrinsically higher resolution limit and directly interpretable, compositionally sensitive imaging, allow a new level of insight into the atomic configurations of extended defects in silicon. This experimental technique has been combined with theoretical calculations (a combination of first principles, tight binding, and classical methods) to extend this level of insight by obtaining the energetic and electronic structure of the defects.

  1. Scanning probe microscopy of oxide surfaces: atomic structure and properties

    International Nuclear Information System (INIS)

    The intersection of two fields, oxide surface science and scanning probe microscopy (SPM), has yielded considerable insight on atomic processes at surfaces. Oxide surfaces, especially those containing transition metals, offer a rich variety of structures and localized physical phenomena that are exploited in a wide range of applications. Nonlinear optics, superconductivity, ferroelectricity and chemical catalytic activity are but a few. Furthermore, the challenges and solutions associated with the chemistry of these surfaces and particularly the solutions to these problems have led to important understanding of tip-surface interactions that can inform SPM studies of all materials. Here, the development of understanding of the model systems TiO2 and SrTiO3 are considered in detail, to demonstrate the role of nonstoichiometry in surface structure evolution and the approach to interpreting structure at the atomic level. Then a combination of scanning tunneling microscopy, noncontact atomic force microscopy and theory are applied to a variety of oxide systems including Al2O3, NiO, ferroelectric BaTiO3, tungstates and molybdates. Recently developed sophisticated probes of local properties include spin-polarized tunneling, Fourier mapping of charge density waves, band gap mapping of superconductors and ultra fast imaging of atomic diffusion. The impact of these studies on our understanding of the behavior of oxides and of tip-surface interactions is summarized

  2. Optomechanical self-structuring in cold atomic gases

    CERN Document Server

    Labeyrie, Guillaume; Gomes, Pedro M; Oppo, Gian-Luca; Firth, William J; Robb, Gordon R M; Arnold, Aidan S; Kaiser, Robin; Ackemann, Thorsten

    2013-01-01

    The rapidly developing field of optomechanics aims at the combined control of optical and mechanical (solid-state or atomic) modes. In particular, laser cooled atoms have been used to exploit optomechanical coupling for self-organization in a variety of schemes where the accessible length scales are constrained by a combination of pump modes and those associated to a second imposed axis, typically a cavity axis. Here, we consider a system with many spatial degrees of freedom around a single distinguished axis, in which two symmetries - rotations and translations in the plane orthogonal to the pump axis - are spontaneously broken. We observe the simultaneous spatial structuring of the density of a cold atomic cloud and an optical pump beam. The resulting patterns have hexagonal symmetry. The experiment demonstrates the manipulation of matter by opto-mechanical self-assembly with adjustable length scales and can be potentially extended to quantum degenerate gases.

  3. Structural properties of lithium atom under weakly coupled plasma environment

    Science.gov (United States)

    Dutta, S.; Saha, J. K.; Chandra, R.; Mukherjee, T. K.

    2016-04-01

    The Rayleigh-Ritz variational technique with a Hylleraas basis set is being tested for the first time to estimate the structural modifications of a lithium atom embedded in a weakly coupled plasma environment. The Debye-Huckel potential is used to mimic the weakly coupled plasma environment. The wave functions for both the helium-like lithium ion and the lithium atom are expanded in the explicitly correlated Hylleraas type basis set which fully takes care of the electron-electron correlation effect. Due to the continuum lowering under plasma environment, the ionization potential of the system gradually decreases leading to the destabilization of the atom. The excited states destabilize at a lower value of the plasma density. The estimated ionization potential agrees fairly well with the few available theoretical estimates. The variation of one and two particle moments, dielectric susceptibility and magnetic shielding constant, with respect to plasma density is also been discussed in detail.

  4. Atomic spectroscopy introduction to the theory of hyperfine structure

    CERN Document Server

    Andreev, Anatoli V

    2006-01-01

    Atomic Spectroscopy provides a comprehensive discussion on the general approach to the theory of atomic spectra, based on the use of the Lagrangian canonical formalism. This approach is developed and applied to explain the hydrogenic hyperfine structure associated with the nucleus motion, its finite mass, and spin. The non-relativistic or relativistic, spin or spin-free particle approximations can be used as a starting point of general approach. The special attention is paid to the theory of Lamb shift formation. The formulae for hydrogenic spectrum including the account of Lamb shift are written in simple analytical form. The book is of interest to specialists, graduate and postgraduate students, who are involved into the experimental and theoretical research in the field of modern atomic spectroscopy.

  5. Developing a New Atomic Physics Computer Program (HTAC) to Perform Atomic Structure and Transition Rate Calculations in Three Advanced Methods

    OpenAIRE

    Amani Tahat; Mahmoud Abu-Allaban; Safeia Hamasha

    2011-01-01

    In this study, a new atomic physics program (HTAC) is introduced and tested. It is a utility program designed to automate the computation of various atomic structure and spectral data. It is the first comprehensive code that enables performing atomic calculations based on three advanced theories: the fully relativistic configuration interactions approach, the multi-reference many body perturbation theory and the R-Matrix method. It has been designed to generate tabulated atomic data files tha...

  6. Atomic structure of non-stoichiometric transition metal carbides

    International Nuclear Information System (INIS)

    Different kinds of experimental studies of the atomic arrangement in non-stoichiometric transition metal carbides are proposed: the ordering of carbon vacancies and the atomic static displacements are the main subjects studied. Powder neutron diffraction on TiCsub(1-x) allowed us to determine the order-disorder transition critical temperature -Tsub(c) approximately 7700C- in the TiCsub(0.52-0.67) range, and to analyze at 300 K the crystal structure of long-range ordered samples. A neutron diffuse scattering quantitative study at 300 K of short-range order in TiCsub(0.76), TiCsub(0.79) and NbCsub(0.73) single crystals is presented: as in Ti2Csub(1+x) and Nb6C5 superstructures, vacancies avoid to be on each side of a metal atom. Besides, the mean-square carbon atom displacements from their sites are small, whereas metal atoms move radially about 0.03 A away from vacancies. These results are in qualitative agreement with EXAFS measurements at titanium-K edge of TiCsub(1-x). An interpretation of ordering in term of short-range interaction pair potentials between vacancies is proposed

  7. Interfacial Atomic Structure of Twisted Few-Layer Graphene

    Science.gov (United States)

    Ishikawa, Ryo; Lugg, Nathan R.; Inoue, Kazutoshi; Sawada, Hidetaka; Taniguchi, Takashi; Shibata, Naoya; Ikuhara, Yuichi

    2016-01-01

    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. PMID:26888259

  8. Atomic Structure Control of Silica Thin Films on Pt(111)

    KAUST Repository

    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.

  9. The variational method in the atomic structure calcularion

    International Nuclear Information System (INIS)

    The importance and limitations of variational methods on the atomic structure calculations is set into relevance. Comparisons are made to the Perturbation Theory. Ilustrating it, the method is applied to the H-, H+ and H+2 simple atomic structure systems, and the results are analysed with basis on the study of the associated essential eigenvalue spectrum. Hydrogenic functions (where the screening constants are replaced by variational parameters) are combined to construct the wave function with proper symmetry for each one of the systems. This shows the existence of a bound state for H-, but no conclusions can be made for the others, where it may or may not be necessary to use more flexible wave functions, i.e., with greater number of terms and parameters. (author)

  10. Atomic scale structure investigations of epitaxial Fe/Cr multilayers

    International Nuclear Information System (INIS)

    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.

  11. Study of atomic structure of polycrystalline vanadium molybdate

    International Nuclear Information System (INIS)

    Atomic structure of polycrystalline V0.95Mo0.97O5 (V4+/V5+=0.6) was investigated by the methods of X-ray diffraction analysis, electron microdiffraction and high resolution electron microscopy. Lattice parameters: a=6.3340, b=4.0463, c=3.7255 A, α=90.0, β=107.3, γ=90.5 deg, sp.gr. P1, Z=1. Mo and V atoms substitute statistically each other in two independent octahedral positions: (0.4 Mo + 0.6 V4+) and (0.6 Mo + 0.4 V5+). The compound is refferred to V2O5 structural type

  12. Atomic structure calculations of Mo XV-XL

    International Nuclear Information System (INIS)

    Energy levels and oscillator strengths were calculated for Mo XV - Mo XL. The computer program for atomic structure calculation, developed by Dr. Robert D. Cowan, Los Alamos National Laboratory, was used in the present work. The scaled energy parameters were empirically determined from the observed spectral data. We present wavelengths and transition probabilities of Mo XV-XL. Energy levels and spectral patterns are presented in figures that are useful for the identification of spectral lines. (author)

  13. Atomic structure calculations on the CRAY X-MP

    International Nuclear Information System (INIS)

    Atomic structure calculations require both radial and angular integrations, where the latter are often based on Racah algebra. With relatively minor modifications, good performance is obtained on vector machines for radial integrations. Angular integrations, however, present the bottleneck. In this paper some recent improvements in the algorithms for angular integrations are described, as well as some multitasking experiments on the CRAY X-MP and CRAY 2. These show that the workload can easily be distributed evenly among available processors with dynamic scheduling

  14. Phase Space Structures Explain Hydrogen Atom Roaming in Formaldehyde Decomposition

    OpenAIRE

    Mauguiere, Frederic A L; Collins, Peter R C; Kramer, Zeb C.; Carpenter, Barry K.; Ezra, Gregory S.; Farantos, Stavros; Wiggins, Stephen R

    2015-01-01

    We re-examine the prototypical roaming reaction—hydrogen atom roaming in formaldehyde decomposition—from a phase space perspective. Specifically, we address the question “why do trajectories roam, rather than dissociate through the radical channel?” We describe and compute the phase space structures that define and control all possible reactive events for this reaction, as well as provide a dynamically exact description of the roaming region in phase space. Using these phase space constructs,...

  15. Structural and chemical characterization of complex nanomaterials at atomic resolution

    Science.gov (United States)

    Sanchez, Sergio I.

    Catalytic and energetic nanomaterials are analyzed chemically and structurally in atomistic detail. Examination of the prototypical industrial catalyst Pt catalysts supported on gamma-Al2O3 using X-ray absorption spectroscopy (XAS) and scanning transmission electron microscopy (STEM) revealed non-bulk-like behavior. Anomalous, temperature-dependent structural dynamics were characterized in the form of negative thermal expansion (NTE) and abnormal levels of disorder. To examine a less complex system, electrocatalytically-active, core-shell nanostructures assembled from Pt and Pd were synthesized and subsequently examined using spherical aberration-corrected STEM (Cs-STEM) and high-energy X-ray diffraction (XRD). Atomically resolved micrographs provide significant insight into the differences in crystallinity and metal-atom bonding between Pt and Pd. The apparent structural dichotomy between Pt and Pd was extended to studying the differences in nanostructure between other third row fcc transition metals (3M -- Ir, Pt, and Au) and their second row counterparts (2M -- Rh, Pd, and Ag). With the use of Cs-STEM and atomic pair distribution function (PDF) measurements it was determined that the Au, Pt and Ir nanocrystals were more crystalline than their Ag, Pd and Rh analogues and that the 3M series was capable of imparting its crystal structure onto the atoms from the 2M series. Lastly, we looked at highly-reactive Al crystals and their successive passivation by secondary transition metals (Cu, Ni, Ag, Pd, Au and Pt). Rather than affording a uniform, monolayer coverage, C s-STEM, XRD and energy dispersive X-ray spectroscopy revealed unalloyed, particulate deposits of the secondary metal on the Al.

  16. Development of atomic spectroscopy technologies - Hyperfine structure of 2 period atoms using optogalvanic effects

    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)

  17. The atomic structure of liquid Fe–C alloys

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Shaopeng, E-mail: shaopengpan@gmail.com [College of Materials Science and Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Feng, Shidong [State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004 (China); Qiao, Junwei [College of Materials Science and Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Dong, Bangshao [Advanced Technology & Materials Co., Ltd., China Iron & Steel Research Institute Group, Beijing 100081 (China); Qin, Jingyu, E-mail: qinjy@sdu.edu.cn [Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials (Ministry of Education), Shandong University, Jinan 250061 (China)

    2015-11-05

    The structures of liquid Fe–C alloys in the Fe-rich end were investigated by ab initio molecular dynamics simulations. The trend of intensity of chemical short range order around Fe and C atoms changes at the eutectic composition, indicating the close correlation between liquid structure and phase diagram. The tri-capped trigonal prism (Voronoi index <0,3,6,0>) and mono-capped square archimedean antiprism (Voronoi index <0,4,4,0>) around C atoms have the largest frequency fractions and the longest lifetimes among all the polyhedra. Moreover, they tend to connect with each other to form network structure. The maximum intensity of network structure is located at the 20% C composition, which might be the reason why alloys near eutectic composition have great glass-forming ability. - Highlights: • A new parameter is proposed to describe chemical short range order. • Close correlation between structure and phase diagram is found in Fe–C system. • Close correlation between structure and glass forming ability is also found.

  18. Cavities and atomic packing in protein structures and interfaces.

    Directory of Open Access Journals (Sweden)

    Shrihari Sonavane

    2008-09-01

    Full Text Available A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively is presented. The total volume of cavities increases with the size of the protein (or the interface, though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 A(3 of cavity volume is found to accommodate single water, with another 40-45 A(3 needed for each additional solvent molecule. Polar atoms/residues have a higher propensity to line solvated cavities. Relative to the frequency of occurrence in the whole structure (or interface, residues in beta-strands are found more often lining the cavities, and those in turn and loop the least. Any depression in one chain not complemented by a protrusion in the other results in a cavity in the protein-protein interface. Through the use of the Voronoi volume, the packing of residues involved in protein-protein interaction has been compared to that in the protein interior. For a comparable number of atoms the interface has about twice the number of cavities relative to the tertiary structure.

  19. Atomic and electronic structure of exfoliated black phosphorus

    International Nuclear Information System (INIS)

    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 PO3 or H3PO3 during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time

  20. 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.

  1. Atoms

    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

  2. Atomic structures of peptide self-assembly mimics

    OpenAIRE

    Makabe, Koki; McElheny, Dan; Tereshko, Valentia; Hilyard, Aaron; Gawlak, Grzegorz; Yan, Shude; Koide, Akiko; Koide, Shohei

    2006-01-01

    Although the β-rich self-assemblies are a major structural class for polypeptides and the focus of intense research, little is known about their atomic structures and dynamics due to their insoluble and noncrystalline nature. We developed a protein engineering strategy that captures a self-assembly segment in a water-soluble molecule. A predefined number of self-assembling peptide units are linked, and the β-sheet ends are capped to prevent aggregation, which yields a mono-dispersed soluble p...

  3. Multi-million atom electronic structure calculations for quantum dots

    Science.gov (United States)

    Usman, Muhammad

    Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined

  4. Atomic layer deposition in porous structures: 3D photonic crystals

    International Nuclear Information System (INIS)

    This paper reports recent results from studies of atomic layer deposition for the infiltration of three-dimensional photonic crystals. Infiltration of ZnS:Mn and TiO2 are reported for SiO2-based opal templates. It has been demonstrated that high filling fractions can be achieved and that the infiltrated material can be of high crystalline quality as assessed by photoluminescence measurements. The highly conformal and uniform coatings obtained in these studies are shown to contribute significantly to the photonic band gap properties. These investigations show the advantages of atomic layer deposition (ALD) as a flexible and practical pathway for attaining high performance photonic crystal structures and optical microcavities

  5. Atomic Clocks and Variations of the FIne Structure Constant

    Science.gov (United States)

    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.

  6. Absence of a stable atomic structure in fluorinated graphene.

    Science.gov (United States)

    Boukhvalov, Danil W

    2016-05-21

    Based on the results of first-principles calculations we demonstrate that significant distortion of graphene sheets caused by adsorption of fluorine atoms leads to the formation of metastable patterns for which the next step of fluorination is considerably less energetically favorable. Existence of these stable patterns oriented along the armchair direction makes possible the synthesis of various CFx structures. The combination of strong distortion of the nonfluorinated graphene sheet with the doping caused by the polar nature of C-F bonds reduces the energy cost of migration and the energy of migration barriers, making possible the migration of fluorine atoms on the graphene surface as well as transformation of the shapes of fluorinated areas. The decreasing energy cost of migration with increasing fluorine content also leads to increasing numbers of single fluorine adatoms, which could be the source of magnetic moments. PMID:27116897

  7. Spatial multimode structure of atom-generated squeezed light

    Science.gov (United States)

    Zhang, Mi; Lanning, R. Nicholas; Xiao, Zhihao; Dowling, Jonathan P.; Novikova, Irina; Mikhailov, Eugeniy E.

    2016-01-01

    We investigated the spatial distribution of quantum fluctuations in a squeezed vacuum field, generated via polarization self-rotation (PSR) interaction of an ensemble of Rb atoms and a strong near-resonant linearly polarized laser field. We found that the noise suppression is greatly effected by the transverse profile of a spatial mask, placed in both the squeezed field and the local oscillator, as well as its position along the focused beam near the focal point. These observations indicate the spatial multimode structure of the squeezed vacuum field. We have developed a theoretical model that describes the generation of higher-order Laguerre-Gauss modes as a result of PSR light-atom interaction. The prediction of this model is in a good qualitative agreement with the experimental measurements.

  8. A new approach to the structure of the lightest atoms

    International Nuclear Information System (INIS)

    Full text: Negative ions of the lightest nuclei are often produced in ion sources of modern linear accelerators. Apart from that H- machines are currently used for producing radiopharmaceuticals. The structure of H- atom is missing in many textbooks on quantum mechanics. The H- atom is one of the simplest three-body (or four-body) systems and it is tempting to use the variation method, which leads to the classical formula for the ground state energy of Helium-like atoms: Eo(Z)= -27.2(Z-5/16)2. However, variation methods with 3, 6, and 11 parameters were used in the case of H-. Using the formula, one takes into account the screening of the atomic charge by one electron from the point of view of the other. Nevertheless, the trial function used in classical calculations exhibits the same probability of finding two electrons at the same point as e.g. in two points, where the nucleus in midway between them. This is the reason why one is tempted to modify the classical trial function by the factor s(Z) (r1-r2), in the hope to avoid the necessity of introducing so many variation parameters. In eq.(2) we introduced s(Z) for the new variation parameter and r1 and r2 are position vectors of the two electrons. The expression (2) is zero, when the two electrons coincide. The optimal value of s(1) turns out to be s(1)=0.03037 for Z=1, while for heavier helium-like atoms the optimal s(Z) will be negative. In the case of Z=10, the parameter s(10) reaches almost its asymptotic value Sasmp= -0.0541. The expression for the ground state energy of Helium-like atoms Eo,s(Z) is now, of course, more complicated than eq.(1). In the case of H- we obtain Eo,s(1)=-12.82762 eV, the value slightly smaller than the binding energy of the neutral Hydrogen atom, EH=-13.5985 eV. Since Eo,s(1) is not directly accessible in experiment, we have to start up with the reactions like: H2 + e→H-+H or H2 + e→ H-+H+e. They provide us in fact with the binding energy of H- in the molecule H2, which turns

  9. Atomic Structure of Au−Pd Bimetallic Alloyed Nanoparticles

    KAUST Repository

    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.

  10. An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

    OpenAIRE

    Whitford, Paul C.; Jeffrey K Noel; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

    2009-01-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) 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...

  11. Atomic-resolution structures of prion AGAAAAGA amyloid fibrils

    CERN Document Server

    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.

  12. Atomic structure of Re-Si amorphous alloys

    International Nuclear Information System (INIS)

    The atomic structure of Re100-xSix (x=0, 4, 11, 20, 31, 47, 54, 70, 82, 88, 100) amorphous alloys (AA) was studied by X-ray diffraction. In as-quenched alloys two amorphous phase were observed: the AI-phase-10-90 at.% Si and AII-phase-45-100 at.% Si, especially that in the composition range 45-90 at.% Si is the coexistence of two phase AI and AII. A comparison of the short range order parameters of the AA and those of the corresponding crystalline compounds has been done. The short-range order of AI-phase and coordination polyhedrons of Re5Si3, ReSi2 compounds is similar. Contrary to the Gaskell's model for metal-metalloid AA (trigonal prismatic structural unit) it seems to be tetragonal antiprism. The structure of AII-phase is the same as a-Si. (orig.)

  13. Atomic structures of icosahedral phases of type F and dislocations

    International Nuclear Information System (INIS)

    The object of this thesis is the study of atomic structures of icosahedral phases of type F and their dislocations. In this study, we have first built a prototypical structure that describes the already known F type icosahedral phases. In order to check it we synthesized some of the new compositions predicted by this model. This synthesis led to the discovery of two new quasi-periodical phases of the stoichiometry Al66,08Cu21,35Mn8,29Fe4,28. One of these phases is icosahedral (metastable) of type F and the other one is decagonal (stable). A F-IQC phase is present on these compounds that have a different composition with respect to the ones already studied for the system (Al,Pd,Fe). Globally, these experimental results on new icosahedral phases allowed to prove the viability of the model: on the three samples of new composition, two of them have shown the existence of icosahedral phases of type F and the third one has given a decagonal phase, in relation of canonical orientation with the icosahedral metastable phase (10-fold axis parallel with 5-fold axis). Using this reliable model, we have been able to introduce dislocations. We could thus provide the geometry of dislocations (outside the dislocation core) at atomic scale for F-IQC phases. On this structure we have also identified the distributions of phasons and given some elements of answer for the global dislocations moves. (author)

  14. Refinement of Atomic Structures Against cryo-EM Maps.

    Science.gov (United States)

    Murshudov, G N

    2016-01-01

    This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models. PMID:27572731

  15. Notes on Critical Assessment of Theoretical Calculations of Atomic Structure and Transition Probabilities

    OpenAIRE

    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...

  16. Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii

    CERN Document Server

    Heyrovska, Raji

    2007-01-01

    The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of adenine, guanine, thymine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On examining the bond length data in the literature, it has been found that the averages of the bond lengths are close to the sums of the corresponding atomic covalent radii of carbon, nitrogen, oxygen, hydrogen and phosphorus. Thus, the conventional molecular structures have been resolved here, for the first time, into probable atomic structures.

  17. Ternary atom site location in L12-structured intermetallic compounds

    International Nuclear Information System (INIS)

    Ternary sublattice site occupancy in two L12-structured intermetallic compounds were evaluated by a transmission electron microscope technique called ALCHEMI, or atom site location by channeling enhanced microanalysis, and by x-ray diffractometry, through measuring the relative integrated intensity of fundamental and superlattice x-ray diffraction peaks. The x-ray diffractometry showed that in nickel-rich Ni3Al+Hf hafnium was found to occupy preferentially the aluminum sublattice, and in a multiphase alloy an L12-structured phase with the composition Al74.2Ti19Ni6.8 nickel atoms showed a strong preference for the titanium sublattice. The ALCHEMI data broadly agreed with the x-ray results for Ni3Al but gave completely the opposite result, i.e., a preference of nickel for the titanium sublattice, for Al3Ti. The methods of ALCHEMI and x-ray diffractometry are compared, and it is concluded that ALCHEMI data may be easily convoluted by peak overlap and delocalization effects

  18. Atomic structure of amorphous shear bands in boron carbide.

    Science.gov (United States)

    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. PMID:24052052

  19. The atomic and electronic structure of dislocations in Ga based nitride semiconductors

    OpenAIRE

    BELABBAS, Imad; Ruterana, Pierre; Chen, Jun; NOUET, Gérard

    2006-01-01

    Abstract The atomic and electronic properties of dislocations in III-N semiconductor layers, especially GaN are presented. The atomic structure of the edge threading dislocation is now well established with three different cores (8 or full core, 5/7 or open core and 4 atom ring). The use of atomistic simulations has confirmed these atomic structures and has given a good understanding of the electronic structure of the screw dislocation. Partial dislocations which are mostly confin...

  20. Hyperfine structure near infrared spectrum of atomic iodine

    International Nuclear Information System (INIS)

    The hyperfine structure of spectral lines of neutral iodine (II) in the wavenumber region from 11 300 cm−1 to 13 000 cm−1 was studied using optical heterodyne concentration modulation absorption spectroscopy with a tunable single-mode cw Ti:Sapphire laser. The iodine atoms were produced and excited by a discharge operated in a mixture of helium and iodine vapor. A total of 89 lines were observed and the hyperfine structure of 45 of these lines was studied. For 40 lines, the hyperfine structure was not previously known. The magnetic dipole and the electric quadrupole hyperfine structure constants of 18 even and 28 odd levels were extracted. The constants of one even level and of 16 odd levels are presented for the first time. - Highlights: • Absorption spectrum of neutral iodine (II) between 11 300 cm−1 and 13 000 cm−1. • The hyperfine structures of II are resolved for 45 lines. • Magnetic dipole and the electric quadrupole constants are obtained. • Constants of some levels are newly reported

  1. Atomic structures of Zr-based metallic glasses

    Institute of Scientific and Technical Information of China (English)

    HUI XiDong; LIU Xiongdun; GAO Rui; HOU HuaiYu; FANG HuaZhi; LIU ZiKui; CHEN GuoLiang

    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 lOP 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 (1 D) periodicity, then 2D periodicity, and finally the formation of 3D nanocrystals. It is also noted that these three growth steps are crosslinked.

  2. 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.

  3. Atomic structure and electronic states of extended defects in silicon

    International Nuclear Information System (INIS)

    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-shaped NiSi2 and Cu3Si precipitates with other impurities. This allows to study their intrinsic electrical activity. Comparison of experimental results with numerical simulations enables identification of structural units originating electrical activity and yields first evaluations of extended defect parameters. Accordingly, e.g., in the case of as-quenched NiSi2 it is the dislocation bounding the platelet that provides a one-dimensional distribution of deep electronic states

  4. Electronic Structure of Helium Atom in a Quantum Dot

    Science.gov (United States)

    Jayanta, K. Saha; Bhattacharyya, S.; T. K., Mukherjee

    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

  5. The Atomic scale structure of liquid metal-electrolyte interfaces.

    Science.gov (United States)

    Murphy, B M; Festersen, S; Magnussen, O M

    2016-08-01

    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. PMID:27301317

  6. The Atomic scale structure of liquid metal-electrolyte interfaces

    Science.gov (United States)

    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.

  7. Special Issue on Critical Assessment of Theoretical Calculations of Atomic Structure and Transition Probabilities

    OpenAIRE

    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. [...

  8. First principles calculation of the structural, electronic, and magnetic properties of Au-Pd atomic chains

    International Nuclear Information System (INIS)

    The structural, electronic and magnetic properties of free standing Au-Pd bimetallic atomic chain is studied using ab-initio method. It is found that electronic and magnetic properties of chains depend on position of atoms and number of atoms. Spin polarization factor for different atomic configuration of atomic chain is calculated predicting a half metallic behavior. It suggests a total spin polarised transport in these chains

  9. The International Atomic Energy Agency: Structure, organs, and practice

    International Nuclear Information System (INIS)

    As a special organization of the UN system the International Atomic Energy Agency (IAEA) bears world-wide responsibility for the promotion of peaceful uses of nuclear power as well as for the control of preventing its misuse for non-peaceful purposes. Based on this fundamental objective of the IAEA a survey of structure, organs and practice of the Agency is given. Particularly, those special programmes are detailed which are of importance to the use of nuclear power for energy generation, and those contributions of the IAEA are concerned which it has to make as the international control authority to prevent the proliferation of nuclear weapons. In conclusions, the future activities of the IAEA and the cooperation of the GDR with the IAEA are dealt with. (author)

  10. Atomic and electronic structure of divacancies in carbon nanotubes

    Science.gov (United States)

    Berber, Savas; Oshiyama, Atsushi

    2008-04-01

    We present atomic and electronic structure of divacancies in carbon nanotubes, which is calculated using the density functional theory. Divacancies in carbon nanotubes self-heal by spontaneous reconstructions, which consist of concerted bond formations. Divacancy formation energies EDV , which strongly depend on the divacancy orientation with respect to the tube axis, are in the range of 2.8 4.3 eV for favorable orientations in the nanotubes of 4 9Å diameter, making divacancies more probable than monovacancies in carbon nanotubes. Defect related states lead to a higher density of states around the Fermi level. Semiconducting nanotubes develop midgap levels that may adversely affect the functionality of carbon nanotube based devices. Our spin polarized density functional calculations show that the exchange splitting of defect-related bands in nonsemiconducting defective nanotubes leads to net spin polarizations of ρ↑-ρ↓≤0.5μB per divacancy for some divacancy orientations.

  11. Phase Space Structures Explain Hydrogen Atom Roaming in Formaldehyde Decomposition.

    Science.gov (United States)

    Mauguière, Frédéric A L; Collins, Peter; Kramer, Zeb C; Carpenter, Barry K; Ezra, Gregory S; Farantos, Stavros C; Wiggins, Stephen

    2015-10-15

    We re-examine the prototypical roaming reaction--hydrogen atom roaming in formaldehyde decomposition--from a phase space perspective. Specifically, we address the question "why do trajectories roam, rather than dissociate through the radical channel?" We describe and compute the phase space structures that define and control all possible reactive events for this reaction, as well as provide a dynamically exact description of the roaming region in phase space. Using these phase space constructs, we show that in the roaming region, there is an unstable periodic orbit whose stable and unstable manifolds define a conduit that both encompasses all roaming trajectories exiting the formaldehyde well and shepherds them toward the H2···CO well. PMID:26499774

  12. Atomic and electronic structure of surfaces theoretical foundations

    CERN Document Server

    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.

  13. Structure of Self-Assembled Mn Atom Chains on Si(001).

    Science.gov (United States)

    Villarreal, R; Longobardi, M; Köster, S A; Kirkham, Ch J; Bowler, D; Renner, Ch

    2015-12-18

    Mn has been found to self-assemble into atomic chains running perpendicular to the surface dimer reconstruction on Si(001). They differ from other atomic chains by a striking asymmetric appearance in filled state scanning tunneling microscopy (STM) images. This has prompted complicated structural models involving up to three Mn atoms per chain unit. Combining STM, atomic force microscopy, and density functional theory we find that a simple necklacelike chain of single Mn atoms reproduces all their prominent features, including their asymmetry not captured by current models. The upshot is a remarkably simpler structure for modeling the electronic and magnetic properties of Mn atom chains on Si(001). PMID:26722930

  14. The grasp2K relativistic atomic structure package

    Science.gov (United States)

    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

  15. Dopant distributions in n-MOSFET structure observed by atom probe tomography.

    Science.gov (United States)

    Inoue, K; Yano, F; Nishida, A; Takamizawa, H; Tsunomura, T; Nagai, Y; Hasegawa, M

    2009-11-01

    The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted. PMID:19775815

  16. Dopant distributions in n-MOSFET structure observed by atom probe tomography

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, K., E-mail: koji.inoue@hs3.ecs.kyoto-u.ac.jp [The Oarai Center, Institute for Materials Research, Tohoku University, Oarai, Ibaraki 311-1313 (Japan); Yano, F.; Nishida, A. [MIRAI-Selete, Tsukuba, Ibaraki 305-8569 (Japan); Takamizawa, H. [The Oarai Center, Institute for Materials Research, Tohoku University, Oarai, Ibaraki 311-1313 (Japan); Tsunomura, T. [MIRAI-Selete, Tsukuba, Ibaraki 305-8569 (Japan); Nagai, Y. [The Oarai Center, Institute for Materials Research, Tohoku University, Oarai, Ibaraki 311-1313 (Japan); Hasegawa, M. [Institute for Materials Research, Tohoku University, Sendai, Miyagi 980-8577 (Japan); Cyclotron and Radioisotope Center, Tohoku University, Sendai 980-8578 (Japan)

    2009-11-15

    The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted.

  17. Atomic structure and surface defects at mineral-water interfaces probed by in situ atomic force microscopy

    Science.gov (United States)

    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

  18. Atomic Structures of Riboflavin (Vitamin B2) and its Reduced Form with Bond Lengths Based on Additivity of Atomic Radii

    CERN Document Server

    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.

  19. Atomic Structures of Riboflavin (Vitamin B2) and its Reduced Form with Bond Lengths Based on Additivity of Atomic Radii

    OpenAIRE

    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...

  20. Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii

    OpenAIRE

    Heyrovska, Raji

    2007-01-01

    The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of adenine, guanine, thymine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On examining the bond length data in the literature, it has been found that the averages of the bond lengths are close to the sums of the corresponding atomic covalent radii of carbon, nitrogen, oxygen, hydrogen and phosphorus. Thus, ...

  1. Atomic and electronic structures of montmorillonite in soft rock

    International Nuclear Information System (INIS)

    Montmorillonite is a kind of clay mineral which often causes large deformation in soft-rock tunnel engineering and thus brings about safety problems in practice. To deal with these engineering safety problems, the physical and chemical properties of montmorillonite should be studied from basic viewpoints. We study the atomic and electronic structures of montmorillonite by using density-functional theory within the local-density approximation (LDA). The results of calculation show that Al–O bond lengths are longer than Si–O bond lengths. It is found that both the valence band maximum (VBM) and the conduction band minimum (CBM) of montmorillonite are at point Γ, and the calculated direct band gap of montmorillonite is 5.35 eV. We show that the chemical bonding between cations and oxygen anions in montmorillonite is mainly ionic, accompanied as well by a minor covalent component. It is pointed out that the VBM and CBM of montmorillonite consist of oxygen 2p and cation s states, respectively. Our calculated results help to understand the chemical and physical properties of montmorillonite, and are expected to be a guide for solving the problem of large deformation of soft-rock tunnels. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  2. The Dependence of All-Atom Statistical Potentials on Structural Training Database

    OpenAIRE

    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 ...

  3. New version: GRASP2K relativistic atomic structure package

    Science.gov (United States)

    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

  4. Atomic structure and surface defects at mineral-water interfaces probed by in situ atomic force microscopy.

    Science.gov (United States)

    Siretanu, Igor; van den Ende, Dirk; Mugele, Frieder

    2016-04-14

    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. PMID:27030282

  5. Probing Atomic Structure and Majorana Wavefunctions in Mono-Atomic Fe-chains on Superconducting Pb-Surface

    CERN Document Server

    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.

  6. A new program for calculating matrix elements in atomic structure

    International Nuclear Information System (INIS)

    The solution of many problems concerning the electronic structure of atoms requires the evaluation of the matrix elements of the Hamiltonian operator, including the electrostatic interaction. These matrix elements may be expressed as weighted sums of radial integrals. The program we describe in this paper evaluates the coefficients of the Slater integrals and, if these are given, computes all the matrix elements for a given set of configurations. This program has nearly the same purposes as Hibbert's program and is also based on the Racach techniques. The main difference between this algorithm and the cited one is the method used to calculate the recoupling coefficients. While Hibbert's programs use Burke's algorithm to calculate these coefficients, in our program they are computed using the graphical techniques developed by Jucys et al. According to this method, that we describe in another paper the formulae needed to calculate the recoupling coefficients are previously derived and simplified (as a first step of the program). The use of this method may considerably reduce the running time, specially in the case of large configuration interaction matrices. (orig.)

  7. Electronic structure of helium atom in a quantum dot

    CERN Document Server

    Saha, Jayanta K; Mukherjee, T K

    2015-01-01

    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] configuration 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 representing the quantum dot. It has been explicitly demonstrated that electronic structure properties become a sensitive function of the dot size. It is observed from the calculations of ionization potential that the stability of an impurity ion within 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 wi...

  8. Atomic structures and electronic properties of phosphorene grain boundaries

    Science.gov (United States)

    Guo, Yu; Zhou, Si; Zhang, Junfeng; Bai, Yizhen; Zhao, Jijun

    2016-06-01

    Grain boundary (GB) is one main type of defects in two-dimensional (2D) crystals, and has significant impact on the physical properties of 2D materials. Phosphorene, a recently synthesized 2D semiconductor, possesses a puckered honeycomb lattice and outstanding electronic properties. It is very interesting to know the possible GBs present in this novel material, and how their properties differ from those in the other 2D materials. Based on first-principles calculations, we explore the atomic structure, thermodynamic stability, and electronic properties of phosphorene GBs. A total of 19 GBs are predicted and found to be energetically stable with formation energies much lower than those in graphene. These GBs do not severely affect the electronic properties of phosphorene: the band gap of perfect phosphorene is preserved, and the electron mobilities are only moderately reduced in these defective systems. Our theoretical results provide vital guidance for experimental tailoring the electronic properties of phosphorene as well as the device applications using phosphorene materials.

  9. 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.

  10. Voronoi analysis of the short–range atomic structure in iron and iron–carbon melts

    International Nuclear Information System (INIS)

    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

  11. Atomic structure of "vitreous" interfacial films in sialon

    OpenAIRE

    Thorel, A.; Laval, J; Broussaud, Daniel

    1988-01-01

    Atomic resolution imaging of siliceous interfacial films in a sialon has been achieved using transmission electron microscopy at 1000 KV. Although such films have always been reputed as vitreous, we show that they are at least partially crystallized. An atomic model is proposed and simulated. The stability of these films is discussed when special crystallographic relationships exist between the two adjacent grains.

  12. A curved line search algorithm for atomic structure relaxation

    OpenAIRE

    Chen, Zhanghui; Wang, Linwang; Li, Jingbo; Li, Shushen

    2015-01-01

    Ab initio atomic relaxations often take large numbers of steps and long times to converge. An atomic relaxation method based on on-the-flight force learning and a corresponding new curved line minimization algorithm is presented to dramatically accelerate this process. Results for metal clusters demonstrate the significant speedup of this method compared with conventional conjugate-gradient method.

  13. Atomic structure calculations using the relativistic random phase approximation

    International Nuclear Information System (INIS)

    A brief review is given for the relativistic random phase approximation (RRPA) applied to atomic transition problems. Selected examples of RRPA calculations on discrete excitations and photoionization are given to illustrate the need of relativistic many-body theories in dealing with atomic processes where both relativity and correlation are important

  14. Structure of ultrathin oxide layers on metal surfaces from grazing scattering of fast atoms

    International Nuclear Information System (INIS)

    The structure of ultrathin oxide layers grown on metal substrates is investigated by grazing scattering of fast atoms from the film surface. We present three recent experimental techniques which allow us to study the structure of ordered oxide films on metal substrates in detail. (1) A new variant of a triangulation method with fast atoms based on the detection of emitted electrons, (2) rainbow scattering under axial surface channeling conditions, and (3) fast atom diffraction (FAD) for studies on the structure of oxide films. Our examples demonstrate the attractive features of grazing fast atom scattering as a powerful analytical tool in surface physics.

  15. Quasilattice-conserved optimization of the atomic structure of decagonal Al-Co-Ni quasicrystals

    OpenAIRE

    Li, Xiao-Tian; Yang, Xiao-Bao; Zhao, Yu-Jun

    2014-01-01

    The detailed atomic structure of quasicrystals has been an open question for decades. Here, we present a quasilattice-conserved optimization method (quasiOPT), with particular quasiperiodic boundary conditions. As the atomic coordinates described by basic cells and quasilattices, we are able to maintain the self-similarity characteristics of qusicrystals with the atomic structure of the boundary region updated timely following the relaxing region. Exemplified with the study of decagonal Al-Co...

  16. Vacuum polarization in hydrogen-like relativistic atom: superfine structure

    International Nuclear Information System (INIS)

    One studies contribution of vacuum polarization into superfine splitting of hydrogen-like atom principal state. One presents the general expressions for a single-potential and for bi-potential contributions of vacuum polarization into superfine splitting of hydrogen-like principal state. The expression for correction to energy was derived in the form of Zα parameter explicit function. The final expression derived in terms of the generalized hypergeometrical functions and their derivatives represents the function of particle mass ratio both at the orbit and in a vacuum loop and, thus, is true both for ordinary and for muon atoms. Paper presents, as well, various asymptotics for muon atoms

  17. Atomic shell structure from the Single-Exponential Decay Detector

    International Nuclear Information System (INIS)

    The density of atomic systems is analysed via the Single-Exponential Decay Detector (SEDD). SEDD is a scalar field designed to explore mathematical, rather than physical, properties of electron density. Nevertheless, it has been shown that SEDD can serve as a descriptor of bonding patterns in molecules as well as an indicator of atomic shells [P. de Silva, J. Korchowiec, and T. A. Wesolowski, ChemPhysChem 13, 3462 (2012)]. In this work, a more detailed analysis of atomic shells is done for atoms in the Li–Xe series. Shell populations based on SEDD agree with the Aufbau principle even better than those obtained from the Electron Localization Function, which is a popular indicator of electron localization. A link between SEDD and the local wave vector is given, which provides a physical interpretation of SEDD

  18. Atomic structure affects the directional dependence of friction

    Czech Academy of Sciences Publication Activity Database

    Weymouth, A.J.; Meuer, D.; Mutombo, Pingo; Wutscher, T.; Ondráček, Martin; Jelínek, Pavel; Giessibl, F.J.

    2013-01-01

    Roč. 111, č. 12 (2013), "126103-1"-"126103-4". ISSN 0031-9007 R&D Projects: GA ČR(CZ) GPP204/11/P578 Grant ostatní: GA AV(CZ) M100101207 Institutional support: RVO:68378271 Keywords : atomic scale friction * atomic force microscopy * silicon surface Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 7.728, year: 2013

  19. Smallest Nanoelectronic with Atomic Devices with Precise Structures

    Science.gov (United States)

    Yamada, Toshishige

    2000-01-01

    Since its invention in 1948, the transistor has revolutionized our everyday life - transistor radios and TV's appeared in the early 1960s, personal computers came into widespread use in the mid-1980s, and cellular phones, laptops, and palm-sized organizers dominated the 1990s. The electronics revolution is based upon transistor miniaturization; smaller transistors are faster, and denser circuitry has more functionality. Transistors in current generation chips are 0.25 micron or 250 nanometers in size, and the electronics industry has completed development of 0.18 micron transistors which will enter production within the next few years. Industry researchers are now working to reduce transistor size down to 0.13 micron - a thousandth of the width of a human hair. However, studies indicate that the miniaturization of silicon transistors will soon reach its limit. For further progress in microelectronics, scientists have turned to nanotechnology to advance the science. Rather than continuing to miniaturize transistors to a point where they become unreliable, nanotechnology offers the new approach of building devices on the atomic scale [see sidebar]. One vision for the next generation of miniature electronics is atomic chain electronics, where devices are composed of atoms aligned on top of a substrate surface in a regular pattern. The Atomic Chain Electronics Project (ACEP) - part of the Semiconductor Device Modeling and Nanotechnology group, Integrated Product Team at the NAS Facility has been developing the theory of understanding atomic chain devices, and the author's patent for atomic chain electronics is now pending.

  20. Bloch oscillations of ultracold atoms and measurement of the fine structure constant; Oscillations de Bloch d'atomes ultrafroids et mesure de la constante de structure fine

    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)

  1. Spontaneous emission of a photon: wave packet structures and atom-photon entanglement

    OpenAIRE

    Fedorov, M. V.; Efremov, M. A.; Kazakov, A. E.; Chan, K W; Law, C. K.; Eberly, J. H.

    2004-01-01

    Spontaneous emission of a photon by an atom is described theoretically in three dimensions with the initial wave function of a finite-mass atom taken in the form of a finite-size wave packet. Recoil and wave-packet spreading are taken into account. The total atom-photon wave function is found in the momentum and coordinate representations as the solution of an initial-value problem. The atom-photon entanglement arising in such a process is shown to be closely related to the structure of atom ...

  2. 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

  3. Femtosecond structural dynamics on the atomic length scale

    International Nuclear Information System (INIS)

    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/μm2) 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 VO2 and the ultrafast photo-reduction mechanism of graphene oxide. In regard to FED setups, I have been deeply involved in

  4. A Hartree-Fock program for atomic structure calculations

    International Nuclear Information System (INIS)

    The Hartree-Fock equations for a general open shell atom are described. The matrix equations that result when the single particle orbitals are written in terms of a linear combination of analytic basis functions are derived. Attention is paid to the complexities that occur when open shells are present. The specifics of a working FORTRAN program which is available for public use are described. The program has the flexibility to handle either Slater-type orbitals or Gaussian-type orbitals. It can be obtained over the internet at http://lacebark.ntu.edu.au/j_mitroy/research/atomic.htm Copyright (1999) CSIRO Australia

  5. Furosemide's one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics.

    Science.gov (United States)

    Widdifield, Cory M; Robson, Harry; Hodgkinson, Paul

    2016-05-10

    The potential of NMR crystallography to verify molecular crystal structures deposited in structural databases is evaluated, with two structures of the pharmaceutical furosemide serving as examples. While the structures differ in the placement of one H atom, using this approach, we verify one of the structures in the Cambridge Structural Database using quantitative tools, while establishing that the other structure does not meet the verification criteria. PMID:27115483

  6. Ab initio calculations and modelling of atomic cluster structure

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.;

    2004-01-01

    framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...

  7. Electron structure of atoms in laser plasma: The Debye shielding model

    International Nuclear Information System (INIS)

    The electronic structure and the energy spectra of multielectron atoms in laser plasmas are examined by the Debye shielding model. The effect of the plasma environment on the electrons bound in an atom is taken into account by introducing the screened Coulomb-type potentials into the electronic Hamiltonian of an atom in place of the standard nuclear attraction and electron repulsion potentials. The capabilities of this new Hamiltonian are demonstrated for He and Li in laser plasmas. (author)

  8. GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

    OpenAIRE

    Zhou, Hongyi; Skolnick, Jeffrey

    2011-01-01

    An accurate scoring function is a key component for successful protein structure prediction. To address this important unsolved problem, we develop a generalized orientation and distance-dependent all-atom statistical potential. The new statistical potential, generalized orientation-dependent all-atom potential (GOAP), depends on the relative orientation of the planes associated with each heavy atom in interacting pairs. GOAP is a generalization of previous orientation-dependent potentials th...

  9. Atomic structure of cascades of atomic displacements in metals and alloys after different types of radiation

    Science.gov (United States)

    Ivchenko, V. A.

    2016-02-01

    Using the methods of field ion microscopy, we studied radiation induced defects on an atomically clean surface and within a subsurface volume of platinum initiated by the interaction of neutron (E > 0.1MeV) and Ar+ beams (E = 30 keV). It is shown that the interaction of fast neutrons (E > 0.1 MeV) F = 6.7-1021 m-2, F = 3.5-1022 m-2 with matter leads to the formation in the amount of platinum such as radiation damage which occur after ion irradiation by beams of charged Ar+ ions with E = 30 keV, F = 1020 ion/m2. They are observed at a depth of about 1.5-2 nm irradiated under the surface of Pt by ions Ar+. Thus, we have carried out modeling of neutron impact with matter when replacing the neutron beam by an ion beam that causes the same radiation damage in the bulk of the material. Experimental results on atomic-spatial investigation of radiative defect formation in surface layers of materials, initiated by neutron bombardment (of Pt, E > 0.1 MeV) and ion implantation (in Cu3Au: E = 40 keV, F = 1020 ion/m2, j = 10-3 A/cm2), are considered. Quantitative estimates obtained for the size, shape, and volume fraction of cascades of atomic displacements formed under various types of irradiation in the surface layers of the materials. It is showing that the average size of radiation clusters after irradiation of platinum to a fast neutron fluence of 6.7-1022 m-2 (E > 0.1 MeV) is about 3.2 nm. The experimentally established average size of a radiation cluster (disordered zone) in the alloy after ion bombardment is 4×4×1.5 nm.

  10. The stability and electronic structure of Fe atoms embedded in zigzag graphene nanoribbons

    International Nuclear Information System (INIS)

    The stability and electronic properties of the Fe atoms embedded in divacancy defects in graphene nanoribbons (GNR) with zigzag-shaped edges have been studied by first-principles calculations. When Fe is positioned in the middle of the ribbon, it has little effect on the edge C atoms, which reserves the flat edges of graphene nanoribbons. On the other hand, when Fe atom is near the edge, structural distortion takes place resulting in tilted-edge structure with low energies. This indicates that the Fe atoms prefer to occupy divacancy sites near the edges. This is also in consistent with the analyses of electronic structures. Meanwhile, our results reveal that embedding Fe atom in the graphene nanoribbons is an effective method to make the GNR possessing metallic properties.

  11. Correlation between atomic structure evolution and strength in a bulk metallic glass at cryogenic temperature.

    Science.gov (United States)

    Tan, J; Wang, G; Liu, Z Y; Bednarčík, J; Gao, Y L; Zhai, Q J; Mattern, N; Eckert, J

    2014-01-01

    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. PMID:24469299

  12. The fine structure of niobium condensates deposited from ion-atomic fluxes in helium atmosphere

    International Nuclear Information System (INIS)

    Helium gas influence on the structural characteristics of niobium coatings deposited by low-energy metallic Nb ion-stoic fluxes in He atmosphere is investigated. It is shown that He implantation in Nb films during condensation is accompanied with the decreasing of the mean size of condensate grains. At the same time, He atoms modify no physical processes of the fine structure formation. Using thermodesorption spectroscopy we have determined that He atoms mainly belong to vacancy/vacancy-solute complexes in Nb coatings. Our conclusion is that such complexes play a dominant role in formation of the fine structure of vacuum coatings deposited from ion-atomic fluxes

  13. Undergraduate chemistry students' conceptions of atomic structure, molecular structure and chemical bonding

    Science.gov (United States)

    Campbell, Erin Roberts

    The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from

  14. Atomic Structures of the Amino Acids, Glycine, Alanine and Serine and Their Tripeptide, with Bond Lengths as Sums of Atomic Covalent Radii

    CERN Document Server

    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.

  15. Arguments, Contradictions, Resistances, and Conceptual Change in Students' Understanding of Atomic Structure.

    Science.gov (United States)

    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'…

  16. Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness

    Science.gov (United States)

    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…

  17. Enrichment of true positives from structural alerts through the use of novel atomic fragment based descriptors

    DEFF Research Database (Denmark)

    Long, A.; Rydberg, Patrik

    2013-01-01

    To enhance the discrimination rate for methods applying structural alerts and biotransformation rules in the prediction of toxicity and drug metabolism we have developed a set of novel fragment based atomic descriptors. These atomic descriptors encode the properties of the fragments separating an...

  18. Structure and transport properties of atomic chains and molecules

    DEFF Research Database (Denmark)

    Strange, Mikkel

    2008-01-01

    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 the experimental findings [5]. The observed conductance properties of Metal/CO are shown to be determined by the local d-band at the Metal apex atoms. For carbon nanotubes it is shown that the conductance may be controlled by site selective adsorption of molecules. A model to explain this behavior is verified...... by direct visualization of Kohn-Sham eigenchannel states. The possibility of non-carbon based nanotubes is also discussed. Both calculations of the strain energy of infinite PtO2 nanotubes that this material could be a candidate for non-carbon based nanotubes, as was recently suggested [6]....

  19. Atomic scale modelling of hexagonal structured metallic fission product alloys

    OpenAIRE

    Middleburgh, S. C.; King, D M; Lumpkin, G. R.

    2015-01-01

    Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)—making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperature...

  20. Atomic structure calculations for F-like tungsten

    Science.gov (United States)

    Sunny, Aggarwal

    2014-09-01

    Energy levels, wavefunction compositions and lifetimes have been computed for all levels of 1s22s22p5, 1s22s2p6, 1s22s22p43s, 1s22s22p43p, and 1s22s22p43d configurations in highly charged F-like tungsten ion. The multiconfigurational Dirac—Fock method (MCDF) is adopted to generate the wavefunctions. We have also presented the transition wavelengths, oscillator strengths, transition probabilities, and line strengths for the electric dipole (E1) and magnetic quadrupole (M2) transition from the 1s22s22p5 ground configuration. We have performed parallel calculations with the flexible atomic code (FAC) for comparing the atomic data. The reliability of present data is assessed by comparison with other theoretical and experimental data available in the literature. Good agreement is found between our results and those obtained using different approaches confirm the quality of our results. Additionally, we have predicted some new atomic data for F-like W that were not available so far and may be important for plasma diagnostic analysis in fusion plasma.

  1. Atomically resolved surface structures of vapor deposited amorphous silicon-carbon alloys: An atomic force microscopy and spectroscopic study

    International Nuclear Information System (INIS)

    Silicon carbide alloys are widely used in high-tech applications due to their interesting combination of chemical, mechanical and electronic properties. Growing thin films of this material in a simple and controlled way is a hot topic in modern material's science. In particular, the possibility to tailor the film properties just by tuning the deposition temperature would be an important progress. In the present work amorphous silicon-carbon alloys thin films have been deposited by electron beam sublimation of a poly-crystalline silicon carbide target in vacuum environment. The deposition temperature was varied from Room Temperature to about 1300 K. The resulting films were analyzed by means of Ultra High Vacuum-Atomic Force Microscopy (UHV-AFM) down to even atomic resolution. The observed features agree with literature data, e.g. interatomic bond lengths, as achieved by others methods, and the structural arrangements of silicon and carbon atoms as concluded from IR and Raman spectroscopy measurements carried out on the same samples. The results not only allow a correlation between film properties and deposition temperature but also support the notion of the UHV-AFM images of the amorphous surfaces being atomically resolved.

  2. Ultrathin atomic vapor film transmission spectroscopy: analysis of Dicke narrowing structure

    Science.gov (United States)

    Li, Yuanyuan; Zhang, Yanpeng; Gan, Chenli

    2005-11-01

    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 atom-field 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 < ?/4) in experiments.

  3. Hydrogen atom position in hydrated iodide anion from x-ray absorption near edge structure

    International Nuclear Information System (INIS)

    Hydrogen atom position in the hydrated iodide anion complex is determined from X-ray Absorption Near Edge Structure (XANES) of an aqueous iodide solution at both the K- and L-edges. The spectra are compared with the theoretical ones calculated by using the FEFF method for several model geometries having hydrogen atoms at different positions. Satisfactory agreements are obtained from models with an almost linear alignment of iodine-hydrogen-oxygen atoms, indicating the capability of the XANES analysis when it is combined with the multiple scattering calculations as a method to detect the positions of hydrogen atoms in the first coordination sphere. (author)

  4. Study on structures and electronic properties of NaxV (x = 1-12) atomic clusters

    International Nuclear Information System (INIS)

    Superatoms, novel entities being studied extensively in recent years, can be stabilized by mixing with transition metal atoms. The aim of this paper is to present some recent theoretical results on the application of quantum calculations for examining the atomic clusters NaxV (x = 1-12) made from the mixing of Nax superatoms with vanadium transition metal atom. Optimized structures of NaxV, NaxV+ and NaxV- are determined by using the TPSSTPSS/DZVP DFT calculations. Characteristics of optimized structures, as point group symmetry, chemical hardness (η), absolute electronegativity (χ), electrophilicity index (ω), fragmentation energy (Ef), secondary energy (∆2E), are calculated. The obtained results point out that among different structures of an atomic cluster, the more negative total energy the more stable structure and the Na8V cluster is the most stable in NaxV (x = 1-12) clusters. (author)

  5. On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

    International Nuclear Information System (INIS)

    Details of five very high-resolution accurate structures of bovine trypsin are compared in the context of the reproducibility of models obtained from crystals grown under identical conditions. Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The Cα and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from

  6. On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

    Energy Technology Data Exchange (ETDEWEB)

    Liebschner, Dorothee; Dauter, Miroslawa [Argonne National Laboratory, Argonne, IL 60439 (United States); Brzuszkiewicz, Anna [Argonne National Laboratory, Argonne, IL 60439 (United States); University of Wroclaw, 50-383 Wroclaw (Poland); Dauter, Zbigniew, E-mail: dauter@anl.gov [Argonne National Laboratory, Argonne, IL 60439 (United States)

    2013-08-01

    Details of five very high-resolution accurate structures of bovine trypsin are compared in the context of the reproducibility of models obtained from crystals grown under identical conditions. Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C{sup α} and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained

  7. Simultaneous atomic force- and scanning tunneling microscopy - a new view on two distinct aspects of the atomic structure of matter

    International Nuclear Information System (INIS)

    Full text: Full text: Frequency-modulation AFM can be combined with scanning tunneling microscopy, yielding a simultaneous data set for current and average force gradient. Ternes et al. have shown that for some metallic contacts, force and current are proportional. The figure shows an example, where combined AFM/STM reveals two strongly distinct aspects of the atomic structure of matter. The gray veil depicts the inverted tunneling current between a CO molecule adsorbed on Cu(111) and a tungsten tip, while the colored surface shows the corresponding force profiles, where the left image corresponds to a W tip oriented in a direction, the right to a direction and the bottom to a direction. While the simultaneous acquisition of current and force can reveal new information about the atomic and electronic structure of matter, the tunneling current can modify the atomic forces. This phantom force, a modification of the electrostatic attraction between tip and sample, originates in an alteration of the effective potential difference between tip and sample caused by strongly localized voltage drop induced by the tunneling current. The talk discusses the merits of combined STM/AFM as well as the challenges, in particular with respect to tip preparation and characterization. (author)

  8. Microstructural Characterization of Hierarchical Structured Surfaces by Atomic Force Microscopy

    Science.gov (United States)

    Ponomareva, A. A.; Moshnikov, V. A.; Suchaneck, G.

    2013-12-01

    In this work, we evaluate the hierarchical surface topography of reactively sputtered nanocrystalline Pb(Zr,Ti)O3 and TiO2 thin films as well as plasma-treated antireflective PET films by means of determining the fractal dimension and power spectral density (PSD) of surface topography recorded by atomic force microscopy (AFM). Local fractal dimension was obtained using the triangulation method. The PSDs of all samples were fitted to the k-correlation model (also called ABC model) valid for a self-affine surface topography. Fractal analysis of AFM images was shown to be an appropriate and easy to use tool for the characterization of hierarchical nanostructures.

  9. Atomic-scale nanowires: physical and electronic structure

    International Nuclear Information System (INIS)

    The technology to build and study nanowires with sizes ranging from individual atoms to tens of nanometres has been developing rapidly over the last few years. We survey the motivation behind these developments, and summarize the basics behind quantized conduction. Several of the different experimental techniques and materials systems used in the creation of nanowires are examined, and the range of theoretical methods developed both for examining open systems (especially their conduction properties) and for modelling large systems are considered. We present various noteworthy example results from the field, before concluding with a look at future directions. (topical review)

  10. Microstructural Characterization of Hierarchical Structured Surfaces by Atomic Force Microscopy

    International Nuclear Information System (INIS)

    In this work, we evaluate the hierarchical surface topography of reactively sputtered nanocrystalline Pb(Zr,Ti)O3 and TiO2 thin films as well as plasma-treated antireflective PET films by means of determining the fractal dimension and power spectral density (PSD) of surface topography recorded by atomic force microscopy (AFM). Local fractal dimension was obtained using the triangulation method. The PSDs of all samples were fitted to the k-correlation model (also called ABC model) valid for a self-affine surface topography. Fractal analysis of AFM images was shown to be an appropriate and easy to use tool for the characterization of hierarchical nanostructures

  11. Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality

    CERN Document Server

    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.

  12. Discrimination of native protein structures using atom–atom contact scoring

    OpenAIRE

    McConkey, Brendan J.; Sobolev, Vladimir; Edelman, Marvin

    2003-01-01

    We introduce a method for discriminating correctly folded proteins from well designed decoy structures using atom–atom and atom–solvent contact surfaces. The measure used to quantify contact surfaces integrates the solvent accessible surface and interatomic contacts into one quantity, allowing solvent to be treated as an atom contact. A scoring function was derived from statistical contact preferences within known protein structures and validated by using established protein decoy sets, inclu...

  13. Semiempirical Studies of Atomic Structure. Final Report for July 1, 2000 - June 30, 2003

    International Nuclear Information System (INIS)

    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)

  14. 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).

  15. Structure determination in 55-atom Li-Na and Na-K nanoalloys.

    Science.gov (United States)

    Aguado, Andrés; López, José M

    2010-09-01

    The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions. PMID:20831313

  16. Atomic Structure of Highly Strained BiFeO3 Thin Films

    Energy Technology Data Exchange (ETDEWEB)

    Rossell, M.D. [Lawrence Berkeley National Laboratory (LBNL); Erni, R. [Lawrence Berkeley National Laboratory (LBNL); Prange, Micah P [ORNL; Idrobo Tapia, Juan C [ORNL; Luo, Weidong [ORNL; Zeches, R J [University of California, Berkeley; Pantelides, Sokrates T [ORNL; Ramesh, R [Lawrence Berkeley National Laboratory (LBNL)

    2012-01-01

    We determine the atomic structure of the pseudotetragonal T phase and the pseudorhombohedral R phase in highly strained multiferroic BiFeO3 thin films by using a combination of atomic-resolution scanning transmission electron microscopy and electron energy-loss spectroscopy. The coordination of the Fe atoms and their displacement relative to the O and Bi positions are assessed by direct imaging. These observations allow us to interpret the electronic structure data derived from electron energy-loss spectroscopy and provide evidence for the giant spontaneous polarization in strained BiFeO3 thin films.

  17. 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.

  18. Medium range real atomic structure of face centred icosahedral Ho9Mg26Zn65

    OpenAIRE

    Bruehne, S.; Sterzel, R.; Uhrig, E.; Gross, C.; Assmus, W.

    2003-01-01

    A new approach to solve quasicrystalline atomic structures in 3-dimensional (3D) real space is presented: The atomic pair distribution function (PDF) of face centred icosahedral Ho9Mg26Zn65 [a(6D) = 2x5.18(3)A was obtained from in-house X-ray diffraction data (MoKa1). Starting with rational approximant models, derived from 1/1- and 2/1-Al-Mg-Zn, its local and medium range structure was refined (r < 27A; R = 12.9%) using the PDF data. 85% of all atoms show Frank-Kasper (FK) type coordinations....

  19. Correlation between atomic structure evolution and strength in a bulk metallic glass at cryogenic temperature

    OpenAIRE

    Tan, J.; Wang, G.; Z. Y. LIU; Bednarčík, J.; Gao, Yan; Zhai, Q. J.; Mattern, N.; Eckert, J.

    2014-01-01

    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 res...

  20. Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

    KAUST Repository

    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.

  1. Atomic structures and oxygen dynamics of CeO2 grain boundaries

    Science.gov (United States)

    Feng, Bin; Sugiyama, Issei; Hojo, Hajime; Ohta, Hiromichi; Shibata, Naoya; Ikuhara, Yuichi

    2016-02-01

    Material performance is significantly governed by grain boundaries (GBs), a typical crystal defects inside, which often exhibit unique properties due to the structural and chemical inhomogeneity. Here, it is reported direct atomic scale evidence that oxygen vacancies formed in the GBs can modify the local surface oxygen dynamics in CeO2, a key material for fuel cells. The atomic structures and oxygen vacancy concentrations in individual GBs are obtained by electron microscopy and theoretical calculations at atomic scale. Meanwhile, local GB oxygen reduction reactivity is measured by electrochemical strain microscopy. By combining these techniques, it is demonstrated that the GB electrochemical activities are affected by the oxygen vacancy concentrations, which is, on the other hand, determined by the local structural distortions at the GB core region. These results provide critical understanding of GB properties down to atomic scale, and new perspectives on the development strategies of high performance electrochemical devices for solid oxide fuel cells.

  2. Resonance structure in elastic scattering of electrons from atomic hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Warner, C.D.; King, G.C.; Hammond, P.; Slevin, J.

    1986-10-28

    High-energy-resolution spectra of electrons scattered elastically from atomic hydrogen have been obtained for incident electron energies of 9.2-10.4 eV and at angles of 33/sup 0/, 54/sup 0/, 70/sup 0/ and 90/sup 0/. The energy spread of the incident electron beam is estimated to be typically 25 meV FWHM. In addition to the /sup 1/S and /sup 3/P resonances which have been reported in earlier studies, a /sup 1/D resonance can be clearly seen and there is some evidence of a resonance state at a higher energy, probably corresponding to a /sup 1/S resonance state. The energies and resonance widths of all these features have been determined.

  3. Resonance structure in elastic scattering of electrons from atomic hydrogen

    International Nuclear Information System (INIS)

    High-energy-resolution spectra of electrons scattered elastically from atomic hydrogen have been obtained for incident electron energies of 9.2-10.4 eV and at angles of 330, 540, 700 and 900. The energy spread of the incident electron beam is estimated to be typically 25 meV FWHM. In addition to the 1S and 3P resonances which have been reported in earlier studies, a 1D resonance can be clearly seen and there is some evidence of a resonance state at a higher energy, probably corresponding to a 1S resonance state. The energies and resonance widths of all these features have been determined. (author)

  4. The role and structure of the Atomic Energy Control Board

    International Nuclear Information System (INIS)

    The Atomic Energy Control Board is responsible for the control and supervision of the application and use of nuclear materials and the operation of nuclear facilities to ensure that the health and safety of people are protected and that the nuclear materials and equipment are used only in accordance with the government non-proliferation policy. Requirements for control and supervision are made into regulations subject to approval by the Governor in Council. They are applied through a comprehensive licensing system. The interpretation and implementation of the regulations are contained in a series of regulatory documents published from time to time by the Board. The functional organization of staff that assist the Board for the administration, the assessment and issuance of licenses, compliance and inspection, as well as for the management of the regulatory research program is described. (author)

  5. Atomic Models of Strong Solids Interfaces Viewed as Composite Structures

    Science.gov (United States)

    Staffell, I.; Shang, J. L.; Kendall, K.

    2014-02-01

    This paper looks back through the 1960s to the invention of carbon fibres and the theories of Strong Solids. In particular it focuses on the fracture mechanics paradox of strong composites containing weak interfaces. From Griffith theory, it is clear that three parameters must be considered in producing a high strength composite:- minimising defects; maximising the elastic modulus; and raising the fracture energy along the crack path. The interface then introduces two further factors:- elastic modulus mismatch causing crack stopping; and debonding along a brittle interface due to low interface fracture energy. Consequently, an understanding of the fracture energy of a composite interface is needed. Using an interface model based on atomic interaction forces, it is shown that a single layer of contaminant atoms between the matrix and the reinforcement can reduce the interface fracture energy by an order of magnitude, giving a large delamination effect. The paper also looks to a future in which cars will be made largely from composite materials. Radical improvements in automobile design are necessary because the number of cars worldwide is predicted to double. This paper predicts gains in fuel economy by suggesting a new theory of automobile fuel consumption using an adaptation of Coulomb's friction law. It is demonstrated both by experiment and by theoretical argument that the energy dissipated in standard vehicle tests depends only on weight. Consequently, moving from metal to fibre construction can give a factor 2 improved fuel economy performance, roughly the same as moving from a petrol combustion drive to hydrogen fuel cell propulsion. Using both options together can give a factor 4 improvement, as demonstrated by testing a composite car using the ECE15 protocol.

  6. Prediction of structural and mechanical properties of atom-decorated porous graphene via density functional calculations

    Science.gov (United States)

    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).

  7. Atomic structure and chemistry of human serum albumin

    Science.gov (United States)

    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.

  8. Atomic structure of Fe thin-films on Cu(0 0 1) studied with stereoscopic photography

    Energy Technology Data Exchange (ETDEWEB)

    Hattori, Azusa N. [Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192 (Japan); Fujikado, M. [Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192 (Japan); Uchida, T. [Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192 (Japan); Okamoto, S. [Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192 (Japan); Fukumoto, K. [Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192 (Japan); Guo, F.Z. [Japan Synchrotron Radiation Research Institute, Kouto, Mikazuki, Sayo, Hyogo 679-5198 (Japan); Matsui, F. [Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192 (Japan); CREST, Japan Science and Technology Agency (Japan); Nakatani, K. [Japan Synchrotron Radiation Research Institute, Kouto, Mikazuki, Sayo, Hyogo 679-5198 (Japan); Matsushita, T. [Japan Synchrotron Radiation Research Institute, Kouto, Mikazuki, Sayo, Hyogo 679-5198 (Japan); Hattori, K. [Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192 (Japan); CREST, Japan Science and Technology Agency (Japan); Daimon, H. [Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192 (Japan); CREST, Japan Science and Technology Agency (Japan)

    2004-10-15

    The complex magnetic properties of Fe films epitaxially grown on Cu(0 0 1) have been discussed in relation to their atomic structure. We have studied the Fe films on Cu(0 0 1) by a new direct method for three-dimensional (3D) atomic structure analysis, so-called 'stereoscopic photography'. The forward-focusing peaks in the photoelectron angular distribution pattern excited by the circularly polarized light rotate around the light axis in either clockwise or counterclockwise direction depending on the light helicity. By using a display-type spherical mirror analyzer for this phenomenon, we can obtain stereoscopic photographs of atomic structure. The photographs revealed that the iron structure changes from bcc to fcc and almost bcc structure with increasing iron film thickness.

  9. Correlating Atomic Structure and Transport in Suspended Graphene Nanoribbons

    OpenAIRE

    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

    2014-01-01

    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 (

  10. Atomic and electronic structure of MoS2 nanoparticles

    OpenAIRE

    Bollinger, Mikkel; Jacobsen, Karsten Wedel; Nørskov, Jens Kehlet

    2003-01-01

    Using density-functional theory (DFT) we present a detailed theoretical study of MoS2 nanoparticles. We focus on the edge structures, and a number of different edge terminations are investigated. Several, but not all, of these configurations have one-dimensional metallic states localized 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 th...

  11. Bloch oscillations of ultracold atoms and measurement of the fine structure constant

    International Nuclear Information System (INIS)

    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 10-9, in conjunction with a careful study of systematic effects (5 10-9), has led us to a determination of alpha with an uncertainty of 6.7 10-9: α-1(Rb) = 137.03599878 (91). This uncertainty is similar to the uncertainty of the best determinations of alpha based on atom interferometry. (author)

  12. Pre-service physics teachers' ideas on size, visibility and structure of the atom

    International Nuclear Information System (INIS)

    Understanding the atom gives the opportunity to both understand and conceptually unify the various domains of science, such as physics, chemistry, biology, astronomy and geology. Among these disciplines, physics teachers are expected to be particularly well educated in this topic. It is important that pre-service physics teachers know what sort of theories regarding the atom they will bring into their own classrooms. Six tasks were developed, comprising size, visibility and structure of the atom. These tasks carried out by pre-service physics teachers were examined by content analysis and six categories were determined. These are size, visibility, subatomic particles, atom models, electron orbit and electron features. Pre-service physics teachers' ideas about the atom were clarified under these categories.

  13. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    OpenAIRE

    Sha, Wei

    2008-01-01

    In this seminar, I will talk about the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscopy (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics simulations were then carried out to investigate the ...

  14. 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 ...... depleted of particles. We propose that the halo-like structures are a result of electrostatic forces acting between the incoming charged clusters and charged regions on the surface. A simple computer simulation supports this suggestion....

  15. On the hyperfine structures of the ground state(s) in the ${}^{6}$Li and ${}^{7}$Li atoms

    CERN Document Server

    Frolov, Alexei M

    2016-01-01

    Hyperfine structure of the ground $2^{2}S-$states of the three-electron atoms and ions is investigated. By using our recent numerical values for the doublet electron density at the atomic nucleus we determine the hyperfine structure of the ground (doublet) $2^{2}S-$state(s) in the ${}^{6}$Li and ${}^{7}$Li atoms.

  16. Atomic and electronic structure of MoS2 nanoparticles

    DEFF Research Database (Denmark)

    Bollinger, Mikkel; Jacobsen, Karsten Wedel; Nørskov, Jens Kehlet

    2003-01-01

    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...

  17. 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.

  18. Halo-like structures studied by atomic force microscopy

    DEFF Research Database (Denmark)

    Sørensen, Alexis Hammer; Kyhle, Anders; Hansen, L. Theil; Busch, Henrik; Christiansen, L. Jin; Mikkelsen, J.; Herholdt-Rasmussen, N.; Mørch, Knud Aage; Bohr, Jakob

    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 be...

  19. Theoretical calculations on the atomic and electronic structure of β-SiC(110) surface

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    We present a theoretical calculation of the atomic and electronic structure of β-SiC and its non-polar (110) surface using the full potential linear augmented plane wave (FPLAPW) approach. The calculated lattice constant and bulk modulus of β-SiC crystal are in excellent agreement with experimental data. The atomic and electronic structure of β-SiC(110) surface has been calculated by employing the slab and supercell model. It is found that the surface is characterized by a top-layer bond-length-contracting rotation relaxation in which the Si-surface atom moves closer towards the substrate while the C-surface atom moves outward. This relaxation is analogous to that of Ⅲ-Ⅴ semi-conductor surface. The driving mechanism for this atomic rearrangement is that the Si atom tends to a planar sp2-like bonding situation with its three N neighbors and the N atom tends to a p3-like bonding with its three Si neighbors. Furthermore, surface relaxation induces the change from metallic to semiconducting characterization.

  20. Synthesis and atomic structure determination of Al8V5 gamma-brass

    International Nuclear Information System (INIS)

    Many structurally complex compounds like quasicrystals and their approximants are known to be stabilized at a particular electron per atom ratio e/a, regardless of constituent elements involved. This has been often referred to as the Hume-Rothery electron concentration rule. We consider the understanding of the Hume-Rothery stabilization mechanism to be best deepened by performing both ab initio LMTO-ASA and FLAPW band calculations for the complex compound whose atomic structure is experimentally determined. Admittedly, however, a computing time increases rapidly beyond practical level with increasing the number of atoms in a unit cell. Among various candidates, we chose a series of gamma-brasses containing 52 atoms in a unit cell by taking a full advantage of the facts that it exists in as many as 24 binary alloy systems and that its unit cell is just in size to be handled even in more time-consuming FLAPW method. We have so far studied the stability mechanism of Cu5Zn8 and Cu9Al4, both being regarded as its prototype, and TM2Zn11 gamma-brasses containing late transition elements TM=Fe, Co, Ni and Pd. In the present work, we chose the gamma-brass consisting of early transition metal element V and trivalent element Al. An almost single phase Al8V5 gamma-brass was ultimately synthesized by overcoming metallurgical difficulties encountered. Its atomic structure was determined by using the Brandon model as a starting structure in the Rietveld structure analysis for powdered diffraction spectra taken at the beam line BL02B2 of 8 GeV synchrotron radiation facility, SPring-8, Japan. The atomic structure suitable for band calculations was then proposed by eliminating quenched-in chemical disorder, i.e., partial mixing of Al and V atoms at given sites with minimum sacrifice. (author)

  1. Chemical Structure and Properties: A Modified Atoms-First, One-Semester Introductory Chemistry Course

    Science.gov (United States)

    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…

  2. Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method

    DEFF Research Database (Denmark)

    Valentin, Jan B.; Andreetta, Christian; Boomsma, Wouter;

    2014-01-01

    We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length s...

  3. A Real-Time All-Atom Structural Search Engine for Proteins

    OpenAIRE

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designabilit...

  4. Structures of Molecules at the Atomic Level: Caffeine and Related Compounds

    CERN Document Server

    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.

  5. Erosion of Carbon-based spacecraft structures in LEO by Atomic Oxygen

    DEFF Research Database (Denmark)

    Jørgensen, John Leif

    1998-01-01

    Atomic oxygen is constantly generated on the topside of the atmosphere by ionizing radiation. The ionizing solar radiation, UV and particles, will on impact dissociate molecular oxygen to atomic oxygen. However, due to the ratio between the UV and the particle flux from the sun, and due to...... comparable cross sections for the reactions, the UV generation largely dominates. Atomic oxygen is very reactive, and will enter into chemical reactions with most materials. This is especially true for earth orbiting spacecraft structures, as the orbital velocity corresponds to a kinetic energy released at...

  6. Study of BCC and FCC crystal atomic structure under instant plastic deformation

    International Nuclear Information System (INIS)

    Evolution of atomic structure of BCC and FCC crystals under conditions of pulsed external loads and great plastic deformations on the basis of computerized experiments is studied. Deformation of crystals was carried out stage-by-stage up to 32%. The results of computerized experiments showed that by instantaneous external loads plastic deformation, depending on its stage, may proceed either on the account of partial dislocations motion, or on account of twinning , or by means of atomic planes turn and shift. Regularities of the system potential energy turn angle of atomic planes change in dependence on the value of the crystal plastic deformation are determined

  7. Energy losses of fast heavy multiply charged structural ions in collisions with complex atoms

    Science.gov (United States)

    Matveev, V. I.; Sidorov, D. B.

    2007-07-01

    A nonperturbatve theory of energy losses of fast heavy multiply charged structural ions in collisions with neutral complex atoms is elaborated with allowance for simultaneous excitations of ionic and atomic electron shells. Formulas for the effective deceleration that are similar to the well-known Bethe-Bloch formulas are derived. By way of example, the energy lost by partially stripped U q+ ions (10 ≤ q ≤ 70) colliding with argon atoms and also the energy lost by Au, Pb, and Bi ions colliding with various targets are calculated. The results of calculation are compared with experimental data.

  8. Critical Assessment of Theoretical Calculations of Atomic Structure and Transition Probabilities: An Experimenter’s View

    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.

  9. Critical Assessment of Theoretical Calculations of Atomic Structure and Transition Probabilities: An Experimenter’s View

    OpenAIRE

    Elmar Träbert

    2014-01-01

    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 need...

  10. Atomic oxygen fine-structure splittings with tunable far-infrared spectroscopy

    Science.gov (United States)

    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.

  11. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    International Nuclear Information System (INIS)

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample

  12. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    Science.gov (United States)

    Wu, X.; Sha, W.

    2008-12-01

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.

  13. Structural fluctuation and atom-permutation in transition-metal clusters

    International Nuclear Information System (INIS)

    The atomic structure and thermodynamic properties of transition-metal clusters containing N atoms are investigated for N=6 and 7 using the method of molecular dynamics, where Gupta's potential taking into account many-body interaction is employed. The caloric curve (total energy-temperature curve) and the structural fluctuations are studied. The 'fluctuating state' is found for N=6 in the region of the temperature near below the melting point, where clusters undergo structural transition from one isomer to others without making any topological change. The fluctuating state differs from the coexistence state in that the former involves no atomic diffusion, and goes to a structural phase transition of the bulk when N is increased. On the other hand, the motion of atom-permutation is found in the low-temperature region of the liquid state, being induced by the cooperative motion of two atoms. It is discussed that such a motion easily occurs along the surface and may be considered to be one of the characteristics of small clusters. The fluctuating state is discussed in relation to the structural fluctuation of gold clusters observed experimentally. (orig.)

  14. Structure and stability of a silicon cluster on sequential doping with carbon atoms

    Science.gov (United States)

    AzeezullaNazrulla, Mohammed; Joshi, Krati; Israel, S.; Krishnamurty, Sailaja

    2016-02-01

    SiC is a highly stable material in bulk. On the other hand, alloys of silicon and carbon at nanoscale length are interesting from both technological as well fundamental view point and are being currently synthesized by various experimental groups (Truong et. al., 2015 [26]). In the present work, we identify a well-known silicon cluster viz., Si10 and dope it sequentially with carbon atoms. The evolution of electronic structure (spin state and the structural properties) on doping, the charge redistribution and structural properties are analyzed. It is interesting to note that the ground state SiC clusters prefer to be in the lowest spin state. Further, it is seen that carbon atoms are the electron rich centres while silicon atoms are electron deficient in every SiC alloy cluster. The carbon-carbon bond lengths in alloy clusters are equivalent to those seen in fullerene molecules. Interestingly, the carbon atoms tend to aggregate together with silicon atoms surrounding them by donating the charge. As a consequence, very few Si-Si bonds are noted with increasing concentrations of C atoms in a SiC alloy. Physical and chemical stability of doped clusters is studied by carrying out finite temperature behaviour and adsorbing O2 molecule on Si9C and Si8C2 clusters, respectively.

  15. Fractional Band Filling in an Atomic Chain Structure

    Science.gov (United States)

    Crain, J. N.; Kirakosian, A.; Altmann, K. N.; Bromberger, C.; Erwin, S. C.; McChesney, J. L.; Lin, J.-L.; Himpsel, F. J.

    2003-05-01

    A new chain structure of Au is found on stepped Si(111) which exhibits a 1/4-filled band and a pair of ≥1/2-filled bands with a combined filling of 4/3. Band dispersions and Fermi surfaces for Si(553)-Au are obtained by photoemission and compared to that of Si(557)-Au. The dimensionality of both systems is determined using a tight binding fit. The fractional band filling makes it possible to preserve metallicity in the presence of strong correlations.

  16. Mossbauer analysis of the atomic and magnetic structure of alloys

    CERN Document Server

    Ovchinnikov, VV

    2007-01-01

    The monograph indicates the key problems that have to be solved for the further development of the Mössbauer methods for analysis of the nuclear and magnetic structure of alloys, and offer solution variants for some of these problems based on the generalised results of a wide range of theoretical and experimental investigations,including original work by the author of the book and his colleagues. Contents 1. Description of the nature of the Mössbauer effect 2. Interpretation of the ossbauer spectra of alloys 3.Electrical and magnetics hyperfine interactions of resonant nuclei in metals and

  17. Unravelling CSH atomic structure via computational and experimental physical chemistry

    OpenAIRE

    Abdolhosseini Qomi, Mohammad Javad; Pellenq, Roland; Ulm, Franz

    2014-01-01

    Calcium Silicate Hydrate (CSH) is the main binding phase for the cement paste, which is responsible for its strength and creep behavior. This is a nonstoichiometric hydration phase with calcium to silicon ratio (C/S) ranging from 1 to 2.2. At low C/S ratios, the molecular structure of CSH resembles to that of Tobermorite minerals, whereas in high C/S ratios it mostly looks like disordered glasses. By taking advantage of tools of statistical physics, it is shown that CSH at a given C/S can be ...

  18. Study of the Adsorption of Atoms and Molecules on Silicon Surfaces Crystallographics and Electronic Structure

    CERN Document Server

    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...

  19. The atomic structure of Pt on Si(1 1 1) studied by scanning tunneling microscopy

    International Nuclear Information System (INIS)

    Highlights: • Two kinds of ordered reconstruction surface were prepared on Pt/Si(1 1 1) surface. • The atomic structures were observed and verified by STM. • Calculation results confirmed the bonding energy between Si and Pt atoms. - Abstract: Two kinds of ordered reconstruction surface (√3 × √3) R30° and (√7 × √7) R19.1°, are prepared by depositing different amounts of Pt on Si(1 1 1). The atomic structure and electronic properties are studied by scanning tunneling microscopy and X-ray photoelectron spectroscopy. Then two models are built to explain the results. And the calculated results using density functional theory based first principle calculation show that the distance between Pt and Si atoms in (√7 × √7) R19.1° structure is smaller than that in (√3 × √3) R30° structure, which can increase the bonding energy between Pt and Si atoms

  20. Properties and atomic structure of amorphous early transition metals

    International Nuclear Information System (INIS)

    Recently, we studied the properties of amorphous Zr-TL alloys (TL = Ni, Cu) in order to obtain parameters associated with the electronic structure and interatomic bonding of amorphous Zr. Here, we provide new data for the magnetic, superconducting and mechanical properties of amorphous Hf-TL and Ti-TL alloys. We combine our results with published data in order to obtain parameters appropriate to hypothetical amorphous Hf and Ti. These parameters are very different from those of the stable crystalline phases (hcp) of Hf and Ti and indicate, as for Zr, an fcc-like short range order for amorphous Hf and Ti. This results in an enhanced electronic density of states at the Fermi level, but in weakened interatomic bonding.

  1. Direct observation of defect structure in protein crystals by atomic force and transmission electron microscopy.

    OpenAIRE

    Devaud, G; Furcinitti, P S; Fleming, J. C.; Lyon, M K; Douglas, K

    1992-01-01

    We have examined the structure of S-layers isolated from Sulfolobus acidocaldarius using atomic force microscopy (AFM) and transmission electron microscopy (TEM). From the AFM images, we were able to directly observe individual dimers of the crystal, defects in the crystal structure, and twin boundaries. We have identified two types of boundaries, one defined by a mirror plane and the other by a glide plane. This work shows that twin boundaries are highly structured regions that are directly ...

  2. Atomic Structures of all the Twenty Essential Amino Acids and a Tripeptide, with Bond Lengths as Sums of Atomic Covalent Radii

    OpenAIRE

    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, t...

  3. The development of high-resolution spectroscopic methods and their use in atomic structure studies

    International Nuclear Information System (INIS)

    This thesis discusses work performed during the last nine years in the field of atomic spectroscopy. Several high-resolution techniques, ranging from quantum beats, level crossings, rf-laser double resonances to nonlinear field atom interactions, have been employed. In particular, these methods have been adopted and developed to deal with fast accelerated atomic or ionic beams, allowing studies of problems in atomic-structure theory. Fine- and hyperfine-structure determinations in the He I and Li I isoelectronic sequences, in 51V I, and in 235U I, II have permitted a detailed comparison with ab initio calculations, demonstrating the change in problems when going towards heavier elements or higher ionization stage. The last part of the thesis is concerned with the fundamental question of obtaining very high optical resolution in the interaction between a fast accelerated atom or ion beam and a laser field, this problem being the core in the continuing development of atomic spectroscopy necessary to challenge the more precise and sophisticated theories advanced. (Auth.)

  4. Atomic calculations and search for variation of the fine-structure constant in quasar absorption spectra

    Science.gov (United States)

    Dzuba, V. A.; Flambaum, V. V.

    A brief review of the search for variation of the fine structure constant in quasar absorption spectra is presented. Special consideration is given to the role of atomic calculations in the analysis of the observed data. A range of methods which allow to perform calculations for atoms or ions with different electron structure and which cover practically all periodic table of elements is discussed. Critical compilation of the results of the calculations as well as a review of the most recent results of the analysis are presented.

  5. Atomic calculations and search for variation of the fine structure constant in quasar absorption spectra

    CERN Document Server

    Dzuba, V A

    2008-01-01

    A brief review of the search for variation of the fine structure constant in quasar absorption spectra is presented. Special consideration is given to the role of atomic calculations in the analysis of the observed data. A range of methods which allow to perform calculations for atoms or ions with different electron structure and which cover practically all periodic table of elements is discussed. Critical compilation of the results of the calculations as well as a review of the most recent results of the analysis are presented.

  6. Effects of Contact Atomic Structure on Electronic Transport in Molecular Junction

    International Nuclear Information System (INIS)

    Based on nonequilibrium Green's function and first-principles calculations, we investigate the change in molecular conductance caused by different adsorption sites with the presence of additional Au atom around the metal-molecule contact in the system that benzene sandwiched between two Au(111) leads. The motivation is the variable situations that may arise in break junction experiments. Numerical results show that the enhancement of conductance induced by the presence of additional Au is dependent on the adsorption sites of anchoring atom. When molecule is located on top site with the presence of additional Au atoms, it can increase molecular conductance remarkably and present negative differential resistance under applied bias which cannot be found in bridge and hollow sites. Furthermore, the effects of different distance between additional Au and sulfur atoms in these three adsorption sites are also discussed. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  7. Systematic Study of Information Measures, Statistical Complexity and Atomic Structure Properties

    Science.gov (United States)

    Chatzisavvas, K. Ch.; Tserkis, S. T.; Panos, C. P.; Moustakidis, Ch. C.

    2015-05-01

    We present a comparative study of several information and statistical complexity measures in order to examine a possible correlation with certain experimental properties of atomic structure. Comparisons are also carried out quantitatively using Pearson correlation coefficient. In particular, it is shown that Fisher information in momentum space is very sensitive to shell effects. It is also seen that three measures expressed in momentum space that is Fisher information, Fisher-Shannon plane and LMC complexity are associated with atomic radius, ionization energy, electronegativity, and atomic dipole polarizability. Our results indicate that a momentum space treatment of atomic periodicity is superior to a position space one. Finally we present a relation that emerges between Fisher information and the second moment of the probability distribution in momentum space i.e. an energy functional of interest in (e,2e) experiments.

  8. A knowledge-based structure-discriminating function that requires only main-chain atom coordinates

    Directory of Open Access Journals (Sweden)

    Itoh Nobuya

    2008-10-01

    Full Text Available Abstract Background The use of knowledge-based potential function is a powerful method for protein structure evaluation. A variety of formulations that evaluate single or multiple structural features of proteins have been developed and studied. The performance of functions is often evaluated by discrimination ability using decoy structures of target proteins. A function that can evaluate coarse-grained structures is advantageous from many aspects, such as relatively easy generation and manipulation of model structures; however, the reduction of structural representation is often accompanied by degradation of the structure discrimination performance. Results We developed a knowledge-based pseudo-energy calculating function for protein structure discrimination. The function (Discriminating Function using Main-chain Atom Coordinates, DFMAC consists of six pseudo-energy calculation components that deal with different structural features. Only the main-chain atom coordinates of N, Cα, and C atoms for the respective amino acid residues are required as input data for structure evaluation. The 231 target structures in 12 different types of decoy sets were separated into 154 and 77 targets, and function training and the subsequent performance test were performed using the respective target sets. Fifty-nine (76.6% native and 68 (88.3% near-native (α RMSD targets in the test set were successfully identified. The average Cα RMSD of the test set resulted in 1.174 with the tuned parameters. The major part of the discrimination performance was supported by the orientation-dependent component. Conclusion Despite the reduced representation of input structures, DFMAC showed considerable structure discrimination ability. The function can be applied to the identification of near-native structures in structure prediction experiments.

  9. The Structural and Mechanical Properties of Graphene functionalized by Atomic Oxygen

    Directory of Open Access Journals (Sweden)

    I.K. Petrushenko

    2014-01-01

    Full Text Available In this paper, the structural and mechanical properties of graphene functionalized by atomic oxygen are investigated in the framework of the density functional theory. It was determined that the addition of oxygen leads to the deformation of the native graphene structure and reduction of its elastic properties. Here, a small functionalization leads to small structural changes, and, at the same time, to reduction of the Young's modulus of graphene. Larger functionalization causes structural deformation, with no significant changes of Young's modulus. It is shown that induced structural reorganization of the investigated models does not cause a rupture.

  10. Compound semiconductor alloys: From atomic-scale structure to bandgap bowing

    International Nuclear Information System (INIS)

    Compound semiconductor alloys such as InxGa1−xAs, GaAsxP1−x, or CuInxGa1−xSe2 are increasingly employed in numerous electronic, optoelectronic, and photonic devices due to the possibility of tuning their properties over a wide parameter range simply by adjusting the alloy composition. Interestingly, the material properties are also determined by the atomic-scale structure of the alloys on the subnanometer scale. These local atomic arrangements exhibit a striking deviation from the average crystallographic structure featuring different element-specific bond lengths, pronounced bond angle relaxation and severe atomic displacements. The latter, in particular, have a strong influence on the bandgap energy and give rise to a significant contribution to the experimentally observed bandgap bowing. This article therefore reviews experimental and theoretical studies of the atomic-scale structure of III-V and II-VI zincblende alloys and I-III-VI2 chalcopyrite alloys and explains the characteristic findings in terms of bond length and bond angle relaxation. Different approaches to describe and predict the bandgap bowing are presented and the correlation with local structural parameters is discussed in detail. The article further highlights both similarities and differences between the cubic zincblende alloys and the more complex chalcopyrite alloys and demonstrates that similar effects can also be expected for other tetrahedrally coordinated semiconductors of the adamantine structural family

  11. On the effect of atomic structure on the deactivation of catalytic gold nanoparticles

    International Nuclear Information System (INIS)

    Here we present atomic scale studies into the nature of both the internal structure and external surfaces of catalytic Au nanoparticles using aberration corrected in-situ electron microscopy. The activity of catalytic nanoparticles is thought to be highly sensitive to the particles' structure, meaning typical local atomic rearrangements are likely to significantly affect the overall performance of the catalyst. As-deposited Au nanoparticles are found to exhibit a variety of morphologies, with many being internally strained or highly stepped at the surface. Upon heating, surface atoms are observed to minimise the particles' surface energy by restructuring towards planar (111) facets, resulting in the removal of low co-ordinated sites thought to be crucial in catalysis by Au nanoparticles. These results suggest the process of surface energy minimisation made possible by heating may lead to a loss of active sites and consequently contribute to the deactivation of the catalyst.

  12. Adjoint design sensitivity analysis of reduced atomic systems using generalized Langevin equation for lattice structures

    International Nuclear Information System (INIS)

    An efficient adjoint design sensitivity analysis method is developed for reduced atomic systems. A reduced atomic system and the adjoint system are constructed in a locally confined region, utilizing generalized Langevin equation (GLE) for periodic lattice structures. Due to the translational symmetry of lattice structures, the size of time history kernel function that accounts for the boundary effects of the reduced atomic systems could be reduced to a single atom’s degrees of freedom. For the problems of highly nonlinear design variables, the finite difference method is impractical for its inefficiency and inaccuracy. However, the adjoint method is very efficient regardless of the number of design variables since one additional time integration is required for the adjoint GLE. Through numerical examples, the derived adjoint sensitivity turns out to be accurate and efficient through the comparison with finite difference sensitivity

  13. Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

    International Nuclear Information System (INIS)

    Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 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 FeTe1−xSex 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

  14. Current State of Web Sites in Science Education--Focus on Atomic Structure.

    Science.gov (United States)

    Tuvi, Inbal; Nachmias, Rafi

    2001-01-01

    Explores to what extent the web's advanced graphical tools and computational power are implemented in science education. Focuses on the pedagogical and technological characteristics of web sites attempting to teach the subject of atomic structure. (Contains 33 references.) (Author/YDS)

  15. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    Science.gov (United States)

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  16. Supporting Students in Learning with Multiple Representation to Improve Student Mental Models on Atomic Structure Concepts

    Science.gov (United States)

    Sunyono; Yuanita, L.; Ibrahim, M.

    2015-01-01

    The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…

  17. Do General Physics Textbooks Discuss Scientists' Ideas about Atomic Structure? A Case in Korea

    Science.gov (United States)

    Niaz, Mansoor; Kwon, Sangwoon; Kim, Nahyun; Lee, Gyoungho

    2013-01-01

    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 physics textbooks published in Korea based on the eight criteria developed in previous research. The result of this study shows that Korean general…

  18. Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors

    OpenAIRE

    Levashov, Valentin A.

    2015-01-01

    It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of t...

  19. Fine-structure constant variability surprises for laboratory atomic spectroscopy and cosmological evolution of quasar spectra

    CERN Document Server

    Bekenstein, J D

    2003-01-01

    Calculation of the Dirac hydrogen atom spectrum in the framework of dynamical fine structure constant (alpha) variability discloses a small departure in the laboratory from Sommerfeld's formula for the fine structure shifts, possibly measurable today. And for a distant object in the universe, the wavelength shift of a spectral line specifically ascribable to cosmological alpha variation is found to depend differently on the quantum numbers than in the conventional view. This last result clashes with the conventional wisdom that an atom's spectrum can change with cosmological time only through evolution of the alpha parameter in the energy eigenvalue formula, and thus impacts on the Webb group's analysis of fine structure intervals in quasar absorption lines (which has been claimed to disclose cosmological alpha evolution). In particular, analyzing together a mix of quasar absorption lines from different fine structure multiplets can bias estimates of cosmological alpha variability.

  20. Higher order structure of short immunostimulatory oligonucleotides studied by atomic force microscopy

    International Nuclear Information System (INIS)

    Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.

  1. Higher order structure of short immunostimulatory oligonucleotides studied by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Dionne C.G., E-mail: dionne.c.g.klein@ntnu.no [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway); Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Latz, Eicke [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 (United States); Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn (Germany); Espevik, Terje [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Stokke, Bjorn T. [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway)

    2010-05-15

    Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.

  2. Electronic structures and magnetic properties of rare-earth-atom-doped BNNTs

    Science.gov (United States)

    Ren, Juan; Zhang, Ning-Chao; Wang, Peng; Ning, Chao; Zhang, Hong; Peng, Xiao-Juan

    2016-04-01

    Stable geometries, electronic structures, and magnetic properties of (8,0) and (4,4) single-walled BN nanotubes (BNNTs) doped with rare-earth (RE) atoms are investigated using the first-principles pseudopotential plane wave method with density functional theory (DFT). The results show that these RE atoms can be effectively doped in BNNTs with favorable energies. Because of the curvature effect, the values of binding energy for RE-atom-doped (4,4) BNNTs are larger than those of the same atoms on (8,0) BNNTs. Electron transfer between RE-5 d, 6 s, and B-2 p, N-2 p orbitals was also observed. Furthermore, electronic structures and magnetic properties of BNNTs can be modified by such doping. The results show that the adsorption of Ce, Pm, Sm, and Eu atoms can induce magnetization, while no magnetism is observed when BNNTs are doped with La. These results are useful for spintronics applications and for developing magnetic nanostructures.

  3. Electronic structure and magnetic properties of substitutional transition-metal atoms in GaN nanotubes

    International Nuclear Information System (INIS)

    The electronic structure and magnetic properties of the transition-metal (TM) atoms (Sc—Zn, Pt and Au) doped zigzag GaN single-walled nanotubes (NTs) are investigated using first-principles spin-polarized density functional calculations. Our results show that the bindings of all TM atoms are stable with the binding energy in the range of 6–16 eV. The Sc- and V-doped GaN NTs exhibit a nonmagnetic behavior. The GaN NTs doped with Ti, Mn, Ni, Cu and Pt are antiferromagnetic. On the contrary, the Cr-, Fe-, Co-, Zn- and Au-doped GaN NTs show the ferromagnetic characteristics. The Mn- and Co-doped GaN NTs induce the largest local moment of 4μB among these TM atoms. The local magnetic moment is dominated by the contribution from the substitutional TM atom and the N atoms bonded with it. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  4. Generation of atomic four-body statistical potentials derived from the delaunay tessellation of protein structures.

    Science.gov (United States)

    Masso, Majid

    2012-01-01

    Delaunay tessellation of the atomic coordinates for a crystallographic protein structure yields an aggregate of non-overlapping and space-filling irregular tetrahedral simplices. The vertices of each simplex objectively identify a quadruplet of nearest neighbor atoms in the protein. Here we apply Delaunay tessellation to 1417 high-resolution structures of single chains that share low sequence identity, for the purpose of determining the relative frequencies of occurrence for all possible nearest neighbor atomic quadruplet types. Alternative distributions are explored by varying two fundamental parameters: atomic alphabet selection and cutoff length for admissible simplex edges. The distributions are then converted to four-body potential functions by implementing the inverted Boltzmann principle, which requires calculating the distribution of the reference state. Two alternative definitions for the reference state are presented, which introduces a third parameter, and we derive and compare an array of such potential functions. These knowledge-based statistical potentials based on higher-order interactions complement and generalize the more commonly encountered atom-pair potentials, for which a number of approaches are described in the literature. PMID:23367374

  5. Atomic structure and orientation relations of interfaces between Ag and ZnO

    OpenAIRE

    Vellinga, W. P.; de Hosson, J.T.M.

    1997-01-01

    This paper presents the results of investigations of Ag-ZnO interfaces, produced by internal oxidation of an Ag-Zn alloy. ZnO precipitates with the wurtzite structure were found exhibiting mainly one orientation relation with the Ag matrix. However, closely related ORs were found, rotated by small angles from that orientation relation. The atomic structures of several interfaces surrounding these precipitates were studied and compared using HRTEM. The paper concentrates on interfaces between ...

  6. Role of Bhabha Atomic Research Center (BARC) parallel processing system in structural analysis of nuclear components

    International Nuclear Information System (INIS)

    Computational structural analysis of nuclear reactor components requires high speed computing systems. Parallel processing systems, such as ANUPAM developed at Bhabha Atomic Research Centre, have helped immensely in meeting this requirement. The implementation of structural integrity analysis code on ANUPAM is illustrated here by commissioning two in house codes TABS and FAIR. The parallelization strategies and the efficiency of ANUPAM are highlighted. (author). 6 refs., 3 figs

  7. Micropore Structure Representation of Sandstone in Petroleum Reservoirs Using an Atomic Force Microscope

    Institute of Scientific and Technical Information of China (English)

    BAI Yong-Qiang; ZHU Xing; WU Jun-Zheng; BAI Wen-Guang

    2011-01-01

    @@ The pore structure of sandstone in an oil reservoir is investigated using atomic force microscopy(AFM).At nanoscale resolution,AFM images of sandstone show us the fine structure.The real height data of images display the three-dimensional space structure of sandstone effectively.The three-dimensional analysis results show that the AFM images of sandstone have unique characteristics that,like fingerprints,can identify different structural properties of sandstones.The results demonstrate that AFM is an effective method used to represent original sandstone in petroleum reservoirs,and may help geologists to appreciate the sandstone in oil reservoirs fully.

  8. Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies

    Science.gov (United States)

    Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

    2016-05-01

    Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum.Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE

  9. Multiscale structural changes of atomic order in severely deformed industrial aluminum

    Science.gov (United States)

    Samoilenko, Z. A.; Ivakhnenko, N. N.; Pushenko, E. I.; Pashinskaya, E. G.; Varyukhin, V. N.

    2016-02-01

    The regularities of multiscale structural changes in the atomic order of the aluminum alloy AD-1 after a severe cold plastic deformation by conventional rolling in smooth rolls or in rolls with relief recesses favorable for shear deformation have been investigated. It has been found that there are four types of structural fractions that differ in scale and perfection of atomic order: crystallographic planes with a long-range order; nanoscale fragments of the planes ( D = 100-300 Å) with an incipient long-range order; smaller groups of atoms ( D = 20-30 Å) of amorphized structure; and the least ordered structural fraction of intercluster medium, keeping only a short-range atomic order (2-3 interatomic distances, 10 Å). The presence of diffuse halo bands in the region of intense Debye lines indicates phase transitions of the order → disorder type with the formation of one to three groups of amorphous clusters with the dominance, in the nanometer scale, of the atomic order characteristic of the family of planes (111), (220), and (311) of crystalline aluminum. We have found a dynamic phase transition with the changing crystallographic order of aluminum, with the matrix structure of a face-centered cubic (FCC) lattice, in the form of nanosized local groups of atoms, that is, the deformation clusters of aluminum with a simple cubic K6 lattice. In the case of conventional rolling, the development of large clusters 50-500 Å in size is observed; however, in the use of rolls with relief recesses, the difference in the sizes of the clusters is one half as much: 50-250 Å. Based on the analysis of the integrated intensity of incoherent X-ray scattering by the samples, we have elucidated the nature of the lowest measured density for the sample subjected to conventional rolling, which consists in the volume concentration of disorderly arranged atoms, the highest of the compared structures, which indicates the formation therein of the greatest amount of fluctuation "voids."

  10. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    Science.gov (United States)

    Xie, Jianming; Wang, Lei; Wu, Ning; Schultz, Peter G.

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  11. 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.……

  12. Atomic-scale structure of single-layer MoS2 nanoclusters

    DEFF Research Database (Denmark)

    Helveg, S.; Lauritsen, J. V.; Lægsgaard, E.;

    2000-01-01

    We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide (MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2...... nanoparticles synthesized on Au(lll), and establishes a new picture of the active edge sires of the nanoclusters. The results demonstrate a way to get detailed atomic-scale information on catalysts in general....

  13. Atomic structure of Ag(111) saturated with chlorine: Formation of Ag3Cl7 clusters

    Science.gov (United States)

    Andryushechkin, B. V.; Cherkez, V. V.; Gladchenko, E. V.; Zhidomirov, G. M.; Kierren, B.; Fagot-Revurat, Y.; Malterre, D.; Eltsov, K. N.

    2011-08-01

    The structure of saturated chlorine layer on Ag(111) has been studied with low temperature scanning tunneling microscopy and density functional theory. For the first time atomic-resolution STM images of saturated chlorine coverage have been obtained. STM images demonstrate coexistence of the domain with (3 × 3)-like reconstruction and numerous bright objects identified as Ag3Cl7 clusters. According to our model supported by DFT calculations, clusters are formed on the boundaries between the adjacent (3×3) antiphase domains. These boundaries have a characteristic triangular shape and are formed by six chlorine atoms chemisorbed on the triangular silver island with local periodicity (1 × 1).

  14. Atomic-scale structure of single-layer MoS2 nanoclusters

    OpenAIRE

    Helveg, S.; Lauritsen, J.V.; Lægsgaard, E.; Stensgaard, I.; Nørskov, Jens Kehlet; Clausen, B.S, Helveg S; Topsøe, H.; Besenbacher, Flemming

    2000-01-01

    We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide (MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2 nanoparticles synthesized on Au(lll), and establishes a new picture of the active edge sires of the nanoclusters. The results demonstrate a way to get detailed atomic-scale information on catalysts in ...

  15. Electronic and atomic structure of the AlnHn+2 clusters

    DEFF Research Database (Denmark)

    Martinez, Jose Ignacio; Alonso, J.A.

    2008-01-01

    polyhedron of n vertices and n H atoms form strong H-Al terminal bonds; one pair of electrons is involved in each of those bonds. The remaining n+1 electron pairs form a delocalized cloud over the surface of the Al cage. The clusters fulfilling the Wade-Mingos rule have wider HOMO-LUMO gaps and are......The electronic and atomic structure of the family of hydrogenated Al clusters AlnHn+2 with n=4-11 has been studied using the density functional theory with the generalized gradient approximation (GGA) for exchange and correlation. All these clusters have substantial gaps between the highest...

  16. Correspondences between the Classical Electrostatic Thomson Problem and Atomic Electronic Structure

    CERN Document Server

    LaFave, Tim

    2014-01-01

    Correspondences between the Thomson Problem and atomic electron shell-filling patterns are observed as systematic non-uniformities in the distribution of potential energy necessary to change configurations of $N\\le 100$ electrons into discrete geometries of neighboring $N-1$ systems. These non-uniformities yield electron energy pairs, intra-subshell pattern similarities with empirical ionization energy, and a salient pattern that coincides with size-normalized empirical ionization energies. Spatial symmetry limitations on discrete charges constrained to a spherical volume are conjectured as underlying physical mechanisms responsible for shell-filling patterns in atomic electronic structure and the Periodic Law.

  17. 'Sub-atomic' resolution of non-contact atomic force microscope images induced by a heterogeneous tip structure: a density functional theory study

    Energy Technology Data Exchange (ETDEWEB)

    Campbellova, Anna; Klapetek, Petr [Czech Metrology Institute, OkruznI 31, 638 00, Brno (Czech Republic); Ondracek, Martin; JelInek, Pavel [Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnicka 10, 162 00 Prague (Czech Republic); Pou, Pablo; Perez, Ruben, E-mail: jelinekp@fzu.cz [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, 28049 Madrid (Spain)

    2011-07-22

    A Si adatom on a Si(111)-(7 x 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.

  18. Influence of the plasma environment on atomic structure using an ion-sphere model

    International Nuclear Information System (INIS)

    Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al

  19. Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies.

    Science.gov (United States)

    Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

    2016-05-19

    Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum. PMID:27160891

  20. Atomic-scale structure of grain boundaries: Correlations to grain boundary properties

    International Nuclear Information System (INIS)

    It is generally believed that many properties of solid interfaces are ultimately determined by their structure and composition at the atomic level. We report here on work in two areas of grain boundary (GB) research in which structure-property correlations have been investigated recently. HREM observations in connection with computer modeling of GBs in fcc metals have given considerable insight into correlations between GB energy and atomic-scale GB structure. Efforts to understand and possibly control the supercurrent transport behavior across GBs in high-temperature superconductors require the combination of microstructure characterizations with investigations of electric transport properties. In both areas considerable progress is being made and has already lead to important insights concerning interfacial properties

  1. Atomic-scale observation of dynamical fluctuation and three-dimensional structure of gold clusters

    Energy Technology Data Exchange (ETDEWEB)

    Li, Junjie [Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, Department of Physics, East China Normal University, North Zhongshan Road 3663, Shanghai 200062 (China); Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Yin, Deqiang [School of Manufacturing Science and Engineering, Sichuan University, Chengdu 610064 (China); Chen, Chunlin; Lin, Liyang; Wang, Zhongchang, E-mail: zcwang@wpi-aimr.tohoku.ac.jp [Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Li, Qiang [School of Materials Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China); Sun, Rong [Institute of Engineering Innovation, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-8656 (Japan); Huang, Sumei, E-mail: smhuang@phy.ecnu.edu.cn [Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, Department of Physics, East China Normal University, North Zhongshan Road 3663, Shanghai 200062 (China)

    2015-02-28

    Unravelling three-dimensional structures and dynamical fluctuation of metal nanoclusters is critical to understanding reaction process and the origin of catalytic activity in many heterogeneous catalytic systems. We obtain three-dimensional structures of ultra-small Au clusters by combining aberration-corrected scanning transmission electron microscopy, density functional theory calculations, and imaging simulations. The configurations of unique Au clusters are revealed at the atomic scale and the corresponding electronic states are given. The sequential observations reveal a transition of ultra-small Au clusters with about 25 atoms from a near-square to an elongated structure. We also find a transition from two dimensions to three dimensions for the Au clusters. The obtained three-dimensional geometry and associated electronic states help to clarify atomistic mechanism of shape- and number-dependent catalytic activities of Au clusters.

  2. Atomic Structure of the Anatase TiO2(001) Surface

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Yaobiao; Zhu, Ke; Kaspar, Tiffany C.; Du, Yingge; Birmingham, Blake; Park, Kenneth T.; Zhang, Zhenrong

    2013-08-16

    Understanding the structure of well-defined anatase TiO2 surfaces is critical for deciphering site-specific thermal and photo- reaction mechanisms on anatase TiO2. Using UHV scanning tunneling microscopy (STM), we have studied the atomic structure of anatase TiO2(001) epitaxial thin films grown by oxygen plasma assisted molecular beam epitaxy. Bright rows of the (1×4) reconstructed surface are resolved as three types of features with different sizes. High-resolution STM images taken from the same area at different bias voltages show that these individual features are originated from combinations of two basic atomic building blocks. We propose a modified added molecule model for the anatase TiO2 (001) surface structure.

  3. Size and shape of grain boundary network components and their atomic structures in polycrystalline nanoscale materials

    International Nuclear Information System (INIS)

    Microstructure in polycrystalline materials is composed of grain boundary plane, triple junction line, and vertex point. They are the integral parts of the grain boundary network structure and the foundation for the structure-property relations. In polycrystalline, especially nanocrystalline, materials, it becomes increasingly difficult to probe the atomistic structure of the microstructure components directly in experiment due to the size limitation. Here, we present a numerical approach using pair correlation function from atomistic simulation to obtain the detailed information for atomic order and disorder in the grain boundary network in nanocrystalline materials. We show that the atomic structures in the different microstructural components are related closely to their geometric size and shape, leading to unique signatures for atomic structure in microstructural characterization at nanoscales. The dependence varies systematically with the characteristic dimension of the microstructural component: liquid-like disorder is found in vertex points, but a certain order persists in triple junctions and grain boundaries along the extended dimensions of these microstructure components

  4. The structure determination of Al20Cu2Mn3 by near atomic resolution chemical mapping

    International Nuclear Information System (INIS)

    Highlights: • The structure of Al20Cu2Mn3 with a space group of Bbmm is completely determined. • The actual formula of Al20Cu2Mn3 is Al31Cu3Mn5. • Al20Cu2Mn3 is formed by a parallel tessellation of hexagon subunits. • Al20Cu2Mn3 is prone to twinning by an alternate tessellation of hexagon subunits. • The Al20Cu2Mn3 is coherent with α-Al along its longitudinal axis. - Abstract: Al20Cu2Mn3 phase is one kind of common dispersoids in aluminum alloys; however, the atomic arrangement of Al20Cu2Mn3 has not yet been clearly identified. Combining the atomic resolution high angle annular dark field and chemical composition quantitative results, three structure models of Al20Cu2Mn3 were derived basing on the isostructural Mn11Ni4Al60. The formation enthalpies and total energy were calculated using the first-principles approach. The structure of the Al20Cu2Mn3 phase with the minimal energy was identified, giving a fully relaxed structure with lattice parameters of a = 23.98 Å, b = 12.54 Å, c = 7.66 Å, which belongs to a space group of Bbmm. The determined structure is in excellent agreement with the near atomic resolution chemical mapping results

  5. Longitudinal structure in atomic oxygen concentrations observed with WINDII on UARS. [Wind Imaging Interferometer

    Science.gov (United States)

    Shepherd, G. G.; Thuillier, G.; Solheim, B. H.; Chandra, S.; Cogger, L. L.; Duboin, M. L.; Evans, W. F. J.; Gattinger, R. L.; Gault, W. A.; Herse, M.

    1993-01-01

    WINDII, the Wind Imaging Interferometer on the Upper Atmosphere Research Satellite, began atmospheric observations on September 28, 1991 and since then has been collecting data on winds, temperatures and emissions rates from atomic, molecular and ionized oxygen species, as well as hydroxyl. The validation of winds and temperatures is not yet complete, and scientific interpretation has barely begun, but the dominant characteristic of these data so far is the remarkable structure in the emission rate from the excited species produced by the recombination of atomic oxygen. The latitudinal and temporal variability has been noted before by many others. In this preliminary report on WINDII results we draw attention to the dramatic longitudinal variations of planetary wave character in atomic oxygen concentration, as reflected in the OI 557.7 nm emission, and to similar variations seen in the Meine1 hydroxyl band emission.

  6. Atomic structure of the SbCu surface alloy: A surface X-ray diffraction study

    DEFF Research Database (Denmark)

    Meunier, I.; Gay, J.M.; Lapena, L.; Aufray, B.; Oughaddou, H.; Landemark, E.; Falkenberg, G.; Lottermoser, L.; Johnson, R.L.

    The dissolution at 400 degrees C of an antimony layer deposited at room temperature on a Cu(111) substrate leads to a surface alloy with a p(root 3x root 3)R 30 degrees x 30 degrees superstructure and a Sb composition of 1/3.We present here a structural study of this Sb-Cu compound by surface X......-ray diffraction (SXRD). The best agreement is obtained for a Cu,Sb surface layer with Sb atoms substituting 1/3 of the Cu atoms, over an essentially unperturbed Cu(111) plane. The largest relaxation is undergone by the Sb atoms which rise by 0.32+0.02 Angstrom over the mean plane of its Cu neighbours. No...

  7. Atomic beam magnetic resonance apparatus for systematic measurement of hyperfine structure anomalies (Bohr-Weisskopf effect)

    International Nuclear Information System (INIS)

    An atomic beam magnetic resonance (ABMR) apparatus has been constructed at Orsay, and has been installed at the CERN PS Booster ISOLDE mass separator facility for 'on-line' work with radioactive isotopes in a program to measure hyperfine structure anomalies (the Bohr-Weisskopf effect) over long isotopic chains. The hfs anomalies result from the effect of the spatial distribution of the nuclear magnetization on the atomic hfs interaction. Constructional details of the system are described: Emphasis is placed on the measurement of nuclear g-factors by a triple resonance, laser state selected, ABMR method. A precision better than 10-4 for gI values has been obtained in stable atomic beam tests, leading to hfs anomaly measurements better than 10%. Two types of detection systems are described: Laser fluorescence and surface ionization coupled with mass spectrometry. (orig.)

  8. Atomic structure of the SbCu surface alloy: A surface X-ray diffraction study

    DEFF Research Database (Denmark)

    Meunier, I.; Gay, J.M.; Lapena, L.;

    1999-01-01

    The dissolution at 400 degrees C of an antimony layer deposited at room temperature on a Cu(111) substrate leads to a surface alloy with a p(root 3x root 3)R 30 degrees x 30 degrees superstructure and a Sb composition of 1/3.We present here a structural study of this Sb-Cu compound by surface X......-ray diffraction (SXRD). The best agreement is obtained for a Cu,Sb surface layer with Sb atoms substituting 1/3 of the Cu atoms, over an essentially unperturbed Cu(111) plane. The largest relaxation is undergone by the Sb atoms which rise by 0.32+0.02 Angstrom over the mean plane of its Cu neighbours. No...

  9. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

    OpenAIRE

    Jonikas, Magdalena A; RADMER, RANDALL J.; Altman, Russ B

    2009-01-01

    Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. Results: We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA ...

  10. Analysis of atomic structures as the development of Belov’s “lattice” crystallography

    International Nuclear Information System (INIS)

    The theorems of lattice crystallography, which was developed by N.V. Belov, and the wave-mechanical concept of the crystalline state lie in the basis of the crystallographic analysis of structures, which determines the results of atomic ordering by sets of crystallographic planes with the formation of pseudotranslational sublattices (force skeletons of structures). The role of cationic and anionic sublattices is shown by the example of structures of natural sulfides: heyrovskyite Pb6Bi2S9 and cannizzarite (Pb,Cd)5(Bi,In)6(S,Se)14.

  11. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob; Jacobsen, Karsten Wedel; Braun, K.F.; Rieder, K.H.; Laegsgaard, E.; Besenbacher, Flemming

    2002-01-01

    The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations, the...... simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

  12. Atomic-scale structure of disordered Ga1-xInxP alloys

    International Nuclear Information System (INIS)

    Extended x-ray-absorption fine-structure experiments have previously demonstrated that for each composition x, the sample average of all nearest-neighbor A-C distances in an A1-xBxC semiconductor alloy is closer to the values in the pure (x→0) AC compound than to the composition-weighted (virtual) lattice average. Such experiments do not reveal, however, the distribution of atomic positions in an alloy, so the principle displacement directions and the degrees of correlation among such atomic displacements remain unknown. Here we calculate both structural and thermodynamic properties of Ga1-xInxP alloys using an explicit occupation- and position-dependent energy functional. The latter is taken as a modified valence force field, carefully fit to structural energies determined by first-principles local-density calculations. Configurational and vibrational degrees of freedom are then treated via the continuous-space Monte Carlo approach. We find good agreement between the calculated and measured mixing enthalpy of the random alloy, nearest-neighbor bond lengths, and temperature-composition phase diagram. In addition, we predict yet unmeasured quantities such as (a) distributions, fluctuations, and moments of first- and second-neighbor bond lengths as well as bond angles, (b) radial distribution functions, (c) the dependence of short-range order on temperature, and (d) the effect of temperature on atomic displacements. Our calculations provide a detailed picture of how atoms are arranged in substitutionally random but positionally relaxed alloys, and offer an explanation for the effects of site correlations, static atomic relaxations, and dynamic vibrations on the phase-diagram and displacement maps. (Abstract Truncated)

  13. Quantitative Subsurface Atomic Structure Fingerprint for 2D Materials and Heterostructures by First-Principles-Calibrated Contact-Resonance Atomic Force Microscopy.

    Science.gov (United States)

    Tu, Qing; Lange, Björn; Parlak, Zehra; Lopes, Joao Marcelo J; Blum, Volker; Zauscher, Stefan

    2016-07-26

    Interfaces and subsurface layers are critical for the performance of devices made of 2D materials and heterostructures. Facile, nondestructive, and quantitative ways to characterize the structure of atomically thin, layered materials are thus essential to ensure control of the resultant properties. Here, we show that contact-resonance atomic force microscopy-which is exquisitely sensitive to stiffness changes that arise from even a single atomic layer of a van der Waals-adhered material-is a powerful experimental tool to address this challenge. A combined density functional theory and continuum modeling approach is introduced that yields sub-surface-sensitive, nanomechanical fingerprints associated with specific, well-defined structure models of individual surface domains. Where such models are known, this information can be correlated with experimentally obtained contact-resonance frequency maps to reveal the (sub)surface structure of different domains on the sample. PMID:27263541

  14. Microtraps for neutral atoms using superconducting structures in the critical state

    International Nuclear Information System (INIS)

    Recently demonstrated superconducting atom chips provide a platform for trapping atoms and coupling them to solid-state quantum systems. Controlling these devices requires a full understanding of the supercurrent distribution in the trapping structures. For type-II superconductors, this distribution is hysteretic in the critical state due to the partial penetration of the magnetic field in the thin superconducting film through pinned vortices. We report here an experimental observation of this memory effect. Our results are in good agreement with the predictions of the Bean model of the critical state without adjustable parameters. The memory effect allows to write and store permanent currents in micron-sized superconducting structures and paves the way toward engineered trapping potentials.

  15. Investigations of the atomic structure of amorphous ytterbium-alloys by Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    Atomic-scale structures of the amorphous alloys Yb80X20 (X = Cu, Ag, Au, Pd, Bi) have been investigated with a 174Yb-Moessbauer source. The distribution of the quadrupole splitting parameters obtained from the analysis of the Moessbauer spectra was compared with the theoretical function for a charge distribution corresponding to dense random packing (DRP) of ions. The atomic structure deduced from the distribution of splitting parameters was consistent with the DRP-model in the amorphous alloys Yb80Cu20, Yb80Ag20, Yb80Au20, Yb80Pd20. In contrast the Moessbauer spectrum of the amorphous alloy Yb80Bi20 showed clear evidence of short range order. This is presumably due to the tendency of bismuth to form covalent bondings. (orig./GSCH)

  16. Atomically resolved structural determination of graphene and its point defects via extrapolation assisted phase retrieval

    International Nuclear Information System (INIS)

    Previously reported crystalline structures obtained by an iterative phase retrieval reconstruction of their diffraction patterns seem to be free from displaying any irregularities or defects in the lattice, which appears to be unrealistic. We demonstrate here that the structure of a nanocrystal including its atomic defects can unambiguously be recovered from its diffraction pattern alone by applying a direct phase retrieval procedure not relying on prior information of the object shape. Individual point defects in the atomic lattice are clearly apparent. Conventional phase retrieval routines assume isotropic scattering. We show that when dealing with electrons, the quantitatively correct transmission function of the sample cannot be retrieved due to anisotropic, strong forward scattering specific to electrons. We summarize the conditions for this phase retrieval method and show that the diffraction pattern can be extrapolated beyond the original record to even reveal formerly not visible Bragg peaks. Such extrapolated wave field pattern leads to enhanced spatial resolution in the reconstruction

  17. Do general physics textbooks discuss scientists’ ideas about atomic structure? A case in Korea

    Science.gov (United States)

    Niaz, Mansoor; Kwon, Sangwoon; Kim, Nahyun; Lee, Gyoungho

    2013-01-01

    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 physics textbooks published in Korea based on the eight criteria developed in previous research. The result of this study shows that Korean general physics textbooks often lack detail about the history and philosophy of science. This result is quite similar to those published for the USA. Furthermore, chemistry textbooks published in the USA, Turkey and Venezuela are quite similar to the physics textbooks. This is a cause for concern as textbooks present theories as facts and ignore the historical reconstructions based on the development of scientific theories that frequently involve controversies and conflicts among scientists. The inclusion of historical reconstructions of ideas about atomic structure can provide students with a better appreciation of the dynamics of scientific progress.

  18. Hybrid inorganic–organic superlattice structures with atomic layer deposition/molecular layer deposition

    OpenAIRE

    Tynell, Tommi; Yamauchi, Hisao; Karppinen, Maarit

    2014-01-01

    A combination of the atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques is successfully employed to fabricate thin films incorporating superlattice structures that consist of single layers of organic molecules between thicker layers of ZnO. Diethyl zinc and water are used as precursors for the deposition of ZnO by ALD, while three different organic precursors are investigated for the MLD part: hydroquinone, 4-aminophenol and 4,4′-oxydianiline. The successful superla...

  19. Stable-isotope ratio analysis based on atomic hyperfine structure and optogalvanic spectroscopy

    International Nuclear Information System (INIS)

    Atomic hyperfine structures were measured for the Cu I transition at 5782 A by optogalvanic spectroscopy at high resolution, with a cw dye laser. Samples were electro-deposited on the demountable cathode of a home-made hollow-cathode lamp. By spectral deconvolution, the relative isotopic abundances of 63Cu and 65Cu could be determined with good accuracy and precision. The technique is applicable to copper concentrations as low as 1.6 ppm. (author)

  20. 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.

  1. Evaluation of Biofield Treatment on Physical, Atomic and Structural Characteristics of Manganese (II, III) Oxide

    OpenAIRE

    Trivedi, Mahendra Kumar

    2015-01-01

    In Mn3O4, the crystal structure, dislocation density, particle size and spin of the electrons plays crucial role in modulating its magnetic properties. Present study investigates impact of Biofield treatment on physical and atomic properties of Mn3O4. X-ray diffraction revealed the significant effect of biofield on lattice parameter, unit cell volume, molecular weight, crystallite sizes and densities of treated Mn3O4. XRD analysis confirmed that crystallinity was enhanced and dislocation dens...

  2. A robust and general Schrödinger and Dirac solver for atomic structure calculations

    Czech Academy of Sciences Publication Activity Database

    Čertík, O.; Pask, J.E.; Vackář, Jiří

    2013-01-01

    Roč. 184, č. 7 (2013), s. 1777-1791. ISSN 0010-4655 R&D Projects: GA MŠk(CZ) LC06040; GA ČR GA101/09/1630 Institutional support: RVO:68378271 Keywords : atom * electronic structure * Dirac equation * density -functional theory Subject RIV: BE - Theoretical Physics Impact factor: 2.407, year: 2013 http://www.sciencedirect.com/science/article/pii/S0010465513000714

  3. Structure of Alzheimer’s disease amyloid precursor protein copper-binding domain at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Geoffrey Kwai-Wai; Adams, Julian J. [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Cappai, Roberto [Department of Pathology and Centre for Neuroscience, The University of Melbourne, Victoria 3010 (Australia); The Mental Health Research Institute of Victoria, Parkville, Victoria 3052 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia); Parker, Michael W., E-mail: mparker@svi.edu.au [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia)

    2007-10-01

    An atomic resolution structure of the copper-binding domain of the Alzheimer’s disease amyloid precursor protein is presented. Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer’s disease, as its cleavage generates the Aβ peptide that is toxic to cells. APP is able to bind Cu{sup 2+} and reduce it to Cu{sup +} through its copper-binding domain (CuBD). The interaction between Cu{sup 2+} and APP leads to a decrease in Aβ production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 Å) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu{sup 2+} reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Aβ production.

  4. Structure of Alzheimer’s disease amyloid precursor protein copper-binding domain at atomic resolution

    International Nuclear Information System (INIS)

    An atomic resolution structure of the copper-binding domain of the Alzheimer’s disease amyloid precursor protein is presented. Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer’s disease, as its cleavage generates the Aβ peptide that is toxic to cells. APP is able to bind Cu2+ and reduce it to Cu+ through its copper-binding domain (CuBD). The interaction between Cu2+ and APP leads to a decrease in Aβ production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 Å) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu2+ reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Aβ production

  5. Atomic-scale mapping of electronic structures across heterointerfaces by cross-sectional scanning tunneling microscopy

    Science.gov (United States)

    Chiu, Ya-Ping; Huang, Bo-Chao; Shih, Min-Chuan; Huang, Po-Cheng; Chen, Chun-Wei

    2015-09-01

    Interfacial science has received much attention recently based on the development of state-of-the-art analytical tools that can create and manipulate the charge, spin, orbital, and lattice degrees of freedom at interfaces. Motivated by the importance of nanoscale interfacial science that governs device operation, we present a technique to probe the electronic characteristics of heterointerfaces with atomic resolution. In this work, the interfacial characteristics of heteroepitaxial structures are investigated and the fundamental mechanisms that pertain in these systems are elucidated through cross-sectional scanning tunneling microscopy (XSTM). The XSTM technique is employed here to directly observe epitaxial interfacial structures and probe local electronic properties with atomic-level capability. Scanning tunneling microscopy and spectroscopy experiments with atomic precision provide insight into the origin and spatial distribution of electronic properties across heterointerfaces. The first part of this report provides a brief description of the cleavage technique and spectroscopy analysis in XSTM measurements. The second part addresses interfacial electronic structures of several model heterostructures in current condensed matter research using XSTM. Topics to be discussed include high-κ‘s/III-V’s semiconductors, polymer heterojunctions, and complex oxide heterostructures, which are all material systems whose investigation using this technique is expected to benefit the research community. Finally, practical aspects and perspectives of using XSTM in interface science are presented.

  6. Atomic-scale mapping of electronic structures across heterointerfaces by cross-sectional scanning tunneling microscopy

    International Nuclear Information System (INIS)

    Interfacial science has received much attention recently based on the development of state-of-the-art analytical tools that can create and manipulate the charge, spin, orbital, and lattice degrees of freedom at interfaces. Motivated by the importance of nanoscale interfacial science that governs device operation, we present a technique to probe the electronic characteristics of heterointerfaces with atomic resolution. In this work, the interfacial characteristics of heteroepitaxial structures are investigated and the fundamental mechanisms that pertain in these systems are elucidated through cross-sectional scanning tunneling microscopy (XSTM). The XSTM technique is employed here to directly observe epitaxial interfacial structures and probe local electronic properties with atomic-level capability. Scanning tunneling microscopy and spectroscopy experiments with atomic precision provide insight into the origin and spatial distribution of electronic properties across heterointerfaces. The first part of this report provides a brief description of the cleavage technique and spectroscopy analysis in XSTM measurements. The second part addresses interfacial electronic structures of several model heterostructures in current condensed matter research using XSTM. Topics to be discussed include high-κ‘s/III–V’s semiconductors, polymer heterojunctions, and complex oxide heterostructures, which are all material systems whose investigation using this technique is expected to benefit the research community. Finally, practical aspects and perspectives of using XSTM in interface science are presented. (topical review)

  7. Atomic density functional and diagram of structures in the phase field crystal model

    Science.gov (United States)

    Ankudinov, V. E.; Galenko, P. K.; Kropotin, N. V.; Krivilyov, M. D.

    2016-02-01

    The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindrical tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.

  8. Atomic structures of a liquid-phase bonded metal/nitride heterointerface

    Science.gov (United States)

    Kumamoto, Akihito; Shibata, Naoya; Nayuki, Kei-Ichiro; Tohei, Tetsuya; Terasaki, Nobuyuki; Nagatomo, Yoshiyuki; Nagase, Toshiyuki; Akiyama, Kazuhiro; Kuromitsu, Yoshirou; Ikuhara, Yuichi

    2016-03-01

    Liquid-phase bonding is a technologically important method to fabricate high-performance metal/ceramic heterostructures used for power electronic devices. However, the atomic-scale mechanisms of how these two dissimilar crystals specifically bond at the interfaces are still not well understood. Here we analyse the atomically-resolved structure of a liquid-phase bonded heterointerface between Al alloy and AlN single crystal using aberration corrected scanning transmission electron microscopy (STEM). In addition, energy-dispersive X-ray microanalysis, using dual silicon drift X-ray detectors in STEM, was performed to analyze the local chemistry of the interface. We find that a monolayer of MgO is spontaneously formed on the AlN substrate surface and that a polarity-inverted monolayer of AlN is grown on top of it. Thus, the Al alloy is bonded with the polarity-inverted AlN monolayer, creating a complex atomic-scale layered structure, facilitating the bonding between the two dissimilar crystals during liquid-phase bonding processes. Density-functional-theory calculations confirm that the bonding stability is strongly dependent on the polarity and stacking of AlN and MgO monolayers. Understanding the spontaneous formation of layered transition structures at the heterointerface will be key in fabricating very stable Al alloy/AlN heterointerface required for high reliability power electronic devices.

  9. Bulk metallic glassy surface native oxide: Its atomic structure, growth rate and electrical properties

    International Nuclear Information System (INIS)

    Formation of a native oxide layer on the surface of bulk metallic glasses (BMGs) influences significantly the nanoscale tribological properties and mechanical behavior of the BMGs used in nanodevices. However, our knowledge of the native oxidation process on the BMG surface and structure of the corresponding oxides remains limited because the oxide layer is very thin. Here we conducted a combined state-of-the-art experimental technique study of the atomic structure, oxidations states and electrical conductivity of the native surface oxides on a Cu−Zr−Al BMG formed at ambient conditions by aberration-corrected scanning transmission electron microscopy (STEM), X-ray photoelectron spectroscopy (XPS) and conductive atomic force microscopy (AFM). This allowed shedding light on the atomic structure, metal oxidation state, growth behavior and nanoscale electrical properties of the surface oxide. The conductive AFM measurements reveal that the electrical conductivity of the native oxide layer transits from the initially metallic to a nonlinear one after some air exposure, and finally changes to insulative state. These findings represent a significant step forward in the knowledge of surface oxides and open up the possibility of fabricating nanoscale electrical devices based on BMGs with controllable conductivity

  10. Atomic structures of a liquid-phase bonded metal/nitride heterointerface.

    Science.gov (United States)

    Kumamoto, Akihito; Shibata, Naoya; Nayuki, Kei-Ichiro; Tohei, Tetsuya; Terasaki, Nobuyuki; Nagatomo, Yoshiyuki; Nagase, Toshiyuki; Akiyama, Kazuhiro; Kuromitsu, Yoshirou; Ikuhara, Yuichi

    2016-01-01

    Liquid-phase bonding is a technologically important method to fabricate high-performance metal/ceramic heterostructures used for power electronic devices. However, the atomic-scale mechanisms of how these two dissimilar crystals specifically bond at the interfaces are still not well understood. Here we analyse the atomically-resolved structure of a liquid-phase bonded heterointerface between Al alloy and AlN single crystal using aberration corrected scanning transmission electron microscopy (STEM). In addition, energy-dispersive X-ray microanalysis, using dual silicon drift X-ray detectors in STEM, was performed to analyze the local chemistry of the interface. We find that a monolayer of MgO is spontaneously formed on the AlN substrate surface and that a polarity-inverted monolayer of AlN is grown on top of it. Thus, the Al alloy is bonded with the polarity-inverted AlN monolayer, creating a complex atomic-scale layered structure, facilitating the bonding between the two dissimilar crystals during liquid-phase bonding processes. Density-functional-theory calculations confirm that the bonding stability is strongly dependent on the polarity and stacking of AlN and MgO monolayers. Understanding the spontaneous formation of layered transition structures at the heterointerface will be key in fabricating very stable Al alloy/AlN heterointerface required for high reliability power electronic devices. PMID:26961157

  11. Structural and Magnetic Evolution of Bimetallic MnAu Clusters Driven by Asymmetric Atomic Migration

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Xiaohui; Zhou, Rulong; Lefebvre, Williams; He, Kai; Le Roy, Damien; Skomski, Ralph; Li, Xingzhong; Shield, Jeffrey E; Kramer, Matthew J; Chen, Shuang; Zeng, Xiao Cheng; Sellmyer, David J

    2014-03-12

    The nanoscale structural, compositional, and magnetic properties are examined for annealed MnAu nanoclusters. The MnAu clusters order into the L10 structure, and monotonic size-dependences develop for the composition and lattice parameters, which are well reproduced by our density functional theory calculations. Simultaneously, Mn diffusion forms 5 Å nanoshells on larger clusters inducing significant magnetization in an otherwise antiferromagnetic system. The differing atomic mobilities yield new cluster nanostructures that can be employed generally to create novel physical properties.

  12. Spin-flip induction of Fano resonance upon electron tunneling through atomic-scale spin structures

    Energy Technology Data Exchange (ETDEWEB)

    Val' kov, V. V., E-mail: vvv@iph.krasn.ru; Aksenov, S. V., E-mail: asv86@iph.krasn.ru [Russian Academy of Sciences, Siberian Branch, Kirensky Institute of Physics (Russian Federation); Ulanov, E. A. [Siberian State Aerospace University (Russian Federation)

    2013-05-15

    The inclusion of inelastic spin-dependent electron scatterings by the potential profiles of a single magnetic impurity and a spin dimer is shown to induce resonance features due to the Fano effect in the transport characteristics of such atomic-scale spin structures. The spin-flip processes leading to a configuration interaction of the system's states play a fundamental role for the realization of Fano resonance and antiresonance. It has been established that applying an external magnetic field and a gate electric field allows the conductive properties of spin structures to be changed radically through the Fano resonance mechanism.

  13. Graph of atomic orbitals and the molecular structure-descriptors based on it

    Directory of Open Access Journals (Sweden)

    ANDREY A. TOROPOV

    2005-04-01

    Full Text Available The graph of atomic orbitals (GAO is a novel type of molecular graph, recently proposed by one of the authors. Various molecular structure-descriptors computed for GAO are compared with their analogs computed for ordinary molecular graphs. The quality of these structure-descriptors was tested for correlation with the normal boiling points of alkanes and cycloalkanes. In all the studied cases, the results based on GAO are similar to, and usually slightly better than, those obtained by means of ordinary molecular graps.

  14. Atomic structure of the cross-[beta] spine of islet amyloid polypeptide (amylin)

    Energy Technology Data Exchange (ETDEWEB)

    Wiltzius, J.J.; Sievers, S.A.; Sawaya, M.R.; Cascio, D.; Popov, D.; Riekel, C.; Eisenberg, D. (UCLA); (ESRF)

    2009-03-27

    Human islet amyloid polypeptide (IAPP or amylin) is a 37-residue hormone found as fibrillar deposits in pancreatic extracts of nearly all type II diabetics. Although the cellular toxicity of IAPP has been established, the structure of the fibrillar form found in these deposits is unknown. Here we have crystallized two segments from IAPP, which themselves form amyloid-like fibrils. The atomic structures of these two segments, NNFGAIL and SSTNVG, were determined, and form the basis of a model for the most commonly observed, full-length IAPP polymorph.

  15. What is matter? The fundamental ontology of atomism and structural realism

    CERN Document Server

    Esfeld, Michael; Oldofredi, Andrea

    2015-01-01

    We set out a fundamental ontology of atomism in terms of matter points. While being most parsimonious, this ontology is able to match both classical and quantum mechanics, and it remains a viable option for any future theory of cosmology that goes beyond current quantum physics. The matter points are structurally individuated: all there is to them are the spatial relations in which they stand; neither a commitment to intrinsic properties nor to an absolute space is required. The spatial relations change. All that is needed to capture change is a dynamical structure, namely dynamical relations as expressed in terms of the dynamical parameters of a physical theory.

  16. Crystal and local atomic structure of Co-doped MgFeBO_4 warwickites

    OpenAIRE

    Kazak, N. V.; Platunov, M. S.; Knyazev, Yu. V.; Ivanova, N. B.; Zubavichus, Y. V.; Veligzhanin, A. A.; Vasiliev, A. D.; Bezmaternykh, L. N.; Bayukov, O. A.; Arauzo, A.; Bartolomé, J.; Lamonova, K. V.; Ovchinnikov, S. G.

    2014-01-01

    Single crystalline MgFeBO_4, Mg_0.5Co_0.5FeBO_4 and CoFeBO_4 have been grown by the flux method. The samples have been characterized by X-ray spectral analysis, X-ray diffraction and X-ray absorption spectroscopy. The X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectra have been measured at the Fe andCoK-edges over a wide temperature range (6.5 - 300 K). The composition, the charge state and local environment of both Fe and Co atoms have b...

  17. Local atomic arrangements and electronic structure of Zr-Ni-Al bulk metallic glass

    International Nuclear Information System (INIS)

    Internal energy of a bulk metallic glass (BMG) was investigated by making full use of its relevant crystals. The local atomic arrangements commonly existing both in the BMG and the relevant crystals were identified using experimentally determined radial distribution functions. The electronic structure of the relevant crystals was investigated by discrete variational X alpha (DVXα) cluster calculations and high-resolution photoemission spectroscopy. The present analysis on the electronic structure revealed that the simultaneous formations of characteristic cluster levels and a pseudogap at the Fermi level effectively reduce the internal energy to stabilize BMGs

  18. Atomic structure of a peptide coated gold nanocluster identified using theoretical and experimental studies

    Science.gov (United States)

    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

  19. Nonstationary structure of atomic and molecular layers in electrothermal. Atomic absorption spectrometry: formation of atomic and molecular absorbing layers of gallium and indium

    International Nuclear Information System (INIS)

    The dynamics of the formation of absorbing layers of gallium and indium atoms and their compounds in a graphite tubular atomizer was investigated by the shadow spectral filming method. These compounds are localozed in the central part of the furnace over the platform and dissapear ay the hotter walls. It the case of gallium and indium atomization, the effects of chemical reactions between the vapor and the walls of the furnace on the formation of absorbing layers are stronger than that of diffusion and convective mass-transfer processes, which are common to all of the elements. Atom propagation from the center to the stomizer ends proceeds through the cascade mechanism because of its relatively low rate of warming up and strong longitudinal anisothermicity

  20. Atomic mechanisms of formation and structure relaxation of Fe83M17 (M: C, B, P) metallic glass

    International Nuclear Information System (INIS)

    The individual characteristic properties of local atomic ordering of structure forming in Fe83M17 (M: C, B, P) metallic glass have been indicated by a computer simulation method. It is proved that carbon atoms 'prefer' to take up the interstitial positions in atomic configurations based on a distorted octahedron and trigonal prism while boron atoms tend to occupy the centres of a distorted Archymedian antiprism. Phosphorus atoms are able to take up both the interstitial and the substitutional positions and the short-range ordering around them is mainly icosahedrical. The interrelationship between the atomic structure of Fe83M17 (M: C, B, P) amorphous metallic alloys and their vitrification ability has been determined

  1. Formation and atomic structure of tetrahedral carbon onion produced by electron-beam irradiation

    International Nuclear Information System (INIS)

    Full text: Various fullerene structures has been designed and produced after the discovery of C60. These fullerene materials are good candidates as nanoscale devises such as single-electron devices, nano-diode, nano-transistor, nano-ball bearing and insulator lubricant. The onion structures, which generally consist of some quasi-spherical fullerene group, are also discovered and studied in detail. The tetrahedral carbon onions had been calculated to be unstable compared to the spherical onions due to the rigidity. The purpose of the present work is to produce new carbon onion by high-energy electron-irradiation on amorphous carbon at 1250 kV, and to investigate atomic structures and stability of the new carbon onion cluster by high-resolution electron microscopy (HREM) and molecular orbital/mechanics calculations. To confirm the structure model from HREM data, HREM image simulation were carried out. The tetrahedral carbon onion was successfully produced by high-energy electron-irradiation. A HREM image of tetrahedral carbon onion would consist of pentagonal and hexagonal rings. The HREM result indicates that new fullerene structures formed into the carbon onion. Molecular mechanics calculations (MM2), semi-empirical molecular orbital calculations (PM3), and density functional theory (DFT) were used to get structure optimization about first and second internal shell. The energy levels and density of states were also calculated by the first principles method (DV-Xα). The smallest tetrahedral onion in the HREM image agreed well with the proposed structure model of C84atC276. Each vertex consists of a hexagonal ring, and three pentagonal rings exist around the vertex along the edge. In summary, the tetrahedral carbon cluster was produced by energy transfer of electron-irradiation, and the new atomic structure model of tetrahedral carbon onion was proposed. The electronic structures were also calculated theoretically. Copyright (2002) Australian Society for Electron

  2. Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

    Science.gov (United States)

    McBriarty, Martin E.

    Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

  3. Program package for semi-empirical analysis of the fine- and hyperfine structure of complex atoms

    International Nuclear Information System (INIS)

    The experimental work combined with semi-empirical calculations is a very efficient tool for the investigations of the fine- and hyperfine structure of the complex atoms. We present a set of programs for the analysis of the fine- and hyperfine structure. The input data for the calculations are: the fine structure energy levels, the gJ-factors and the hyperfine structure (hfs) A and B constants of experimentally observed levels. The programs are used for the analysis of electron systems containing any number of configurations up to four open shells. In the energy matrix generated, all kinds of electrostatic, magnetic and correlated electrostatic and magnetic interaction, up to second order perturbation theory, were included. As a result, we obtain predicted energy values for all the levels of the system considered, their exact spectroscopic description and also gJ-factors and hfs A and B constants

  4. Atomic force microscopy study of chromosome surface structure changed by protein extraction

    International Nuclear Information System (INIS)

    We applied atomic force microscopy (AFM) to investigate the surface structure of barley chromosome in combination with a chemical treatment method. As a result, we have obtained high-resolution topographic images of granular structures with a diameter of ca. 50 nm on the surface of critical-point dried metaphase chromosomes. Treatment with 2 M NaCl significantly modified the chromosome surface structure: surface roughness was increased and chromosome thickness was decreased. The NaCl treatment extracted two major proteins with molecular weights of 4000 and 20,000 Da. These proteins might be belonging to non-histone protein families that do not contain any aromatic amino acid. The results demonstrate the advantage of the combined method of high-resolution AFM imaging and chemical treatments for understanding nano-scale surface structures of the chromosome

  5. Atomic-resolution STM structure of DNA and localization of the retinoic acid binding site

    International Nuclear Information System (INIS)

    Single-molecule imaging by scanning tunnelling microscopy (STM) yields the atomic-resolution (0.6 A) structure of individual B-type DNA molecules. The strong correlation between these STM structures and those predicted from the known base sequence indicates that sequencing of single DNA molecules using STM may be feasible. There is excellent agreement between the STM and X-ray structures, but subtle differences exist due to radial distortions. We show that the interactions of other molecules with DNA, their binding configurations, and the structure of these complexes can be studied at the single-molecule level. The anti-cancer drug retinoic acid (RA) binds selectively to the minor groove of DNA with up to 6 RA molecules per DNA turn and with the plane of the RA molecule approximately parallel to the DNA symmetry axis. Similar studies for other drug molecules will be valuable in the a priori evaluation of the effectiveness of anti-cancer drugs

  6. Interfacial atomic structure analysis at sub-angstrom resolution using aberration-corrected STEM

    Science.gov (United States)

    2014-01-01

    The atomic structure of a SiGe/Si epitaxial interface grown via molecular beam epitaxy on a single crystal silicon substrate was investigated using an aberration-corrected scanning transmittance electron microscope equipped with a high-angle annular dark-field detector and an energy-dispersive spectrometer. The accuracy required for compensation of the various residual aberration coefficients to achieve sub-angstrom resolution with the electron optics system was also evaluated. It was found that the interfacial layer was composed of a silicon single crystal, connected coherently to epitaxial SiGe nanolaminates. In addition, the distance between the dumbbell structures of the Si and Ge atoms was approximately 0.136 nm at the SiGe/Si interface in the [110] orientation. The corresponding fast Fourier transform exhibited a sub-angstrom scale point resolution of 0.78 Å. Furthermore, the relative positions of the atoms in the chemical composition line scan signals could be directly interpreted from the corresponding incoherent high-angle annular dark-field image. PMID:25426003

  7. Dynamic and structural studies of molecular or atomic systems through the generation of high order harmonics

    International Nuclear Information System (INIS)

    High harmonic generation is a well known phenomenon explained by a three step model: because of the high intensity field generated by an ultrashort laser pulse, an atom or a molecule can be tunnel ionized. The ejected electron is then accelerated by the intense electric field, and eventually can recombine on its parent ion, leading to the emission of a XUV photon. Because of the generating process in itself, this light source is a promising candidate to probe the electronic structure of atoms and molecules, with an atto-second/sub-nanometer potential resolution (1 as=10-18 s). In this work, we have studied the sensitivity of the emitted light (in terms of amplitude, but also phase and polarization) towards the electronic structure of the generating medium. We have first worked on atomic medium, then on molecules (N2, CO2, O2). Comparing the experimental results with numerical simulations shows the necessity to model finely the generation process and to go beyond commonly used approximations. We have also shown the possibility to perform high harmonic spectroscopy in order to measure dynamics of complex molecules, such as Nitrogen Dioxide (NO2). This technic has obtained complementary results compared to classical spectroscopy and has revealed dynamics of the electronic wave packet along a conical intersection. In this experiment, we have adapted conventional optical spectroscopy technic to the XUV spectral area, which significantly improved the signal over noise ratio. (author)

  8. A real-time all-atom structural search engine for proteins.

    Directory of Open Access Journals (Sweden)

    Gabriel Gonzalez

    2014-07-01

    Full Text Available Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license, https://github.com/Gabriel439/suns-cmd (command line client, BSD license, and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license.

  9. Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface

    Science.gov (United States)

    Sun, Ce; Paulauskas, Tadas; Sen, Fatih G.; Lian, Guoda; Wang, Jinguo; Buurma, Christopher; Chan, Maria K. Y.; Klie, Robert F.; Kim, Moon J.

    2016-01-01

    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. PMID:27255415

  10. Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface.

    Science.gov (United States)

    Sun, Ce; Paulauskas, Tadas; Sen, Fatih G; Lian, Guoda; Wang, Jinguo; Buurma, Christopher; Chan, Maria K Y; Klie, Robert F; Kim, Moon J

    2016-01-01

    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. PMID:27255415

  11. Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface

    Science.gov (United States)

    Sun, Ce; Paulauskas, Tadas; Sen, Fatih G.; Lian, Guoda; Wang, Jinguo; Buurma, Christopher; Chan, Maria K. Y.; Klie, Robert F.; Kim, Moon J.

    2016-06-01

    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.

  12. Correlation between morphology, electron band structure, and resistivity of Pb atomic chains on the Si(5 5 3)-Au surface.

    Science.gov (United States)

    Jałochowski, M; Kwapiński, T; Łukasik, P; Nita, P; Kopciuszyński, M

    2016-07-20

    Structural and electron transport properties of multiple Pb atomic chains fabricated on the Si(5 5 3)-Au surface are investigated using scanning tunneling spectroscopy, reflection high electron energy diffraction, angular resolved photoemission electron spectroscopy and in situ electrical resistance. The study shows that Pb atomic chains growth modulates the electron band structure of pristine Si(5 5 3)-Au surface and hence changes its sheet resistivity. Strong correlation between chains morphology, electron band structure and electron transport properties is found. To explain experimental findings a theoretical tight-binding model of multiple atomic chains interacting on effective substrate is proposed. PMID:27228462

  13. Tailoring atomic structure to control the electronic transport in zigzag graphene nanoribbon

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Hui [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Zhao, Jun, E-mail: zhaojun@yangtzeu.edu.cn [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Wei, Jianwei [College of Optoelectronic Information, Chongqing University of Technology, Chongqing 400054 (China); Zeng, Xianliang [College of Physical Science and Technology, Yangtze University, Jingzhou, Hubei 434023 (China); Xu, Yang [Department of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, Zhejiang 310027 (China)

    2012-10-01

    We have performed ab initio density functional theory calculation to study the electronic transport properties of the tailored zigzag-edged graphene nanoribbon (ZGNR) with particular electronic transport channels. Our results demonstrated that tailoring the atomic structure had significantly influenced the electronic transport of the defective nanostructures, and could lead to the metal-semiconducting transition when sufficient atoms are tailored. The asymmetric I–V characteristics as a result of symmetry breaking have been exhibited, which indicates the route to utilize GNR as a basic component for novel nanoelectronics. -- Highlights: ► M–S transition induced by tailoring nanostructure. ► Asymmetric I–V curve due to symmetry breaking. ► Controllable electron transport by designing nanofiguration.

  14. Mechanical and structural characterization of atomic layer deposition-based ZnO films

    International Nuclear Information System (INIS)

    Zinc oxide thin films were deposited by atomic layer deposition (ALD). The structural and mechanical properties of the thin films were investigated by x-ray diffraction, transmission electron microscopy, atomic force microscopy, and nanoindentation. Diethyl zinc was used as the chemical precursor for zinc and water vapor was used as the oxidation agent. The samples were deposited at 150 °C and at a pressure of 2.1 × 10−1 Torr in the ALD reactor. A growth rate of 2 Å per cycle was calculated in the ALD process window. The Nano Indenter XP was used in conjunction with the continuous stiffness method in depth control mode in order to measure and to analyze the mechanical properties of hardness and modulus of ALD ZnO thin film samples. For comparison, we benchmarked the mechanical properties of single crystal bulk ZnO samples against those of our ALD ZnO thin films

  15. Mechanical and structural characterization of atomic layer deposition-based ZnO films

    Science.gov (United States)

    Tapily, K.; Gu, D.; Baumgart, H.; Namkoong, G.; Stegall, D.; Elmustafa, A. A.

    2011-11-01

    Zinc oxide thin films were deposited by atomic layer deposition (ALD). The structural and mechanical properties of the thin films were investigated by x-ray diffraction, transmission electron microscopy, atomic force microscopy, and nanoindentation. Diethyl zinc was used as the chemical precursor for zinc and water vapor was used as the oxidation agent. The samples were deposited at 150 °C and at a pressure of 2.1 × 10-1 Torr in the ALD reactor. A growth rate of 2 Å per cycle was calculated in the ALD process window. The Nano Indenter XP was used in conjunction with the continuous stiffness method in depth control mode in order to measure and to analyze the mechanical properties of hardness and modulus of ALD ZnO thin film samples. For comparison, we benchmarked the mechanical properties of single crystal bulk ZnO samples against those of our ALD ZnO thin films.

  16. Adhesion and Atomic Structures of Gold on Ceria Nanostructures:The Role of Surface Structure and Oxidation State of Ceria Supports

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yuyuan [Northwestern University, Evanston; Wu, Zili [ORNL; Wen, Jianguo [Argonne National Laboratory (ANL); Poeppelmeier, Kenneth R [Northwestern University, Evanston; Marks, Laurence D [Northwestern University, Evanston

    2015-01-01

    Recent advances in heterogeneous catalysis have demonstrated that oxides supports with the same material but different shapes can result in metal catalysts with distinct catalytic properties. The shape-dependent catalysis was not well-understood owing to the lack of direct visualization of the atomic structures at metal-oxide interface. Herein, we utilized aberration-corrected electron microscopy and revealed the atomic structures of gold particles deposited on ceria nanocubes and nanorods with {100} or {111} facets exposed. For the ceria nanocube support, gold nanoparticles have extended atom layers at the metal-support interface. In contrast, regular gold nanoparticles and rafts are present on the ceria nanorod support. After hours of water gas shift reaction, the extended gold atom layers and rafts vanish, which is associated with the decrease of the catalytic activities. By understanding the atomic structures of the support surfaces, metal-support interfaces, and morphologies of the gold particles, a direct structure-property relationship is established.

  17. Local atomic structure inheritance in Ag{sub 50}Sn{sub 50} melt

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Yanwen; Bian, Xiufang, E-mail: xfbian@sdu.edu.cn; Qin, Jingyu; Hu, Lina; Yang, Jianfei; Zhang, Kai; Zhao, Xiaolin; Yang, Chuncheng [Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Zhang, Shuo; Huang, Yuying [Shanghai Synchrotron Radiation Facilities, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204 (China)

    2014-01-28

    Local structure inheritance signatures were observed during the alloying process of the Ag{sub 50}Sn{sub 50} melt, using high-temperature X-ray diffraction and ab initio molecular dynamics simulations. The coordination number N{sub m} around Ag atom is similar in the alloy and in pure Ag melts (N{sub m} ∼ 10), while, during the alloying process, the local structure around Sn atoms rearranges. Sn-Sn covalent bonds were substituted by Ag-Sn chemical bonds, and the total coordination number around Sn increases by about 70% as compared with those in the pure Sn melt. Changes in the electronic structure of the alloy have been studied by Ag and Sn K-edge X-ray absorption spectroscopy, as well as by calculations of the partial density of states. We propose that a leading mechanism for local structure inheritance in Ag{sub 50}Sn{sub 50} is due to s-p dehybridization of Sn and to the interplay between Sn-s and Ag-d electrons.

  18. Fabrication and design of metal nano-accordion structures using atomic layer deposition and interference lithography

    Science.gov (United States)

    Min, J.-H.; Bagal, A.; Mundy, J. Z.; Oldham, C. J.; Wu, B.-I.; Parsons, G. N.; Chang, C.-H.

    2016-02-01

    Metal nanostructures have attractive electrical and thermal properties as well as structural stability, and are important for applications in flexible conductors. In this study, we have developed a method to fabricate and control novel complex platinum nanostructures with accordion-like profile using atomic layer deposition on lithographically patterned polymer templates. The template removal process results in unique structural transformation of the nanostructure profile, which has been studied and modeled. Using different template duty cycles and aspect ratios, we have demonstrated a wide variety of cross-sectional profiles from wavy geometry to pipe array patterns. These complex thin metal nanostructures can find applications in flexible/stretchable electronics, photonics and nanofluidics.Metal nanostructures have attractive electrical and thermal properties as well as structural stability, and are important for applications in flexible conductors. In this study, we have developed a method to fabricate and control novel complex platinum nanostructures with accordion-like profile using atomic layer deposition on lithographically patterned polymer templates. The template removal process results in unique structural transformation of the nanostructure profile, which has been studied and modeled. Using different template duty cycles and aspect ratios, we have demonstrated a wide variety of cross-sectional profiles from wavy geometry to pipe array patterns. These complex thin metal nanostructures can find applications in flexible/stretchable electronics, photonics and nanofluidics. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08566g

  19. Nuclear structure of light thallium isotopes as deduced from laser spectroscopy on a fast atom beam

    International Nuclear Information System (INIS)

    After optimizing the system by experiments on /sup 201,203,205/Tl, the neutron-deficient isotopes 189-193Tl have been studied using the collinear fast atom beam laser spectroscopy system at UNISOR on-line to the Holifield Heavy Ion Research Facility. A sensitive system for the measurements was developed since the light isotopes were available in mass-separated beams of only 7 x 104 to 4 x 105 atoms per second. By laser excitation of the 535 nm atomic transitions of atoms in the beam, the 6s27s 2S/sub 1/2/ and 6s26s 2P/sub 3/2/ hyperfine structures were measured, as were the isotope shifts of the 535 nm transitions. From these, the magnetic dipole moments, spectroscopic quadrupole moments and isotopic changes in mean-square charge radius were deduced. The magnetic dipole moments are consistent with previous data. The /sup 190,192/Tl isotopes show a considerable difference in quadrupole deformations as well as an anomalous isotope shift with respect to 194Tl. A large isomer shift in 193Tl is observed implying a larger deformation in the 9/2- isomer than in the 1/2+ ground state. The /sup 189,191,193/Tl isomers show increasing deformation away from stability. A deformed shell model calculation indicates that this increase in deformation can account for the dropping of the 9/2- band in these isotopes while an increase in neutron pairing correlations, having opposite and compensating effects on the rotational moment of inertia, maintains the 9/2- strong-coupled band structure. 105 refs., 27 figs

  20. Atomic structure of nanometer-sized amorphous TiO2

    Science.gov (United States)

    Zhang, Hengzhong; Chen, Bin; Banfield, Jillian F.; Waychunas, Glenn A.

    2008-12-01

    Amorphous titania (TiO2) is an important precursor for synthesis of single-phase nanocrystalline anatase. We synthesized amorphous titania by hydrolysis of titanium ethoxide at the ice point. Transmission electron microscopy examination and nitrogen gas adsorption indicated that the particle size of the synthesized titania is ˜2nm . Synchrotron wide-angle x-ray scattering (WAXS) was used to probe the atomic correlations in this amorphous sample. Atomic pair-distribution function (PDF) derived from Fourier transform of the WAXS data was used for reverse Monte Carlo (RMC) simulations of the atomic structure of the amorphous TiO2 nanoparticles. Molecular-dynamics simulations were used to generate input structures for the RMC. X-ray-absorption spectroscopy (XAS) simulations were used to screen candidate structures obtained from the RMC by comparing with experimental XAS data. The structure model that best describes both the WAXS and XAS data shows that amorphous TiO2 particles consist of a highly distorted shell and a small strained anataselike crystalline core. The average coordination number of Ti is 5.3 and most Ti-O bonds are populated around 1.940Å . Relative to bulk TiO2 , the reduction in the coordination number is primarily due to the truncation of the Ti-O octahedra at the amorphous nanoparticle surface and the shortening of the Ti-O bond length to the bond contraction in the distorted shell. The pre-existence of the anataselike core may be critical to the formation of single-phase nanocrystalline anatase in crystallization of amorphous TiO2 upon heating.

  1. Wigner’s phase-space function and atomic structure: II. Ground states for closed-shell atoms

    DEFF Research Database (Denmark)

    Springborg, Michael; Dahl, Jens Peder

    1987-01-01

    display and analyze the function for the closed-shell atoms helium, beryllium, neon, argon, and zinc in the Hartree-Fock approximation. The quantum-mechanical exact results are compared with those obtained with the approximate Thomas-Fermi description of electron densities in phase space.......We present formulas for reduced Wigner phase-space functions for atoms, with an emphasis on the first-order spinless Wigner function. This function can be written as the sum of separate contributions from single orbitals (the natural orbitals). This allows a detailed study of the function. Here we...

  2. Fabrication and atomic structure of size-selected, layered MoS2 clusters for catalysis.

    Science.gov (United States)

    Cuddy, Martin J; Arkill, Kenton P; Wang, Zhi Wei; Komsa, Hannu-Pekka; Krasheninnikov, Arkady V; Palmer, Richard E

    2014-11-01

    Well defined MoS2 nanoparticles having a layered structure and abundant edges would be of considerable interest for applications including photocatalysis. We report the atomic structure of MoS2 size-selected clusters with mass in a range all the way from 50 to ∼2000 MoS2 units. The clusters were prepared by magnetron sputtering and gas condensation prior to size selection and soft landing on carbon supports. Aberration-corrected scanning transmission electron microscopy (STEM) in high-angle annular dark-field (HAADF) mode reveals a layered structure and Mo-Mo spacing similar to the bulk material. The mean number of layers in these lamellar clusters increases from one to three with increasing mass, consistent with density functional theory calculations of the balance between edge energies and interlayer binding. PMID:25226541

  3. Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

    Science.gov (United States)

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

    2015-07-01

    Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)-(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule.

  4. HYPERFINE STRUCTURE CONSTANTS OF ENERGETICALLY HIGH-LYING LEVELS OF ODD PARITY OF ATOMIC VANADIUM

    International Nuclear Information System (INIS)

    High-resolution Fourier transform spectra of a vanadium-argon plasma have been recorded in the wavelength range of 365-670 nm (15,000-27,400 cm–1). Optical bandpass filters were used in the experimental setup to enhance the sensitivity of the Fourier transform spectrometer. In total, 138 atomic vanadium spectral lines showing resolved or partially resolved hyperfine structure have been analyzed to determine the magnetic dipole hyperfine structure constants A of the involved energy levels. One of the investigated lines has not been previously classified. As a result, the magnetic dipole hyperfine structure constants A for 90 energy levels are presented: 35 of them belong to the configuration 3d 34s4p and 55 to the configuration 3d 44p. Of these 90 constants, 67 have been determined for the first time, with 23 corresponding to the configuration 3d 34s4p and 44 to 3d 44p

  5. Potential antitumor gold drugs: DFT and XANES studies of local atomic and electronic structure

    International Nuclear Information System (INIS)

    Geometry structure optimization of the potential antitumor agent Au(bipy)(OH)2 was carried out by means of density functional theory simulations. The experimental Au L3-edge X-ray absorption near edge structure (XANES) spectrum of Au(bipy)(OH)2 was obtained. The theoretical Au L3-XANES spectra of the gold(III) complex Au(bipy)(OH)2 were simulated using both the self-consistent real-space full multiple scattering theory within the muffin-tin approximation for the potential shape and the full-potential finite difference method. The comparison of the theoretical spectra with the experimental XANES is discussed. The exact local atomic structure of gold complex Au(bipy)(OH)2 has been defined by two independent ab initio methods.

  6. Controlling the Atomic Structure of Au30 Nanoclusters by a Ligand-Based Strategy.

    Science.gov (United States)

    Higaki, Tatsuya; Liu, Chong; Zeng, Chenjie; Jin, Renxi; Chen, Yuxiang; Rosi, Nathaniel L; Jin, Rongchao

    2016-06-01

    We report the X-ray structure of a gold nanocluster with 30 gold atoms protected by 18 1-adamantanethiolate ligands (formulated as Au30 (S-Adm)18 ). This nanocluster exhibits a threefold rotationally symmetrical, hexagonal-close-packed (HCP) Au18 kernel protected by six dimeric Au2 (SR)3 staple motifs. This new structure is distinctly different from the previously reported Au30 S(S-(t) Bu)18 nanocluster protected by 18 tert-butylthiolate ligands and one sulfido ligand with a face-centered cubic (FCC) Au22 kernel. The Au30 (S-Adm)18 nanocluster has an anomalous solubility (it is only soluble in benzene but not in other common solvents). This work demonstrates a ligand-based strategy for controlling nanocluster structure and also provides a method for the discovery of possibly overlooked clusters because of their anomalous solubility. PMID:27099989

  7. Atomic structure of "multilayer silicene" grown on Ag(111): Dynamical low energy electron diffraction analysis

    Science.gov (United States)

    Kawahara, Kazuaki; Shirasawa, Tetsuroh; Lin, Chun-Liang; Nagao, Ryo; Tsukahara, Noriyuki; Takahashi, Toshio; Arafune, Ryuichi; Kawai, Maki; Takagi, Noriaki

    2016-09-01

    We have investigated the atomic structure of the "multilayer silicene" grown on the Ag(111) single crystal surface by using low energy electron diffraction (LEED) and scanning tunneling microscopy (STM). We measured the intensity of the LEED spot as a function of the incident electron energy (I-V curve) and analyzed the I-V curve using a dynamical LEED theory. We have found that the Si(111)(√{ 3} ×√{ 3})-Ag model well reproduces the I-V curve whereas the models consisting of the honeycomb structure of Si do not. The bias dependence of the STM image of multilayer silicene agrees with that of the Si(111)(√{ 3} ×√{ 3})-Ag reconstructed surface. Consequently, we have concluded that the multilayer silicene grown on Ag(111) is identical to the Si(111)(√{ 3} ×√{ 3})-Ag reconstructed structure.

  8. Composite organic-inorganic butterfly scales: production of photonic structures with atomic layer deposition.

    Science.gov (United States)

    Gaillot, Davy P; Deparis, Olivier; Welch, Victoria; Wagner, Brent K; Vigneron, Jean Pol; Summers, Christopher J

    2008-09-01

    Recent advances in the photonics and optics industries have produced great demand for ever more sophisticated optical devices, such as photonic crystals. However, photonic crystals are notoriously difficult to manufacture. Increasingly, therefore, researchers have turned towards naturally occurring photonic structures for inspiration and a wide variety of elaborate techniques have been attempted to copy and harness biological processes to manufacture artificial photonic structures. Here, we describe a simple, direct process for producing an artificial photonic device by using a naturally occurring structure from the wings of the butterfly Papilio blumei as a template and low-temperature atomic layer deposition of TiO2 to create a faithful cast of the structure. The optical properties of the organic-inorganic diffraction structures produced are assessed by normal-incidence specular reflectance and found to be well described by multilayer computation method using a two-dimensional photonic crystal model. Depending on the structural integrity of the initially sealed scale, it was found possible not only to replicate the outer but also the inner and more complex surfaces of the structure, each resulting in distinct multicolor optical behavior as revealed by experimental and theoretical data. In this paper, we also explore tailoring the process to design composite skeleton architectures with desired optical properties and integrated multifunctional (mechanical, thermal, optical, fluidic) properties. PMID:18851080

  9. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

    Science.gov (United States)

    Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

    2016-01-01

    A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data. PMID:26697868

  10. Influence of the atomic structure of crystal surfaces on the surface diffusion in medium temperature range

    International Nuclear Information System (INIS)

    In this work, we have studied the influence of atomic structure of crystal surface on surface self-diffusion in the medium temperature range. Two ways are followed. First, we have measured, using a radiotracer method, the self-diffusion coefficient at 820 K (0.6 T melting) on copper surfaces both the structure and the cleanliness of which were stable during the experiment. We have shown that the interaction between mobile surface defects and steps can be studied through measurements of the anisotropy of surface self diffusion. Second, the behavior of an adatom and a surface vacancy is simulated via a molecular dynamics method, on several surfaces of a Lennard Jones crystal. An inventory of possible migration mechanisms of these surface defects has been drawn between 0.35 and 0.45 Tsub(m). The results obtained with both the methods point out the influence of the surface atomic structure in surface self-diffusion in the medium temperature range

  11. Observations of resonance-like structures for positron-atom scattering at intermediate energies

    International Nuclear Information System (INIS)

    Absolute values of elastic differential cross sections (DCS's) are measured for position (e+) scattering by argon (8.7-300 eV) krypton (6.7-400 eV) and also neon (13.6-400 eV) using a crossed-beam experimental setup. When the DCS's are plotted at fixed scattering angles of 30 degrees, 60 degrees, 90 degrees and 120 degrees versus energy it has been found that well-defined resonance-like structures are found at an energy of 55-60 eV for argon and at 25 and 200 eV for krypton, with a broader structure found between 100-200 eV for neon. These observed resonance-like structures are unusual because they occur at energies well above the known inelastic thresholds for these atoms. They may represent examples of open-quotes coupled channel shape resonancesclose quotes, first predicted by Higgins and Burke [1] for e+-H scattering in the vicinity of 36 eV (width ∼ 4 eV), which occurs only when both the elastic and positronium formation scattering channels are considered together. A more recent e+-H calculation by Hewitt et al. [2] supports the Higgins and Burke prediction. These predictions and the present observations suggest the existence of a new type of atomic scattering resonance

  12. Atomic layer deposition TiO2 coated porous silicon surface: Structural characterization and morphological features

    International Nuclear Information System (INIS)

    TiO2 thin films were grown on highly-doped p-Si (100) macro- and mesoporous structures by atomic layer deposition (ALD) using TiCl4 and deionized water as precursors at 300 °C. The crystalline structure, chemical composition, and morphology of the deposited films and initial silicon nanostructures were investigated by scanning electron microscopy, transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, micro-Raman spectroscopy and X-ray diffraction (XRD). The mean size of TiO2 crystallites was determined by TEM, XRD and Raman spectroscopy. It was shown that the mean crystallite size and the crystallinity of the TiO2 are influenced dramatically by the morphology of the porous silicon, with the mesoporous silicon resulting in a much finer grain size and amorphous structure than the macroporous silicon having a partially crystal anatase phase. A simple model of the ALD layer growth inside the pores was presented. - Highlights: • The morphology and chemical composition of TiO2 and porous Si were established. • The approximate size of TiO2 nanocrystals was estimated. • The model of the atomic layer deposition coating in the porous Si was presented

  13. Structural properties of organic Langmuir-Blodgett thin films using atomic force microscopy

    International Nuclear Information System (INIS)

    The Langmuir-Blodgett (LB) thin film deposition technique is an elegant method in thin film technology to fabricate ultra-thin organic LB films on the nanoscale. This technique allows us to make monolayer or multilayer ultra-thin LB films by sequentially transferring monolayers from a water surface onto a solid substrate. During the last decade many scientists have a significant interest in Langmuir-Blodgett films because of potential applications of such films, which have many potential applications in physics, chemistry, biology and molecular electronics. There are a number of techniques such as Atomic Force Microscopy, Surface Plasmon Resonance, X-ray diffraction, Infra-red and Raman Spectroscopy, Ellipsometry etc that can be used to characterise and evaluate the optical and structural information of monolayer and multilayer organic LB films. In this work organic materials have been used to fabricate an ultra-thin LB film using a computer controlled alternate layer Langmuir-Blodgett trough. Atomic Force Microscopy (AFM) is employed to investigate the structural properties of such LB films. All results of the structural properties for organic ultra-thin LB films will be discussed in this paper

  14. The multi-scattering-Xα method for analysis of the electronic structure of atomic clusters

    International Nuclear Information System (INIS)

    A computer program, MSXALPHA, has been developed to carry out a quantum-mechanical analysis of the electronic structure of molecules and atomic clusters using the Multi-Scattering-Xα (MSXα) method. The MSXALPHA program is based on a code obtained from the University of Alberta; several improvements and new features were incorporated to increase generality and efficiency. The major ones are: (1) minimization of core memory usage, (2) reduction of execution time, (3) introduction of a dynamic core allocation scheme for a large number of arrays, (4) incorporation of an atomic program to generate numerical orbitals used to construct the initial molecular potential, and (5) inclusion of a routine to evaluate total energy. This report is divided into three parts. The first discusses the theory of the MSXα method. The second gives a detailed description of the program, MSXALPHA. The third discusses the results of calculations carried out for the methane molecule (CH4) and a four-atom zirconium cluster (Zr4)

  15. Atomic structure calculations and identification of EUV and SXR spectral lines in Sr XXX

    Science.gov (United States)

    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.

  16. Atomic and electronic structures of a-SiC:H from tight-binding molecular dynamics

    CERN Document Server

    Ivashchenko, V I; Shevchenko, V I; Ivashchenko, L A; Rusakov, G V

    2003-01-01

    The atomic and electronic properties of amorphous unhydrogenated (a-SiC) and hydrogenated (a-SiC:H) silicon carbides are studied using an sp sup 3 s sup * tight-binding force model with molecular dynamics simulations. The parameters of a repulsive pairwise potential are determined from ab initio pseudopotential calculations. Both carbides are generated from dilute vapours condensed from high temperature, with post-annealing at low temperature for a-SiC:H. A plausible model for the inter-atomic correlations and electronic states in a-SiC:H is suggested. According to this model, the formation of the amorphous network is weakly sensitive to the presence of hydrogen. Hydrogen passivates effectively only the weak bonds of threefold-coordinated atoms. Chemical ordering is very much affected by the cooling rate and the structure of the high-temperature vapour. The as-computed characteristics are in rather good agreement with the results for a-SiC and a-Si:H from ab initio calculations.

  17. Tuning the atomic and domain structure of epitaxial films of multiferroic BiFeO3

    OpenAIRE

    Daumont, C. J. M.; Farokhipoor, S.; Ferri, A; Wojdel, J. C.; Iniguez, Jorge; Kooi, B. J.; Noheda, Beatriz; Wojdeł, J.C.

    2010-01-01

    Recent works have shown that the domain walls of room-temperature multiferroic BiFeO3 (BFO) thin films can display distinct and promising functionalities. It is thus important to understand the mechanisms underlying domain formation in these films. High-resolution x-ray diffraction and piezoforce microscopy, combined with first-principles simulations, have allowed us to characterize both the atomic and domain structure of BFO films grown under compressive strain on (001)-SrTiO3, as a function...

  18. On the representation matrices of the spin permutation group. [for atomic and molecular electronic structures

    Science.gov (United States)

    Wilson, S.

    1977-01-01

    A method is presented for the determination of the representation matrices of the spin permutation group (symmetric group), a detailed knowledge of these matrices being required in the study of the electronic structure of atoms and molecules. The method is characterized by the use of two different coupling schemes. Unlike the Yamanouchi spin algebraic scheme, the method is not recursive. The matrices for the fundamental transpositions can be written down directly in one of the two bases. The method results in a computationally significant reduction in the number of matrix elements that have to be stored when compared with, say, the standard Young tableaux group theoretical approach.

  19. 3D mechanical measurements with an atomic force microscope on 1D structures

    DEFF Research Database (Denmark)

    Kallesøe, Christian; Larsen, Martin Benjamin Barbour Spanget; Bøggild, Peter; Mølhave, Kristian

    2012-01-01

    We have developed a simple method to characterize the mechanical properties of three dimensional nanostructures, such as nanorods standing up from a substrate. With an atomic force microscope the cantilever probe is used to deflect a horizontally aligned nanorod at different positions along the...... nanorod, using the apex of the cantilever itself rather than the tip normally used for probing surfaces. This enables accurate determination of nanostructures' spring constant. From these measurements, Young's modulus is found on many individual nanorods with different geometrical and material structures...

  20. Atom-Generated Spatial Multi-Mode Structure of Squeezed Light

    CERN Document Server

    Zhang, Mi; Xiao, Zhihao; Dowling, Jonathan P; Novikova, Irina; Mikhailov, Eugeniy E

    2015-01-01

    We generate a squeezed vacuum field via an interaction between a laser beam and an atomic ensemble. A measurement of the quantum noise of a spatially modified squeezed field is conducted. We find the noise suppression to be greatly affected by the transverse profile of the spatial mask and its position along the propagation direction. We have developed a multimode model to describe the mode structure of the light fields which qualitatively explains the quadrature noise behavior in terms of higher-order Laguerre-Gauss modes.

  1. Structure and Thermodynamic Properties of Liquid Transition Metals with Different Embedded-Atom Method Models

    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.

  2. EF-hands at atomic resolution: The structure of human psoriasin (S100A7) solved by MAD phasing

    DEFF Research Database (Denmark)

    Brodersen, Ditlev Egeskov; Etzerodt, Michael; Madsen, Peder Søndergaard; Thøgersen, Hans Christian; Celis, J. E.; Nyborg, Jens; Kjeldgaard, Morten

    1998-01-01

    holmium-substituted psoriasin has been determined by multiple anomalous wavelength dispersion (MAD) phasing and refined to atomic resolution (1.05 A). The structure represents the most accurately determined structure of a calcium-binding protein. Although the overall structure of psoriasin is similar to...

  3. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    International Nuclear Information System (INIS)

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT

  4. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    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

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT

  5. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    Science.gov (United States)

    Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-01

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

  6. Atomic and electronic structure transformations of silver nanoparticles under a rapid cooling conditions

    International Nuclear Information System (INIS)

    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 x 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 x 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. (orig.)

  7. Structure investigation of ultra-small CdSe nanoparticles using the atomic PDF

    Science.gov (United States)

    Masadeh, Ahmad S.; Billinge, Simon J. L.; Bozin, Emil S.; McBride, James R.; Rosenthal, Sandra J.

    2011-03-01

    The size-dependent structure of CdSe nanoparticles, with diameter ranging from 1.5 to 3.6 nm, has been studied using the atomic pair distribution function (PDF) method. The samples are prepared by the methods of Peng et al, with modifications. The structure of the smallest stable size, (~ 1.5 nm), have been found to posses locally distorted wurtzite structure, with no clear evidence of a heavily disordered surface region. The PDF data of the smallest particle show an extra structural peak appears around r = 3.5 A indicates there is structure modification happened in this sample. This peak start appearing the nanoparticles PDF data gradually as nanoparticle size decreases. The structural parameters are reported quantitatively. We measure a size-dependent strain on the Cd-Se bond which reaches 1.0% at the smallest particle size. The size of the well-ordered core extracted directly from the data agrees with the size determined from other methods.

  8. Impact-collision ion scattering spectroscopy applied to the determination of atomic surface structure

    International Nuclear Information System (INIS)

    The technique of impact collision ion scattering spectroscopy (ICISS) was used to investigate the atomic structure and low energy ion scattering dynamics from various surfaces. A new formalism for calculating the three-dimensional cross section for an ion to scatter sequentially and classically from two atoms has been developed. This method can be used to assist in the interpretation of ICISS data in terms of quantitative surface-structure models. In an ICISS investigation of the Ag(110) surface, a surface flux peak analysis demonstrated that the surface was not a complete monolayer, but rather contained 10-15% random vacancies. Subsurface Li+ scattering results confirmed the oscillatory relaxation of the first two atomic layers of the surface, with Δ12 = -7.5% and Δ23 = 4.0%. Modeling of the neutralization mechanism for the He+ scattering gave a best fit time-dependent Auger neutralization time constant of 0.84 ± 0.08 fs. A neutralization study of 5 keV He+ ions scattered from Au adatoms on the Si(111)-√3 x √3-Au surface showed the He+ ICISS data contained false shadowing features that were actually the result of local neutralization effects. A detailed examination of the Si(111)-√3 x √3-Ag surface was also made. The 5 keV Li+ ICISS data gave evidence for Ag island formation at single monolayer coverages of silver, while the LEED, AES and LEIS data showed that at relatively high coverages of Ag (35 ML) small areas of √3 x √3 character were still present

  9. Atomic structure calculations and identification of EUV and SXR spectral lines in Sr XXX

    International Nuclear Information System (INIS)

    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. - Highlights: • 113 Lowest levels for Sr XXX are calculated. • Extreme Ultraviolet (EUV) and soft-X ray (SXR) spectral lines are identified. • Wavelengths of EUV and SXR spectral lines are reported. • E1, E2, M1 and M2 transition rates, oscillator strengths and lines strengths for lowest 113 levels are presented. • Lifetimes for lowest 113 fine structure levels are provided

  10. Atomic study on the ordered structure in Al melts induced by liquid/substrate interface with Ti solute

    International Nuclear Information System (INIS)

    Atomic ordering in Al melts induced by liquid/substrate interface with Ti solute was investigated by ab initio molecular dynamics simulations and in-situ synchrotron X-ray diffraction. It is predicted that deformed nanoscale ordering Al layers with a rhombohedral-centered hexagonal structure (R3¯m space group) instead of the intrinsic fcc structure (Fm3¯m space group) form on substrate at temperature above Al liquids. With Al atoms stacking away from the interface, the ordering structure reaches a critical thickness, which inhibits the consecutive stacking of Al atoms on substrates. The locally stacking reconstruction induced by Ti atom relieves the accumulated elastic strain energy in ordered Al layers, facilitating fully heterogeneous nucleation on substrate beyond the deformed ordering Al layer around the melting point. The roles of liquid/substrate interface with Ti solute in the physical behavior of heterogeneous nucleation on substrate were discussed

  11. Local atomic structure of martensitic Ni2+xMn1-xGa: An EXAFS study

    International Nuclear Information System (INIS)

    The local atomic structure of Ni2+xMn1-xGa with 0≤x≤0.16 alloys was explored using Mn and Ga K-edge extended x-ray-absorption fine-structure (EXAFS) measurement. In order to study the atomic re-arrangements that occur upon martensitic transformation, room-temperature and low-temperature EXAFS were recorded. The changes occurring in the L21 unit cell and the bond lengths obtained from the analysis enables us to determine the modulation amplitudes over which the constituent atoms move giving rise to the shuffling of the atomic planes in the modulated structure. The EXAFS analysis also suggests the changes in hybridization of Ga-p and Ni-d orbitals associated with the local symmetry breaking upon undergoing martensitic transition

  12. Atomic structure and oxygen deficiency of the ultrathin aluminium oxide barrier in Al/AlOx/Al Josephson junctions.

    Science.gov (United States)

    Zeng, Lunjie; Tran, Dung Trung; Tai, Cheuk-Wai; Svensson, Gunnar; Olsson, Eva

    2016-01-01

    Al/AlOx/Al Josephson junctions are the building blocks of a wide range of superconducting quantum devices that are key elements for quantum computers, extremely sensitive magnetometers and radiation detectors. The properties of the junctions and the superconducting quantum devices are determined by the atomic structure of the tunnel barrier. The nanoscale dimension and disordered nature of the barrier oxide have been challenges for the direct experimental investigation of the atomic structure of the tunnel barrier. Here we show that the miniaturized dimension of the barrier and the interfacial interaction between crystalline Al and amorphous AlOx give rise to oxygen deficiency at the metal/oxide interfaces. In the interior of the barrier, the oxide resembles the atomic structure of bulk aluminium oxide. Atomic defects such as oxygen vacancies at the interfaces can be the origin of the two-level systems and contribute to decoherence and noise in superconducting quantum circuits. PMID:27403611

  13. Change in the local atomic and crystal structures in a martensitic transformation in TiNiCu shape memory alloys

    International Nuclear Information System (INIS)

    Changes in the local and crystal structures of Ti, Ni, and Cu atoms in Ti50Ni25Cu25 shape memory alloys have been investigated using X-ray diffraction and extended X-ray absorption fine structure spectroscopy (EXAFS) in the temperature range of direct and inverse martensitic transformations. The analysis of the EXAFS spectra shows that the bonds involving Ni atoms have the highest degree of disorder and the change in the local environment of Ni atoms is significant for the occurrence of the shape memory effect, while Cu atoms occupy the normal positions in the crystallographic structure and have the lowest displacement amplitude leading to the stabilization of both phases

  14. The atomic structure of the Si(111) (2 root 3x2 root 3)R30 degrees-Sn reconstruction

    DEFF Research Database (Denmark)

    Levermann, A.H.; Howes, P.B.; Edwards, K.A.; Anyele, H.T.; Matthai, C.C.; Macdonald, J.E.; Feidenhans'l, R.; Lottermoser, L.; Seehofer, L.; Falkenberg, G.; Johnson, R.L.

    We have studied the atomic structure of the (2 root 3x2 root)R30 degrees reconstruction induced by adsorption of about 1.1 monolayers of Sn on Si(lll) using surface X-ray diffraction (SXRD) and scanning tunnelling microscopy (STM). The experimentally obtained structure factors in SXRD are in...... contradiction with existing models in the literature and we conclude the need for a new surface atomic structure model. We have been able to determine a number of properties of an appropriate surface model to allow a better fit to the experimental structure factors....

  15. Evolution of symmetry-broken states in the pseudogap regime of cuprates - the atomic structure footprints

    Science.gov (United States)

    Bozin, Emil; Zhong, R.; Knox, K. R.; Winn, B. L.; Gu, G. D.; Hill, J. P.; Tranquada, J. M.; Billinge, S. J. L.

    2015-03-01

    Revealing the nature of the symmetry broken states in strongly correlated electron systems in general, and in the pseudo-gap (PG) phase of cuprates in particular, is instrumental in understanding the underlying properties. To that effect the knowledge of the local atomic structure may reveal relevant details important for more comprehensive understanding of the character of symmetry broken states in strongly correlated electron systems. Atomic pair distribution function (PDF) is one of the few experimental methods that can speak to this problem. Mounting experimental evidence suggests that the pseudogap phase may represent an electronic state in which the four-fold rotational symmetry of the CuO2 planes is broken, pointing to stripe or nematic character. Systematic approach has been taken in charting both long and short range structural orders, on an equal footing, across the (x, T) phase diagrams of cuprates. For example, in La2-xBaxCuO4, by combining inelastic neutron scattering and neutron PDF approaches, we find evidence consistent with there being a dynamic symmetry breaking well above the charge ordering temperature and within the pseudogap regime. The response has non-monotonic doping dependence that peaks at 1/8 composition. Work at Brookhaven National Laboratory was supported by US DOE, Office of Science, Office of Basic Energy Sciences (DOE-BES) under Contract DE-AC02-98CH10886.

  16. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

    Directory of Open Access Journals (Sweden)

    Bickerton George R

    2011-07-01

    Full Text Available Abstract Background Structural studies are increasingly providing huge amounts of information on multi-protein assemblies. Although a complete understanding of cellular processes will be dependent on an explicit characterization of the intermolecular interactions that underlie these assemblies and mediate molecular recognition, these are not well described by standard representations. Results Here we present PICCOLO, a comprehensive relational database capturing the details of structurally characterized protein-protein interactions. Interactions are described at the level of interacting pairs of atoms, residues and polypeptide chains, with the physico-chemical nature of the interactions being characterized. Distance and angle terms are used to distinguish 12 different interaction types, including van der Waals contacts, hydrogen bonds and hydrophobic contacts. The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces. This is exemplified by an analysis of residue propensity and interface contact preferences derived from a much larger data set than previously reported. However, PICCOLO also supports detailed inspection of particular systems of interest. Conclusions The current PICCOLO database comprises more than 260 million interacting atom pairs from 38,202 protein complexes. A web interface for the database is available at http://www-cryst.bioc.cam.ac.uk/piccolo.

  17. Spin structure of harmonically trapped one-dimensional atoms with spin-orbit coupling

    Science.gov (United States)

    Guan, Q.; Blume, D.

    2015-08-01

    We introduce a theoretical approach to determine the spin structure of harmonically trapped atoms with two-body zero-range interactions subject to an equal mixture of Rashba and Dresselhaus spin-orbit coupling created through Raman coupling of atomic hyperfine states. The spin structure of bosonic and fermionic two-particle systems with finite and infinite two-body interaction strength g is calculated. Taking advantage of the fact that the N -boson and N -fermion systems with infinitely large coupling strength g are analytically solvable for vanishing spin-orbit coupling strength kso and vanishing Raman coupling strength Ω , we develop an effective spin model that is accurate to second order in Ω for any kso and infinite g . The three- and four-particle systems are considered explicitly. It is shown that the effective spin Hamiltonian, which contains a Heisenberg exchange term and an anisotropic Dzyaloshinskii-Moriya exchange term, describes the transitions that these systems undergo with the change of kso as a competition between independent spin dynamics and nearest-neighbor spin interactions.

  18. Hybrid inorganic–organic superlattice structures with atomic layer deposition/molecular layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Tynell, Tommi; Yamauchi, Hisao; Karppinen, Maarit, E-mail: maarit.karppinen@aalto.fi [Department of Chemistry, Aalto University, FI-00076 Aalto (Finland)

    2014-01-15

    A combination of the atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques is successfully employed to fabricate thin films incorporating superlattice structures that consist of single layers of organic molecules between thicker layers of ZnO. Diethyl zinc and water are used as precursors for the deposition of ZnO by ALD, while three different organic precursors are investigated for the MLD part: hydroquinone, 4-aminophenol and 4,4′-oxydianiline. The successful superlattice formation with all the organic precursors is verified through x-ray reflectivity studies. The effects of the interspersed organic layers/superlattice structure on the electrical and thermoelectric properties of ZnO are investigated through resistivity and Seebeck coefficient measurements at room temperature. The results suggest an increase in carrier concentration for small concentrations of organic layers, while higher concentrations seem to lead to rather large reductions in carrier concentration.

  19. Hybrid inorganic–organic superlattice structures with atomic layer deposition/molecular layer deposition

    International Nuclear Information System (INIS)

    A combination of the atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques is successfully employed to fabricate thin films incorporating superlattice structures that consist of single layers of organic molecules between thicker layers of ZnO. Diethyl zinc and water are used as precursors for the deposition of ZnO by ALD, while three different organic precursors are investigated for the MLD part: hydroquinone, 4-aminophenol and 4,4′-oxydianiline. The successful superlattice formation with all the organic precursors is verified through x-ray reflectivity studies. The effects of the interspersed organic layers/superlattice structure on the electrical and thermoelectric properties of ZnO are investigated through resistivity and Seebeck coefficient measurements at room temperature. The results suggest an increase in carrier concentration for small concentrations of organic layers, while higher concentrations seem to lead to rather large reductions in carrier concentration

  20. Structural evaluation of probucol nanoparticles in water by atomic force microscopy.

    Science.gov (United States)

    Moribe, Kunikazu; Limwikrant, Waree; Higashi, Kenjirou; Yamamoto, Keiji

    2012-05-10

    Structural evaluation of probucol nanoparticles coground with polyvinylpyrrolidone K17 and sodium dodecyl sulfate for 90 min was performed by solid-state nuclear magnetic resonance (NMR) spectroscopy and atomic force microscopy (AFM) with force-distance curve analysis. The results of solid-state NMR indicated that the cogrinding changed crystalline probucol to amorphous form. The number-averaged mean heights of probucol particles in the ground mixture (GM) suspension were determined by AFM to be 6 and 15 nm for freshly prepared and 24h-stored samples, respectively. Nucleation and the subsequent crystal growth might have occurred after the GM was dispersed in water. The presence of probucol nanocrystals and agglomeration of the primary probucol nanoparticles were recognized by AFM force-distance curve analysis. AFM could be a promising tool to evaluate the structure of nanoparticles as well as their agglomeration behavior in aqueous media. PMID:22370474

  1. Observations and morphological analysis of supermolecular structure of natural bitumens by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Yevgeny A. Golubev; Olga V. Kovaleva; Nikolay P. Yushkin [Institute of Geology of RAS, Syktyvkar (Russian Federation)

    2008-01-15

    The supermolecular structures of natural bitumens of the thermal consequent row asphaltites lower kerites (albertites), higher kerites (impsonites), anthraxolites from the Timan-Pechora petroleum province and Karelian shungite rocks, Russia, were studied in details. The experimental technique used was atomic force microscopy (AFM), following fracture preparation. The element distribution of the sample surfaces was analyzed by an X-ray microanalyser 'Link ISIS', combined with a scanning electron microscope (SEM). In this work, we characterized the supermolecular evolution of natural solid bitumens in the carbonization sequence by quantitative parameters. We showed that supermolecular structure can be important in defining to which classification group solid bitumens belong. 29 refs., 7 figs., 2 tabs.

  2. Probing the local structure of doped manganites using the atomic pair distribution function

    International Nuclear Information System (INIS)

    We have used atomic pair distribution function (PDF) analysis based on neutron powder diffraction data to investigate the local structure of the colossal magnetoresistant manganite La0.75Ca0.25MnO3 as a function of temperature. In the doping range 0.173+ ions. A two-phase model based on the local structures of the FM and PI phases was used to refine the experimental PDFs quantitatively. We observe the co-existence of both phases over a wide temperature range: approximately 10% of the localized JT phase (PI) is present even at the lowest temperature (T=20 K), whereas at room temperature nearly half of the sample remains in the delocalized (FM) phase. (orig.)

  3. Chain-Branching Control of the Atomic Structure of Alkanethiol-Based Gold–Sulfur Interfaces

    DEFF Research Database (Denmark)

    Wang, Yun; Chi, Qijin; Zhang, Jingdong; Hush, Noel S.; Reimers, Jeffrey R.; Ulstrup, Jens

    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......): 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......, 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....

  4. 3D structural and atomic-scale analysis of lath martensite: Effect of the transformation sequence

    International Nuclear Information System (INIS)

    To improve the fundamental understanding of the multi-scale characteristics of martensitic microstructures and their micro-mechanical properties, a multi-probe methodology is developed and applied to low-carbon lath martensitic model alloys. The approach is based on the joint employment of electron channeling contrast imaging (ECCI), electron backscatter diffraction (EBSD), transmission electron microscopy (TEM), atom probe tomography (APT) and nanoindentation, in conjunction with high precision and large field-of-view 3D serial sectioning. This methodology enabled us to resolve (i) size variations of martensite sub-units, (ii) associated dislocation sub-structures, (iii) chemical heterogeneities, and (iv) the resulting local mechanical properties. The identified interrelated microstructure heterogeneity is discussed and related to the martensitic transformation sequence, which is proposed to intrinsically lead to formation of a nano-composite structure in low-carbon martensitic steels

  5. GRASP92: a package for large-scale relativistic atomic structure calculations

    Science.gov (United States)

    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

  6. Local atomic order, electronic structure and electron transport properties of Cu-Zr metallic glasses

    International Nuclear Information System (INIS)

    We studied atomic and electronic structures of binary Cu-Zr metallic glasses (MGs) using combined experimental and computational methods including X-ray absorption fine structure spectroscopy, electrical resistivity, thermoelectric power (TEP) measurements, molecular dynamics (MD) simulations, and ab-initio calculations. The results of MD simulations and extended X-ray absorption fine structure analysis indicate that atomic order of Cu-Zr MGs and can be described in terms of interpenetrating icosahedral-like clusters involving five-fold symmetry. MD configurations were used as an input for calculations of theoretical electronic density of states (DOS) functions which exhibits good agreement with the experimental X-ray absorption near-edge spectra. We found no indication of minimum of DOS at Fermi energy predicted by Mott's nearly free electron (NFE) model for glass-forming alloys. The theoretical DOS was subsequently used to test Mott's model describing the temperature variation of electrical resistivity and thermoelectric power of transition metal-based MGs. We demonstrate that the measured temperature variations of electrical resistivity and TEP remain in a contradiction with this model. On the other hand, the experimental temperature dependence of electrical resistivity can be explained by incipient localization of conduction electrons. It is shown that weak localization model works up to relatively high temperatures when localization is destroyed by phonons. Our results indicate that electron transport properties of Cu-Zr MGs are dominated by localization effects rather than by electronic structure. We suggest that NFE model fails to explain a relatively high glass-forming ability of binary Cu-Zr alloys.

  7. Mesoscale effects in electrochemical conversion: coupling of chemistry to atomic- and nanoscale structure in iron-based electrodes.

    Science.gov (United States)

    Wiaderek, Kamila M; Borkiewicz, Olaf J; Pereira, Nathalie; Ilavsky, Jan; Amatucci, Glenn G; Chupas, Peter J; Chapman, Karena W

    2014-04-30

    The complex coupling of atomic, chemical, and electronic transformations across multiple length scales underlies the performance of electrochemical energy storage devices. Here, the coupling of chemistry with atomic- and nanoscale structure in iron conversion electrodes is resolved by combining pair distribution function (PDF) and small-angle X-ray scattering (SAXS) analysis for a series of Fe fluorides, oxyfluorides, and oxides. The data show that the anion chemistry of the initial electrode influences the abundance of atomic defects in the Fe atomic lattice. This, in turn, is linked to different atom mobilities and propensity for particle growth. Competitive nanoparticle growth in mixed anion systems contributes to a distinct nanostructure, without the interconnected metallic nanoparticles formed for single anion systems. PMID:24735418

  8. Atomic physics

    CERN Document Server

    Born, Max

    1989-01-01

    The Nobel Laureate's brilliant exposition of the kinetic theory of gases, elementary particles, the nuclear atom, wave-corpuscles, atomic structure and spectral lines, electron spin and Pauli's principle, quantum statistics, molecular structure and nuclear physics. Over 40 appendices, a bibliography, numerous figures and graphs.

  9. The asymmetrical structure of Golgi apparatus membranes revealed by in situ atomic force microscope.

    Directory of Open Access Journals (Sweden)

    Haijiao Xu

    Full Text Available The Golgi apparatus has attracted intense attentions due to its fascinating morphology and vital role as the pivot of cellular secretory pathway since its discovery. However, its complex structure at the molecular level remains elusive due to limited approaches. In this study, the structure of Golgi apparatus, including the Golgi stack, cisternal structure, relevant tubules and vesicles, were directly visualized by high-resolution atomic force microscope. We imaged both sides of Golgi apparatus membranes and revealed that the outer leaflet of Golgi membranes is relatively smooth while the inner membrane leaflet is rough and covered by dense proteins. With the treatment of methyl-β-cyclodextrin and Triton X-100, we confirmed the existence of lipid rafts in Golgi apparatus membrane, which are mostly in the size of 20 nm -200 nm and appear irregular in shape. Our results may be of significance to reveal the structure-function relationship of the Golgi complex and pave the way for visualizing the endomembrane system in mammalian cells at the molecular level.

  10. Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors

    CERN Document Server

    Levashov, Valentin A

    2015-01-01

    It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a model 3D binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. Thus correlations relevant to the Green-Kubo expression for viscosity are interpreted in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonst...

  11. Atomic and electronic structure of the SrNbO3/SrNbO3.4 interface

    International Nuclear Information System (INIS)

    We have determined the atomic-scale structure of the SrNbO3/SrNbO3.4 interface and related it to the electronic structure. Experimentally, transmission electron microscopy observations reveal that SrNbO3 and SrNbO3.4 show orientation relationships [1¯10]SrNbO3 // [010]SrNbO3.4 and (110)SrNbO3 // (001)SrNbO3.4, and that their interface is coherent and atomically abrupt. Theoretically, this interface is found to be strongly anisotropic in electronic structure, and takes on quasi-one-dimensional nature. We also find that the interface impacts greatly the electron occupation of Nb d orbitals, particularly dz2 orbital. The combined study represents a relevant advance in atomically bridging structures to properties of heterointerfaces

  12. Atomic charges in RBa2Cu3O7 superconductor lattices. Electronic structure of the copper atoms

    International Nuclear Information System (INIS)

    The effective atomic charges for all sites of the RBa2Cu3O7 lattices have been found using our Moessbauer data with the 67Cu(67Zn), 133Ba(133Cs), 155Eu(155Gd) isotopes, our calculations of the lattice electric field gradient (EFG) at the lattice sites, as well as the 17O NMR data available in literature. The charges show holes placed in the chain oxygen sublattice mainly. The Cu2+ Sternheimer factor has been estimated and the Cu2+ valence EFG in YBa2Cu3O7 has been found. The z-axes of the total, lattice, and valence EFG tensors for Cu(2) coincide with the crystal axis c. For Cu(1) they coincide with the axes b, a, and a, respectively. (orig.)

  13. Temporal structure of attosecond pulses from intense laser-atom interactions

    International Nuclear Information System (INIS)

    We find that the high harmonics have a power-law spectrum Iω∼ω-3.3±0.25 in a wide frequency domain starting at the ionization potential Ip and down to the plateau beginning. Our spectrotemporal analysis of the emitted radiation displays clear bowlike structures in the (t,ω) plane. These 'bows' correspond to Corkum's reencounters of the freed electron with the atom. We find that the bows are not filled and thus cannot be due to any bremsstrahlung. Rather, it is a resonant process that we call stimulated recombination (SR). It occurs when an electron with momentum p reencounters the incompletely ionized atom, and interferes with itself still remaining in the ground state. The SR leads to a highly efficient resonant emission at (ℎ/2π)ω=p2/2m+Ip in the form of attosecond pulses. The SR relies on a low level of ionization and strongly benefits from the use of few-cycle laser pulses

  14. X-ray crystal structure of anhydrous chitosan at atomic resolution.

    Science.gov (United States)

    Naito, Philip-Kunio; Ogawa, Yu; Sawada, Daisuke; Nishiyama, Yoshiharu; Iwata, Tadahisa; Wada, Masahisa

    2016-07-01

    We determined the crystal structure of anhydrous chitosan at atomic resolution, using X-ray fiber diffraction data extending to 1.17 Å resolution. The unit cell [a = 8.129(7) Å, b = 8.347(6) Å, c = 10.311(7) Å, space group P21 21 21 ] of anhydrous chitosan contains two chains having one glucosamine residue in the asymmetric unit with the primary hydroxyl group in the gt conformation, that could be directly located in the Fourier omit map. The molecular arrangement of chitosan is very similar to the corner chains of cellulose II implying similar intermolecular hydrogen bonding between O6 and the amine nitrogen atom, and an intramolecular bifurcated hydrogen bond from O3 to O5 and O6. In addition to the classical hydrogen bonds, all the aliphatic hydrogens were involved in one or two weak hydrogen bonds, mostly helping to stabilize cohesion between antiparallel chains. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 361-368, 2016. PMID:26930586

  15. Hyperfine structure of the 3d34s4p 6G multiplet of atomic vanadium

    International Nuclear Information System (INIS)

    The spectrum of atomic vanadium was recorded using high-resolution Fourier transform spectroscopy with optical bandpass filters in the wavelength range from 360 to 500 nm. Vanadium atoms are produced and excited in a hollow-cathode discharge. The main focus lies on the determination of the magnetic dipole hyperfine constants A of the lowest multiplet of odd parity, the 6G of the configuration 3d34s4p, the hyperfine structure (HFS) of which was unknown to date. The HFS of the lines, connecting this multiplet with the multiplets 3d34s5s 6F, 3d34s4d 6H and 3d34s4d 6G, was observed and analysed. New results are presented for all six levels belonging to 3d34s4p 6G as well as for seven high-lying levels belonging to 3d34s4d 6H and 3d34s4d 6G. The experimental results for the lowest multiplet of odd parity are compared with calculated magnetic dipole hyperfine constants which were estimated using the effective-operator formalism in the pure LS coupling case.

  16. Characterization of atomic-level structure in Fe-based amorphous and nanocrystalline alloy by experimental and modeling methods

    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.

  17. Characterization of atomic-level structure in Fe-based amorphous and nanocrystalline alloy by experimental and modeling methods

    International Nuclear Information System (INIS)

    The atomic structure of Fe70Nb10B20 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

  18. Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

    Science.gov (United States)

    Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H

    2016-05-01

    Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species. PMID:27070292

  19. Casimir-Polder force on a V -type three-level atom near a structure containing left-handed materials

    Science.gov (United States)

    Xu, Jingping; Chang, Shenglong; Yang, Yaping; Al-amri, M.

    2016-01-01

    The Casimir-Polder (CP) force acting on a V -type three-level atom which is initially prepared in two different kinds of superposition states, i.e., subradiant and superradiant states, is investigated. The influence of quantum interference on force evolution due to two-dipole transitions is analyzed in detail. It is found that the orientation of the atomic dipole moment has significant influence on the Casimir-Polder force and consequently its evolution. For the ideal degenerate V -type atom with two parallel dipoles, quantum interference leads to population trapping as well as the cancellation of the CP force when the atom is prepared initially in a subradiant state. However, the result changes when we consider the practical Zeeman V -type atom whose two dipole moments are perpendicular to each other. Since quantum interference in such an atom must occur in an anisotropic environment, it is possible to trap atomic population and enhance the CP force simultaneously by preparing the atom initially in sub-radiant states. In principle, our results can be found in an arbitrary anisotropic environment, and here we describe a structure containing left-handed materials to highlight our findings.

  20. Atomic Physics

    CERN Document Server

    Foot, Christopher J

    2007-01-01

    This text will thoroughly update the existing literature on atomic physics. Intended to accompany an advanced undergraduate course in atomic physics, the book will lead the students up to the latest advances and the applications to Bose-Einstein Condensation of atoms, matter-wave inter-ferometry and quantum computing with trapped ions. The elementary atomic physics covered in the early chapters should be accessible to undergraduates when they are first introduced to the subject. To complement. the usual quantum mechanical treatment of atomic structure the book strongly emphasizes the experimen

  1. Research Investigation Directed Toward Extending the Useful Range of the Electromagnetic Spectrum. [atomic spectra and electronic structure of alkali metals

    Science.gov (United States)

    Hartmann, S. R.; Happer, W.

    1974-01-01

    The report discusses completed and proposed research in atomic and molecular physics conducted at the Columbia Radiation Laboratory from July 1972 to June 1973. Central topics described include the atomic spectra and electronic structure of alkali metals and helium, molecular microwave spectroscopy, the resonance physics of photon echoes in some solid state systems (including Raman echoes, superradiance, and two photon absorption), and liquid helium superfluidity.

  2. Investigation of the structure change of atomic shells due to uranium ionization by the Dirac-Fock-Slater method

    International Nuclear Information System (INIS)

    The influence of outer vacancies in the atomic shells of uranium on the atomic shell structure is claculated by the Dirac-Fock-Slater method. It is found out that the energy of the X-ray transitions increases due to the detachment of the electrons with the lowest binding energies. The electron detachment from the subshells of the 4f level gives rise to negative energy shifts of the X-ray transitions.(author)

  3. Structure-Property Relationships in Atomic-Scale Junctions: Histograms and Beyond.

    Science.gov (United States)

    Hybertsen, Mark S; Venkataraman, Latha

    2016-03-15

    Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure-function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, the scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics. Such link groups (amines, methylsuflides, pyridines, etc.) maintain a stable lone pair configuration that selectively bonds to specific, undercoordinated transition metal atoms available following rupture of a metal point contact in the STM-BJ experiments. This basic chemical principle rationalizes the observation of highly reproducible conductance signatures. Subsequently, the method has been extended to probe a variety of physical phenomena ranging from basic I-V characteristics to more complex properties such as thermopower and electrochemical response. By adapting the technique to a conducting cantilever atomic force microscope (AFM-BJ), simultaneous measurement of the mechanical characteristics of nanoscale junctions as they

  4. β-SiC(100) surface: atomic structures and electronic properties

    International Nuclear Information System (INIS)

    This review organizes and presents the state of the art of research related to the composition, atomic and electronic structure, and electronic properties of various superstructures that were recently shown to exist on clean β-SiC(100) surfaces. In the past 10 years, considerable experimental and theoretical progress in clean β-SiC(100) surfaces has been made. In particular, various surface reconstructions have been identified and studied, and the controlled formation of highly stable, very long straight lines of Si dimers self-organizing on a β-SiC(100) surface have been found, with the line separation being determined by the annealing time and temperature. Many aspects of the field (composition, unit cell models, etc.) are still subject to debate, however. (reviews of topical problems)

  5. Comparing two iteration algorithms of Broyden electron density mixing through an atomic electronic structure computation

    Science.gov (United States)

    Man-Hong, Zhang

    2016-05-01

    By performing the electronic structure computation of a Si atom, we compare two iteration algorithms of Broyden electron density mixing in the literature. One was proposed by Johnson and implemented in the well-known VASP code. The other was given by Eyert. We solve the Kohn-Sham equation by using a conventional outward/inward integration of the differential equation and then connect two parts of solutions at the classical turning points, which is different from the method of the matrix eigenvalue solution as used in the VASP code. Compared to Johnson’s algorithm, the one proposed by Eyert needs fewer total iteration numbers. Project supported by the National Natural Science Foundation of China (Grant No. 61176080).

  6. Atomic-Resolution Structure of an N(5) Flavin Adduct in D-Arginine Dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Guoxing; Yuan, Hongling; Wang, Siming; Gadda, Giovanni; Weber, Irene T. (GSU)

    2011-09-06

    D-Arginine dehydrogenase (DADH) catalyzes the flavin-dependent oxidative deamination of D-arginine and other D-amino acids to the corresponding imino acids. The 1.07 {angstrom} atomic-resolution structure of DADH crystallized with D-leucine unexpectedly revealed a covalent N(5) flavin adduct, instead of the expected iminoleucine product in the active site. This acyl adduct has been successfully reproduced by photoreduction of DADH in the presence of 4-methyl-2-oxopentanoic acid (ketoleucine). The iminoleucine may be released readily because of weak interactions in the binding site, in contrast to iminoarginine, converted to ketoleucine, which reacts with activated FAD to form the covalently linked acyl adduct.

  7. Atomic-resolution structure of an N5 flavin adduct in D-arginine dehydrogenase.

    Science.gov (United States)

    Fu, Guoxing; Yuan, Hongling; Wang, Siming; Gadda, Giovanni; Weber, Irene T

    2011-07-26

    D-Arginine dehydrogenase (DADH) catalyzes the flavin-dependent oxidative deamination of D-arginine and other D-amino acids to the corresponding imino acids. The 1.07 Å atomic-resolution structure of DADH crystallized with D-leucine unexpectedly revealed a covalent N(5) flavin adduct, instead of the expected iminoleucine product in the active site. This acyl adduct has been successfully reproduced by photoreduction of DADH in the presence of 4-methyl-2-oxopentanoic acid (ketoleucine). The iminoleucine may be released readily because of weak interactions in the binding site, in contrast to iminoarginine, converted to ketoleucine, which reacts with activated FAD to form the covalently linked acyl adduct. PMID:21707047

  8. Atomic-scale simulation of nano-grains:structure and diffusion properties

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Nanograins are characterized by a typical grain size from 1 to 100 nm. Molecular dynamics simulations have been carried out for the nanograin sphere with the diameters from 1.45 to 10.12 nm. We study the influence of grain size on structure and diffusion properties of the nanograins. The results reveal that as the grain size is reduced, the fraction of grain surface increases significantly, and the surface width is approximately constant; the mean atomic energy of the surface increases distinctly, but that of the grain interior varies insignificantly; the diffusion coefficient is increased sharply, and the relation of the diffusion coefficient and the grain size is close to exponential relation below 10 nm.

  9. Spectroscopic investigation of the electronic structure of thin atomic layer deposition HfO2 films

    International Nuclear Information System (INIS)

    The electronic structure of HfO2 thin films is investigated employing resonant photoelectron spectroscopy (resPES). The detailed analysis of the O1s resonance profile enables the determination of the partial density of states for the valence and the conduction bands as well as the electronic band gap to be 6.2 eV. The position of the charge neutrality level is evaluated. Thereby, it is demonstrated that the resPES data are able to combine information both for the valence as well as for the conduction band states. In addition, evidences for intrinsic in-gap states attributed to polaronic and charge transfer states are given. Electronic charges within the atomic layer deposition-HfO2 films are identified, pointing out that the amount of charges is essential to determine the accurate position of the surface potentials

  10. The local atomic structure of di-alanine amino acid derivative of protoporphyrin IX

    International Nuclear Information System (INIS)

    The photophysical and photochemical properties of photosensitizers bearing potential for photodynamic diagnosis (PDD) and treatment (PDT) of malignant tissues strictly depend on the details of their chemical processing. In this work, the x-ray absorption spectroscopy (XAFS) and electron spin resonance (ESR) techniques were applied to determine the nearest neighbourhood of iron in the di-alanine amino acid derivative of protoporphyrin IX (L-alanine diprotoporphyrinate). The investigated compound is a technological precursor for novel-class, highly water-soluble protoporphyrin IX-based photosensitizers, which have potential for applications in PDD and PDT and have just entered phase I clinical trials. Knowing the chemical content and exact atomic structures of the technological precursor, as well as of the high-purity final product, which all might contain some contamination, is a prerequisite for preparing photosensitizers for preliminary clinical tests

  11. Atomic and electronic structure of clusters from car-Parrinello method

    International Nuclear Information System (INIS)

    With the development of ab-initio molecular dynamics method, it has now become possible to study the static and dynamical properties of clusters containing up to a few tens of atoms. Here I present a review of the method within the framework of the density functional theory and pseudopotential approach to represent the electron-ion interaction and discuss some of its applications to clusters. Particular attention is focussed on the structure and bonding properties of clusters as a function of their size. Applications to clusters of alkali metals and Al, non-metal - metal transition in divalent metal clusters, molecular clusters of carbon and Sb are discussed in detail. Some results are also presented on mixed clusters. (author). 121 refs, 24 ifigs

  12. Study on Fine Structure of Gas Atomized LaNi5-based Alloys

    Institute of Scientific and Technical Information of China (English)

    Hai JING; Hong GUO; Shuguang ZHANG; Zili MA; Shaoming ZHANG

    2003-01-01

    The fine structure of hydrogen storage alloy powders MINi4.3-xCoxMn0.4Al0.3(x=0.75, 0.45, 0.10; MI: La-rich mischmetal) prepared by rapidly solidifying gas atomization was investigated using a Rietveld analysis method. Two setsof CaCu5-type crystal constants were observed in the studied alloys and one set was larger than the other. Withdecreasing powder radius the solidification rate of powder increased, and so did the percentage of a particle partwith larger crystal constants. The reason why there were two sets of crystal constants might be the difference ofsolidification rate between the outside and inside of a particle.

  13. Atomic structure of the Σ = 2 twist carbide grain boundary in WC-Co alloys

    Science.gov (United States)

    Lay, Sabine; Missiaen, Jean-Michel

    2013-04-01

    The Σ = 2 twist carbide grain boundary with a (10 ? 0) habit plane was investigated by high resolution transmission electron microscopy in a WC-Co alloy. The atomic structure at the boundary was determined by comparing experimental images and simulations. It corresponds to the boundary model with the lowest energy according to atomistic calculations. Periodic monolayer interfacial steps, compensating for the parametric misfit at the boundary were studied. The displacement field around the defects was simulated and corresponds to a dislocation with a mixed character and a Burgers vectors equal to 1/6⟨ ? 2 ? 3⟩ lying in the boundary plane. Another step with a larger height and connected to a stacking fault was analyzed. It likely arises from the interaction of a matrix dislocation with the boundary. The observations suggest that the migration of Σ = 2 grain boundaries can be induced by the glide of the monolayer steps along the grain boundary.

  14. Highly charged ions for atomic clocks and search for variation of the fine structure constant

    CERN Document Server

    Dzuba, V A

    2015-01-01

    We review a number of highly charged ions which have optical transitions suitable for building extremely accurate atomic clocks. This includes ions from Hf$^{12+}$ to U$^{34+}$, which have the $4f^{12}$ configuration of valence electrons, the Ir$^{17+}$ ion, which has a hole in almost filled $4f$ subshell, the Ho$^{14+}$, Cf$^{15+}$, Es$^{17+}$ and Es$^{16+}$ ions. Clock transitions in most of these ions are sensitive to variation of the fine structure constant, $\\alpha$ ($\\alpha = e^2/\\hbar c$). E.g., californium and einsteinium ions have largest known sensitivity to $\\alpha$-variation while holmium ion looks as the most suitable ion for experimental study. We study the spectra of the ions and their features relevant to the use as frequency standards.

  15. The local atomic structure of di-alanine amino acid derivative of protoporphyrin IX

    Energy Technology Data Exchange (ETDEWEB)

    Walczak, M S [Institute of Physics PAS, Aleja Lotnikow 32/46, 02-668 Warsaw (Poland); Lawniczak-Jablonska, K [Institute of Physics PAS, Aleja Lotnikow 32/46, 02-668 Warsaw (Poland); Sienkiewicz, A [Institute of Physics PAS, Aleja Lotnikow 32/46, 02-668 Warsaw (Poland); Czuba, M [Institute of Optoelectronics MUT, ulica Stefana Kaliskiego 2, 00-908 Warsaw (Poland); Klepka, M [Institute of Physics PAS, Aleja Lotnikow 32/46, 02-668 Warsaw (Poland); Graczyk, A [Institute of Optoelectronics MUT, ulica Stefana Kaliskiego 2, 00-908 Warsaw (Poland)

    2007-07-18

    The photophysical and photochemical properties of photosensitizers bearing potential for photodynamic diagnosis (PDD) and treatment (PDT) of malignant tissues strictly depend on the details of their chemical processing. In this work, the x-ray absorption spectroscopy (XAFS) and electron spin resonance (ESR) techniques were applied to determine the nearest neighbourhood of iron in the di-alanine amino acid derivative of protoporphyrin IX (L-alanine diprotoporphyrinate). The investigated compound is a technological precursor for novel-class, highly water-soluble protoporphyrin IX-based photosensitizers, which have potential for applications in PDD and PDT and have just entered phase I clinical trials. Knowing the chemical content and exact atomic structures of the technological precursor, as well as of the high-purity final product, which all might contain some contamination, is a prerequisite for preparing photosensitizers for preliminary clinical tests.

  16. Molecular dynamic simulation of the atomic structure of aluminum solid–liquid interfaces

    International Nuclear Information System (INIS)

    In this paper, molecular dynamic (MD) simulation was used to investigate the equilibrium atomic arrangement at aluminum solid–liquid (S/L) interfaces with {111}, {110} and {100} orientations. The simulation results reveal that the aluminum S/L interfaces are diffuse for all the orientations, and extend up to 7 atomic layers. Within the diffuse interfaces there exists substantial atomic ordering, which is manifested by atomic layering perpendicular to the interface and in-plane atomic ordering parallel to the interface. Atomic layering can be quantified by the atomic density profile (ρ(z)) while the in-plane atomic ordering can be described by the in-plane ordering parameter (S(z)). The detailed MD simulation suggests that atomic layering at the interface always occurs within 7 atomic layers independent of the interface orientation while the in-plane ordering is highly dependent on the interface orientations, with the {111} interface being less diffuse than the {100} and {110} interfaces. This study demonstrates clearly that the physical origin of the diffuse interface is atomic layering and in-plane atomic ordering at the S/L interfaces. It is suggested that the difference in atomic layering and in-plane ordering at the S/L interface with different orientations is responsible for the observed growth anisotropy. (papers)

  17. Possible atomic structures responsible for the sub-bandgap absorption of chalcogen-hyperdoped silicon

    International Nuclear Information System (INIS)

    Single-crystal silicon was hyperdoped with sulfur, selenium, and tellurium using ion implantation and nanosecond laser melting. The hyperdoping of such chalcogen elements led to strong and wide sub-bandgap light absorption. Annealing the hyperdoped silicon, even at low temperatures (such as 200–400 °C), led to attenuation of the sub-bandgap absorption. To explain the attenuation process, we modeled it as chemical decomposition reaction from an optically absorbing structure to a non-absorbing structure. Attenuation of the experimental absorption coefficient was fit using the Arrhenius equation. From the fitted data, we extracted the reaction activation energies of S-, Se-, and T-hyperdoped silicon as 0.338 ± 0.029 eV, 0.471 ± 0.040 eV, and 0.357 ± 0.028 eV, respectively. We discuss these activation energies in terms of the bond energies of chalcogen–Si metastable bonds, and suggest that several high-energy interstitial sites, rather than substitutional sites, are candidates for the atomic structures that are responsible for the strong sub-bandgap absorption of chalcogen hyperdoped silicon

  18. Possible atomic structures responsible for the sub-bandgap absorption of chalcogen-hyperdoped silicon

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ke-Fan [Institute for Computational Materials Science, School of Physics and Electronics, Henan University, Kaifeng 475004 (China); Key Laboratory of Semiconductor Materials Science, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China); Shao, Hezhu [Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China); Liu, Kong; Qu, Shengchun, E-mail: qsc@semi.ac.cn, E-mail: wangyx@henu.edu.cn; Wang, Zhanguo [Key Laboratory of Semiconductor Materials Science, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China); Wang, Yuanxu, E-mail: qsc@semi.ac.cn, E-mail: wangyx@henu.edu.cn [Institute for Computational Materials Science, School of Physics and Electronics, Henan University, Kaifeng 475004 (China)

    2015-09-14

    Single-crystal silicon was hyperdoped with sulfur, selenium, and tellurium using ion implantation and nanosecond laser melting. The hyperdoping of such chalcogen elements led to strong and wide sub-bandgap light absorption. Annealing the hyperdoped silicon, even at low temperatures (such as 200–400 °C), led to attenuation of the sub-bandgap absorption. To explain the attenuation process, we modeled it as chemical decomposition reaction from an optically absorbing structure to a non-absorbing structure. Attenuation of the experimental absorption coefficient was fit using the Arrhenius equation. From the fitted data, we extracted the reaction activation energies of S-, Se-, and T-hyperdoped silicon as 0.338 ± 0.029 eV, 0.471 ± 0.040 eV, and 0.357 ± 0.028 eV, respectively. We discuss these activation energies in terms of the bond energies of chalcogen–Si metastable bonds, and suggest that several high-energy interstitial sites, rather than substitutional sites, are candidates for the atomic structures that are responsible for the strong sub-bandgap absorption of chalcogen hyperdoped silicon.

  19. Atomic structure of high-coercivity cobalt-carbide nanoparticles ensembles

    Science.gov (United States)

    Arena, D. A.; Sterbinsky, G.; Stephens, P. W.; Carroll, K. J.; Yoon, H.; Meng, S.; Huba, Z.; Carpenter, E. E.

    2013-03-01

    Permanent magnets are increasingly important in numerous applications, including the quickly expanding area of green technologies (e . g . high efficiency electric car motors and wind turbine power systems). We present studies of novel permanent magnet materials based on cobalt carbide nanoparticles (NPs), where the energy product (BHmax) exceeds 20 kJ / m3. The NPs are synthesized via a polyol process, which offers a flexible approach to modify the Co-carbide phase (Co2C and Co3C), and NP morphology, size and size dispersion. The Co2C and Co3C phases have unique magnetic properties, and the combination exhibits the high BHmax . We present a detailed assessment of the structure of mixtures of Co2C and Co3 NPs, measured by high-resolution, synchrotron based powder x-ray diffraction (p-XRD). Both the Co2C and Co3 phases exhibit an orthorhombic structure (Pnnm and Pnma space groups, respectively). The high-resolution p-XRD facilitates identification of mixed phase samples, enabling detailed comparisons of the atomic structure with the magnetic properties, measured by both lab-based magnetometry and x-ray spectroscopy (soft x-ray XAS & XMCD).

  20. Epitaxial B-Graphene: Large-Scale Growth and Atomic Structure.

    Science.gov (United States)

    Usachov, Dmitry Yu; Fedorov, Alexander V; Petukhov, Anatoly E; Vilkov, Oleg Yu; Rybkin, Artem G; Otrokov, Mikhail M; Arnau, Andrés; Chulkov, Evgueni V; Yashina, Lada V; Farjam, Mani; Adamchuk, Vera K; Senkovskiy, Boris V; Laubschat, Clemens; Vyalikh, Denis V

    2015-07-28

    Embedding foreign atoms or molecules in graphene has become the key approach in its functionalization and is intensively used for tuning its structural and electronic properties. Here, we present an efficient method based on chemical vapor deposition for large scale growth of boron-doped graphene (B-graphene) on Ni(111) and Co(0001) substrates using carborane molecules as the precursor. It is shown that up to 19 at. % of boron can be embedded in the graphene matrix and that a planar C-B sp(2) network is formed. It is resistant to air exposure and widely retains the electronic structure of graphene on metals. The large-scale and local structure of this material has been explored depending on boron content and substrate. By resolving individual impurities with scanning tunneling microscopy we have demonstrated the possibility for preferential substitution of carbon with boron in one of the graphene sublattices (unbalanced sublattice doping) at low doping level on the Ni(111) substrate. At high boron content the honeycomb lattice of B-graphene is strongly distorted, and therefore, it demonstrates no unballanced sublattice doping. PMID:26121999

  1. Nanoimaging and ultra structure of Entamoeba histolytica and its pseudopods by using atomic force microscope

    Science.gov (United States)

    Joshi, Narahari V.; Medina, Honorio; Urdaneta, H.; Barboza, J.

    2000-04-01

    Nan-imaging of Entamoeba histolytica was carried out by using Atomic Force Microscope (AFM). The structure of the nucleus, endoplasm and ectoplasm were studied separately. The diameter of the nucleus in living E. histolytica was found to be of the order of 10 micrometers which is slightly higher than the earlier reported value. The presence of karysome was detected in the nucleus. Well-organized patterns of chromatoid bodies located within the endoplasm, were detected and their repetitive patterns were examined. The organized structure was also extended within the ectoplasm. The dimensions and form of the organization suggest that chromatic bodies are constituted with ribosomes ordered in the form of folded sheet. Such structures were found to be absent in non-living E. histolytica. AFM images were also captured just in the act when ameba was extending its pseudopods. Alteration in the ultrastructure caused during the process of extension was viewed. Well marked canals of width 694.05 nm. And height 211.05 nm are clearly perceptible towards the direction of the pseudopods. 3D images are presented to appreciate the height variation, which can not be achieved by conventional well-established techniques such as electron microscopy.

  2. The Structure of Light Nuclei and Its Effect on Precise Atomic Measurements

    OpenAIRE

    Friar, J. L.

    2002-01-01

    My talk will consist of three parts: (a) what every atomic physicist needs to know about the physics of light nuclei [and no more]; (b) what nuclear physicists can do for atomic physics; (c) what atomic physicists can do for nuclear physics. A brief qualitative overview of the nuclear force and calculational techniques for light nuclei will be presented, with an emphasis on debunking myths and on recent progress in the field. Nuclear quantities that affect precise atomic measurements will be ...

  3. The Structure of Light Nuclei and Its Effect on Precise Atomic Measurements

    OpenAIRE

    Friar, J. L.

    2002-01-01

    This review consists of three parts: (a) what every atomic physicist needs to know about the physics of light nuclei; (b) what nuclear physicists can do for atomic physics; (c) what atomic physicists can do for nuclear physics. A brief qualitative overview of the nuclear force and calculational techniques for light nuclei will be presented, with an emphasis on debunking myths and on recent progress in the field. Nuclear quantities that affect precise atomic measurements will be discussed, tog...

  4. Atomically resolved FeSe/SrTiO3(001) interface structure by scanning transmission electron microscopy

    Science.gov (United States)

    Li, Fangsen; Zhang, Qinghua; Tang, Chenjia; Liu, Chong; Shi, Jinan; Nie, CaiNa; Zhou, Guanyu; Li, Zheng; Zhang, Wenhao; Song, Can-Li; He, Ke; Ji, Shuaihua; Zhang, Shengbai; Gu, Lin; Wang, Lili; Ma, Xu-Cun; Xue, Qi-Kun

    2016-06-01

    Interface-enhanced high-temperature superconductivity in one unit-cell FeSe films on SrTiO3(001) (STO) substrate has recently attracted much attention in condensed matter physics and material science. By combined in situ scanning tunneling microscopy/spectroscopy and ex situ scanning transmission electron microscopy studies, we report on atomically resolved structure including both lattice constants and actual atomic positions of the FeSe/STO interface under both non-superconducting and superconducting states. We observed TiO2 double layers and significant atomic displacements in the top two layers of STO, lattice compression of the Se-Fe-Se triple layer, and relative shift between bottom Se and topmost Ti atoms. By imaging the interface structures under various superconducting states, we unveil a close correlation between interface structure and superconductivity. Our atomic-scale identification of FeSe/STO interface structure provides insight on investigating the pairing mechanism of this interface-enhanced high-temperature superconducting system.

  5. Molecular Dynamics Simulation of Atomic Force Microscopy at the Water-Muscovite Interface: Hydration Layer Structure and Force Analysis.

    Science.gov (United States)

    Kobayashi, Kazuya; Liang, Yunfeng; Amano, Ken-Ichi; Murata, Sumihiko; Matsuoka, Toshifumi; Takahashi, Satoru; Nishi, Naoya; Sakka, Tetsuo

    2016-04-19

    With the development of atomic force microscopy (AFM), it is now possible to detect the buried liquid-solid interfacial structure in three dimensions at the atomic scale. One of the model surfaces used for AFM is the muscovite surface because it is atomically flat after cleavage along the basal plane. Although it is considered that force profiles obtained by AFM reflect the interfacial structures (e.g., muscovite surface and water structure), the force profiles are not straightforward because of the lack of a quantitative relationship between the force and the interfacial structure. In the present study, molecular dynamics simulations were performed to investigate the relationship between the muscovite-water interfacial structure and the measured AFM force using a capped carbon nanotube (CNT) AFM tip. We provide divided force profiles, where the force contributions from each water layer at the interface are shown. They reveal that the first hydration layer is dominant in the total force from water even after destruction of the layer. Moreover, the lateral structure of the first hydration layer transcribes the muscovite surface structure. It resembles the experimentally resolved surface structure of muscovite in previous AFM studies. The local density profile of water between the tip and the surface provides further insight into the relationship between the water structure and the detected force structure. The detected force structure reflects the basic features of the atomic structure for the local hydration layers. However, details including the peak-peak distance in the force profile (force-distance curve) differ from those in the density profile (density-distance curve) because of disturbance by the tip. PMID:27018633

  6. Determination of interfacial atomic structure, misfits and energetics of Ω phase in Al–Cu–Mg–Ag alloy

    International Nuclear Information System (INIS)

    The interfacial atomic structure and misfits of Ω precipitates formed in the face-centered cubic Al in the Al–Cu–Mg–Ag alloy have been determined by combining scanning transmission electron microscopy (STEM) Z-contrast imaging with chemical analysis and ab initio density functional theory (DFT) calculations. Precipitates of several thicknesses formed after heat treatment at 250 °C, starting from 0 to 2 unit cells of Ω phase, were examined by STEM in four different projections. The results show that a remarkably stable double-layered interface is formed at all observed thicknesses, which separates the Ω phase from the Al matrix. The outermost interfacial layer next to Al is composed of Ag atoms in a hexagonal structure and Mg or Cu atoms below the center of the hexagon. Structural models constructed based on the experimental data were relaxed using DFT-based molecular dynamics calculations. The results show that interfacial Mg atoms, together with Ag atoms, greatly stabilize the interface structure and consequently the Ω phase on the Al {1 1 1} habit planes. Comparison between the measured and calculated precipitate misfit along the thickness direction suggests that atomic substitutions of light atoms, Al and Mg, at the interface mediate the misfit strain and free energy, which is further supported by experimental evidence obtained from STEM. Thus, we have identified here: (i) the driving force for the Ag and Mg segregation in the formation of the Ω phase; (ii) the precipitation sequence characterized by a stable interfacial double-layer; and (iii) an interfacial substitution mechanism for misfit accommodation

  7. Raman spectroscopy as a tool to investigate the structure and electronic properties of carbon-atom wires

    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.

  8. A method for the calculation of collision strengths for complex atomic structures based on Slater parameter optimisation

    International Nuclear Information System (INIS)

    This report presents details of a new method to enable the computation of collision strengths for complex ions which is adapted from long established optimisation techniques previously applied to the calculation of atomic structures and oscillator strengths. The procedure involves the adjustment of Slater parameters so that they determine improved energy levels and eigenvectors. They provide a basis for collision strength calculations in ions where ab initio computations break down or result in reducible errors. This application is demonstrated through modifications of the DISTORTED WAVE collision code and SUPERSTRUCTURE atomic-structure code which interface via a transformation code JAJOM which processes their output. (author)

  9. Local Atomic Structure of Martensitic Ni$_{2+x}$Mn$_{1-x}$Ga: An EXAFS Study

    OpenAIRE

    Bhobe, P. A.; Priolkar, K. R.; Sarode, P R

    2006-01-01

    The local atomic structure of Ni$_{2+x}$Mn$_{1-x}$Ga with 0 $\\le$ $x$ $\\le$ 0.16 alloys was explored using Mn and Ga K-edge Extended X-ray Absorption Fine Structure (EXAFS) measurement. Inorder to study the atomic re-arrangements that occur upon martensitic transformation, room temperature and low temperature EXAFS were recorded. The changes occurring in the L2$_1$ unit cell and the bond lengths obtained from the analysis enables us to determine the modulation amplitudes over which the consti...

  10. Atomic structure and electronic properties of the SixSb100-x phase-change memory material

    DEFF Research Database (Denmark)

    Verma, Ashok K.; Modak, Paritosh; Svane, Axel;

    2011-01-01

    The electronic and structural properties of SixSb100-x (x∼16) materials are investigated using first-principles molecular dynamics simulations. Crystalline-liquid-amorphous phase transitions are examined and remarkable changes in the local structure around the Si atoms are found. The average Si...... coordination number 6 (3 long + 3 short Si-Sb bonds) of the crystalline phase changes to 4 (3 long Si-Sb + 1 short Si-Si bonds) by preserving three Si-Sb bonds in both the liquid and the amorphous phases. In the amorphous phase ∼90% of the Si atoms are fourfold coordinated compared to 40% in the liquid. The...

  11. Formation, atomic structure, and electronic properties of GaSb quantum dots in GaAs

    Energy Technology Data Exchange (ETDEWEB)

    Timm, R.

    2007-12-14

    In this work, cross-sectional scanning tunneling microscopy and spectroscopy are used for the first time to study the shape, size, strain, chemical composition, and electronic properties of capped GaSb/GaAs QDs at the atomic scale. By evaluating such structural results on a variety of nanostructures built using different epitaxy methods and growth conditions, details on the underlying QD formation processes can be revealed. A cross-over from flat quantum wells (QWs) to optically active QDs can be observed in samples grown by metalorganic chemical vapor deposition (MOCVD) with increasing amount of GaSb, including self-assembled Sb accumulations within a still two-dimensional layer and tiny three-dimensional GaSb islands probably acting as precursor structures. The QWs consist of significantly intermixed material with stoichiometries of maximally 50% GaSb, additionally exhibiting small gaps filled with GaAs. A higher GaSb content up to nearly pure material is found in the QDs, being characterized by small sizes of up to 8 nm baselength and about 2 nm height. In spite of the intermixing, all nanostructures have rather abrupt interfaces, and no significant Sb segregation in growth direction is observed. This changes completely when molecular beam epitaxy (MBE) is used as growth method, in which case individual Sb atoms are found to be distributed over several nm above the nanostructures. Massive group-V atomic exchange processes are causing this strong inter-mixing and Sb segregation during GaAs overgrowth. In combination with the large strain inherent to GaSb/GaAs QDs, this segregation upon overgrowth is assumed to be the reason for a unique structural phenomenon: All MBE-grown QDs, independent of the amount of deposited GaSb, exhibit a ring structure, consisting of a ring body of high GaSb content and a more or less extended central gap filled with GaAs. These rings have formed in a self-assembled way even when the initial GaSb layer was overgrown considerably fast

  12. Atomic and electronic structure of hydrogen on ZnO (1bar 100) surface: ab initio hybrid calculations

    Science.gov (United States)

    Usseinov, A. B.; Kotomin, E. A.; Zhukovskii, Yu F.; Purans, J.; Sorokin, A. V.; Akilbekov, A. T.

    2013-12-01

    Hydrogen atoms unavoidably incorporated into ZnO during growth of bulk samples and thin films considerably affect their electrical conductivity. The results of first principles hybrid LCAO calculations are discussed for hydrogen atoms in the bulk and on the non-polar ZnO (1bar 100) surface. The incorporation energy, the atomic relaxation, the electronic density redistribution and the electronic structure modifications are compared for the surface adsorption and bulk interstitial H positions. It is shown that hydrogen has a strong binding with the surface O ions (2.7 eV) whereas its incorporation into bulk is energetically unfavorable. Surface hydrogen atoms are very shallow donors, thus, contributing to the electronic conductivity.

  13. 2nd International Symposium "Atomic Cluster Collisions : Structure and Dynamics from the Nuclear to the Biological Scale"

    CERN Document Server

    Solov'yov, Andrey; ISACC 2007; Latest advances in atomic cluster collisions

    2008-01-01

    This book presents a 'snapshot' of the most recent and significant advances in the field of cluster physics. It is a comprehensive review based on contributions by the participants of the 2nd International Symposium on Atomic Cluster Collisions (ISACC 2007) held in July 19-23, 2007 at GSI, Darmstadt, Germany. The purpose of the Symposium is to promote the growth and exchange of scientific information on the structure and properties of nuclear, atomic, molecular, biological and complex cluster systems studied by means of photonic, electronic, heavy particle and atomic collisions. Particular attention is devoted to dynamic phenomena, many-body effects taking place in cluster systems of a different nature - these include problems of fusion and fission, fragmentation, collective electron excitations, phase transitions, etc.Both the experimental and theoretical aspects of cluster physics, uniquely placed between nuclear physics on the one hand and atomic, molecular and solid state physics on the other, are discuss...

  14. Atomic force microscopy of collagen structure in bone and dentine revealed by osteoclastic resorption

    International Nuclear Information System (INIS)

    Mineralised tissues such as bone consist of two material phases: collagen protein fibrils, secreted by osteoblasts, form model structures for subsequent deposition of mineral, calcium hydroxyapatite. Collagen and mineral are removed in a three-dimensional manner by osteoclasts during bone turnover in skeletal growth or repair. Bone active drugs have recently been developed for skeletal diseases, and there is revived interest in changes in the structure of mineralised tissues seen in disease and upon treatment. The resolution of atomic force microscopy and use of unmodified samples has enabled us to image bone and dentine collagen exposed by the natural process of cellular dissolution of mineralised matrix. The morphology of bone and dentine has been analysed when fully mineralised and after osteoclast-mediated bone resorption, and compared with results from other microscopy techniques. Banded type I collagen, with 66.5±1.4 nm axial D-periodicity and 62.2±7.0 nm diameter, has been identified within resorption lacunae in bone and 69.4±4.3 nm axial D-periodicity and 140.6±12.4 nm diameter in dentine substrates formed by human and rabbit osteoclasts, respectively. This observation suggests a route by which the material and morphological properties of bone collagen can be analysed in situ, compared with collagen from non-skeletal sites, and contrasted in diseases of medical importance, such as osteoporosis, where skeletal tissue is mechanically weakened

  15. Surface Structure of Lithium Doped Potassium Tantalate (KLT) using Helium Atom Scattering.

    Energy Technology Data Exchange (ETDEWEB)

    Fatema, Rifat [Florida State University; Van Winkle, David [Florida State University; Skofronick, J. G. [Florida State University; Sanfron, Sanford a [Department of Chemistry and Biochemistry, Florida State University; Flaherty, F. A. [Valdosta State University, Valdosta, GA; Boatner, Lynn A [ORNL

    2013-01-01

    The structures of the (001) surface of potassium tantalate doped with nominally 2, 4 and 7% lithium have been investigated using high resolution helium atom scattering. The surfaces were prepared by cleaving single crystal samples in situ under UHV conditions. Diraction measurements in the region around the He specular re ection angle soon after cleaving yielded specular peaks initially with broad shoulders. However, over a period of about an hour, the widths of these specular peaks decreased markedly as the shoulders diminished into the background. Drift spectra measurements of the stabilized surfaces revealed that the step heights separating surface terraces were predominantly multiples of the cubic unit cell dimension, about 4A, rather than multiples of a half unit cell, 2A, expected from the cleaving of these crystals. Together these results suggest that after cleaving these surfaces are rapidly modied by migration of ions to the surface from the near-surface. Further, half-order diraction peaks were observed in the <100> azimuth a short time after cleaving samples at room temperature, indicating that domains with (21) structure had formed.

  16. Chiral Nematic Structure of Cellulose Nanocrystal Suspensions and Films; Polarized Light and Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Derek G. Gray

    2015-11-01

    Full Text Available Cellulosic liquid crystalline solutions and suspensions form chiral nematic phases that show a rich variety of optical textures in the liquid crystalline state. These ordered structures may be preserved in solid films prepared by evaporation of solvent or suspending medium. Film formation from aqueous suspensions of cellulose nanocrystals (CNC was investigated by polarized light microscopy, optical profilometry and atomic force microscopy (AFM. An attempt is made to interpret qualitatively the observed textures in terms of the orientation of the cellulose nanocrystals in the suspensions and films, and the changes in orientation caused by the evaporative process. Mass transfer within the evaporating droplet resulted in the formation of raised rings whose magnitude depended on the degree of pinning of the receding contact line. AFM of dry films at short length scales showed a radial orientation of the CNC at the free surface of the film, along with a radial height variation with a period of approximately P/2, ascribed to the anisotropic shrinkage of the chiral nematic structure.

  17. Atomic structure and crystallization processes of amorphous (Co,Ni)–P metallic alloy

    Energy Technology Data Exchange (ETDEWEB)

    Modin, Evgeny B., E-mail: modin.eb@dvfu.ru [Far Eastern Federal University, Shukhanova 8, Vladivostok 690950 (Russian Federation); Pustovalov, Evgeny V.; Fedorets, Aleksander N.; Dubinets, Aleksander V.; Grudin, Boris N.; Plotnikov, Vladimir S. [Far Eastern Federal University, Shukhanova 8, Vladivostok 690950 (Russian Federation); Grabchikov, Sergey S. [Scientific and Practical Centre of Material Science, Belarus National Academy of Sciences, P. Brovki 19, Minsk 220072 (Belarus)

    2015-08-25

    Highlights: • The CoP–CoNiP amorphous alloys were studied by the Cs-corrected high resolution transmission electron microscopy. • In situ heating experiments showed that crystallization starts at 200–250 °C on the network frame and cell boundaries. • Crystal growth occurs at the free surface, then the remaining material in the volume is crystallized. • Adding nickel to the CoP alloy leads to higher thermal stability. • At the beginning of crystallization there are high diffusion coefficients, 1.2–2.4 ∗ 10{sup −18} m{sup 2}/s at 250 °C. - Abstract: This work concerns the in situ investigation of the atomic structure of (Co,Ni)–P alloys during relaxation and crystallization by high resolution transmission electron microscopy. The CoP–CoNiP alloys, in the initial state, have a hierarchical network-like disordered structure. Crystallization starts at 200–250 °C on the network frame and cell boundaries. In the early stages, crystal growth occurs at the free surface, then the remaining material in the volume is crystallized. The diffusion coefficient at the start of crystallization is 1.2–2.4 × 10{sup −18} m{sup 2}/s at 250 °C and we assume that the high diffusion speed is due to surface diffusion.

  18. Distortions of the calcite and aragonite atomic structures from interstitial water

    International Nuclear Information System (INIS)

    Amorphous calcium carbonate (ACC), as observed by diffraction or infra-red spectroscopy, is especially significant as a precursor in biomineralization. The atomic structure and mechanisms for transformation to the crystalline phases are still unknown. It is conceivable that insertion of water molecules could give rise to distortions that result in the observed diffraction patterns and infrared spectra. We use the VASP density functional theory code to relax model supercells with 24 formula units of CaCO3 where we have inserted up to 5 water molecules, corresponding to 3.75 wt%. The main effect is tilting of the carbonate planes, which can be as high as 50°. This leads to a range of Ca–O distances that are consistent with the observed changes in the IR spectra in ACC. The spread in cation–cation distances is not enough to destroy coherent diffraction from regions 70 nm across, and so does not explain amorphous diffraction profiles. - Highlights: • Low concentrations of water in the calcite or aragonite structures lead to tilting of the carbonate planes. • This is consistent with IR observations from amorphous calcium carbonate. • It does not explain amorphous diffraction patterns

  19. Local atomic and electronic structure of boron chemical doping in monolayer graphene.

    Science.gov (United States)

    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

    2013-10-01

    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. PMID:24032458

  20. Electronic and atomic structure modifications of copper nitride films by ion impact and phase separation

    International Nuclear Information System (INIS)

    We have studied electronic and atomic structure modifications of Cu3N films under 100 keV Ne and 100 MeV Xe ion impact. Cu3N films were prepared on R(11-2 surface)-cut-Al2O3 substrates at 250 deg. C by using a RF-magnetron sputter deposition method. X-ray diffraction (XRD) shows that unirradiated films are polycrystalline with (1 0 0) orientation of cubic structure. We find that the electrical resistivity (∼10 Ω cm before ion impact) decreases by more than two orders of magnitude after the Ne impact at a fluence of ∼1013 cm-2, where no Cu phase separation is observed. For further ion impact (larger than ∼1015 cm-2), XRD shows Cu diffraction peak (Cu phase separation), and the resistivity decreases further (three orders of magnitude). Decomposition and phase separation are discussed based on these results, as well as temperature dependence of the resistivity and optical absorption. The results of 100 MeV Xe ion impact are compared with those of Ne ion impact.

  1. Electronic and atomic structure modifications of copper nitride films by ion impact and phase separation

    Energy Technology Data Exchange (ETDEWEB)

    Matsunami, N. [EcoTopia Science Institute (ESI), Nagoya University, Nagoya 464-8603 (Japan)], E-mail: n-matsunami@esi.nagoya-u.ac.jp; Kakiuchida, H.; Tazawa, M. [National Institute of Advanced Industrial Science and Technology (AIST), Nagoya 463-8650 (Japan); Sataka, M.; Sugai, H.; Okayasu, S. [Japan Atomic Energy Agency (JAEA), Tokai 319-1195 (Japan)

    2009-08-15

    We have studied electronic and atomic structure modifications of Cu{sub 3}N films under 100 keV Ne and 100 MeV Xe ion impact. Cu{sub 3}N films were prepared on R(11-2 surface)-cut-Al{sub 2}O{sub 3} substrates at 250 deg. C by using a RF-magnetron sputter deposition method. X-ray diffraction (XRD) shows that unirradiated films are polycrystalline with (1 0 0) orientation of cubic structure. We find that the electrical resistivity ({approx}10 {omega} cm before ion impact) decreases by more than two orders of magnitude after the Ne impact at a fluence of {approx}10{sup 13} cm{sup -2}, where no Cu phase separation is observed. For further ion impact (larger than {approx}10{sup 15} cm{sup -2}), XRD shows Cu diffraction peak (Cu phase separation), and the resistivity decreases further (three orders of magnitude). Decomposition and phase separation are discussed based on these results, as well as temperature dependence of the resistivity and optical absorption. The results of 100 MeV Xe ion impact are compared with those of Ne ion impact.

  2. Groundwater Arsenic Adsorption on Granular TiO2: Integrating Atomic Structure, Filtration, and Health Impact.

    Science.gov (United States)

    Hu, Shan; Shi, Qiantao; Jing, Chuanyong

    2015-08-18

    A pressing challenge in arsenic (As) adsorptive filtration is to decipher how the As atomic surface structure obtained in the laboratory can be used to accurately predict the field filtration cycle. The motivation of this study was therefore to integrate molecular level As adsorption mechanisms and capacities to predict effluent As from granular TiO2 columns in the field as well as its health impacts. Approximately 2,955 bed volumes of groundwater with an average of 542 μg/L As were filtered before the effluent As concentration exceeded 10 μg/L, corresponding to an adsorption capacity of 1.53 mg As/g TiO2. After regeneration, the TiO2 column could treat 2,563 bed volumes of groundwater, resulting in an As load of 1.36 mg/g TiO2. Column filtration and EXAFS results showed that among coexisting ions present in groundwater, only Ca(2+), Si(OH)4, and HCO3(-) would interfere with As adsorption. The compound effects of coexisting ions and molecular level structural information were incorporated in the PHREEQC program to satisfactorily predict the As breakthrough curves. The total urinary As concentration from four volunteers of local residences, ranging from 972 to 2,080 μg/L before groundwater treatment, decreased to the range 31.7-73.3 μg/L at the end of the experimental cycle (15-33 days). PMID:26198737

  3. Atomic structure of a rhinovirus C, a virus species linked to severe childhood asthma.

    Science.gov (United States)

    Liu, Yue; Hill, Marchel G; Klose, Thomas; Chen, Zhenguo; Watters, Kelly; Bochkov, Yury A; Jiang, Wen; Palmenberg, Ann C; Rossmann, Michael G

    2016-08-01

    Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma exacerbations. The RV-C have been refractory to structure determination because they are difficult to propagate in vitro. Here, we report the cryo-EM atomic structures of the full virion and native empty particle (NEP) of RV-C15a. The virus has 60 "fingers" on the virus outer surface that probably function as dominant immunogens. Because the NEPs also display these fingers, they may have utility as vaccine candidates. A sequence-conserved surface depression adjacent to each finger forms a likely binding site for the sialic acid on its receptor. The RV-C, unlike other EVs, are resistant to capsid-binding antiviral compounds because the hydrophobic pocket in VP1 is filled with multiple bulky residues. These results define potential molecular determinants for designing antiviral therapeutics and vaccines. PMID:27511920

  4. Distortions of the calcite and aragonite atomic structures from interstitial water

    Energy Technology Data Exchange (ETDEWEB)

    Sinha, S.; Rez, P., E-mail: Peter.Rez@asu.edu

    2015-05-01

    Amorphous calcium carbonate (ACC), as observed by diffraction or infra-red spectroscopy, is especially significant as a precursor in biomineralization. The atomic structure and mechanisms for transformation to the crystalline phases are still unknown. It is conceivable that insertion of water molecules could give rise to distortions that result in the observed diffraction patterns and infrared spectra. We use the VASP density functional theory code to relax model supercells with 24 formula units of CaCO{sub 3} where we have inserted up to 5 water molecules, corresponding to 3.75 wt%. The main effect is tilting of the carbonate planes, which can be as high as 50°. This leads to a range of Ca–O distances that are consistent with the observed changes in the IR spectra in ACC. The spread in cation–cation distances is not enough to destroy coherent diffraction from regions 70 nm across, and so does not explain amorphous diffraction profiles. - Highlights: • Low concentrations of water in the calcite or aragonite structures lead to tilting of the carbonate planes. • This is consistent with IR observations from amorphous calcium carbonate. • It does not explain amorphous diffraction patterns.

  5. Atomic structure and crystallization processes of amorphous (Co,Ni)–P metallic alloy

    International Nuclear Information System (INIS)

    Highlights: • The CoP–CoNiP amorphous alloys were studied by the Cs-corrected high resolution transmission electron microscopy. • In situ heating experiments showed that crystallization starts at 200–250 °C on the network frame and cell boundaries. • Crystal growth occurs at the free surface, then the remaining material in the volume is crystallized. • Adding nickel to the CoP alloy leads to higher thermal stability. • At the beginning of crystallization there are high diffusion coefficients, 1.2–2.4 ∗ 10−18 m2/s at 250 °C. - Abstract: This work concerns the in situ investigation of the atomic structure of (Co,Ni)–P alloys during relaxation and crystallization by high resolution transmission electron microscopy. The CoP–CoNiP alloys, in the initial state, have a hierarchical network-like disordered structure. Crystallization starts at 200–250 °C on the network frame and cell boundaries. In the early stages, crystal growth occurs at the free surface, then the remaining material in the volume is crystallized. The diffusion coefficient at the start of crystallization is 1.2–2.4 × 10−18 m2/s at 250 °C and we assume that the high diffusion speed is due to surface diffusion

  6. Characterization of iron ferromagnetism by the local atomic volume: from three-dimensional structures to isolated atoms

    Czech Academy of Sciences Publication Activity Database

    Zhang, L.; Šob, Mojmír; Wu, Z.; Zhang, Y.; Lu, G-H.

    2014-01-01

    Roč. 26, č. 8 (2014), 086002-1-086002-17. ISSN 0953-8984 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP108/12/0311; GA AV ČR IAA100100920 Institutional support: RVO:68081723 Keywords : electronic structure * magnetism * iron * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.346, year: 2014

  7. Atomic structure of shear bands in Cu64Zr36 metallic glasses studied by molecular dynamics simulations

    International Nuclear Information System (INIS)

    Graphical abstract: Figure shows that atoms in the shear band (SB) moved desultorily compared with those in the matrix. These atoms seriously interacted with each other similar to the grain boundary in crystalline materials. Figuratively, if these atoms wanted to “pass” the shear band, they should arrange their irritations. However, stress concentrations and high energy were observed in SB, which resulted in instability in the deformation process and finally led to a disastrously brittle fracture. - Abstract: Molecular dynamics simulations on the atomic structure of shear bands (SBs) in Cu64Zr36 metallic glasses are presented. Results show that the atoms in the SB move desultorily, in contrast to those in the matrix. The saturated degree of bonded pairs considering the “liquid-like” character of SB quantitatively provides important details in extending earlier studies on SBs. Zr-centered 〈0, 2, 8, 5〉 clusters exhibit strong spatial correlations and tendency to connect with each other in short-range order. The 〈0, 2, 8, 5〉 cluster-type medium-range order is the main feature inside the SB relative to the matrix. The fractal results demonstrate the planar-like fashion of the 〈0, 2, 8, 5〉 network in SB, forming an interpenetrating solid-like backbone. Such heterogeneous structure provides a fundamental structural perspective of mechanical instability in SB

  8. Atomic-level structure characterization of an ultrafast folding mini-protein denatured state.

    Directory of Open Access Journals (Sweden)

    Per Rogne

    Full Text Available Atomic-level analyses of non-native protein ensembles constitute an important aspect of protein folding studies to reach a more complete understanding of how proteins attain their native form exhibiting biological activity. Previously, formation of hydrophobic clusters in the 6 M urea-denatured state of an ultrafast folding mini-protein known as TC5b from both photo-CIDNP NOE transfer studies and FCS measurements was observed. Here, we elucidate the structural properties of this mini-protein denatured in 6 M urea performing (15N NMR relaxation studies together with a thorough NOE analysis. Even though our results demonstrate that no elements of secondary structure persist in the denatured state, the heterogeneous distribution of R(2 rate constants together with observing pronounced heteronuclear NOEs along the peptide backbone reveals specific regions of urea-denatured TC5b exhibiting a high degree of structural rigidity more frequently observed for native proteins. The data are complemented with studies on two TC5b point mutants to verify the importance of hydrophobic interactions for fast folding. Our results corroborate earlier findings of a hydrophobic cluster present in urea-denatured TC5b comprising both native and non-native contacts underscoring their importance for ultra rapid folding. The data assist in finding ways of interpreting the effects of pre-existing native and/or non-native interactions on the ultrafast folding of proteins; a fact, which might have to be considered when defining the starting conditions for molecular dynamics simulation studies of protein folding.

  9. The structure and stability of phospholipid bilayers by atomic force microscopy.

    Science.gov (United States)

    Hui, S W; Viswanathan, R; Zasadzinski, J A; Israelachvili, J N

    1995-01-01

    Atomic force microscopy (AFM) was used to investigate the structure, stability, and defects of the hydrophilic surfaces of Langmuir-Blodgett bilayer films of distearoylphosphatidylcholine (DSPC) and dipalmitoylphosphatidylethanolamine (DPPE) in the solid phase, and dilinoleoylphosphatidylethanolamine (DLPE) in the fluid phase. Their relative resilience to external mechanical stress by the scanning tip and by fluid exchange were also investigated. DPPE monolayers showed parallel ridges at the surface with a period of 0.49 nm, corresponding to the rows of aligned headgroups consistent with the known crystallographic structure. DSPC and DLPE monolayers did not show any periodic order. The solid DSPC and DPPE monolayers were stable to continued rastering by the AFM tip; however, the stability of DLPE monolayers depended on the pH of the aqueous environment. Structural defects in the form of monolayer gaps and holes were observed after fluid exchange, but the defects in DLPE monolayer at pH 11 were stable during consecutive scanning. At pH 9 and below, the defects induced by fluid exchange over DLPE monolayers were more extensive and were deformed easily by consecutive scanning of the AFM tip at a force of 10 nN. The pH dependence of resilience was explained by the increasing bending energy or frustration due to the high spontaneous curvature of DLPE monolayers at low pH. The tangential stress exerted by the AFM tip on the deformable monolayers eventually produced a ripple pattern, which could be described as a periodic buckling known as Shallamach waves. PMID:7711239

  10. Magnetically driven anisotropic structural changes in the atomic laminate M n2GaC

    Science.gov (United States)

    Dahlqvist, M.; Ingason, A. S.; Alling, B.; Magnus, F.; Thore, A.; Petruhins, A.; Mockute, A.; Arnalds, U. B.; Sahlberg, M.; Hjörvarsson, B.; Abrikosov, I. A.; Rosen, J.

    2016-01-01

    Inherently layered magnetic materials, such as magnetic Mn +1A Xn (MAX) phases, offer an intriguing perspective for use in spintronics applications and as ideal model systems for fundamental studies of complex magnetic phenomena. The MAX phase composition Mn+1A Xn consists of Mn +1Xn blocks separated by atomically thin A -layers where M is a transition metal, A an A-group element, X refers to carbon and/or nitrogen, and n is typically 1, 2, or 3. Here, we show that the recently discovered magnetic M n2GaC MAX phase displays structural changes linked to the magnetic anisotropy, and a rich magnetic phase diagram which can be manipulated through temperature and magnetic field. Using first-principles calculations and Monte Carlo simulations, an essentially one-dimensional (1D) interlayer plethora of two-dimensioanl (2D) Mn-C-Mn trilayers with robust intralayer ferromagnetic spin coupling was revealed. The complex transitions between them were observed to induce magnetically driven anisotropic structural changes. The magnetic behavior as well as structural changes dependent on the temperature and applied magnetic field are explained by the large number of low energy, i.e., close to degenerate, collinear and noncollinear spin configurations that become accessible to the system with a change in volume. These results indicate that the magnetic state can be directly controlled by an applied pressure or through the introduction of stress and show promise for the use of M n2GaC MAX phases in future magnetoelectric and magnetocaloric applications.

  11. Comparative semi-empirical and ab initio atomic structure calculations in Yb-like tungsten W4+

    International Nuclear Information System (INIS)

    In this paper, we report on extensive calculations of radiative data in Yb-like tungsten ion using several independent atomic structure methods, i.e. the relativistic Hartree–Fock approach, the flexible atomic code and the multiconfiguration Dirac–Fock method. This multi-platform approach allowed us to check the consistency of our results. Advantages and shortcomings of semi-empirical and ab initio methods for atomic structure calculations in such a complex heavy ion are also discussed in detail. A new set of transition probabilities and oscillator strengths is reported for electric dipole lines together with magnetic dipole and electric quadrupole lines in this ion of interest for fusion plasma diagnostics. (paper)

  12. Packing schemes of cavities in selected clathrasils and zeolites and the analogous packings of atoms in crystal structures

    DEFF Research Database (Denmark)

    Hem, Caroline Piper; Makovicky, Emil; Balic Zunic, Tonci

    2010-01-01

    ] cages, associated with other cavity types. The packing of cavities in melanophlogite is analogous to the packing of atoms in the structure of Cr3Si, where the Cr atoms form icosahedra around the Si sites. Dodecasil 3C has a cubic arrangement of [512] cavities, which is described as ABC stacking of...... kagome nets and its cavity packing is an analog to the packing scheme of atoms in the cubic Laves phase MgCu2. Dodecasil 1H has an arrangement of [512] cavities in an AA stacking of kagome nets and is analogous to the alloy structure type CaZn5. Edingtonite and natrolite are built from two types of...

  13. Atomic structure and pressure-induced phase transformations in a phase-change alloy

    Science.gov (United States)

    Xu, Ming

    Phase-change materials exist in at least two phases under the ambient condition. One is the amorphous state and another is crystalline phase. These two phases have vastly different physical properties, such as electrical conductivity, optical reflectivity, mass density, thermal conductivity, etc. The distinct physical properties and the fast transformation between amorphous and crystalline phases render these materials the ability to store information. For example, the DVD and the Blue-ray discs take advantage of the optical reflectivity contrast, and the newly developed solid-state memories make use of the large conductivity difference. In addition, both the amorphous and crystalline phases in phase-change memories (PCMs) are very stable at room temperature, and they are easy to be scaled up in the production of devices with large storage density. All these features make phase-change materials the ideal candidates for the next-generation memories. Despite of the fast development of these new memory materials in industry, many fundamental physics problems underlying these interesting materials are still not fully resolved. This thesis is aiming at solving some of the key issues in phase-change materials. Most of phase-change materials are composed of Ge-Sb-Te constituents. Among all these Ge-Sb-Te based materials, Ge2Sb2Te5 (GST) has the best performance and has been frequently studied as a prototypical phase-change material. The first and foremost issue is the structure of the two functioning phases. In this thesis, we investigate the unique atomic structure and bonding nature of amorphous GST (a-GST) and crystalline GST ( c-GST), using ab initio tools and X-ray diffraction (XRD) methods. Their local structures and bonding scenarios are then analyzed using electronic structure calculations. In order to gain insight into the fast phase transformation mechanism, we also carried out a series of high-pressure experiments on GST. Several new polymorphs and their

  14. How in Spite of the Rhetoric, History of Chemistry Has Been Ignored in Presenting Atomic Structure in Textbooks.

    Science.gov (United States)

    Rodriguez, Maria A.; Niaz, Mansoor

    2002-01-01

    Reports on a study designed to: (a) show how the importance of the history of chemistry has been recognized in the classroom; (b) demonstrate how criteria based on history and philosophy of science can be used to evaluate the presentation of atomic structure in general chemistry textbooks; and (c) compare new (1970-1992) and old textbooks…

  15. Students' Representations of the Atomic Structure--The Effect of Some Individual Differences in Particular Task Contexts

    Science.gov (United States)

    Papageorgiou, George; Markos, Angelos; Zarkadis, Nikolaos

    2016-01-01

    The current study aims to investigate students' representations of the atomic structure in a number of student cohorts with specific characteristics concerning age, grade, class curriculum and some individual differences, such as formal reasoning and field dependence/independence. Two specific task contexts, which were designed in accordance with…

  16. Atomic structure of screw dislocations intersecting the Au(111) surface: A combined scanning tunneling microscopy and molecular dynamics study

    DEFF Research Database (Denmark)

    Engbæk, Jakob; Schiøtz, Jakob; Dahl-Madsen, Bjarke; Horch, Sebastian

    2006-01-01

    The atomic-scale structure of naturally occurring screw dislocations intersecting a Au(111) surface has been investigated both experimentally by scanning tunneling microscopy (STM) and theoretically using molecular dynamics (MD) simulations. The step profiles of 166 dislocations were measured using...

  17. Effect of Programmed Instruction on Students' Attitude towards Structure of the Atom and the Periodic Table among Kenyan Secondary Schools

    Science.gov (United States)

    Wangila, M. J.; Martin, W.; Ronald, M.

    2015-01-01

    This study examined the effect of Programmed Instruction on students' attitude towards Structure of the Atom and the Periodic Table (SAPT) among mixed (co-educational) secondary schools of Butere district, Kakamega county, Kenya. The quasi-experimental research design was adopted, using the nonrandomized Solomon four-group as a model. The sample…

  18. Some consequences of a Universal Tension arising from Dark Energy for structures from Atomic Nuclei to Galaxy Clusters

    CERN Document Server

    Sivaram, C; V., Kiren O

    2013-01-01

    In recent work, a new cosmological paradigm implied a mass-radius relation, suggesting a universal tension related to the background dark energy (cosmological constant), leading to an energy per unit area that holds for structures from atomic nuclei to clusters of galaxies. Here we explore some of the consequences that arise from such a universal tension.

  19. Semiconductor microfabrication and ultraprecise quantum dots by atom manipulation. 2. Finish. Semiconductor quantum structure with exact fidelity

    International Nuclear Information System (INIS)

    This paper introduces a latest experiment, where the preparation of ultraprecise quantum dots without error of even one atom and their integration were successfully made. In an experiment of In atoms (N=6), the observed spectral peak showed the quantum level, where free electronic state of InAs side as a substrate was formed by being trapped inside the potential well. In addition, it was suggested that there was surface electron accumulation layer on InAs substrate surface. When double quantum dot molecules were formed using two ultraprecise quantum dots (N=6), new molecule like electronic states of bonding and antibonding character were formed, through the interaction between electronic states in each quantum dot, as if the case of two hydrogen (H) atoms to form H2 molecule. The illustrated local electron density of state (electron existence probability distribution) image was visualized by utilizing the magnitude of differential conductance (dI/dV) in the tunnel current. This study also examined the trimers that used three ultraprecise quantum dots (N=6). It was shown that in the ultraprecise structure due to atomic manipulation, the circuit using electron effect has a potential to be operated at room temperature, by embedding the atomically manipulated atoms on the substrate side. (J.P.N.)

  20. Effects of atomic geometry and electronic structure of platinum surfaces on molecular adsorbates studied by gap-mode SERS.

    Science.gov (United States)

    Hu, Jian; Tanabe, Masahiro; Sato, Jun; Uosaki, Kohei; Ikeda, Katsuyoshi

    2014-07-23

    Surface enhanced Raman scattering (SERS) spectra of organic monolayers were measured on various types of polycrystalline and single crystalline Pt substrates with nanometric or atomic surface features, including heteroepitaxial Pt monolayers, using sphere-plane type nanogap structures. Although atomic geometry and electronic structures of a metal surface significantly influence metal-molecule interactions, such effects are often hindered in conventional SERS measured on a roughened surface because of the spectral information averaging at various adsorption sites. In this study, the use of atomically defined Pt surfaces revealed detailed surface effects; the observed preferential adsorption geometry on each surface was well explained by atomic surface arrangements. The peak shift of the intramolecular vibration in the anchor group was in good agreement with the variation of the d-band center of Pt substrates. Moreover, in electrochemical SERS study the Stark shift of an extramolecular vibrational mode at around 400 cm(-1), which is not accessible in infrared absorption spectroscopy, was monitored on an atomically defined heteroepitaxial Pt monolayer electrode. PMID:24802029

  1. Weak links between fast mobility and local structure in molecular and atomic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Bernini, S. [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); Puosi, F. [Laboratoire de Physique de l’École Normale Supérieure de Lyon, UMR CNRS 5672, 46 allée d’Italie, 69007 Lyon (France); Leporini, D., E-mail: dino.leporini@df.unipi.it [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); IPCF-CNR, UOS Pisa, Pisa (Italy)

    2015-03-28

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  2. Lipid memberane:inelastic deformation of surface structure by an atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The stability of the 1,2-Dioleoyl-sn-Glycero-3-[phospho-rac-1-Glycerol-Na] liposome in the liquid crystalline state have been investigated using an atomic force microscope(AFM),We have observed the inelastic deformation of the sample surface,The AFM tip causes persistent deformation of the surface of the lipid membrane,in which some of the lipid molecules are eventually pushed or dragged by the AFM tip.The experiment shows how the surface structure of the lipid membrane can be created by the interaction between the AFM tip and lipid membrane.When the operating force exceeds 10-8N,it leads to large deformations of the surface.A squareregion of about 1×1um2 is created by the scanning probe on the surface,When the operating force is between 10-11N and 10-8N,it can image the topography of the surface of the lipid membrane.The stability of the sample is related to the concentration of the medium in which the sample is prepared.

  3. Lipid membrane: inelastic deformation of surface structure by an atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    张静; 孙润广

    2002-01-01

    The stability of the 1,2-Dioleoyl-sn-Glycero-3-[phospho-rac-1-Glycerol-Na] liposome in the liquid crystalline statehave been investigated using an atomic force microscope (AFM). We have observed the inelastic deformation of thesample surface. The AFM tip causes persistent deformation of the surface of the lipid membrane, in which some of thelipid molecules are eventually pushed or dragged by the AFM tip. The experiment shows how the surface structure ofthe lipid membrane can be created by the interaction between the AFM tip and lipid membrane. When the operatingforce exceeds 10-8 N, it leads to large deformations of the surface. A square region of about 1×1μm2 is created by thescanning probe on the surface. When the operating force is between 10-11N and 10-8N, it can image the topographyof the surface of the lipid membrane. The stability of the sample is related to the concentration of the medium in whichthe sample is prepared.

  4. The orbital minimization method for electronic structure calculations with finite-range atomic basis sets

    CERN Document Server

    Corsetti, Fabiano

    2014-01-01

    The implementation of the orbital minimization method (OMM) for solving the self-consistent Kohn-Sham (KS) problem for electronic structure calculations in a basis of non-orthogonal numerical atomic orbitals of finite-range is reported. We explore the possibilities for using the OMM as an exact cubic-scaling solver for the KS problem, and compare its performance with that of explicit diagonalization in realistic systems. We analyze the efficiency of the method depending on the choice of line search algorithm and on two free parameters, the scale of the kinetic energy preconditioning and the eigenspectrum shift. The results of several timing tests are then discussed, showing that the OMM can achieve a noticeable speedup with respect to diagonalization even for minimal basis sets for which the number of occupied eigenstates represents a significant fraction of the total basis size (>15%). We investigate the hard and soft parallel scaling of the method on multiple cores, finding a performance equal to or better ...

  5. Weak links between fast mobility and local structure in molecular and atomic liquids

    International Nuclear Information System (INIS)

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes

  6. Electronic structure calculations of atomic transport properties in uranium dioxide: influence of strong correlations

    International Nuclear Information System (INIS)

    Uranium dioxide UO2 is the standard nuclear fuel used in pressurized water reactors. During in-reactor operation, the fission of uranium atoms yields a wide variety of fission products (FP) which create numerous point defects while slowing down in the material. Point defects and FP govern in turn the evolution of the fuel physical properties under irradiation. In this study, we use electronic structure calculations in order to better understand the fuel behavior under irradiation. In particular, we investigate point defect behavior, as well as the stability of three volatile FP: iodine, krypton and xenon. In order to take into account the strong correlations of uranium 5f electrons in UO2, we use the DFT+U approximation, based on the density functional theory. This approximation, however, creates numerous metastable states which trap the system and induce discrepancies in the results reported in the literature. To solve this issue and to ensure the ground state is systematically approached as much as possible, we use a method based on electronic occupancy control of the correlated orbitals. We show that the DFT+U approximation, when used with electronic occupancy control, can describe accurately point defect and fission product behavior in UO2 and provide quantitative information regarding point defect transport properties in the oxide fuel. (author)

  7. Atomic structure of the i-R -Cd quasicrystals and consequences for magnetism

    Science.gov (United States)

    Yamada, T.; Takakura, H.; Kong, T.; Das, P.; Jayasekara, W. T.; Kreyssig, A.; Beutier, G.; Canfield, P. C.; de Boissieu, M.; Goldman, A. I.

    2016-08-01

    We report on the six-dimensional (6D) structural refinement of three members of the i-R -Cd quasicrystals (R = Gd, Dy, Tm) via synchrotron x-ray diffraction from single-grain samples, and show that this series is isostructural to the i-YbCd5.7 quasicrystal. However, our refinements suggest that the R occupancy on the Yb icosahedron sites within the Tsai-type atomic cluster is approximately 80%, with the balance taken up by Cd. Similarities between the i-R -Cd series and i-ScZn7.33, and their differences with i-YbCd5.7 and i-Ca15Cd85 , indicate that there are at least two subclasses of Tsai-type icosahedral quasicrystals. We further show from x-ray resonant magnetic scattering (XRMS) measurements on a set of closely related Tb1 -xYxCd6 1/1 approximants that the dilution of the magnetic R ions on the icosahedron within the Tsai-type cluster by nonmagnetic Y disrupts the commensurate magnetic ordering in the approximant phase.

  8. Anomalous Hyperfine Structure of the $^{229}$Th Ground-State Doublet in Muonic Atom

    CERN Document Server

    Tkalya, E V

    2016-01-01

    The hyperfine splitting of the ground and low-energy $3/2^+(7.8 \\pm 0.5$ eV) levels in the $^{229}$Th nucleus in muonic atom ($\\mu^-_{1S_{1/2}}{}^{229}$Th$)^*$ has been calculated considering the distribution of the nuclear magnetization in the framework of collective nuclear model with the wave functions of the Nilsson model for the unpaired neutron. It is shown that (a) the hyperfine splitting of the $3/2^+$ isomeric state is anomalously weak, and the reduction of hyperfine structure in comparison with the model of a point nuclear magnetic dipole is close to 100\\%, (b) partial inversion of levels of the $^{229}$Th ground-state doublet and spontaneous decay of the ground state with excitation of the isomeric state take place, (c) the energy of the isomeric transition lies in the range of 120--140 eV, which makes possible the direct observation of the transition, registration of conversion electrons and measurement of the nuclear matrix element.

  9. Arecibo Multi-Epoch HI Absorption Measurements Against Pulsars: Tiny-Scale Atomic Structure

    CERN Document Server

    Stanimirovic, S; Pei, Z; Tuttle, K; Green, J T

    2010-01-01

    We present results from multi-epoch neutral hydrogen (HI) absorption observations of six bright pulsars with the Arecibo telescope. Moving through the interstellar medium (ISM) with transverse velocities of 10--150 AU/yr, these pulsars have swept across 1--200 AU over the course of our experiment, allowing us to probe the existence and properties of the tiny scale atomic structure (TSAS) in the cold neutral medium (CNM). While most of the observed pulsars show no significant change in their HI absorption spectra, we have identified at least two clear TSAS-induced opacity variations in the direction of B1929+10. These observations require strong spatial inhomogeneities in either the TSAS clouds' physical properties themselves or else in the clouds' galactic distribution. While TSAS is occasionally detected on spatial scales down to 10 AU, it is too rare to be characterized by a spectrum of turbulent CNM fluctuations on scales of 10-1000 AU, as previously suggested by some work. In the direction of B1929+10, an...

  10. ARECIBO MULTI-EPOCH H I ABSORPTION MEASUREMENTS AGAINST PULSARS: TINY-SCALE ATOMIC STRUCTURE

    International Nuclear Information System (INIS)

    We present results from multi-epoch neutral hydrogen (H I) absorption observations of six bright pulsars with the Arecibo telescope. Moving through the interstellar medium (ISM) with transverse velocities of 10-150 AU yr-1, these pulsars have swept across 1-200 AU over the course of our experiment, allowing us to probe the existence and properties of the tiny-scale atomic structure (TSAS) in the cold neutral medium (CNM). While most of the observed pulsars show no significant change in their H I absorption spectra, we have identified at least two clear TSAS-induced opacity variations in the direction of B1929+10. These observations require strong spatial inhomogeneities in either the TSAS clouds' physical properties themselves or else in the clouds' galactic distribution. While TSAS is occasionally detected on spatial scales down to 10 AU, it is too rare to be characterized by a spectrum of turbulent CNM fluctuations on scales of 101-103 AU, as previously suggested by some work. In the direction of B1929+10, an apparent correlation between TSAS and interstellar clouds inside the warm Local Bubble (LB) indicates that TSAS may be tracing the fragmentation of the LB wall via hydrodynamic instabilities. While similar fragmentation events occur frequently throughout the ISM, the warm medium surrounding these cold cloudlets induces a natural selection effect wherein small TSAS clouds evaporate quickly and are rare, while large clouds survive longer and become a general property of the ISM.

  11. Anomalous magnetic hyperfine structure of the 229Th ground-state doublet in muonic atoms

    Science.gov (United States)

    Tkalya, E. V.

    2016-07-01

    The magnetic hyperfine (MHF) splitting of the ground and low-energy 3 /2+(7.8 ±0.5 eV) levels in the 229Th nucleus in the muonic atom (μ1S1 /2 -229Th) * is calculated considering the distribution of the nuclear magnetization in the framework of the collective nuclear model with wave functions of the Nilsson model for the unpaired neutron. It is shown that (a) deviation of the MHF structure of the isomeric state exceeds 100% from its value for a pointlike nuclear magnetic dipole (the order of sublevels is reversed); (b) partial inversion of levels of the 229Th ground-state doublet and spontaneous decay of the ground state to the isomeric state occur; (c) the E 0 transition, which is sensitive to differences in the mean-square charge radii of the doublet states, is possible between mixed sublevels with F =2 ; and (d) MHF splitting of the 3 /2+ isomeric state may be in the optical range for certain values of the intrinsic gK factor and a reduced probability of a nuclear transition between the isomeric and the ground states.

  12. Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys

    International Nuclear Information System (INIS)

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by “dynamic heterogeneity” in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract “cooperatively rearranging regions” of AG. We also find coexisting clusters of relatively “immobile” atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of “mobile” atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized (“immobile”) and wandering (“mobile”) particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations

  13. Investigation of structural change of purple membrane in storage by transmission electron microscope and atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The structural change of purple membrane during storage has been investigated by means of transmission electron microscope and atomic force microscope. It is found that many liposomes have spontaneously evolved from the purple membrane sheets isolated three years ago. The membrane proteins on the liposomes, bacteriorhodopsin, are still presented as trimers in 2-D hexagonal structure, which is the same as that in natural cell membrane. However, the cytoplasmic surface of purple membrane faced outside on the liposomes.

  14. Effect of atom dimension of metalloid on structure of metallic glasses Fe83M17 (M: C, B, P)

    International Nuclear Information System (INIS)

    With the use of molecular dynamics and static relaxation methods a computer experiment is accomplished aimed to study the influence of nonmetal atomic size on the structure of iron base amorphous alloys Fe83M17 (M - C, B, P). Experimental results show that the absence of vitrification in Fe-C binary alloys unlike easily vitrifying Fe-B and Fe-P alloys is explained by the occurrence of similar local structural units as in crystal so in amorphous states

  15. Novel mesoscale defect structure on NiO(1 0 0) surfaces by atomic force microscopy

    Science.gov (United States)

    Petitto, S. C.; Berrie, C. L.; Langell, M. A.

    2006-09-01

    Cleaved NiO(1 0 0) surfaces were imaged with atomic force microscopy (AFM) to determine defect concentrations and morphology. Random and oriented steps, which have been previously characterized, were the most common defect observed on the cleaved surface and formed with step heights in multiples of 2.1 Å, the Ni-O nearest-neighbor distance, and terrace widths in the range of 25-100 nm. In addition, the surface showed novel mesoscale (˜0.5-2 μm) square pyramidal defects with the pyramid base oriented along symmetry related directions. Upon etching, the pyramidal defects converted to more stable cubic pits, consistent with (1 0 0) symmetry related walls. The square pyramidal pits tended to cluster or to form along step edges, where the weakened structure is more susceptible to surface deformations. Also, a small concentration of square pyramidal pits, oriented with the base of the pyramid along , was observed on the cleaved NiO surfaces. For comparison purposes, chemical mechanical polished (CMP) NiO(1 0 0) substrates were imaged with AFM. Defect concentrations were of comparable levels to the cleaved surface, but showed a different distribution of defect types. Long-ranged stepped defects were much less common on CMP substrates, and the predominant defects observed were cubic pits with sidewalls steeper than could be accurately measured by the AFM tip. These defects were similar in size and structure to those observed on cleaved NiO(1 0 0) surfaces that had been acid etched, although pit clustering was more pronounced for the CMP surfaces.

  16. Electronic structure investigation of atomic layer deposition ruthenium(oxide) thin films using photoemission spectroscopy

    Science.gov (United States)

    Schaefer, Michael; Schlaf, Rudy

    2015-08-01

    Analyzing and manipulating the electronic band line-up of interfaces in novel micro- and nanoelectronic devices is important to achieve further advancement in this field. Such band alignment modifications can be achieved by introducing thin conformal interfacial dipole layers. Atomic layer deposition (ALD), enabling angstrom-precise control over thin film thickness, is an ideal technique for this challenge. Ruthenium (Ru0) and its oxide (RuO2) have gained interest in the past decade as interfacial dipole layers because of their favorable properties like metal-equivalent work functions, conductivity, etc. In this study, initial results of the electronic structure investigation of ALD Ru0 and RuO2 films via photoemission spectroscopy are presented. These experiments give insight into the band alignment, growth behavior, surface structure termination, and dipole formation. The experiments were performed in an integrated vacuum system attached to a home-built, stop-flow type ALD reactor without exposing the samples to the ambient in between deposition and analysis. Bis(ethylcyclopentadienyl)ruthenium(II) was used as precursor and oxygen as reactant. The analysis chamber was outfitted with X-ray photoemission spectroscopy (LIXPS, XPS). The determined growth modes are consistent with a strong growth inhibition situation with a maximum average growth rate of 0.21 Å/cycle for RuO2 and 0.04 Å/cycle for Ru.0 An interface dipole of up to -0.93 eV was observed, supporting the assumption of a strongly physisorbed interface. A separate experiment where the surface of a RuO film was sputtered suggests that the surface is terminated by an intermediate, stable, non-stoichiometric RuO2/OH compound whose surface is saturated with hydroxyl groups.

  17. Numerical study of the atomic and electronic structure of some silicon grain boundaries

    International Nuclear Information System (INIS)

    This work contributes to the theoretical study of extended defects in covalent materials. The study is especially devoted to the tilt grain boundaries in silicon as a model material. The theoretical model is based on the self-consistent tight-binding approximation and is applied within two numerical techniques: the fast 'order N' density-matrix method and the diagonalization technique which allows the sampling of the reciprocal space. Total energy parameters of the model have been fitted in order to reproduce the silicon band structure (with a correct gap value) and the transferability of crystalline and mechanical properties of this material. A new type of boundary conditions is proposed and tested. These conditions, named 'ante-periodic' or 'Moebius', allow only one grain boundary per box instead of two and decrease the CPU time by a factor of two. The model is then applied to the study of the Σ=25 [001] (710) grain boundary. The results show the possible presence in this boundary of low energy non-reconstructed atomic structures which are electrically active. This confirms what had been suggested by some experimental observations. The same study is also performed for the Σ=13 [001] (510) grain boundary. In order to compare the intrinsic electrical activity in the previous grain boundaries with the one induced by impurities, a total energy parametrization for the silicon-nickel bond is achieved and used in preliminary calculations. Finally the two variants of the Σ=11 [011] (2-33) interface are studied, especially their respective interfacial energies. The result disagrees with previous calculations using phenomenological potentials. (author)

  18. Electronic structure investigation of atomic layer deposition ruthenium(oxide) thin films using photoemission spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, Michael, E-mail: mvschaefer@mail.usf.edu, E-mail: schlaf@mail.usf.edu [Department of Physics, University of South Florida, Tampa, Florida 33620 (United States); Schlaf, Rudy, E-mail: mvschaefer@mail.usf.edu, E-mail: schlaf@mail.usf.edu [Department of Electrical Engineering, University of South Florida, Tampa, Florida 33620 (United States)

    2015-08-14

    Analyzing and manipulating the electronic band line-up of interfaces in novel micro- and nanoelectronic devices is important to achieve further advancement in this field. Such band alignment modifications can be achieved by introducing thin conformal interfacial dipole layers. Atomic layer deposition (ALD), enabling angstrom-precise control over thin film thickness, is an ideal technique for this challenge. Ruthenium (Ru{sup 0}) and its oxide (RuO{sub 2}) have gained interest in the past decade as interfacial dipole layers because of their favorable properties like metal-equivalent work functions, conductivity, etc. In this study, initial results of the electronic structure investigation of ALD Ru{sup 0} and RuO{sub 2} films via photoemission spectroscopy are presented. These experiments give insight into the band alignment, growth behavior, surface structure termination, and dipole formation. The experiments were performed in an integrated vacuum system attached to a home-built, stop-flow type ALD reactor without exposing the samples to the ambient in between deposition and analysis. Bis(ethylcyclopentadienyl)ruthenium(II) was used as precursor and oxygen as reactant. The analysis chamber was outfitted with X-ray photoemission spectroscopy (LIXPS, XPS). The determined growth modes are consistent with a strong growth inhibition situation with a maximum average growth rate of 0.21 Å/cycle for RuO{sub 2} and 0.04 Å/cycle for Ru.{sup 0} An interface dipole of up to −0.93 eV was observed, supporting the assumption of a strongly physisorbed interface. A separate experiment where the surface of a RuO film was sputtered suggests that the surface is terminated by an intermediate, stable, non-stoichiometric RuO{sub 2}/OH compound whose surface is saturated with hydroxyl groups.

  19. Electronic structure investigation of atomic layer deposition ruthenium(oxide) thin films using photoemission spectroscopy

    International Nuclear Information System (INIS)

    Analyzing and manipulating the electronic band line-up of interfaces in novel micro- and nanoelectronic devices is important to achieve further advancement in this field. Such band alignment modifications can be achieved by introducing thin conformal interfacial dipole layers. Atomic layer deposition (ALD), enabling angstrom-precise control over thin film thickness, is an ideal technique for this challenge. Ruthenium (Ru0) and its oxide (RuO2) have gained interest in the past decade as interfacial dipole layers because of their favorable properties like metal-equivalent work functions, conductivity, etc. In this study, initial results of the electronic structure investigation of ALD Ru0 and RuO2 films via photoemission spectroscopy are presented. These experiments give insight into the band alignment, growth behavior, surface structure termination, and dipole formation. The experiments were performed in an integrated vacuum system attached to a home-built, stop-flow type ALD reactor without exposing the samples to the ambient in between deposition and analysis. Bis(ethylcyclopentadienyl)ruthenium(II) was used as precursor and oxygen as reactant. The analysis chamber was outfitted with X-ray photoemission spectroscopy (LIXPS, XPS). The determined growth modes are consistent with a strong growth inhibition situation with a maximum average growth rate of 0.21 Å/cycle for RuO2 and 0.04 Å/cycle for Ru.0 An interface dipole of up to −0.93 eV was observed, supporting the assumption of a strongly physisorbed interface. A separate experiment where the surface of a RuO film was sputtered suggests that the surface is terminated by an intermediate, stable, non-stoichiometric RuO2/OH compound whose surface is saturated with hydroxyl groups

  20. Tailoring characteristic thermal stability of Ni-Au binary nanocrystals via structure and composition engineering: theoretical insights into structural evolution and atomic inter-diffusion

    International Nuclear Information System (INIS)

    We report on the structural evolution and atomic inter-diffusion characteristics of the bimetallic Ni-Au nanocrystals (NCs) by molecular dynamics simulations studies. Our results reveal that the thermal stability dynamics of Ni-Au NCs strongly depends on the atomic configurations. By engineering the structural construction with Ni:Au = 1:1 atomic composition, compared with core-shell Au@Ni and alloy NCs, the melting point of core-shell Ni@Au NCs is significantly enhanced up to 1215 K. Unexpectedly, with atomic ratio of Au:Ni= 1:9, the melting process initiates from the atoms in the shell of Ni@Au and alloy NCs, while starts from the core of Au@Ni NCs. The corresponding features and evolution process of structural motifs, mixing and segregation are illustrated via a series of dynamic simulations videos. Moreover, our results revealed that the face centered cubic phase Au0.75Ni0.25 favorably stabilizes in NCs form but does not exist in the bulk counterpart, which elucidates the anomalies of previously reported experimental results on such bimetallic NCs

  1. Tailoring characteristic thermal stability of Ni-Au binary nanocrystals via structure and composition engineering: theoretical insights into structural evolution and atomic inter-diffusion

    Directory of Open Access Journals (Sweden)

    Bangquan Li

    2014-11-01

    Full Text Available We report on the structural evolution and atomic inter-diffusion characteristics of the bimetallic Ni-Au nanocrystals (NCs by molecular dynamics simulations studies. Our results reveal that the thermal stability dynamics of Ni-Au NCs strongly depends on the atomic configurations. By engineering the structural construction with Ni:Au = 1:1 atomic composition, compared with core-shell Au@Ni and alloy NCs, the melting point of core-shell Ni@Au NCs is significantly enhanced up to 1215 K. Unexpectedly, with atomic ratio of Au:Ni= 1:9, the melting process initiates from the atoms in the shell of Ni@Au and alloy NCs, while starts from the core of Au@Ni NCs. The corresponding features and evolution process of structural motifs, mixing and segregation are illustrated via a series of dynamic simulations videos. Moreover, our results revealed that the face centered cubic phase Au0.75Ni0.25 favorably stabilizes in NCs form but does not exist in the bulk counterpart, which elucidates the anomalies of previously reported experimental results on such bimetallic NCs.

  2. Surface structure of polymers and their model compounds observed by atomic force microscopy

    NARCIS (Netherlands)

    Stocker, W.; Bickmann, B.; Magonov, S.N.; Cantow, H.-J.; Lotz, B.; Wittmann, J.-C.; Möller, M.

    1992-01-01

    Results of atomic force microscopy (AFM) of normal alkanes, polyethylene, isotactic polypropylene and of a diblock copolymer are presented. Various types of surfaces - naturally and epitaxially grown on different substrates - have been examined from hundreds of nanometers down to the atomic scale. S

  3. Atomic structure of the non-polar GaN(anti 2110) surface by cross-sectional scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Krueger, David; Kuhr, Simon; Schmidt, Thomas; Hommel, Detlef; Falta, Jens [Institute of Solid State Physics, University of Bremen (Germany)

    2009-05-15

    The (anti 2110) plane of gallium nitride, exposed by cleaving a GaN single crystal under ultra-high vacuum conditions, has been atomically resolved for the first time, using cross-sectional scanning tunneling microscopy. The spatial period length supports a (1 x 1) unit mesh size, i.e., the absence of a reconstruction. The contrast observed in the experimental data is well explained by the atomic arrangement expected for a truncated-bulk structure. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  4. Atomic structure of a stable high-index Ge surface: G2(103)-(4x1)

    DEFF Research Database (Denmark)

    Seehofer, L.; Bunk, O.; Falkenberg, G.; Lottermoser, L.; Feidenhans'l, R.; Landemark, E.; Nielsen, M.; Johnson, R.L.

    Based on scanning tunneling microscopy and surface X-ray diffraction, we propose a complex structural model for the Ge(103)-(4 x 1) reconstruction. Each unit cell contains two (103) double steps, which gives rise to the formation of stripes of Ge atoms oriented in the [<(3)over bar 01>] direction....... The stripes and the spaces between them are covered with threefold-coordinated Ge adatoms. Charge is transferred from the bulk-like edge atoms of the double steps to the adatoms. The formation of the reconstruction can be explained in terms of stress relief, charge transfer, and minimization of the...

  5. {2p_\\pi}-{2p_\\sigma} crossing in heavy symmetric ion-atom collisions: I. Level structure

    OpenAIRE

    Morovi´c, Tihomir; Sepp, Wolf-Dieter; Fricke, Burkhard

    1982-01-01

    Ab initio self-consistent DFS calculations are performed for five different symmetric atomic systems from Ar-Ar to Pb-Pb. The level structure for the {2p_\\pi}-{2p_\\sigma} crossing as function of the united atomic charge Z_u is studied and interpreted. Manybody effects, spin-orbit splitting, direct relativistic effects as well as indirect relativistic effects are differently important for different Z_u. For the I-I system a comparison with other calculations is given.

  6. Quantitative structure determination using grazing scattering of fast atoms: Oxygen-induced missing-row reconstruction of Mo(112)

    Science.gov (United States)

    Seifert, J.; Winter, H.

    2016-05-01

    We present an extensive study on the structure of oxygen adsorbates on Mo(112) by means of grazing scattering of fast hydrogen and helium atoms and low-energy electron diffraction. For projectile energies less than 2 keV, fast atom diffraction provides information on the surface unit cell and on adsorption sites for low coverages. In the classical scattering regime, we employed so-called triangulation techniques where for an azimuthal rotation of the target axial surface channels are identified. From comparison with computer simulation positions of surface atoms can be derived. Aside from the detection scheme of projectile-induced electron emission, we present details for a new variant of triangulation based on the detection of angular distributions of scattered particles. The different sensitivity of the methods to the topmost surface layers allows us to efficiently set up structural models for four adsorbate phases for which contradicting models exist in literature. The c (4 ×2 ) phase is revealed to be one step in the formation of a missing-row reconstruction with p (1 ×2 ) unit cell. Our studies demonstrate the potential of grazing scattering of fast atoms for quantitative structure analysis.

  7. Understanding atomic structures of amorphous C-doped Ge2Sb2Te5 phase-change memory materials

    International Nuclear Information System (INIS)

    The atomic structure of thin films of the carbon-doped Ge2Sb2Te5 (GST) rapid phase-change memory material Ge2Sb2Te5C (10% C-GST) was investigated by reverse Monte Carlo refinement using experimental electron diffraction reduced scattering data accompanied by density functional theory (DFT) molecular dynamics (MD) simulations and energy optimizations. For comparison, the structure of amorphous Ge2Sb2Te5C2 (18% C-GST) was obtained by DFT MD simulation of cooling from the melt. The results suggest that the carbon dopant forms atomic scale carbon clusters coordinated predominantly by Ge atoms. This becomes more evident with increasing carbon concentration. For 10% C-GST the building blocks of the matrix can be identified as squares of Ge(Sb)-Te-Sb(Ge)-Te atoms, related to the elementary building blocks of the corresponding crystalline structure of the metastable cubic phase of pure GST. The increased contribution of homopolar Te-Te bonds and Sb(Te)-Te-Sb(Te)-Te square fragments is suggested with the higher dopant level in 18% C-GST.

  8. Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.

    Science.gov (United States)

    Agirrezabala, Xabier; Velázquez-Muriel, Javier A; Gómez-Puertas, Paulino; Scheres, Sjors H W; Carazo, José M; Carrascosa, José L

    2007-04-01

    The existence of similar folds among major structural subunits of viral capsids has shown unexpected evolutionary relationships suggesting common origins irrespective of the capsids' host life domain. Tailed bacteriophages are emerging as one such family, and we have studied the possible existence of the HK97-like fold in bacteriophage T7. The procapsid structure at approximately 10 A resolution was used to obtain a quasi-atomic model by fitting a homology model of the T7 capsid protein gp10 that was based on the atomic structure of the HK97 capsid protein. A number of fold similarities, such as the fitting of domains A and P into the L-shaped procapsid subunit, are evident between both viral systems. A different feature is related to the presence of the amino-terminal domain of gp10 found at the inner surface of the capsid that might play an important role in the interaction of capsid and scaffolding proteins. PMID:17437718

  9. Resistive switching in HfO2-based atomic layer deposition grown metal–insulator–metal structures

    International Nuclear Information System (INIS)

    Highlights: • We have prepared Pt/HfO2/TiN MIM structures with very thin HfO2 films. • HfO2 films were prepared by thermal, ozone and plasma assisted atomic layer deposition. • Stable bipolar resistive switching characteristics were obtained. • Forming voltage scales with the HfO2 film thickness. • 104 consecutive resistive switching operations were attained in ms pulsed regime without degradation. - Abstract: We prepared Pt/HfO2/TiN metal–insulator–metal structures for resistive switching experiments. The HfO2 films were prepared by thermal, ozone and plasma assisted atomic layer deposition. The deposition techniques yielded HfO2 films that were conducive to stable and reproducible bipolar resistive switching. We observed that the forming voltage scaled with the HfO2 film thickness. The structures did not show degradation after 104 consecutive resistive switching operations in a millisecond pulsed regime

  10. Atomic resolution structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A2

    International Nuclear Information System (INIS)

    The atomic resolution crystal structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A2 is reported. The structure of the double mutant K53,56M has previously been refined at 1.9 Å resolution using room-temperature data. The present paper reports the crystal structure of the same mutant K53,56M refined against 1.1 Å data collected using synchrotron radiation. A total of 116 main-chain atoms from 29 residues and 44 side chains are modelled in alternate conformations. Most of the interfacial binding residues are found to be disordered and alternate conformations could be recognized. The second calcium ion-binding site residue Glu92 adopts two alternate conformations. The minor and major conformations of Glu92 correspond to the second calcium ion bound and unbound states

  11. Order within disorder: The atomic structure of ion-beam sputtered amorphous tantala (a-Ta2O5)

    Science.gov (United States)

    Bassiri, Riccardo; Liou, Franklin; Abernathy, Matthew R.; Lin, Angie C.; Kim, Namjun; Mehta, Apurva; Shyam, Badri; Byer, Robert L.; Gustafson, Eric K.; Hart, Martin; MacLaren, Ian; Martin, Iain W.; Route, Roger K.; Rowan, Sheila; Stebbins, Jonathan F.; Fejer, Martin M.

    2015-03-01

    Amorphous tantala (a-Ta2O5) is a technologically important material often used in high-performance coatings. Understanding this material at the atomic level provides a way to further improve performance. This work details extended X-ray absorption fine structure measurements of a-Ta2O5 coatings, where high-quality experimental data and theoretical fits have allowed a detailed interpretation of the nearest-neighbor distributions. It was found that the tantalum atom is surrounded by four shells of atoms in sequence; oxygen, tantalum, oxygen, and tantalum. A discussion is also included on how these models can be interpreted within the context of published crystalline Ta2O5 and other a-T2O5 studies.

  12. Order within disorder: The atomic structure of ion-beam sputtered amorphous tantala (a-Ta2O5

    Directory of Open Access Journals (Sweden)

    Riccardo Bassiri

    2015-03-01

    Full Text Available Amorphous tantala (a-Ta2O5 is a technologically important material often used in high-performance coatings. Understanding this material at the atomic level provides a way to further improve performance. This work details extended X-ray absorption fine structure measurements of a-Ta2O5 coatings, where high-quality experimental data and theoretical fits have allowed a detailed interpretation of the nearest-neighbor distributions. It was found that the tantalum atom is surrounded by four shells of atoms in sequence; oxygen, tantalum, oxygen, and tantalum. A discussion is also included on how these models can be interpreted within the context of published crystalline Ta2O5 and other a-T2O5 studies.

  13. Tunable electronic structures of germanium monochalcogenide nanosheets via light non-metallic atom functionalization: a first-principles study.

    Science.gov (United States)

    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. PMID:27491896

  14. Probing electronic and structural properties of single molecules on the atomic scale

    OpenAIRE

    Mohn, Fabian

    2012-01-01

    In this thesis work, a combination of low-temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM) was used to study single atoms and molecules on thin insulating films. We show that noncontact-AFM can yield important additional information for these systems, which had previously been studied only with STM. In particular, we demonstrate that the charge states of single gold adatoms can be detected with Kelvin probe force microscopy (KPFM). Furthermore, it is descr...

  15. Atomic structure and one-dimensional ionic conductivity of LiB3O5

    International Nuclear Information System (INIS)

    X-ray diffraction and electrophysical investigations into lithium triborate (LiB3O5) are presented. Specification of the atomic model is performed using the least square method in the full-matrix variant with regard to the atom thermal oscillation anisotropy in harmonic approximation. The results of investigations conducted allow one to conclude that conductivity in LiB3O5 is conditioned by Li+ ion mobility

  16. Operando atomic structure and active sites of TiO2(110)-supported gold nanoparticles during carbon monoxide oxidation.

    Science.gov (United States)

    Saint-Lager, Marie-Claire; Laoufi, Issam; Bailly, Aude

    2013-01-01

    It is well known that gold nanoparticles supported on TiO2 act as a catalyst for CO oxidation, even below room temperature. Despite extensive studies, the origin of this catalytic activity remains under debate. Indeed, when the particle size decreases, many changes may occur; thus modifying the nanoparticles' electronic properties and consequently their catalytic performances. Thanks to a state-of-the-art home-developed setup, model catalysts can be prepared in ultra-high vacuum and their morphology then studied in operando conditions by Grazing Incidence Small Angle X-ray Scattering, as well as their atomic structure by Grazing Incidence X-ray Diffraction as a function of their catalytic activity. We previously reported on the existence of a catalytic activity maximum observed for three-dimensional gold nanoparticles with a diameter of 2-3 nm and a height of 6-7 atomic planes. In the present work we correlate this size dependence of the catalytic activity to the nanoparticles' atomic structure. We show that even when their size decreases below the optimum diameter, the gold nanoparticles keep the face-centered cubic structure characteristic of bulk gold. Nevertheless, for these smallest nanoparticles, the lattice parameter presents anisotropic strains with a larger contraction in the direction perpendicular to the surface. Moreover a careful analysis of the atomic-scale morphology around the catalytic activity maximum tends to evidence the role of sites with a specific geometry at the interface between the nanoparticles and the substrate. This argues for models where atoms at the interface periphery act as catalytically active sites for carbon monoxide oxidation. PMID:24015583

  17. Structural evolution and strain induced mixing in Cu–Co composites studied by transmission electron microscopy and atom probe tomography

    International Nuclear Information System (INIS)

    A Cu–Co composite material is chosen as a model system to study structural evolution and phase formations during severe plastic deformation. The evolving microstructures as a function of the applied strain were characterized at the micro-, nano-, and atomic scale-levels by combining scanning electron microscopy and transmission electron microscopy including energy-filtered transmission electron microscopy and electron energy-loss spectroscopy. The amount of intermixing between the two phases at different strains was examined at the atomic scale using atom probe tomography as complimentary method. It is shown that Co particles are dissolved in the Cu matrix during severe plastic deformation to a remarkable extent and their size, number, and volume fraction were quantitatively determined during the deformation process. From the results, it can be concluded that supersaturated solid solutions up to 26 at.% Co in a fcc Cu–26 at.% Co alloy are obtained during deformation. However, the distribution of Co was found to be inhomogeneous even at the highest degree of investigated strain. - Highlights: • Structural evolution in a deformed Cu–Co composite is studied on all length scales. • Amount of intermixing is examined by atom-probe tomography. • Supersaturated solid solutions up to 26 at.% Co in Cu are observed

  18. Atomic-scale chemical imaging and quantification of metallic alloy structures by energy-dispersive X-ray spectroscopy.

    Science.gov (United States)

    Lu, Ping; Zhou, Lin; Kramer, M J; Smith, David J

    2014-01-01

    Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L2(1) phase with Ni0.48Co0.52 at A-sites, Al at B(Ι)-sites and Fe0.20Ti0.80 at B(ΙΙ)-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems. PMID:24492747

  19. A DFT study of atomic structure and adhesion at the Fe(BCC)/Fe3O4 interfaces

    Science.gov (United States)

    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.

  20. Catalytic Activity and Stability of Oxides: The Role of Near-Surface Atomic Structures and Compositions.

    Science.gov (United States)

    Feng, Zhenxing; Hong, Wesley T; Fong, Dillon D; Lee, Yueh-Lin; Yacoby, Yizhak; Morgan, Dane; Shao-Horn, Yang

    2016-05-17

    Electrocatalysts play an important role in catalyzing the kinetics for oxygen reduction and oxygen evolution reactions for many air-based energy storage and conversion devices, such as metal-air batteries and fuel cells. Although noble metals have been extensively used as electrocatalysts, their limited natural abundance and high costs have motivated the search for more cost-effective catalysts. Oxides are suitable candidates since they are relatively inexpensive and have shown reasonably high activity for various electrochemical reactions. However, a lack of fundamental understanding of the reaction mechanisms has been a major hurdle toward improving electrocatalytic activity. Detailed studies of the oxide surface atomic structure and chemistry (e.g., cation migration) can provide much needed insights for the design of highly efficient and stable oxide electrocatalysts. In this Account, we focus on recent advances in characterizing strontium (Sr) cation segregation and enrichment near the surface of Sr-substituted perovskite oxides under different operating conditions (e.g., high temperature, applied potential), as well as their influence on the surface oxygen exchange kinetics at elevated temperatures. We contrast Sr segregation, which is associated with Sr redistribution in the crystal lattice near the surface, with Sr enrichment, which involves Sr redistribution via the formation of secondary phases. The newly developed coherent Bragg rod analysis (COBRA) and energy-modulated differential COBRA are uniquely powerful ways of providing information about surface and interfacial cation segregation at the atomic scale for these thin film electrocatalysts. In situ ambient pressure X-ray photoelectron spectroscopy (APXPS) studies under electrochemical operating conditions give additional insights into cation migration. Direct COBRA and APXPS evidence for surface Sr segregation was found for La1-xSrxCoO3-δ and (La1-ySry)2CoO4±δ/La1-xSrxCoO3-δ oxide thin films, and

  1. Local conditions for the Pauli potential in order to yield self-consistent electron densities exhibiting proper atomic shell structure

    International Nuclear Information System (INIS)

    The local conditions for the Pauli potential that are necessary in order to yield self-consistent electron densities from orbital-free calculations are investigated for approximations that are expressed with the help of a local position variable. It is shown that those local conditions also apply when the Pauli potential is given in terms of the electron density. An explicit formula for the Ne atom is given, preserving the local conditions during the iterative procedure. The resulting orbital-free electron density exhibits proper shell structure behavior and is in close agreement with the Kohn-Sham electron density. This study demonstrates that it is possible to obtain self-consistent orbital-free electron densities with proper atomic shell structure from simple one-point approximations for the Pauli potential at local density level

  2. Pressure/temperature fluid cell apparatus for the neutron powder diffractometer instrument: Probing atomic structure in situ

    Science.gov (United States)

    Wang, Hsiu-Wen; Fanelli, Victor R.; Reiche, Helmut M.; Larson, Eric; Taylor, Mark A.; Xu, Hongwu; Zhu, Jinlong; Siewenie, Joan; Page, Katharine

    2014-12-01

    This contribution describes a new local structure compatible gas/liquid cell apparatus for probing disordered materials at high pressures and variable temperatures in the Neutron Powder Diffraction instrument at the Lujan Neutron Scattering Center, Los Alamos National Laboratory. The new sample environment offers choices for sample canister thickness and canister material type. Finite element modeling is utilized to establish maximum allowable working pressures of 414 MPa at 15 K and 121 MPa at 600 K. High quality atomic pair distribution function data extraction and modeling have been demonstrated for a calibration standard (Si powder) and for supercritical and subcritical CO2 measurements. The new sample environment was designed to specifically target experimental studies of the local atomic structures involved in geologic CO2 sequestration, but will be equally applicable to a wide variety of energy applications, including sorption of fluids on nano/meso-porous solids, clathrate hydrate formation, catalysis, carbon capture, and H2 and natural gas uptake/storage.

  3. Atomic-level structural and chemical analysis of Cr-doped Bi2Se3 thin films

    Science.gov (United States)

    Ghasemi, A.; Kepaptsoglou, D.; Collins-McIntyre, L. J.; Ramasse, Q.; Hesjedal, T.; Lazarov, V. K.

    2016-05-01

    We present a study of the structure and chemical composition of the Cr-doped 3D topological insulator Bi2Se3. Single-crystalline thin films were grown by molecular beam epitaxy on Al2O3 (0001), and their structural and chemical properties determined on an atomic level by aberration-corrected scanning transmission electron microscopy and electron energy loss spectroscopy. A regular quintuple layer stacking of the Bi2Se3 film is found, with the exception of the first several atomic layers in the initial growth. The spectroscopy data gives direct evidence that Cr is preferentially substituting for Bi in the Bi2Se3 host. We also show that Cr has a tendency to segregate at internal grain boundaries of the Bi2Se3 film.

  4. Analysis of Local Structures around Ni Atoms Doped in ZnO-Based Diluted Magnetic Semiconductors by Fluorescence EXAFS

    Institute of Scientific and Technical Information of China (English)

    LI Bin-Bin; XIU Xiang-Qian; ZHANG Rong; TAO Zhi-Kuo; CHEN Lin; XIE Zi-Li; ZHENG You-Dou; HE Bo

    2006-01-01

    @@ Zn1-xNixO (x = 0.001, 0.01, 0.02, 0.05 and 0.20) powders are prepared by sol-gel method. An extended x-ray absorption fine structure technique (EXAFS) for the Ni K-edge is employed to probe the local structures around Ni atoms doped in ZnO powders by fluorescence mode. The near edge EXAFS of the samples does not change in the range of Ni concentration from x = 0.001 to 0.05, which is consistent with the results of x-ray diffraction of the samples. The simulation results for the first shell EXAFS signals indicated that Ni atoms are substituted in Zn sites.

  5. The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies

    Science.gov (United States)

    Hawelek, L.; Brodka, A.; Dore, J. C.; Honkimaki, V.; Burian, A.

    2013-11-01

    The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp3 defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.

  6. Non-local physics: Applications from the universe evolution to the atom structure in the frame of the unified theory

    Science.gov (United States)

    Alexeev, B. V.

    2013-10-01

    The main principles of the non-local physics are delivered. The unified theory of transport processes is applicable to the physical systems in tremendous diapason of scales - from atom structures to the Universe evolution. The origin of difficulties connected with the hypothetical dark matter and dark energy consists in the total Oversimplification following from the principles of local physics and reflects the general shortcomings of the local kinetic transport theory.

  7. Bloch space structure, the qutrit wave function and atom-field entanglement in three-level systems

    OpenAIRE

    Sen, Surajit; Nath, Mihir Ranjan; Dey, Tushar Kanti; Gangopadhyay, Gautam

    2011-01-01

    We have given a novel formulation of the exact solutions for the lambda, vee and cascade three-level systems where the Hamiltonian of each configuration is expressed in the SU(3) basis. The solutions are discussed from the perspective of the Bloch equation and the atom-field entanglement scenario. For the semiclassical systems, the Bloch space structure of each configuration is studied by solving the corresponding Bloch equation and it is shown that at resonance, the eight-dimensional Bloch s...

  8. Atomic core structure of 90°(c)-bent screw threading dislocations in wurtzite GaN

    Institute of Scientific and Technical Information of China (English)

    BELABBAS Imad; CHEN Jun; RUTERANA Pierre; YU Guanghui; NOUET Gérard

    2006-01-01

    The atomic and electronic structures of the c threading dislocations with an edge or screw character were compared using a tight binding formalism which takes into account charge transfer.The two dislocations do not exhibit dangling bonds.While the screw dislocation contains only constrained Ga-N bonds, the edge dislocation contains Ga-Ga and N-N wrong bonds.Both dislocations are found to induce shallow and deep gap states.

  9. Catalytic activity of bimetallic catalysts highly sensitive to the atomic composition and phase structure at the nanoscale

    Science.gov (United States)

    Shan, Shiyao; Petkov, Valeri; Prasai, Binay; Wu, Jinfang; Joseph, Pharrah; Skeete, Zakiya; Kim, Eunjoo; Mott, Derrick; Malis, Oana; Luo, Jin; Zhong, Chuan-Jian

    2015-11-01

    The ability to determine the atomic arrangement in nanoalloy catalysts and reveal the detailed structural features responsible for the catalytically active sites is essential for understanding the correlation between the atomic structure and catalytic properties, enabling the preparation of efficient nanoalloy catalysts by design. Herein we describe a study of CO oxidation over PdCu nanoalloy catalysts focusing on gaining insights into the correlation between the atomic structures and catalytic activity of nanoalloys. PdCu nanoalloys of different bimetallic compositions are synthesized as a model system and are activated by a controlled thermochemical treatment for assessing their catalytic activity. The results show that the catalytic synergy of Pd and Cu species evolves with both the bimetallic nanoalloy composition and temperature of the thermochemical treatment reaching a maximum at a Pd : Cu ratio close to 50 : 50. The nanoalloys are characterized structurally by ex situ and in situ synchrotron X-ray diffraction, including atomic pair distribution function analysis. The structural data show that, depending on the bimetallic composition and treatment temperature, PdCu nanoalloys adopt two different structure types. One features a chemically ordered, body centered cubic (B2) type alloy consisting of two interpenetrating simple cubic lattices, each occupied with Pd or Cu species alone, and the other structure type features a chemically disordered, face-centered cubic (fcc) type of alloy wherein Pd and Cu species are intermixed at random. The catalytic activity for CO oxidation is strongly influenced by the structural features. In particular, it is revealed that the prevalence of chemical disorder in nanoalloys with a Pd : Cu ratio close to 50 : 50 makes them superior catalysts for CO oxidation in comparison with the same nanoalloys of other bimetallic compositions. However, the catalytic synergy can be diminished if the Pd50Cu50 nanoalloys undergo phase

  10. Atomic Structures of Graphene, Benzene and Methane with Bond Lengths as Sums of the Single, Double and Resonance Bond Radii of Carbon

    CERN Document Server

    Heyrovska, Raji

    2008-01-01

    Two dimensional layers of graphene are currently drawing a great attention in fundamental and applied nanoscience. Graphene consists of interconnected hexagons of carbon atoms as in graphite. This article presents for the first time the structures of graphene at the atomic level and shows how it differs from that of benzene, due to the difference in the double bond and resonance bond based radii of carbon. The carbon atom of an aliphatic compound such as methane has a longer covalent single bond radius as in diamond. All the atomic structures presented here have been drawn to scale.

  11. Local 3D real space atomic structure of the simple icosahedral Ho11Mg15Zn74 quasicrystal from PDF data

    OpenAIRE

    Bruehne, S.; Uhrig, E.; Gross, C.; Assmus, W.

    2003-01-01

    We present a new complementary strategy to quasicrystalline structure determination: The local atomic structure of simple icosahedral (si) Ho11Mg15Zn74 [a(6D)=5.144(3)A] in a sphere of up to r=17A was refined using the atomic pair distribution function (PDF) from in-house X-ray powder diffraction data (MoKa1, Qmax=13.5A-1; R=20.4%). The basic building block is a 105-atom Bergman-Cluster {Ho8Mg12Zn85}. Its center is occupied by a Zn atom - in contrast to a void in face centred icosahedral (fci...

  12. Crystal structure of post-perovskite-type CaIrO3 reinvestigated: new insights into atomic thermal vibration behaviors

    Directory of Open Access Journals (Sweden)

    Akihiko Nakatsuka

    2015-09-01

    Full Text Available Single crystals of the title compound, the post-perovskite-type CaIrO3 [calcium iridium(IV trioxide], have been grown from a CaCl2 flux at atmospheric pressure. The crystal structure consists of an alternate stacking of IrO6 octahedral layers and CaO8 hendecahedral layers along [010]. Chains formed by edge-sharing of IrO6 octahedra (point-group symmetry 2/m.. run along [100] and are interconnected along [001] by sharing apical O atoms to build up the IrO6 octahedral layers. Chains formed by face-sharing of CaO8 hendecahedra (point-group symmetry m2m run along [100] and are interconnected along [001] by edge-sharing to build up the CaO8 hendecahedral layers. The IrO6 octahedral layers and CaO8 hendecahedral layers are interconnected by sharing edges. The present structure refinement using a high-power X-ray source confirms the atomic positions determined by Hirai et al. (2009 [Z. Kristallogr. 224, 345–350], who had revised our previous report [Sugahara et al. (2008. Am. Mineral. 93, 1148–1152]. However, the displacement ellipsoids of the Ir and Ca atoms based on the present refinement can be approximated as uniaxial ellipsoids elongating along [100], unlike those reported by Hirai et al. (2009. This suggests that the thermal vibrations of the Ir and Ca atoms are mutually suppressed towards the Ir...Ca direction across the shared edge because of the dominant repulsion between the two atoms.

  13. Crystal structure of post-perovskite-type CaIrO3 reinvestigated: new insights into atomic thermal vibration behaviors.

    Science.gov (United States)

    Nakatsuka, Akihiko; Sugiyama, Kazumasa; Yoneda, Akira; Fujiwara, Keiko; Yoshiasa, Akira

    2015-09-01

    Single crystals of the title compound, the post-perovskite-type CaIrO3 [calcium iridium(IV) trioxide], have been grown from a CaCl2 flux at atmospheric pressure. The crystal structure consists of an alternate stacking of IrO6 octa-hedral layers and CaO8 hendeca-hedral layers along [010]. Chains formed by edge-sharing of IrO6 octa-hedra (point-group symmetry 2/m..) run along [100] and are inter-connected along [001] by sharing apical O atoms to build up the IrO6 octa-hedral layers. Chains formed by face-sharing of CaO8 hendeca-hedra (point-group symmetry m2m) run along [100] and are inter-connected along [001] by edge-sharing to build up the CaO8 hendeca-hedral layers. The IrO6 octa-hedral layers and CaO8 hendeca-hedral layers are inter-connected by sharing edges. The present structure refinement using a high-power X-ray source confirms the atomic positions determined by Hirai et al. (2009 ▸) [Z. Kristallogr. 224, 345-350], who had revised our previous report [Sugahara et al. (2008 ▸). Am. Mineral. 93, 1148-1152]. However, the displacement ellipsoids of the Ir and Ca atoms based on the present refinement can be approximated as uniaxial ellipsoids elongating along [100], unlike those reported by Hirai et al. (2009 ▸). This suggests that the thermal vibrations of the Ir and Ca atoms are mutually suppressed towards the Ir⋯Ca direction across the shared edge because of the dominant repulsion between the two atoms. PMID:26396860

  14. Relating Electronic and Geometric Structure of Atomic Layer Deposited BaTiO3 to its Electrical Properties.

    Science.gov (United States)

    Torgersen, Jan; Acharya, Shinjita; Dadlani, Anup Lal; Petousis, Ioannis; Kim, Yongmin; Trejo, Orlando; Nordlund, Dennis; Prinz, Fritz B

    2016-04-21

    Atomic layer deposition allows the fabrication of BaTiO3 (BTO) ultrathin films with tunable dielectric properties, which is a promising material for electronic and optical technology. Industrial applicability necessitates a better understanding of their atomic structure and corresponding properties. Through the use of element-specific X-ray absorption near edge structure (XANES) analysis, O K-edge of BTO as a function of cation composition and underlying substrate (RuO2 and SiO2) is revealed. By employing density functional theory and multiple scattering simulations, we analyze the distortions in BTO's bonding environment captured by the XANES spectra. The spectral weight shifts to lower energy with increasing Ti content and provides an atomic scale (microscopic) explanation for the increase in leakage current density. Differences in film morphologies in the first few layers near substrate-film interfaces reveal BTO's homogeneous growth on RuO2 and its distorted growth on SiO2. This work links structural changes to BTO thin-film properties and provides insight necessary for optimizing future BTO and other ternary metal oxide-based thin-film devices. PMID:27009677

  15. Computational insights into the effect of carbon structures at the atomic level for non-aqueous sodium-oxygen batteries

    Science.gov (United States)

    Jiang, H. R.; Wu, M. C.; Zhou, X. L.; Yan, X. H.; Zhao, T. S.

    2016-09-01

    Carbon materials have been widely used to form air cathodes for non-aqueous sodium-oxygen (Nasbnd O2) batteries due to their large specific surface area, high conductivity and low cost. However, the effect of carbon structures at the atomic level remains poorly understood. In this work, a first-principles study is conducted to investigate how representative carbon structures, including graphite (0001) surface, point defects and fractured edge, influence the discharge and charge processes of non-aqueous Nasbnd O2 batteries. It is found that the single vacancy (SV) defect has the largest adsorption energy (5.81 eV) to NaO2 molecule among the structures studied, even larger than that of the NaO2 molecule on NaO2 crystal (2.81 eV). Such high adsorption energy is attributed to two factors: the dangling atoms in SV defects decrease the distance from NaO2 molecules, and the attachment through oxygen atoms increases the electrons transfer. The findings suggest that SV defects can act as the nucleation sites for NaO2 in the discharge process, and increasing the number of SV defects can facilitate the uniform formation of small-sized particles. The uniformly distributed discharge products lower the possibility for pore clogging, leading to an increased discharge capacity and improved cyclability for non-aqueous Nasbnd O2 batteries.

  16. Atomic-Scale Structure and Local Chemistry of CoFeB-MgO Magnetic Tunnel Junctions.

    Science.gov (United States)

    Wang, Zhongchang; Saito, Mitsuhiro; McKenna, Keith P; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi

    2016-03-01

    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. PMID:26905782

  17. Electronic structure and binding energy relaxation of ScZr atomic alloying

    Science.gov (United States)

    Bo, Maolin; Guo, Yongling; Yang, Xuexian; He, Junjie; Liu, Yonghui; Peng, Cheng; Huang, Yongli; Sun, Chang Q.

    2016-07-01

    We examined the combined effect of atomic under- and hetero-coordination on the bond relaxation and electronic binding energy of Sc, Zr, and ScZr alloying using a combination of the bond-order-length-strength (BOLS) correlation and density functional theory (DFT) calculations. Observations strongly emphasize the relevance of core-level shifts as reliable X-ray photoelectron spectroscopy experimental descriptors of core-shell catalysis reactivity, along with under-coordinated atoms in bimetallic transition metal systems. The BOLS-DFT method provides enhanced catalysis reactivity and detects surface and alloy configurations, opening up the possibility to investigate more complex systems with irregularly under- and hetero-coordinated atoms.

  18. Electronic structure and Moessbauer isomer shift of the iron atom isolated in crystalline argon matrix

    International Nuclear Information System (INIS)

    Multiple Scattering calculations were performed on an FeAr12 cluster in order to describe the iron atom trapped in a crystalline argon matrix. The total electron densities at the iron nucleus derived from these calculations are used to interpret Moessbauer Isomer Shift data. The different bonding mechanisms contributing to the metal atom-rare gas matrix interaction are also investigated. The overlap distorsion effect of the metal wave functions is found to play a major role in the calculated electron densities. The iron isomer shift calibration constant was found to be -0.22 a3 sub(o) mm sec-1. (Author)

  19. Strong field atomic ionization: Origin of high-energy structures in photoelectron spectra

    International Nuclear Information System (INIS)

    Two distinct interpretations have been proposed to account for conspicuous enhancements of the ionization peaks in the high energy part of above-threshold ionization spectra. One of them ascribes the enhancement to a multiphoton resonance involving an excited state, while other analysis performed for zero-range model potential link it to 'channel closings', i.e., to the change in the number of photons needed to ionize the atom when the laser intensity increases. We report the results of model calculations that confirm the existence of a resonant process in atoms and shed light on why short-range potential models can mimic the experimental observations

  20. Structures of Molecules at the Atomic Level: Caffeine and Related Compounds

    OpenAIRE

    Heyrovska, Raji; Narayan, Saraswathi

    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...