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. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. Atomic and Electronic Structures of Zr Atomic Chains

    Institute of Scientific and Technical Information of China (English)

    林益寿; 李爱玉; 朱梓忠

    2004-01-01

    The atomic, binding and electronic structures of very thin Zr chains are studied by the first-principles densityfunctional method. The present calculations reveal that zirconium can form planar chains in zigzag, dimer and ladder structures. The zigzag geometry has two minima. The most stable geometry is the zigzag one with a unit cell rather close to equilateral triangles with four nearest neighbours. The other stable zigzag structure has a wide bond angle and allows for two nearest neighbours. An intermediary structure has the ladder geometry and is formed by two strands. The dimer structure is also found to be more stable than the truly linear chain. All these planar geometries are more favourable energetically than the linear chain. We also show that by going from Zr bulk to a Zr chain, the characters of bonding do not change significantly.

  12. Atomic structures of 13-atom clusters by density functional theory

    Science.gov (United States)

    Chen, Hsin-Yi; Wei, Ching-Ming

    2007-03-01

    The 13-atom cluster structures of the alkaline metals, alkaline earth metals, boron group, 3d, 4d, and 5d transition metals in the periodic table, and Pb are investigated by density functional theory with three kinds of exchange correlation approximation: i) LDA (Local Density Approximation), ii) GGA (Generalized Gradient Approximation) [1], and iii) PBE (Perdew-Burke-Ernzerhof) [2]. The results mainly focus on five 3-D structures: icosahedral, cuboctahedral, hexagonal-closed packed, body-center cubic, decahedral, and the other two layer structures: buckled biplanar (bbp) and garrison-cap biplanar (gbp) structures. Limited by accuracy of exchange correlation approximation, two interesting results are found. The ground states of Ca13, Sr13, Ba13, Sc13, Y13, La13, Ti13, Zr13, and Hf13 are icosahedral structures. The clusters of Ir13, Pt13, Cu13, Ag13, and Au13 are more favorable for layer structures (i.e. bbp and gbp) than the other five 3-D structures. [1] J. P. Perdew et al., Phys. Rev. B 46, 6671 (1992). [2] J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996).

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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...

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. Big Atoms for Small Children: Building Atomic Models from Common Materials to Better Visualize and Conceptualize Atomic Structure

    Science.gov (United States)

    Cipolla, Laura; Ferrari, Lia A.

    2016-01-01

    A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).

  5. 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.

  6. 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...

  7. 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.

  8. 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.

  9. 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…

  10. 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.

  11. 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...

  12. 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)

  13. 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,…

  14. 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.

  15. 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.

  16. Fluctuations of spacetime and hyperfine structure of the hydrogen atom

    Energy Technology Data Exchange (ETDEWEB)

    Goeklue, Ertan [ZARM-Universitaet Bremen (Germany); Rivas, Juan Israel; Camacho, Abel [Universidad Autonoma Metropolitana-Iztapalapa, Mexico (Mexico)

    2012-07-01

    We consider the consequences of the presence of metric fluctuations upon the properties of a hydrogen atom. Particularly, we introduce these metric fluctuations in the corresponding effective Schroedinger equation and deduce the modifications that they entail upon the hyperfine structure related to a hydrogen atom. We will find the change that these effects imply for the ground state energy of the system and obtain a bound for its size comparing our theoretical predictions against the experimental uncertainty reported in the literature.

  17. 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...

  18. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    None

    1981-03-01

    The conference is an attempt to gather state-of-the-art information to understand the theory of relativistic atomic structure beyond the framework of the original Dirac theory. Abstracts of twenty articles from the conference were prepared separately for the data base. (GHT)

  20. 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...

  1. 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.

  2. 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

    The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...... framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....

  3. The shells of atomic structure in metallic glasses

    Science.gov (United States)

    Pan, S. P.; Feng, S. D.; Qiao, J. W.; Dong, B. S.; Qin, J. Y.

    2016-02-01

    We proposed a scheme to describe the spatial correlation between two atoms in metallic glasses. Pair distribution function in a model iron was fully decomposed into several shells and can be presented as the spread of nearest neighbor correlation via distance. Moreover, angle distribution function can also be decomposed into groups. We demonstrate that there is close correlation between pair distribution function and angle distribution function for metallic glasses. We think that our results are very helpful understanding the atomic structure of metallic glasses.

  4. 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.

  5. Volcano structure in atomic resolution core-loss images

    Energy Technology Data Exchange (ETDEWEB)

    D' Alfonso, A.J.; Findlay, S.D. [School of Physics, University of Melbourne, Victoria, 3010 (Australia); Oxley, M.P. [Materials Science and Technology Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 (United States); Allen, L.J. [School of Physics, University of Melbourne, Victoria, 3010 (Australia)], E-mail: lja@physics.unimelb.edu.au

    2008-06-15

    A feature commonly present in simulations of atomic resolution electron energy loss spectroscopy images in the scanning transmission electron microscope is the volcano or donut structure. In the past this has been understood in terms of a geometrical perspective using a dipole approximation. It is shown that the dipole approximation for core-loss spectroscopy begins to break down as the probe forming aperture semi-angle increases, necessitating the inclusion of higher order terms for a quantitative understanding of volcano formation. Using such simulations we further investigate the mechanisms behind the formation of such structures in the single atom case and extend this to the case of crystals. The cubic SrTiO{sub 3} crystal is used as a test case to show the effects of nonlocality, probe channelling and absorption in producing the volcano structure in crystal images.

  6. 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.

  7. 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

  8. Stable atomic structure of NiTi austenite

    Energy Technology Data Exchange (ETDEWEB)

    Zarkevich, Nikolai A [Ames Laboratory; Johnson, Duane D [Ames Laboratory

    2014-08-01

    Nitinol (NiTi), the most widely used shape-memory alloy, exhibits an austenite phase that has yet to be identified. The usually assumed austenitic structure is cubic B2, which has imaginary phonon modes, hence it is unstable. We suggest a stable austenitic structure that “on average” has B2 symmetry (observed by x-ray and neutron diffraction), but it exhibits finite atomic displacements from the ideal B2 sites. The proposed structure has a phonon spectrum that agrees with that from neutron scattering, has diffraction spectra in agreement with x-ray diffraction, and has an energy relative to the ground state that agrees with calorimetry data.

  9. 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

  10. 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.

  11. 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

  12. 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)

  13. 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)

  14. 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)

  15. 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,...

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. The crystal structure of samarosporin I at atomic resolution.

    Science.gov (United States)

    Gessmann, Renate; Axford, Danny; Evans, Gwyndaf; Brückner, Hans; Petratos, Kyriacos

    2012-11-01

    The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.

  1. 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...

  2. Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy

    Science.gov (United States)

    Urban, Knut W.

    2008-07-01

    Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations.

  3. 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.

  4. 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.

  5. 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...

  6. 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.

  7. 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.

  8. 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

  9. Understanding the structure of the first atomic contact in gold.

    Science.gov (United States)

    Sabater, Carlos; Caturla, María José; Palacios, Juan José; Untiedt, Carlos

    2013-01-01

    : We have studied experimentally jump-to-contact (JC) and jump-out-of-contact (JOC) phenomena in gold electrodes. JC can be observed at first contact when two metals approach each other, while JOC occurs in the last contact before breaking. When the indentation depth between the electrodes is limited to a certain value of conductance, a highly reproducible behaviour in the evolution of the conductance can be obtained for hundreds of cycles of formation and rupture. Molecular dynamics simulations of this process show how the two metallic electrodes are shaped into tips of a well-defined crystallographic structure formed through a mechanical annealing mechanism. We report a detailed analysis of the atomic configurations obtained before contact and rupture of these stable structures and obtained their conductance using first-principles quantum transport calculations. These results help us understand the values of conductance obtained experimentally in the JC and JOC phenomena and improve our understanding of atomic-sized contacts and the evolution of their structural characteristics. PMID:23718316

  10. AMO Database in KAERI and Atomic Structure Studies

    Science.gov (United States)

    Rhee, Yongjoo; Park, H. M.; Kwon, D. H.

    2005-05-01

    Atomic spectroscopy studies carried out at the Laboratory for Quantum Optics in Korea Atomic Energy Research Institute are introduced together with the AMO (Atomic, Molecular, and Optical) database established based upon those studies.

  11. Direct observation of a long-lived single-atom catalyst chiseling atomic structures in graphene.

    Science.gov (United States)

    Wang, Wei Li; Santos, Elton J G; Jiang, Bin; Cubuk, Ekin Dogus; Ophus, Colin; Centeno, Alba; Pesquera, Amaia; Zurutuza, Amaia; Ciston, Jim; Westervelt, Robert; Kaxiras, Efthimios

    2014-02-12

    Fabricating stable functional devices at the atomic scale is an ultimate goal of nanotechnology. In biological processes, such high-precision operations are accomplished by enzymes. A counterpart molecular catalyst that binds to a solid-state substrate would be highly desirable. Here, we report the direct observation of single Si adatoms catalyzing the dissociation of carbon atoms from graphene in an aberration-corrected high-resolution transmission electron microscope (HRTEM). The single Si atom provides a catalytic wedge for energetic electrons to chisel off the graphene lattice, atom by atom, while the Si atom itself is not consumed. The products of the chiseling process are atomic-scale features including graphene pores and clean edges. Our experimental observations and first-principles calculations demonstrated the dynamics, stability, and selectivity of such a single-atom chisel, which opens up the possibility of fabricating certain stable molecular devices by precise modification of materials at the atomic scale.

  12. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    Science.gov (United States)

    Colvin, Michael T; Silvers, Robert; Ni, Qing Zhe; Can, Thach V; Sergeyev, Ivan; Rosay, Melanie; Donovan, Kevin J; Michael, Brian; Wall, Joseph; Linse, Sara; Griffin, Robert G

    2016-08-01

    Amyloid-β (Aβ) is a 39-42 residue protein produced by the cleavage of the amyloid precursor protein (APP), which subsequently aggregates to form cross-β amyloid fibrils that are a hallmark of Alzheimer's disease (AD). The most prominent forms of Aβ are Aβ1-40 and Aβ1-42, which differ by two amino acids (I and A) at the C-terminus. However, Aβ42 is more neurotoxic and essential to the etiology of AD. Here, we present an atomic resolution structure of a monomorphic form of AβM01-42 amyloid fibrils derived from over 500 (13)C-(13)C, (13)C-(15)N distance and backbone angle structural constraints obtained from high field magic angle spinning NMR spectra. The structure (PDB ID: 5KK3 ) shows that the fibril core consists of a dimer of Aβ42 molecules, each containing four β-strands in a S-shaped amyloid fold, and arranged in a manner that generates two hydrophobic cores that are capped at the end of the chain by a salt bridge. The outer surface of the monomers presents hydrophilic side chains to the solvent. The interface between the monomers of the dimer shows clear contacts between M35 of one molecule and L17 and Q15 of the second. Intermolecular (13)C-(15)N constraints demonstrate that the amyloid fibrils are parallel in register. The RMSD of the backbone structure (Q15-A42) is 0.71 ± 0.12 Å and of all heavy atoms is 1.07 ± 0.08 Å. The structure provides a point of departure for the design of drugs that bind to the fibril surface and therefore interfere with secondary nucleation and for other therapeutic approaches to mitigate Aβ42 aggregation. PMID:27355699

  13. A theoretical study of the atomic and electronic structures of three prospective atomic scale wire systems

    CERN Document Server

    Shevlin, S A

    2001-01-01

    transport properties of the line are also calculated. Finally we find which of the two models of the (4x1)-Si(111)-ln reconstruction is thermodynamically favoured in a supercell geometry. We use ab initio plane wave techniques in the Local-Density-Approximation, and calculate and compare the electronic structure of the two models with respect to the characteristic energies for electron dispersion along and across the chain structures. We also consider the effects of electronic structure on the in-plane transport properties of the indium lines. The structural and electronic properties of several candidate atomic scale wires are analysed. Three candidates are studied: the trans-polyacetylene molecule, the silicon line on the (001) face of cubic silicon carbide (the (nx2) series of reconstructions) and the indium chain on the (111) face of silicon carbide (the (4x1) reconstruction). We use the polyacetylene molecule as a test-bed for the techniques that we use to calculate transport properties in an empirically ...

  14. 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...

  15. 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

  16. 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.

  17. Embedded atom study of dislocation core structure in Fe

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D.; Rodriguez, P.L. (Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering Centro Atomico Bariloche (Argentina))

    1994-04-01

    The relaxed atomistic structure of dislocation cores in body centered cubic metals was investigated many years ago, using pair potentials. These studies are now classic and have been the basis for understanding mechanical behavior of these materials. They constitute the classic example of the importance of non-elastic core effect for the dislocations responsible for deformation, as described in several reviews written on the subject. Volume-dependent interatomic potentials were introduced in 1984. Despite the importance of the results obtained with pair potentials, no calculation of dislocation cores in pure bcc metals using volume-dependent interatomic potentials has yet been performed. The purpose of the present investigation is to compute the structures of 1/2[111] screw dislocation cores Fe. The objective is to compare these results with the structures obtained with pair potentials. The computation of Peierls stresses with pair potentials usually gives an overestimate of the actual Peierls stress. In the present work, they also use an improved boundary condition technique for the simulation of the dislocation cores can give more accurate Peierls stresses using manageable atomic block sizes. They also use a more recent graphical method for the representation of the core structures to obtain the information on the core structures and their relationship to the various crystallographic planes in the material and to analyze the shape of core in relation with the possible glide planes of the dislocation.

  18. 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. [...

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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...

  12. 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, ...

  13. Rotational Spectrum and Carbon Atom Structure of Dihydroartemisinic Acid

    Science.gov (United States)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Dihydroartemisinic acid (DHAA, C15H24O2, five chiral centers) is a precursor in proposed low-cost synthetic routes to the antimalarial drug artemisinin. In one reaction process being considered in pharmaceutical production, DHAA is formed from an enantiopure sample of artemisinic acid through hydrogenation of the alkene. This reaction needs to properly set the stereochemistry of the asymmetric carbon for the synthesis to produce artemisinin. A recrystallization process can purify the diastereomer mixture of the hydrogenation reaction if the unwanted epimer is produced in less than 10% abundance. There is a need in the process analytical chemistry to rapidly (less than 1 min) measure the diastereomer excess and current solutions, such a HPLC, lack the needed measurement speed. The rotational spectrum of DHAA has been measured at 300:1 signal-to-noise ratio in a chirped-pulsed Fourier transform microwave spectrometer operating from 2-8 GHz using simple heating of the compound. The 13C isotope analysis provides a carbon atom structure that confirms the diastereomer. This structure is in excellent agreement with quantum chemistry calculations at the B2PLYPD3/ 6-311++G** level of theory. The DHAA spectrum is expected to be fully resolved from the unwanted diastereomer raising the potential for fast diastereomer excess measurement by rotational spectroscopy in the pharmaceutical production process.

  14. A near atomic structure of the active human apoptosome

    Science.gov (United States)

    Cheng, Tat Cheung; Hong, Chuan; Akey, Ildikó V; Yuan, Shujun; Akey, Christopher W

    2016-01-01

    In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease. DOI: http://dx.doi.org/10.7554/eLife.17755.001

  15. 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

  16. 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.

  17. 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.

  18. Voronoi analysis of the short-range atomic structure in iron and iron-carbon melts

    Science.gov (United States)

    Sobolev, Andrey; Mirzoev, Alexander

    2015-08-01

    In this work, we simulated the atomic structure of liquid iron and iron-carbon alloys by means of ab initio molecular dynamics. Voronoi analysis was used to highlight changes in the close environments of Fe atoms as carbon concentration in the melt increases. We have found, that even high concentrations of carbon do not affect short-range atomic order of iron atoms — it remains effectively the same as in pure iron melts.

  19. Atomic structure of intracellular amorphous calcium phosphate deposits.

    Science.gov (United States)

    Betts, F; Blumenthal, N C; Posner, A S; Becker, G L; Lehninger, A L

    1975-06-01

    The radial distribution function calculated from x-ray diffraction of mineralized cytoplasmic structures isolated from the hepatopancreas of the blue crab (Callinectes sapidus) is very similar to that previously found for synthetic amorphous calcium phosphate. Both types of mineral apparently have only short-range atomic order, represented as a neutral ion cluster of about 10 A in longest dimension, whose probable composition is expressed by the formula Ca9(PO4)6. The minor differences observed are attributed to the presence in the biological mineral of significant amounts of Mg-2+ and ATP. Synthetic amorphous calcium phosphate in contact with a solution containing an amount of ATP equivalent to that of the biological mineral failed to undergo conversion to the thermodynamically more stable hydroxyapatite. The amorphous calcium phosphate of the cytoplasmic mineral granules is similarly stable, and does not undergo conversion to hydroxyapatite, presumably owing to the presence of ATP and Mg-2+, known in inhibitors of the conversion process. The physiological implications of mineral deposits consisting of stabilized calcium phosphate ion clusters are discussed.

  20. 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

  1. 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.

  2. 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.

  3. Atomic structure of machined semiconducting chips: An x-ray absorption spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Paesler, M.; Sayers, D.

    1988-12-01

    X-ray absorption spectroscopy (XAS) has been used to examine the atomic structure of chips of germanium that were produced by single point diamond machining. It is demonstrated that although the local (nearest neighbor) atomic structure is experimentally quite similar to that of single crystal specimens information from more distant atoms indicates the presence of considerable stress. An outline of the technique is given and the strength of XAS in studying the machining process is demonstrated.

  4. 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...

  5. 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

  6. 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)

  7. Analysis of Nanometer Structure for Chromium Atoms in Gauss Standing Laser Wave

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wen-Tao; ZHU Bao-Hua; XIONG Xian-Ming

    2010-01-01

    @@ The equation of motion of two-level chromium atoms in Gauss standing laser wave is discussed and the distribution of chromium atoms is given under different transverse velocity conditions.The results show that the focusing position of atoms will be affected by the transverse velocity of atoms.Based on the four-order Runge-Kutta method,the locus of chromium atoms in Gauss standing laser wave is simulated.The three-dimensional characteristics of nanometer structures are stimulated under perfect and emanative conditions.

  8. 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.

  9. 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

  10. Structure and transport properties of atomic chains and molecules

    DEFF Research Database (Denmark)

    Strange, Mikkel

    2008-01-01

    of atomically thin, suspended chains containing silver and oxygen atoms in an alternating sequence has been studied. The conductances of the chains exhibit weak even-odd oscillations around an anomalously low value of 0.1G0 (G0 = 2e2/h) in agreement with experiments [1] in the long chain limit. These unusual...... conductance properties are explained in terms of a resonating-chain model, which takes the reflection probability and phase-shift of a single bulk-chain interface as the only input. The stability of silver-oxygen chains was studied with a thermodynamic model. This model has been developed in this work...... plane-wave code Dacapo [2] in combination with maximally localized Wannier functions and the norm-conserving pseudopotential code Siesta [3]which applies an atomic orbital basis set. For the systems studied we find that the Siesta transmission functions converge toward the plane-wave result...

  11. Atomic structure of threading dislocations in AlN thin films

    Energy Technology Data Exchange (ETDEWEB)

    Tokumoto, Yuki, E-mail: y.tokumoto@imr.tohoku.ac.j [Institute for Materials Research, Tohoku University, 2-1-2, Katahira, Aoba-ku, Sendai 980-8577 (Japan); Shibata, Naoya [Institute of Engineering Innovation, School of Engineering, University of Tokyo, 2-11-16, Yayoi, Bunkyo, Tokyo 113-8656 (Japan); PRESTO, JST, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012 (Japan); Mizoguhci, Teruyasu [Institute of Engineering Innovation, School of Engineering, University of Tokyo, 2-11-16, Yayoi, Bunkyo, Tokyo 113-8656 (Japan); Yamamoto, Takahisa [Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8651 (Japan); Ikuhara, Yuichi [Institute of Engineering Innovation, School of Engineering, University of Tokyo, 2-11-16, Yayoi, Bunkyo, Tokyo 113-8656 (Japan); WPI Advanced Institute for Materials Research, Tohoku University, 2-1-2, Katahira, Aoba-ku, Sendai 980-8577 (Japan)

    2009-12-15

    The core structure of threading dislocations in AlN films was investigated by atomic-resolution scanning transmission electron microscopy. The threading dislocations in the AlN films were found to be mostly edge-type perfect dislocations. It was directly revealed that the edge dislocation core has the 8-atom ring structure which is an energetically favorable structure predicted by previous theoretical studies.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. Boundary Collisions of Slow Atoms with Two-dimensional Hexagonal Structure

    Directory of Open Access Journals (Sweden)

    A.S. Dolgov

    2014-11-01

    Full Text Available It is shown that location of target atoms, specified by the structure geometry, define the distribution of impact parameters and energy transfer which strongly differs from the distribution of random location of targets. Considering model of solid spheres, energy spectrum of reflected atoms and probability of single or multiple collisions with the structure are found. Increase in the energy efficiency with respect to the disordered structure is established. Possibility and conditions of realizations of collisions with the second layer atoms omitting first ones are demonstrated.

  17. Realizing high magnetic moments in fcc Fe nanoparticles through atomic structure stretch.

    Science.gov (United States)

    Baker, S H; Roy, M; Thornton, S C; Binns, C

    2012-05-01

    We describe the realization of a high moment state in fcc Fe nanoparticles through a controlled change in their atomic structure. Embedding Fe nanoparticles in a Cu(1-x)Au(x) matrix causes their atomic structure to switch from bcc to fcc. Extended x-ray absorption fine structure (EXAFS) measurements show that the structure in both the matrix and the Fe nanoparticles expands as the amount of Au in the matrix is increased, with the data indicating a tetragonal stretch in the Fe nanoparticles. The samples were prepared directly from the gas phase by co-deposition, using a gas aggregation source and MBE-type sources respectively for the nanoparticle and matrix materials. The structure change in the Fe nanoparticles is accompanied by a sharp increase in atomic magnetic moment, ultimately to values of ~2.5 ± 0.3 μ(B)/atom .

  18. 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...

  19. 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'…

  20. 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…

  1. 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.

  2. 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.

  3. 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).

  4. 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)

  5. 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.

  6. 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)

  7. 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.

  8. 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...

  9. 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.

  10. 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.

  11. 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).

  12. 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.

  13. 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)

  14. 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.

  15. 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.

  16. 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.

  17. 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)

  18. 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...

  19. Spectral fine structure of the atomic ground states based on full relativistic theory

    Institute of Scientific and Technical Information of China (English)

    Zhenghe Zhu; Yongjian Tang

    2011-01-01

    @@ We focus on the full relativistic quantum mechanical calculations from boron to fluorine atoms with electronic configuration of 1s22s22pn (n = 1, 2, 3, 4, and 5), where 1s22s2 is the closed shell and 2pn is the open shell. Their active electrons in the open shell occupy all the six spinors as far as possible.Therefore, we suggest a new rule called "maximum probability" for the full symmetry group relativistic theory. Furthermore, the spectral fine structure of the atomic ground states based on the full relativistic theory and their intervals of L-S splitting are all reasonable. It is impossible to calculate the L-S splitting through non-relativistic quantum mechanics. The relativistic effect of atomic mass is increased significantly by about 12 folds from boron atom to fluorine atom.%We focus on the full relativistic quantum mechanical calculations from boron to fluorine atoms with electronic configuration of 1s22s22pn (n = 1, 2, 3, 4, and 5), where 1s22s2 is the closed shell and 2pn is the open shell. Their active electrons in the open shell occupy all the six spinors as far as possible.Therefore, we suggest a new rule called "maximum probability" for the full symmetry group relativistic theory. Furthermore, the spectral fine structure of the atomic ground states based on the full relativistic theory and their intervals of L-S splitting are all reasonable. It is impossible to calculate the L-S splitting through non-relativistic quantum mechanics. The relativistic effect of atomic mass is increased significantly by about 12 folds from boron atom to fluorine atom.

  20. 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.

  1. Local atomic structure in equilibrium and supercooled liquid Zr(75.5)Pd(24.5).

    Science.gov (United States)

    Mauro, N A; Fu, W; Bendert, J C; Cheng, Y Q; Ma, E; Kelton, K F

    2012-07-28

    Atomic structures were obtained in equilibrium and supercooled eutectic Zr(75.5)Pd(24.5) liquids by in situ high-energy synchrotron diffraction measurements using the beamline electrostatic levitation (BESL) technique, which provides a high-vacuum, containerless, environment. Reverse Monte Carlo fits to the x-ray static structure factors, constrained using partial pair correlation functions obtained from ab initio molecular dynamics simulations, indicate the presence of medium-range order (MRO) in the form of a strong tendency for Pd-Pd (solute-solute) avoidance. This order persists over the entire temperature range studied, from 170 °C above the equilibrium liquidus temperature to 263 °C below it. Further, a quantitative analysis of the atomic structures obtained indicates a modest degree of icosahedral-like local order around Pd atoms, with the clusters showing an increased tendency for face-sharing to form more extended structures with decreasing temperature. PMID:22852625

  2. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis

    Science.gov (United States)

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-01-01

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts. PMID:27650485

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

    Institute of Scientific and Technical Information of China (English)

    Yuanyuan Li; Yanpeng Zhang; Chenli Gan

    2005-01-01

    Transmission sub-Doppler spectroscopy with confined atomic vapor film between two dielectric walls is theoretically studied. Because of atoms flying from wall to wall, where they get de-excited, the atomfield interaction time is anisotropic so that the contribution of slow atoms is enhanced, a sub-Doppler transmission spectroscopy (Dicke narrowing effect) can be obtained when the thickness of the film is much small or comparable with the wavelength even at small angle oblique incidence. It is feasible to get a sub-Doppler structure in a new region (L <λ/4) in experiments.

  5. 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

  6. 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.

  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. Atomic and electronic structure of MoS2 nanoparticles

    DEFF Research Database (Denmark)

    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 e......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...

  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. 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.

  12. 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…

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

    DEFF Research Database (Denmark)

    Wang, Yun; Chi, Qijin; Zhang, Jingdong;

    2011-01-01

    Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111): di...

  14. Atomic structure of (111) twist grain boundaries in f.c.c. metals

    NARCIS (Netherlands)

    Hosson, J.Th.M. De; Vitek, V.

    1990-01-01

    In this paper we have studied the atomic structures of (111) twist boundaries and investigated the applicability of the structural unit model which has previously been established for tilt boundaries and (001) twist boundaries. The calculations were carried out using two different descriptions of in

  15. 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 ...

  16. 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.

  17. Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Nina A. Filenko

    2012-01-01

    Full Text Available Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their population was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.

  18. Correlating atomic structure and transport in suspended graphene nanoribbons.

    Science.gov (United States)

    Qi, Zhengqing John; Rodríguez-Manzo, Julio A; Botello-Méndez, Andrés R; Hong, Sung Ju; Stach, Eric A; Park, Yung Woo; Charlier, Jean-Christophe; Drndić, Marija; Johnson, A T Charlie

    2014-08-13

    Graphene nanoribbons (GNRs) are promising candidates for next generation integrated circuit (IC) components; this fact motivates exploration of the relationship between crystallographic structure and transport of graphene patterned at IC-relevant length scales (edges after current annealing, presenting a pathway for the controlled fabrication of semiconducting GNRs with known edge geometry. Finally, we report on simulations of quantum transport in GNRs that are in qualitative agreement with the observations.

  19. 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...

  20. 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

  1. 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.

  2. 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 ...

  3. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    Science.gov (United States)

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous-crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  4. 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...

  5. Atomic structure of icosahedral B4C boron carbide from a first principles analysis of NMR spectra.

    Science.gov (United States)

    Mauri, F; Vast, N; Pickard, C J

    2001-08-20

    Density functional theory is demonstrated to reproduce the 13C and 11B NMR chemical shifts of icosahedral boron carbides with sufficient accuracy to extract previously unresolved structural information from experimental NMR spectra. B4C can be viewed as an arrangement of 3-atom linear chains and 12-atom icosahedra. According to our results, all the chains have a CBC structure. Most of the icosahedra have a B11C structure with the C atom placed in a polar site, and a few percent have a B (12) structure or a B10C2 structure with the two C atoms placed in two antipodal polar sites.

  6. 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.)

  7. 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.

  8. 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.

  9. Interaction and dynamics of add-atoms with 2-dimensional structures

    CERN Multimedia

    The interaction and dynamics of add-atoms with graphene, graphene-derivate structures and, later, MoSi$_2$, two-dimensional – single and few – atomic layers will be studied with the Perturbed Angular Correlation – PAC – technique. Graphene is also envisaged as new platform for growing semiconductor nanostructure devices, such as quantum dots and as a particularly powerful catalyst. Understanding nucleation of nanostructures and clusters on graphene and related phases in wet conditions as they are used in chemical methods in research and industry require complementary studies. These systems will therefore be studied systematically using radioactive probe atoms attaching via a transfer media (e.g., water in catalysis process) or being deposited with soft-landing techniques under vacuum and UHV conditions, as put in place at the ASPIC setup at ISOLDE. The hyperfine fields obtained under different environments are expected to reveal basic information on the rich atomic and physical mechanisms associated w...

  10. Local atomic structure in tetragonal pure ZrO{sub 2} nanopowders

    Energy Technology Data Exchange (ETDEWEB)

    Acuna, Leandro M.; Lamas, Diego G.; Fuentes, Rodolfo O.; Fabregas, Ismael O. [CITEFA-CONICET, Villa Martelli, Provincia de Buenos Aires (AR). CINSO (Centro de Investigaciones en Solidos); Fantini, Marcia C.A.; Craievich, Aldo F. [Universidade de Sao Paulo (Brazil). Inst. de Fisica; Prado, Rogerio J. [Universidade Federal de Mato Grosso (UFMT), Cuiaba (Brazil). Inst. de Fisica

    2010-04-15

    The local atomic structures around the Zr atom of pure (undoped) ZrO{sub 2} nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wetchemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO{sub 2} nanopowders can be described by a model consisting of two oxygen subshells (4+4 atoms) with different Zr-O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye-Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4+2+2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments. (orig.)

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

    Energy Technology Data Exchange (ETDEWEB)

    Schnohr, C. S., E-mail: c.schnohr@uni-jena.de [Institut für Festkörperphysik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena (Germany)

    2015-09-15

    Compound semiconductor alloys such as In{sub x}Ga{sub 1−x}As, GaAs{sub x}P{sub 1−x}, or CuIn{sub x}Ga{sub 1−x}Se{sub 2} 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-VI{sub 2} 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.

  12. 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.

  13. The role of Co atoms in spin dependent electronic properties of graphite-like ZnO structures

    Energy Technology Data Exchange (ETDEWEB)

    Caliskan, S., E-mail: scaliskan@fatih.edu.tr; Guner, S.

    2015-01-01

    A first principles study is employed to reveal the electronic properties of graphite-like Co doped ZnO structures composed of atomic layers when spin property of electrons is involved. The influence of Co atoms, which are substituting the Zn atoms, was addressed through distinct atomic arrangements formed by specific atomic configurations and various Co concentrations. We obtained that the spin dependent behavior is largely determined by the atomic arrangement which can crucially impact the electronic structure for a certain spin orientation. It was observed that atomic configuration is an essential factor which may reduce or enhance the minority-spin energy gap relative to majority one. It was shown that the emerging spin polarization can be manipulated by the atomic arrangement of the layered structures. Both the spin polarization and the magnetic moment were found to be contributed by both Co and O atoms. The stability of a system via formation energy, the role of Co dopants positioned at different Zn sites, the number of both Co atoms and layers in a supercell, and the mechanisms governing the spin dependent behavior of these structures are discussed. - Highlights: • Co dopants at distinct locations yield crucial changes in spin dependent behavior. • Spin dependent behavior is determined by atomic arrangement in Co doped ZnO systems. • Atomic configuration and Co concentration play a crucial role on minority band gap. • The magnetic moment is mostly contributed by Co-3d and O-2p orbitals.

  14. 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.

  15. The Lattice Kinetic Monte Carlo Simulation of Atomic Diffusion and Structural Transition for Gold

    Science.gov (United States)

    He, Xiang; Cheng, Feng; Chen, Zhao-Xu

    2016-01-01

    For the kinetic simulation of metal nanoparticles, we developed a self-consistent coordination-averaged energies for Au atoms based on energy properties of gold bulk phases. The energy barrier of the atom pairing change is proposed and holds for the microscopic reversibility principle. By applying the lattice kinetic Monte Carlo simulation on gold films, we found that the atomic diffusion of Au on the Au(111) surface undergoes a late transition state with an energy barrier of about 0.2 eV and a prefactor between 40~50 Å2/ps. This study also investigates the structural transition from spherical to faceted gold nanoparticles upon heating. The temperatures of structural transition are in agreement with the experimental melting temperatures of gold nanoparticles with diameters ranging from 2 nm to 8 nm. PMID:27629538

  16. The Lattice Kinetic Monte Carlo Simulation of Atomic Diffusion and Structural Transition for Gold.

    Science.gov (United States)

    He, Xiang; Cheng, Feng; Chen, Zhao-Xu

    2016-01-01

    For the kinetic simulation of metal nanoparticles, we developed a self-consistent coordination-averaged energies for Au atoms based on energy properties of gold bulk phases. The energy barrier of the atom pairing change is proposed and holds for the microscopic reversibility principle. By applying the lattice kinetic Monte Carlo simulation on gold films, we found that the atomic diffusion of Au on the Au(111) surface undergoes a late transition state with an energy barrier of about 0.2 eV and a prefactor between 40~50 Å(2)/ps. This study also investigates the structural transition from spherical to faceted gold nanoparticles upon heating. The temperatures of structural transition are in agreement with the experimental melting temperatures of gold nanoparticles with diameters ranging from 2 nm to 8 nm. PMID:27629538

  17. 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...

  18. Atomically precise self-assembly of one-dimensional structures on silicon

    Science.gov (United States)

    Barke, I.; Rügheimer, T. K.; Zheng, Fan; Himpsel, F. J.

    2007-10-01

    This work has three main themes: (1) fabricate atomically precise nanostructures at surfaces, particularly nanowires consisting of atom chains; (2) explore the behavior of one-dimensional electrons in atomic chains; (3) find the fundamental limits of data storage using an atomic scale memory. Semiconductor surfaces lend themselves towards self-assembly, because the broken covalent bonds create elaborate reconstruction patterns to minimize the surface energy. An example is the large 7 × 7 unit cell on Si(1 1 1), which can be used as building block. On semiconductors, the surface electrons completely de-couple from the substrate, as long as their energy lies in the band gap. Angle-resolved photoemission reveals surprising features, such as a fractional band filling and a spin-splitting at a non-magnetic surface. An interesting by-product is a memory structure with self-assembled tracks that are five atom rows wide and store a bit by the presence or absence of a single silicon atom. This toy memory is used to test the fundamental limits of data storage and to see how storage on silicon compares to storage in DNA.

  19. Atomic structure and phason modes of the Sc-Zn icosahedral quasicrystal.

    Science.gov (United States)

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-07-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = -0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye-Waller factor, which explains the vanishing of 'high-Q perp' reflections. PMID:27437112

  20. Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

    Science.gov (United States)

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-01-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of ‘high-Q perp’ reflections. PMID:27437112

  1. 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...

  2. Understanding the proton radius puzzle: Nuclear structure effects in light muonic atoms

    CERN Document Server

    Ji, Chen; Dinur, Nir Nevo; Bacca, Sonia; Barnea, Nir

    2015-01-01

    We present calculations of nuclear structure effects to the Lamb shift in light muonic atoms. We adopt a modern ab-initio approach by combining state-of-the-art nuclear potentials with the hyperspherical harmonics method. Our calculations are instrumental to the determination of nuclear charge radii in the Lamb shift measurements, which will shed light on the proton radius puzzle.

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

    Directory of Open Access Journals (Sweden)

    Oscar Martínez-Santiago

    2016-05-01

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

  4. Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

    Directory of Open Access Journals (Sweden)

    Tsunetomo Yamada

    2016-07-01

    Full Text Available The detailed atomic structure of the binary icosahedral (i ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP, both resulting from a close-packing of a large (Sc and a small (Zn atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K2/K1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason Debye–Waller factor, which explains the vanishing of `high-Qperp' reflections.

  5. Mechanical deformation of atomic-scale metallic contacts: Structure and mechanisms

    DEFF Research Database (Denmark)

    Sørensen, Mads Reinholdt; Brandbyge, Mads; Jacobsen, Karsten Wedel

    1998-01-01

    We have simulated the mechanical deformation of atomic-scale metallic contacts under tensile strain using molecular dynamics and effective medium theory potentials. The evolution of the structure of the contacts and the underlying deformation mechanisms are described along with the calculated ele...

  6. Imaging the atomic surface structures of CeO2 nanoparticles

    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

    2014-01-01

    Atomic surface structures of CeO2 nanoparticles are under debate owing to the lack of clear experimental determination of the positions of the surface oxygen atoms. Particularly controversial is the (100) surface structure of this material. In this study, with oxygen atoms clearly observed using aberration corrected high resolution electron microscopy, we determined the atomic structures of the (100), (110) and (111) surfaces of CeO2 nanocubes. The predominantly exposed (100) surface has a mixture of Ce, O, and reduced CeO terminations, underscoring the complex structures of this polar surface that previously was often oversimplified. The (110) surface shows saw-like (111) nanofacets and flat CeO2-x terminations with oxygen vacancies. The (111) surface has an O termination. As these three low index surfaces are the most often exposed facets in the majority of CeO2 nanoparticles, these findings can be extended to the surfaces of differently shaped CeO2 nanoparticles as well as provide insight about face-selective catalysis.

  7. 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…

  8. 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)

  9. 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

  10. 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…

  11. 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.

  12. 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.

  13. 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.

  14. 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)

  15. 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

  16. 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.

  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. Infrared image recognition based on structure sparse and atomic sparse parallel

    Science.gov (United States)

    Wu, Yalu; Li, Ruilong; Xu, Yi; Wang, Liping

    2015-12-01

    Use the redundancy of the super complete dictionary can capture the structural features of the image effectively, can achieving the effective representation of the image. However, the commonly used atomic sparse representation without regard the structure of the dictionary and the unrelated non-zero-term in the process of the computation, though structure sparse consider the structure feature of dictionary, the majority coefficients of the blocks maybe are non-zero, it may affect the identification efficiency. For the disadvantages of these two sparse expressions, a weighted parallel atomic sparse and sparse structure is proposed, and the recognition efficiency is improved by the adaptive computation of the optimal weights. The atomic sparse expression and structure sparse expression are respectively, and the optimal weights are calculated by the adaptive method. Methods are as follows: training by using the less part of the identification sample, the recognition rate is calculated by the increase of the certain step size and t the constraint between weight. The recognition rate as the Z axis, two weight values respectively as X, Y axis, the resulting points can be connected in a straight line in the 3 dimensional coordinate system, by solving the highest recognition rate, the optimal weights can be obtained. Through simulation experiments can be known, the optimal weights based on adaptive method are better in the recognition rate, weights obtained by adaptive computation of a few samples, suitable for parallel recognition calculation, can effectively improve the recognition rate of infrared images.

  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

    2016-05-01

    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

  20. 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.……

  1. 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.

  2. 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 ...

  3. 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.

  4. 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

  5. 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 ...

  6. 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.

  7. 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

  8. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    Science.gov (United States)

    Kahn, L. R.

    1981-01-01

    A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

  9. 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.)

  10. 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.

  11. Atom exchange between aqueous Fe(II) and structural Fe in clay minerals.

    Science.gov (United States)

    Neumann, Anke; Wu, Lingling; Li, Weiqiang; Beard, Brian L; Johnson, Clark M; Rosso, Kevin M; Frierdich, Andrew J; Scherer, Michelle M

    2015-03-01

    Due to their stability toward reductive dissolution, Fe-bearing clay minerals are viewed as a renewable source of Fe redox activity in diverse environments. Recent findings of interfacial electron transfer between aqueous Fe(II) and structural Fe in clay minerals and electron conduction in octahedral sheets of nontronite, however, raise the question whether Fe interaction with clay minerals is more dynamic than previously thought. Here, we use an enriched isotope tracer approach to simultaneously trace Fe atom movement from the aqueous phase to the solid ((57)Fe) and from the solid into the aqueous phase ((56)Fe). Over 6 months, we observed a significant decrease in aqueous (57)Fe isotope fraction, with a fast initial decrease which slowed after 3 days and stabilized after about 50 days. For the aqueous (56)Fe isotope fraction, we observed a similar but opposite trend, indicating that Fe atom movement had occurred in both directions: from the aqueous phase into the solid and from the solid into aqueous phase. We calculated that 5-20% of structural Fe in clay minerals NAu-1, NAu-2, and SWa-1 exchanged with aqueous Fe(II), which significantly exceeds the Fe atom layer exposed directly to solution. Calculations based on electron-hopping rates in nontronite suggest that the bulk conduction mechanism previously demonstrated for hematite1 and suggested as an explanation for the significant Fe atom exchange observed in goethite2 may be a plausible mechanism for Fe atom exchange in Fe-bearing clay minerals. Our finding of 5-20% Fe atom exchange in clay minerals indicates that we need to rethink how Fe mobility affects the macroscopic properties of Fe-bearing phyllosilicates and its role in Fe biogeochemical cycling, as well as its use in a variety of engineered applications, such as landfill liners and nuclear repositories.

  12. Structural Evidence for α-Synuclein Fibrils Using in Situ Atomic Force Microscopy

    Institute of Scientific and Technical Information of China (English)

    Feng ZHANG; Li-Na JI; Lin TANG; Jun HU; Hong-Yu HU; Hong-Jie XU; Jian-Hua HE

    2005-01-01

    Human α-synuclein is a presynaptic terminal protein and can form insoluble fibrils that are believed to play an important role in the pathogenesis of several neurodegenerafive diseases such as Parkinson's disease, dementia with Lewy bodies and Lewy body variant of Alzheimer's disease. In this paper, in situ atomic force microscopy has been used to study the structural properties of α-synuclein fibrils in solution using two different atomic force microscopy imaging modes: tapping mode and contact mode. In the in situ contact mode atomic force microscopy experiments α-synuclein fibrils quickly broke into fragments, and a similar phenomenon was found using tapping mode atomic force microscopy in which α-synuclein fibrils were incubated with guanidine hydrochloride (0.6 M). The α-synuclein fibrils kept their original filamentous topography for over 1 h in the in situ tapping mode atomic force microscopy experiments. The present results provide indirect evidence on how β-sheets assemble into α-synuclein fibrils on a nanometer scale.

  13. 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.

  14. Atomic force microscopy studies of domain structures in phase-separated monolayers

    Science.gov (United States)

    Xiao, Shou-Jun; Wu, Hai-Ming; Yang, Xiao-Min; Wei, Yu; Tai, Zi-Hou; Sun, Xing-Zhong

    1994-10-01

    Domain structures were studied with atomic force microscopy (AFM) in binary phase-separated monolayer films composed of 5, 10, 15-triphenyl-20-(4-dl-α-phenylalanylamindo) phenyl porphyrin (TPPP) and one of a series of fatty acids which are arachidic acid (AA), palmitic acid (PA), and lauric acid (LA). The liquid-condensed (LC) domain structures of AA and PA were observed in their corresponding mixed monolayers. However, instead of the fatty acid domain, a liquid-expanded (LE) domain structure of TPPP appears in the mixed monolayer of LA/TPPP.

  15. 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

  16. Atomic-Scale Observations of Catalyst Structures under Reaction Conditions and during Catalysis.

    Science.gov (United States)

    Tao, Franklin Feng; Crozier, Peter A

    2016-03-23

    Heterogeneous catalysis is a chemical process performed at a solid-gas or solid-liquid interface. Direct participation of catalyst atoms in this chemical process determines the significance of the surface structure of a catalyst in a fundamental understanding of such a chemical process at a molecular level. High-pressure scanning tunneling microscopy (HP-STM) and environmental transmission electron microscopy (ETEM) have been used to observe catalyst structure in the last few decades. In this review, instrumentation for the two in situ/operando techniques and scientific findings on catalyst structures under reaction conditions and during catalysis are discussed with the following objectives: (1) to present the fundamental aspects of in situ/operando studies of catalysts; (2) to interpret the observed restructurings of catalyst and evolution of catalyst structures; (3) to explore how HP-STM and ETEM can be synergistically used to reveal structural details under reaction conditions and during catalysis; and (4) to discuss the future challenges and prospects of atomic-scale observation of catalysts in understanding of heterogeneous catalysis. This Review focuses on the development of HP-STM and ETEM, the in situ/operando characterizations of catalyst structures with them, and the integration of the two structural analytical techniques for fundamentally understanding catalysis.

  17. 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

  18. First-principles calculations atomic structure and elastic properties of Ti-Nb alloys

    CERN Document Server

    Timoshevskii, A N; Ivasishin, O M

    2011-01-01

    Elastic properties of Ti based \\beta-alloy were studied by the method of the model structure first principle calculations. Concentrational dependence of Young modulus for the binary \\beta-alloy Ti-Nb was discovered. It is shown that peculiarities visible at 15-18% concentrations can be related to the different Nb atoms distribution. Detailed comparison of the calculation results with the measurement results was done. Young modulus for the set of the ordered structures with different Nb atoms location, which simulate triple \\beta-alloys Ti-29.7%Zr-18.5%Nb and Ti-51.8%Zr-18.5%Nb have been calculated. The results of these calculations allowed us to suggest the concentration region for single-phase ternary \\beta-phase alloys possessing low values of Young's modulus.

  19. 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.

  20. 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...

  1. 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)

  2. Molecular dynamics simulation of atomic-scale frictional behavior of corrugated nano-structured surfaces.

    Science.gov (United States)

    Kim, Hyun-Joon; Kim, Dae-Eun

    2012-07-01

    Surface morphology is one of the critical parameters that affect the frictional behavior of two contacting bodies in relative motion. It is important because the real contact area as well as the contact stiffness is dictated by the micro- and nano-scale geometry of the surface. In this regard, the frictional behavior may be controlled by varying the surface morphology through nano-structuring. In this study, molecular dynamics simulations were conducted to investigate the effects of contact area and structural stiffness of corrugated nano-structures on the fundamental frictional behavior at the atomic-scale. The nano-structured surface was modeled as an array of corrugated carbon atoms with a given periodicity. It was found that the friction coefficient of the nano-structured surface was lower than that of a smooth surface under specific contact conditions. The effect of applied load on the friction coefficient was dependent on the size of the corrugation. Furthermore, stiffness of the nano-structure was identified to be an important variable in dictating the frictional behavior.

  3. 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

  4. 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

  5. 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.

  6. 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...... scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy...

  7. 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...

  8. 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.

  9. 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

  10. 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.

  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

    2016-01-01

    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

  12. 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.

  13. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Belianinov, Alex, E-mail: belianinova@ornl.gov; Ganesh, Panchapakesan; Lin, Wenzhi; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V. [Oak Ridge National Laboratory, Institute for Functional Imaging of Materials, Center for Nanophase Material Science, Oak Ridge, Tennessee 37922 (United States); Sales, Brian C.; Sefat, Athena S. [Oak Ridge National Laboratory, Materials Science and Technology Division, Oak Ridge, Tennessee 37922 (United States)

    2014-12-01

    Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe{sub 1−x}Se{sub x} structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

    Science.gov (United States)

    Teschke, Omar; Soares, David Mendez

    2016-03-29

    Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

  1. Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.

    Directory of Open Access Journals (Sweden)

    Rhiju Das

    Full Text Available Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. Current approaches, such as the protein local optimization protocol or kinematic inversion closure (KIC Monte Carlo, involve stages that coarse-grain proteins, simplifying modeling but precluding a systematic search of all-atom configurations. This article introduces an alternative modeling strategy based on a 'stepwise ansatz', recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include cis-Pro touch turns, loops that pass through tunnels of other side-chains, and loops of lengths up to 24 residues. Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth 'RNA-puzzle' competition. These results establish all-atom enumeration as

  2. 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

  3. Morphology and atomic-scale structure of single-layer WS2 nanoclusters.

    Science.gov (United States)

    Füchtbauer, Henrik G; Tuxen, Anders K; Moses, Poul G; Topsøe, Henrik; Besenbacher, Flemming; Lauritsen, Jeppe V

    2013-10-14

    Two-dimensional sheets of transition metal (Mo and W) sulfides are attracting strong attention due to the unique electronic and optical properties associated with the material in its single-layer form. The single-layer MoS2 and WS2 are already in widespread commercial use in catalytic applications as both hydrotreating and hydrocracking catalysts. Consequently, characterization of the morphology and atomic structure of such particles is of utmost importance for the understanding of the catalytic active phase. However, in comparison with the related MoS2 system only little is known about the fundamental properties of single-layer WS2 (tungstenite). Here, we use an interplay of atom-resolved Scanning Tunneling Microscopy (STM) studies of Au(111)-supported WS2 nanoparticles and calculated edge structures using Density Functional Theory (DFT) to reveal the equilibrium morphology and prevalent edge structures of single-layer WS2. The STM results reveal that the single layer S-W-S sheets adopt a triangular equilibrium shape under the sulfiding conditions of the synthesis, with fully sulfided edges. The predominant edge structures are determined to be the (101[combining macron]0) W-edge, but for the smallest nanoclusters also the (1[combining macron]010) S-edges become important. DFT calculations are used to construct phase diagrams of the WS2 edges, and describe their sulfur and hydrogen coordination under different conditions, and in this way shed light on the catalytic role of WS2 edges.

  4. Ab initio random structure search for 13-atom clusters of fcc elements.

    Science.gov (United States)

    Chou, J P; Hsing, C R; Wei, C M; Cheng, C; Chang, C M

    2013-03-27

    The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd13 and Au13, we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au13, which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons.

  5. Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Liqing, E-mail: chenlq@uah.edu; Wang, Yujun [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Wells, David; Toh, Diana; Harold, Hunt [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Zhou, Jing [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); DiGiammarino, Enrico [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Meehan, Edward J. [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States)

    2006-09-01

    The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.

  6. Atomic structure of the adsorption of transition metals on silicon surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Cocoletzi, G.H. [IF-BUAP, 72000 Puebla (Mexico); Takeuchi, N. [CCMC-UNAM, Ensenada, BCN (Mexico)

    2007-07-01

    Full text: Solid state devices are useful for their high sensitivity in a small volume. Applications of such devices as dose materials include semi-conducting dose-rate, and dose-reading measuring devices. Transition metals (TM) have electronic and atomic properties similar to those of rare earth elements when they are adsorbed on silicon surfaces. The interfaces of transition metals silicides with Si (111) have very small lattice mismatches, sharp interfaces, and low Schottky barrier, making them ideal in electronic devices, such as infrared detectors and rectifying contacts. In this work we shall describe our first principles total energy calculations to investigate structural properties of bulk ScSi and YSi, the two dimensional arrangement of ScSi{sub 2} and YSi{sub 2} on the Si(111) surface, and the growth of a few layers of ScSi{sub 1.7} and YSi{sub 1.7} on the Si(111) surface. Our calculated bulk structural parameters are in excellent agreement with experimental values. It will be shown that one monolayer of a TM on Si( l l 1) yields a two dimensional phase with (lxl) periodicity consisting of a layer of TM atoms on T4 sites and a Si bilayer on top. This double layer of Si atoms is very close to ideal Si(111)-(1x1) surface, but rotated 180 with respect to the rest of the crystal. More layers of TM silicide epitaxially grown on Si(l 11) result in a hexagonal structure similar to bulk ScSi2 and YSi2: graphite-like Si planes (with vacancies) intercalated with TM planes, and forming a ({radical}3x{radical}3) arrangement with a ScSi{sub 1.7} and YSi{sub 1.7} stoichiometry. The top Si layer does not contain vacancies and it does not present a graphite-like structure, but forms a bilayer arrangement as in bulk Si. (Author)

  7. 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....

  8. 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

  9. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.

    Science.gov (United States)

    Schur, Florian K M; Obr, Martin; Hagen, Wim J H; Wan, William; Jakobi, Arjen J; Kirkpatrick, Joanna M; Sachse, Carsten; Kräusslich, Hans-Georg; Briggs, John A G

    2016-07-29

    Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1. PMID:27417497

  10. 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.

  11. 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

  12. Ultralow-Noise Atomic-Scale Structures for Quantum Circuitry in Silicon.

    Science.gov (United States)

    Shamim, Saquib; Weber, Bent; Thompson, Daniel W; Simmons, Michelle Y; Ghosh, Arindam

    2016-09-14

    The atomically precise doping of silicon with phosphorus (Si:P) using scanning tunneling microscopy (STM) promises ultimate miniaturization of field effect transistors. The one-dimensional (1D) Si:P nanowires are of particular interest, retaining exceptional conductivity down to the atomic scale, and are predicted as interconnects for a scalable silicon-based quantum computer. Here, we show that ultrathin Si:P nanowires form one of the most-stable electrical conductors, with the phenomenological Hooge parameter of low-frequency noise being as low as ≈10(-8) at 4.2 K, nearly 3 orders of magnitude lower than even carbon-nanotube-based 1D conductors. A in-built isolation from the surface charge fluctuations due to encapsulation of the wires within the epitaxial Si matrix is the dominant cause for the observed suppression of noise. Apart from quantum information technology, our results confirm the promising prospects for precision-doped Si:P structures in atomic-scale circuitry for the 11 nm technology node and beyond. PMID:27525390

  13. 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.

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

    OpenAIRE

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

    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...

  15. Observation of banded spherulites and lamellar structures by atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    姜勇; 罗艳红; 范泽夫; 王霞瑜; 徐军; 郭宝华; 李林

    2003-01-01

    Lamellar structures of banded spherulites of poly(ε-caprolactone)/poly(vinyl chloride) (PCL/PVC) blends are observed using tapping mode atomic force microscopy (AFM). The surface of the PCL/PVC banded spherulites presents to be concentric periodic ups and downs. The period of the bands corresponds to the extinction rings under the polarized optical microscopy observation. The lamellae with edge-on orientation in the ridges and the flat-on lamellae in the valleys of the banded spherulites are observed clearly. The twisting between the edge-on and flat-on lamellae is also observed.

  16. 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.

  17. 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.

  18. Relativistic corrections in atoms and space-time variation of the fine structure constant

    Energy Technology Data Exchange (ETDEWEB)

    Dzuba, V.A.; Flambaum, V.V.; Murphy, M.T.; Webb, J.K. [School of Physics, Univ. of New South Wales, Sydney, NSW (Australia)

    2001-07-01

    Comparison of quasar absorption line spectra with laboratory spectra provides the best probe for variability of the fine structure constant, {alpha}=e{sup 2}/{Dirac_h}c, over cosmological time-scales. We have demonstrated that high sensitivity to the variation of a can be obtained from a comparison of the spectra of heavy and light atoms and have obtained an order of magnitude gain in precision over previous methods. Our new data hint that a was smaller at earlier epochs. Careful searches have so far not revealed any spurious e.ect that can explain the observations.

  19. 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.

  20. The study of 3-dimensional structures of IgG with atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    YU Yi-gang; XU Ru-xiang; JIANG Xiao-dan; KE Yi-quan

    2005-01-01

    Objective: To detect 3-dimensional images of anti-N-methyl-D-aspartate receptor Nr1 (NMDAr1) polycolonal IgG affixed on mica in physiological environment. Methods: The images and data were obtained from a contact mode and commercial Si3N4 probed tip by using atomic force microscope (AFM). Conclusions: Using AFM to investigate biomacromolecule can make us deeply understand the structure of IgG, which will instruct us to detect the membrane receptor protein as a labelling agent.

  1. 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

  2. Structures of 13-atom clusters of fcc transition metals by ab initio and semiempirical calculations

    Science.gov (United States)

    Longo, R. C.; Gallego, L. J.

    2006-11-01

    We report the results of ab initio calculations of the structures and magnetic moments of Ni13 , Pd13 , Pt13 , Cu13 , Ag13 , and Au13 that were performed using a density-functional method that employs linear combinations of pseudoatomic orbitals as basis sets (SIESTA). Our structural results for Pt13 , Cu13 , Ag13 , and Au13 show that a buckled biplanar structure (BBP) is more stable than the icosahedral configuration, in keeping with results obtained recently by Chang and Chou [Phys. Rev. Lett. 93, 133401 (2004)] using the Vienna ab initio simulation package with a plane-wave basis. However, for Ni13 and Pd13 we found that the icosahedral structure is more stable than BBP. For all these clusters, two semiempirical methods based on spherically symmetric potentials both found the icosahedral structure to be the more stable, while the modified embedded atom model method, which uses a direction-dependent potential, found BBP to be the more stable structure. When low-energy structures found in recent ab initio studies of Pt13 , Cu13 , and Au13 other than Chang and Chou were optimized with SIESTA, those reported for Pt13 and Cu13 were found to be less stable than BBP, but the two-dimensional planar configuration reported for Au13 proved to be more stable than BBP.

  3. Structural investigation of ionic liquid/rubrene single crystal interfaces by using frequency-modulation atomic force microscopy.

    Science.gov (United States)

    Yokota, Yasuyuki; Hara, Hisaya; Harada, Tomohiro; Imanishi, Akihito; Uemura, Takafumi; Takeya, Jun; Fukui, Ken-ichi

    2013-11-21

    Frequency-modulation atomic force microscopy (FM-AFM) was employed to reveal the structural properties of a rubrene single crystal immersed in an ionic liquid. We found large vacancies formed by the anisotropic dissolution of rubrene molecules. Molecular resolution imaging revealed that structures of FM-AFM images deviated from the bulk-terminated structure. PMID:24091742

  4. 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

  5. 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

  6. High-speed atomic force microscopy reveals structural dynamics of amyloid β1-42 aggregates.

    Science.gov (United States)

    Watanabe-Nakayama, Takahiro; Ono, Kenjiro; Itami, Masahiro; Takahashi, Ryoichi; Teplow, David B; Yamada, Masahito

    2016-05-24

    Aggregation of amyloidogenic proteins into insoluble amyloid fibrils is implicated in various neurodegenerative diseases. This process involves protein assembly into oligomeric intermediates and fibrils with highly polymorphic molecular structures. These structural differences may be responsible for different disease presentations. For this reason, elucidation of the structural features and assembly kinetics of amyloidogenic proteins has been an area of intense study. We report here the results of high-speed atomic force microscopy (HS-AFM) studies of fibril formation and elongation by the 42-residue form of the amyloid β-protein (Aβ1-42), a key pathogenetic agent of Alzheimer's disease. Our data demonstrate two different growth modes of Aβ1-42, one producing straight fibrils and the other producing spiral fibrils. Each mode depends on initial fibril nucleus structure, but switching from one growth mode to another was occasionally observed, suggesting that fibril end structure fluctuated between the two growth modes. This switching phenomenon was affected by buffer salt composition. Our findings indicate that polymorphism in fibril structure can occur after fibril nucleation and is affected by relatively modest changes in environmental conditions. PMID:27162352

  7. 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

    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......, and interpreted by comparison with analogous packings of atoms in inorganic compounds and alloys. The topology is described qualitatively as “negative” structures formed by the cavities. Melanophlogite and dodecasils 3C and 1H are all clathrasils with isolated cavities. They all have pentagonal dodecahedral [512......] 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...

  8. 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

  9. 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

    2016-07-01

    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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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...

  17. 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.

  18. Chain-branching control of the atomic structure of alkanethiol-based gold-sulfur interfaces.

    Science.gov (United States)

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

    2011-09-28

    Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111): direct binding to the Au(111) surface without pitting, binding to adatoms above a regular surface with extensive pitting, and binding to adatoms with local surface vacancies and some pitting. Thermal motions are shown to produce some observed STM features, with a very tight energy balance controlling the observed structures. Variation of the degree of substitution on the α carbon is found to significantly change the relative energies for interaction of the different types of adatom structures with the surface, while the nature of the surface cell, controlled primarily by inter-adsorbate steric interactions, controls substrate reorganization energies and adsorbate distortion energies. Most significantly, by manipulating these features, chemical control of the adsorbate can produce stable interfaces with surface pitting eliminated, providing new perspectives for technological applications of SAMs.

  19. Propagation of Structural Disorder in Epitaxially Connected Quantum Dot Solids from Atomic to Micron Scale.

    Science.gov (United States)

    Savitzky, Benjamin H; Hovden, Robert; Whitham, Kevin; Yang, Jun; Wise, Frank; Hanrath, Tobias; Kourkoutis, Lena F

    2016-09-14

    Epitaxially connected superlattices of self-assembled colloidal quantum dots present a promising route toward exquisite control of electronic structure through precise hierarchical structuring across multiple length scales. Here, we uncover propagation of disorder as an essential feature in these systems, which intimately connects order at the atomic, superlattice, and grain scales. Accessing theoretically predicted exotic electronic states and highly tunable minibands will therefore require detailed understanding of the subtle interplay between local and long-range structure. To that end, we developed analytical methods to quantitatively characterize the propagating disorder in terms of a real paracrystal model and directly observe the dramatic impact of angstrom scale translational disorder on structural correlations at hundreds of nanometers. Using this framework, we discover improved order accompanies increasing sample thickness and identify the substantial effect of small fractions of missing epitaxial bonds on statistical disorder. These results have significant experimental and theoretical implications for the elusive goals of long-range carrier delocalization and true miniband formation. PMID:27540863

  20. 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.)

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

    DEFF Research Database (Denmark)

    Martinez, Jose Ignacio; Alonso, J.A.

    2008-01-01

    The electronic and atomic structure of the family of hydrogenated Al clusters AlnHn+2 with n=4-11 has been studied using the density functional theory with the generalized gradient approximation (GGA) for exchange and correlation. All these clusters have substantial gaps between the highest...... occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) and, consequently, they are chemically very stable. The largest gap of 2.81 eV occurs for Al6H8. Five clusters of the family, Al4H6, Al5H7, Al6H8, Al7H9, and Al10H12, fulfill the Wade-Mingos rule. That is, in AlnHn+2, the Al matrix forms...... a polyhedron of n vertices and n H atoms form strong H-Al terminal bonds; one pair of electrons is involved in each of those bonds. The remaining n+1 electron pairs form a delocalized cloud over the surface of the Al cage. The clusters fulfilling the Wade-Mingos rule have wider HOMO-LUMO gaps...

  2. 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

  3. Dispersed-phase structure of pressure-atomized sprays at various gas densities

    Science.gov (United States)

    Tseng, L.-K.; Wu, P.-K.; Faeth, G. M.

    1992-01-01

    The dispersed-phase structure of the dense-spray region of pressure-atomized sprays was studied for atomization breakup conditions, considering large-scale (9.5 mm initial diameter) water jets in still air at ambient pressures of 1, 2, and 4 atm., with both fully-developed turbulent pipe flow and nonturbulent slug flow at the jet exit. Drop sizes and velocities, and liquid volume fractions and fluxes, were measured using holography. Measurements were compared with predictions based on the locally-homogeneous flow approximation as well as recent correlations of drop sizes after primary breakup of turbulent and nonturbulent liquids. The dispersed-flow region beyond the liquid surface was relatively dilute (liquid volume fractions less than 0.1 percent), with significant separated-flow effects throughout, and evidence of near-limit secondary breakup and drop deformation near the liquid surface. Turbulent primary breakup predictions were satisfactory at atmospheric pressure, where the correlation was developed, but failed to predict observed trends of decreasing drop sizes with increasing gas density due to aerodynamic effects; in contrast, the laminar primary breakup predictions successfully treated the relatively small effects of gas density for this breakup mechanism. Effects of liquid turbulence at the jet exit were qualitatively similar to single-phase flows, yielding faster mixing rates with increased turbulence levels even though drop sizes tended to increase as well.

  4. 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.

  5. 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)

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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)

  11. 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.

  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. 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

  14. 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

  15. 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.

  16. 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).

  17. 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 ...

  18. 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...

  19. The chemical structure of a molecule resolved by atomic force microscopy

    NARCIS (Netherlands)

    Gross, L.; Mohn, F.; Moll, N.; Liljeroth, P.; Meyer, G.

    2009-01-01

    Resolving individual atoms has always been the ultimate goal of surface microscopy. The scanning tunneling microscope images atomic-scale features on surfaces, but resolving single atoms within an adsorbed molecule remains a great challenge because the tunneling current is primarily sensitive to the

  20. 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

    -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...

  1. In situ observation of surface structures of cardiovascular endothelial cells with atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    Tong Yin; Jin Luo; YaMin Ma; Xiao-Long Ji; Yu-Sheng Zhao; Shi-Wen Wang

    2009-01-01

    Objective To observe the surface structures of cardiovascular endothelial cells in situ with atomic force microscope (AFM). Methods Fresh aorta and aortic valve were dissected from 10 healthy male New Zealand white rabbits. Before fixed in 1% formaldehyde, the fresh tissues were washed in the buffer phosphate solution. Under general microscope, the fixed aorta or valve was spread on the double side stick tape which had already been stuck on the glass slide. The intima of aorta or the aorta side of valve was towards upside. Then the specimen was dried under 37 degrees centigrade in an attemperator and was washed with pure water. After dried again, the specimen was loaded on the platform ofNanoScope llla AFM and was scanned in tapping mode with the scanning speed of 0.5 HZ. Results The surface structures of endothelial cell on the fixed and dried tissue could be obsserved clearly in situ with AFM. Aortic endothclial cells were large, branched and arranged sparsely and parallel to the direction of blood flow, whereas endothelial cells on aorta valve surface were small, less branched and arranged intensively and vertical to the direction of blood flow. When the scanning range was dwindled, granular ultra-structures could be observed on the surface of endothelial cells, and, as the scanning range was dwindled further, fissure and convolution could be seen on the surface of granules from aortic endothelial cells. Centre cavity and surrounding swelling volcano-like structure could be seen on the surface of granules from endothelial cells of aortic valve. Conclusions It's feasible to observe the surface ultra-structures of cardiovascular endothelial cells in situ with AFM and morphological information provided by A FM might be of clinical value in future histopathological diagnosis.

  2. 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.

  3. 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.

  4. 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

  5. Growth mechanisms for Si epitaxy on O atomic layers: Impact of O-content and surface structure

    Science.gov (United States)

    Jayachandran, Suseendran; Billen, Arne; Douhard, Bastien; Conard, Thierry; Meersschaut, Johan; Moussa, Alain; Caymax, Matty; Bender, Hugo; Vandervorst, Wilfried; Heyns, Marc; Delabie, Annelies

    2016-10-01

    The epitaxial growth of Si layers on Si substrates in the presence of O atoms is generally considered a challenge, as O atoms degrade the epitaxial quality by generating defects. Here, we investigate the growth mechanisms for Si epitaxy on O atomic layers (ALs) with different O-contents and structures. O ALs are deposited by ozone (O3) or oxygen (O2) exposure on H-terminated Si at 50 °C and 300 °C respectively. Epitaxial Si is deposited by chemical vapor deposition using silane (SiH4) at 500 °C. After O3 exposure, the O atoms are uniformly distributed in Si-Si dimer/back bonds. This O layer still allows epitaxial seeding of Si. The epitaxial quality is enhanced by lowering the surface distortions due to O atoms and by decreasing the arrival rate of SiH4 reactants, allowing more time for surface diffusion. After O2 exposure, the O atoms are present in the form of SiOx clusters. Regions of hydrogen-terminated Si remain present between the SiOx clusters. The epitaxial seeding of Si in these structures is realized on H-Si regions, and an epitaxial layer grows by a lateral overgrowth mechanism. A breakdown in the epitaxial ordering occurs at a critical Si thickness, presumably by accumulation of surface roughness.

  6. 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...

  7. 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)

  8. 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...

  9. 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...

  10. 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

  11. 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.

  12. 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

  13. Near-atomic resolution structural model of the yeast 26S proteasome.

    Science.gov (United States)

    Beck, Florian; Unverdorben, Pia; Bohn, Stefan; Schweitzer, Andreas; Pfeifer, Günter; Sakata, Eri; Nickell, Stephan; Plitzko, Jürgen M; Villa, Elizabeth; Baumeister, Wolfgang; Förster, Friedrich

    2012-09-11

    The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. Structure and property of metal melt Ⅲ—Relationship between kinematic viscosity and size of atomic clusters

    Institute of Scientific and Technical Information of China (English)

    POPEL; P; S; KONSTANTINOVA; N; Yu

    2010-01-01

    The method of crucible rotating oscillation damping was employed to measure the kinematic viscosity of aluminum melt,and the curve of viscosity v versus temperature T from 935 to 1383 K was obtained.Besides,based on the calculation model of the evolution behavior of atomic clusters in liquid structure,the curve of atomic clusters size d versus temperature was obtained,and the calculated results are in good agreement with the experimental values.By analyzing experimental data,it was found that both the viscosity and the size of atomic clusters of aluminum melt are monodrome functions of temperature,and the relation between v(T) and d(T) is a linear function,i.e.,v = v 0 + K·d(T).This relation indirectly verifies the calculation model of the structural information of metal melt,which is of great significance for studying the relation between melt microstructure and macro-physical properties.

  19. 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)

  20. 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.

  1. Atom probe tomography characterisation of a laser diode structure grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, Samantha E.; Humphreys, Colin J.; Oliver, Rachel A. [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge, CB2 3QZ (United Kingdom); Smeeton, Tim M.; Hooper, Stewart E.; Heffernan, Jonathan [Sharp Laboratories of Europe Limited, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4GB (United Kingdom); Saxey, David W.; Smith, George D. W. [Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH (United Kingdom)

    2012-03-01

    Atom probe tomography (APT) has been used to achieve three-dimensional characterization of a III-nitride laser diode (LD) structure grown by molecular beam epitaxy (MBE). Four APT data sets have been obtained, with fields of view up to 400 nm in depth and 120 nm in diameter. These data sets contain material from the InGaN quantum well (QW) active region, as well as the surrounding p- and n-doped waveguide and cladding layers, enabling comprehensive study of the structure and composition of the LD structure. Two regions of the same sample, with different average indium contents (18% and 16%) in the QW region, were studied. The APT data are shown to provide easy access to the p-type dopant levels, and the composition of a thin AlGaN barrier layer. Next, the distribution of indium within the InGaN QW was analyzed, to assess any possible inhomogeneity of the distribution of indium (''indium clustering''). No evidence for a statistically significant deviation from a random distribution was found, indicating that these MBE-grown InGaN QWs do not require indium clusters for carrier localization. However, the APT data show steps in the QW interfaces, leading to well-width fluctuations, which may act to localize carriers. Additionally, the unexpected presence of a small amount (x = 0.005) of indium in a layer grown intentionally as GaN was revealed. Finally, the same statistical method applied to the QW was used to show that the indium distribution within a thick InGaN waveguide layer in the n-doped region did not show any deviation from randomness.

  2. 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.

  3. Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

    Directory of Open Access Journals (Sweden)

    Gront Dominik

    2007-06-01

    Full Text Available Abstract Background Although experimental methods for determining protein structure are providing high resolution structures, they cannot keep the pace at which amino acid sequences are resolved on the scale of entire genomes. For a considerable fraction of proteins whose structures will not be determined experimentally, computational methods can provide valuable information. The value of structural models in biological research depends critically on their quality. Development of high-accuracy computational methods that reliably generate near-experimental quality structural models is an important, unsolved problem in the protein structure modeling. Results Large sets of structural decoys have been generated using reduced conformational space protein modeling tool CABS. Subsequently, the reduced models were subject to all-atom reconstruction. Then, the resulting detailed models were energy-minimized using state-of-the-art all-atom force field, assuming fixed positions of the alpha carbons. It has been shown that a very short minimization leads to the proper ranking of the quality of the models (distance from the native structure, when the all-atom energy is used as the ranking criterion. Additionally, we performed test on medium and low accuracy decoys built via classical methods of comparative modeling. The test placed our model evaluation procedure among the state-of-the-art protein model assessment methods. Conclusion These test computations show that a large scale high resolution protein structure prediction is possible, not only for small but also for large protein domains, and that it should be based on a hierarchical approach to the modeling protocol. We employed Molecular Mechanics with fixed alpha carbons to rank-order the all-atom models built on the scaffolds of the reduced models. Our tests show that a physic-based approach, usually considered computationally too demanding for large-scale applications, can be effectively used in such

  4. 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.)

  5. 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…

  6. 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…

  7. Baroque Tower on a Gothic Base: A Lakatosian Reconstruction of Students' and Teachers' Understanding of Structure of the Atom.

    Science.gov (United States)

    Blanco, Rafael; Niaz, Mansoor

    1998-01-01

    Reconstructs students' and teachers' understanding of the structure of the atom based on a framework characterized by considering the history of science as competing research programs and by believing that some great scientific research programs progress on inconsistent foundations. Contains 107 references. (DDR)

  8. 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.

  9. 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…

  10. 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

  11. 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

  12. 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.

  13. Atomic structure of a single large biomolecule from diffraction patterns of random orientations

    CERN Document Server

    Tegze, Miklós

    2012-01-01

    The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the sample. In a single molecule imaging (SMI) experiment thousands of diffraction patterns of single molecules with random orientations are recorded. One of the most challenging problems of SMI is how to assemble these noisy patterns of unknown orientations into a consistent single set of diffraction data. Here we present a new method which can solve the orientation problem of SMI efficiently even for large biological molecules and in the presence of noise. We show on simulated diffraction patterns of a large protein molecule, how the orientations of the patterns can be found and the structure to atomic resolution can be solved. The concept of our algorithm could be also applied to experiments where images of an object are recorded in unknown orientations and/or positions lik...

  14. Atomic force microscopic study on topological structures of pBR322 DNA

    Institute of Scientific and Technical Information of China (English)

    张平城; 白春礼; 成英俊; 方晔; 王中怀; 黄熙泰

    1996-01-01

    Plasmid pBR322 DNA (0.5mg/mL) isolated from Escherichia coli HB101 was suspended in Tris-HCl-EDTA (1 mol/L - 0.1 mol/L, pH8.5); then a drop of the above solution was deposited on freshly cleaved mica substrate. After adsorption for about 1 min, the sample was stained with phosphotungstic acid. The residua] solution was removed with a piece of filter paper. Afterwards the sample was imaged with a home-made atomic force microscope (AFM) in air. The AFM images of pBR322 DNA with a molecular resolution have been obtained. These images show that pBR322 DNA exists in several different topological structures: (i) relaxed circular DNA with a different diameter; (ii) supercondensed DNA with different particle sizes; (iii) dimeric catenane connected by one relaxed circular molecule and another dose-compacted molecule which might be either supercoiled or intramolecular knotted form; (iv) oligomeric catenane with multiple irregular molecules in which DNA is interlocked into a complex oligomer; (v) possibly-existing

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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 ...

  20. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Samuel Paul Jarvis

    2015-08-01

    Full Text Available A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

  1. 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

  2. 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)

  3. 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.

  4. 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.

  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 compar...

  6. 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

  7. Atomic Structure of a Spinel-like Transition Al2O3 (100) Surface

    DEFF Research Database (Denmark)

    Jensen, Thomas Nørregaard; Meinander, Kristoffer; Helveg, Stig;

    2014-01-01

    We study a crystalline epitaxial alumina thin film with the characteristics of a spinel-type transition Al2O3(100) surface by using atom-resolved noncontact atomic force microscopy and density functional theory. It is shown that the films are terminated by an Al-O layer rich in Al vacancies...

  8. 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.

  9. 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.

  10. 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.)

  11. Structural properties of Al and TiAl3 metallic glasses — An embedded atom method study

    Science.gov (United States)

    Tahiri, M.; Trady, S.; Hasnaoui, A.; Mazroui, M.; Saadouni, K.; Sbiaai, K.

    2016-06-01

    In this paper, we investigated the structural properties of metallic glasses (MGs). We emphasized our study on monatomic Al and binary TiAl3 systems. The calculations are performed by using the molecular dynamics (MD) simulation based on semi-empirical many-body potentials derived from the embedded atom method. The structure is analyzed using the radial distribution function (RDF), the common neighbor analysis (CNA) and the coordination numbers (CNs). Our results demonstrated that it is possible to form MGs in both systems upon fast cooling from the liquid state. This is confirmed by the fact that the system energy and/or volume during the cooling stage decrease continuously with a slight change and by atomic scale analysis using the RDF, CNA and CN analyzing techniques. Furthermore, this specific study shows that under the same conditions, the icosahedral structures appeared in TiAl3 are more abundant than in pure Al. Implications of these findings are discussed.

  12. Local atomic and magnetic structure of dilute magnetic semiconductor (Ba ,K ) (Zn,Mn ) 2As2

    Science.gov (United States)

    Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; Banerjee, Soham; Chen, Bijuan; Jin, Changqing; Feygenson, Mikhail; Uemura, Yasutomo J.; Billinge, Simon J. L.

    2016-09-01

    We have studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba ,K )(Zn ,Mn )2As2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. We detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5 Å , resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment of Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. We discuss these results in the context of other experiments and theoretical studies on this system.

  13. Photoluminescence polarization anisotropy for studying long-range structural ordering within semiconductor multi-atomic alloys and organic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Prutskij, T.; Percino, J. [Instituto de Ciencias, BUAP, Privada 17 Norte, No 3417, col. San Miguel Huyeotlipan, 72050, Puebla, Pue. (Mexico); Orlova, T. [Department of Chemical and Biochemical Engineering, University of Notre Dame, Notre Dame, IN (United States); Vavilova, L. [Ioffe Physical-Technical Institute, 26 Polytekhnicheskaya, St Petersburg 194021, Russian Federation (Russian Federation)

    2013-12-04

    Long-range structural ordering within multi-component semiconductor alloys and organic crystals leads to significant optical anisotropy and, in particular, to anisotropy of the photoluminescence (PL) emission. The PL emission of ternary and quaternary semiconductor alloys is polarized if there is some amount of the atomic ordering within the crystal structure. We analyze the polarization of the PL emission from the quaternary GaInAsP semiconductor alloy grown by Liquid Phase Epitaxy (LPE) and conclude that it could be caused by low degree atomic ordering within the crystal structure together with the thermal biaxial strain due to difference between the thermal expansion coefficients of the layer and the substrate. We also study the state of polarization of the PL from organic crystals in order to identify different features of the crystal PL spectrum.

  14. 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

  15. 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.

  16. 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.

  17. Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and Its Precursors on Metal Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, George W [Columbia University

    2015-02-16

    Executive Summary of Final Report for Award DE-FG02-88ER13937 Project Title: Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and its Precursors on Metal Surfaces Applicant/Institution: Columbia University Principal Investigator: George W. Flynn Objectives: The objectives of this project were to reveal the mechanisms and reaction processes that solid carbon materials undergo when combining with gases such as oxygen, water vapor and hydrocarbons. This research was focused on fundamental chemical events taking place on single carbon sheets of graphene, a two-dimensional, polycyclic carbon material that possesses remarkable chemical and electronic properties. Ultimately, this work is related to the role of these materials in mediating the formation of polycyclic aromatic hydrocarbons (PAH’s), their reactions at interfaces, and the growth of soot particles. Our intent has been to contribute to a fundamental understanding of carbon chemistry and the mechanisms that control the formation of PAH’s, which eventually lead to the growth of undesirable particulates. We expect increased understanding of these basic chemical mechanisms to spur development of techniques for more efficient combustion of fossil fuels and to lead to a concomitant reduction in the production of undesirable solid carbon material. Project Description: Our work treated specifically the surface chemistry aspects of carbon reactions by using proximal probe (atomic scale imaging) techniques to study model systems of graphene that have many features in common with soot forming reactions of importance in combustion flames. Scanning tunneling microscopy (STM) is the main probe technique that we used to study the interfacial structure and chemistry of graphene, mainly because of its ability to elucidate surface structure and dynamics with molecular or even atomic resolution. Scanning tunneling spectroscopy (STS), which measures the local density of quantum states over a single

  18. 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

  19. 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.

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

    Institute of Scientific and Technical Information of China (English)

    XIA Cai-Juan; FANG Chang-Feng; HU Gui-chao; ZHAO Peng; WANG Yi-Ming; XIE Shi-Jie; LIU De-Sheng

    2008-01-01

    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 metalmolecule 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.

  1. 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...

  2. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    Science.gov (United States)

    Kahn, L. R.

    1982-01-01

    Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

  3. 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 L21 phase with Ni0.48Co0.52 at A-sites, Al at BΙ-sites and Fe0.20Ti0.80 at BΙΙ-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

  4. Atomic-Scale Chemical Imaging and Quantification of Metallic Alloy Structures by Energy-Dispersive X-Ray Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Ping [Sandia National Laboratories; Zhou, Lin [Ames Laboratory; Kramer, Matthew J. [Ames Laboratory; Smith, David J. [Arizona State University

    2014-02-04

    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 L21 phase with Ni0.48Co0.52 at A-sites, Al at BΙ-sites and Fe0.20Ti0.80 at BΙΙ-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.

  5. 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

  6. Bottom-up Approach Design, Band Structure, and Lithium Storage Properties of Atomically Thin γ-FeOOH Nanosheets.

    Science.gov (United States)

    Song, Yun; Cao, Yu; Wang, Jing; Zhou, Yong-Ning; Fang, Fang; Li, Yuesheng; Gao, Shang-Peng; Gu, Qin-Fen; Hu, Linfeng; Sun, Dalin

    2016-08-24

    As a novel class of soft matter, two-dimensional (2D) atomic nanosheet-like crystals have attracted much attention for energy storage devices due to the fact that nearly all of the atoms can be exposed to the electrolyte and involved in redox reactions. Herein, atomically thin γ-FeOOH nanosheets with a thickness of ∼1.5 nm are synthesized in a high yield, and the band and electronic structures of the γ-FeOOH nanosheet are revealed using density-functional theory calculations for the first time. The rationally designed γ-FeOOH@rGO composites with a heterostacking structure are used as an anode material for lithium-ion batteries (LIBs). A high reversible capacity over 850 mAh g(-1) after 100 cycles at 200 mA g(-1) is obtained with excellent rate capability. The remarkable performance is attributed to the ultrathin nature of γ-FeOOH nanosheets and 2D heterostacking structure, which provide the minimized Li(+) diffusion length and buffer zone for volume change. Further investigation on the Li storage electrochemical mechanism of γ-FeOOH@rGO indicates that the charge-discharge processes include both conversion reaction and capacitive behavior. This synergistic effect of conversion reaction and capacitive behavior originating from 2D heterostacking structure casts new light on the development of high-energy anode materials. PMID:27471909

  7. 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.

  8. 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

  9. 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.

  10. Complementary method to locate atomic coordinates by combined searching method of structure-sensitive indexes based on bond valence method

    Institute of Scientific and Technical Information of China (English)

    宋振; 刘小浪; 何丽珠; 夏志国; 刘泉林

    2015-01-01

    Bond valence method illustrates the relation between valence and length of a particular bond type. This theory has been used to predict structure information, but the effect is very limited. In this paper, two indexes, i.e., global instability index (GII) and bond strain index (BSI), are adopted as a judgment of a search-match program for prediction. The results show that with GII and BSI combined as judgment, the predicted atom positions are very close to real ones. The mechanism and validity of this searching program are also discussed. The GII&BSI distribution contour map reveals that the predicted function is a reflection of exponential feature of bond valence formula. This combined searching method may be integrated with other structure-determination method, and may be helpful in refining and testifying light atom positions.

  11. 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.

  12. Manipulation of adsorbed atoms and creation of new structures on room-temperature surfaces with a scanning tunneling microscope.

    Science.gov (United States)

    Whitman, L J; Stroscio, J A; Dragoset, R A; Celotta, R J

    1991-03-01

    A general method of manipulating adsorbed atoms and molecules on room-temperature surfaces with the use of a scanning tunneling microscope is described. By applying an appropriate voltage pulse between the sample and probe tip, adsorbed atoms can be induced to diffuse into the region beneath the tip. The field-induced diffusion occurs preferentially toward the tip during the voltage pulse because of the local potential energy gradient arising from the interaction of the adsorbate dipole moment with the electric field gradient at the surface. Depending upon the surface and pulse parameters, cesium (Cs) structures from one nanometer to a few tens of nanometers across have been created in this way on the (110) surfaces of gallium arsenide (GaAs) and indium antimonide (InSb), including structures that do not naturally occur.

  13. Variation of local atomic structure due to devitrification of Ni-Zr alloy thin films probed by EXAFS measurements

    Science.gov (United States)

    Bhattacharya, Debarati; Tiwari, Nidhi; Bhattacharyya, Dibyendu; Jha, S. N.; Basu, S.

    2016-05-01

    Thin film metallic glasses (TFMGs) exhibit properties superior to their bulk counterparts allowing them to be potentially useful in many practical applications. Apart from their technological interest, when converted to crystallized state (devitrification) TFMGs can also act as precursors for partially crystallized or fully crystallized forms. Such devitrified forms are attractive due to their novel structural and magnetic properties. The amorphous-to-crystalline transformation of co-sputtered Ni-Zr alloy thin films through annealing was studied using EXAFS (Extended X-ray Absorption Fine Structure) measurements. Investigation through an atomic probe gives a better insight into the local environment of the atomic species, rendering a deeper understanding of thermal evolution of such materials.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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...

  3. 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

  4. Structurally Well-Defined Sigmoidal Gold Clusters: Probing the Correlation between Metal Atom Arrangement and Chiroptical Response.

    Science.gov (United States)

    He, Xin; Wang, Yuechao; Jiang, Hong; Zhao, Liang

    2016-05-01

    Asymmetric arrangement of metal atoms is crucial for understanding the chirality origin of chiral metal nanoclusters and facilitating the design and development of new chiral catalysts and chiroptical devices. Here, we describe the construction of four asymmetric gold and gold-silver clusters by chirality transfer from diimido ligands. The acquired metal clusters show strong circular dichroism (CD) response with large anisotropy factors of up to 6 × 10(-3), larger than the values of most reported chiral gold nanoclusters. Regardless of the same absolute configuration of the applied three diimido ligands, sigmoidal and reverse-sigmoidal arrangements of gold atoms both can be achieved, which resultantly produce an opposite Cotton effect within a specific absorption range. On the basis of the detailed structural characterization via X-ray crystallography and contrast experiments, the chirality contribution of the imido ligand, the asymmetrically arranged metal cluster, and the chiral arrangement of aromatic rings of phosphine ligands have been qualitatively evaluated. Time-dependent DFT calculations reveal that the chiroptical property of the acquired metal clusters is mainly influenced by the asymmetrically arranged metal atoms. Correlation of asymmetric arrangements of metal atoms in clusters with their chiroptical response provides a viable means of fabricating a designable chiral surface of metal nanoclusters and opens a broader prospect for chiral cluster application.

  5. The effect of atomic-scale defects and dopants on phosphorene electronic structure and quantum transport properties.

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Bezanilla, Alejandro

    2016-01-20

    By means of a multi-scale first-principles approach, a description of the local electronic structure of 2D and narrow phosphorene sheets with various types of modifications is presented. Firtly, a rational argument based on the geometry of the pristine and modified P network, and supported by the Wannier functions formalism is introduced to describe a hybridization model of the P atomic orbitals. Ab initio calculations show that non-isoelectronic foreign atoms form quasi-bound states at varying energy levels and create different polarization states depending on the number of valence electrons between P and the doping atom. The quantum transport properties of modified phosphorene ribbons are further described with great accuracy. The distortions on the electronic bands induced by the external species lead to strong backscattering effects on the propagating charge carriers. Depending on the energy of the charge carrier and the type of doping, the conduction may range from the diffusive to the localized regime. Interstitial defects at vacant sites lead to homogeneous transport fingerprints across different types of doping atoms. We suggest that the relatively low values of charge mobility reported in experimental measurements may have its origin in the presence of defects.

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

    Science.gov (United States)

    Levashov, V. A.

    2016-03-01

    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 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity 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 demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.

  7. Atomic Structures of Graphene, Benzene and Methane with Bond Lengths as Sums of the Single, Double and Resonance Bond Radii of Carbon

    OpenAIRE

    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 b...

  8. Atomic structure of the SnO sub 2 (110) surface

    Energy Technology Data Exchange (ETDEWEB)

    Godin, T.J.; LaFemina, J.P.

    1991-12-01

    Using a tight-binding, total-energy model, we examine atomic relaxations of the ideal stoichiometric and reduced tin oxide (11) surfaces. In both cases we find a nearly bond-length conserving rumple of the top layer, and a smaller counter-relaxation of the second layer. These calculations show no evidence of surface states in the band gap for either surface.

  9. Atomic structure of the SnO{sub 2} (110) surface

    Energy Technology Data Exchange (ETDEWEB)

    Godin, T.J.; LaFemina, J.P.

    1991-12-01

    Using a tight-binding, total-energy model, we examine atomic relaxations of the ideal stoichiometric and reduced tin oxide (11) surfaces. In both cases we find a nearly bond-length conserving rumple of the top layer, and a smaller counter-relaxation of the second layer. These calculations show no evidence of surface states in the band gap for either surface.

  10. Pre-Service Physics Teachers' Ideas on Size, Visibility and Structure of the Atom

    Science.gov (United States)

    Unlu, Pervin

    2010-01-01

    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…

  11. SPIRAL STRUCTURE OF M51 - DISTRIBUTION AND KINEMATICS OF THE ATOMIC AND IONIZED HYDROGEN

    NARCIS (Netherlands)

    TILANUS, RPJ; ALLEN, RJ

    1991-01-01

    The atomic hydrogen (H I) and the H-alpha emission lines in the grand-design spiral galaxy M51 have been observed with the Westerbork Synthesis Radio Telescope and the TAURUS Fabry-Perot imaging spectrometer, respectively. Across the inner spiral arms significant tangential and radial velocity gradi

  12. The Materials Chemistry of Atomic Oxygen with Applications to Anisotropic Etching of Submicron Structures in Microelectronics and the Surface Chemistry Engineering of Porous Solids

    Energy Technology Data Exchange (ETDEWEB)

    Koontz, S.L.; Leger, L.J.; Wu, C.; Cross, J.B.; Jurgensen, C.W. [Los Alamos National Lab., NM (United States)]|[Bell Telephone Labs., Inc., Murray Hill, NJ (United States)

    1994-05-01

    Neutral atomic oxygen is the most abundant component of the ionospheric plasma in the low Earth orbit environment (LEO; 200 to 700 kilometers altitude) and can produce significant degradation of some spacecraft materials. In order to produce a more complete understanding of the materials chemistry of atomic oxygen, the chemistry and physics of O-atom interactions with materials were determined in three radically different environments: (1) The Space Shuttle cargo bay in low Earth orbit (the EOIM-3 space flight experiment), (2) a high-velocity neutral atom beam system (HVAB) at Los Alamos National Laboratory (LANL), and (3) a microwave-plasma flowing-discharge system at JSC. The Space Shuttle and the high velocity atom beam systems produce atom-surface collision energies ranging from 0.1 to 7 eV (hyperthermal atoms) under high-vacuum conditions, while the flowing discharge system produces a 0.065 eV surface collision energy at a total pressure of 2 Torr. Data obtained in the three different O-atom environments referred to above show that the rate of O-atom reaction with polymeric materials is strongly dependent on atom kinetic energy, obeying a reactive scattering law which suggests that atom kinetic energy is directly available for overcoming activation barriers in the reaction. General relationships between polymer reactivity with O atoms and polymer composition and molecular structure have been determined. In addition, vacuum ultraviolet photochemical effects have been shown to dominate the reaction of O atoms with fluorocarbon polymers. Finally, studies of the materials chemistry of O atoms have produced results which may be of interest to technologists outside the aerospace industry. Atomic oxygen `spin-off` or `dual use` technologies in the areas of anisotropic etching in microelectronic materials and device processing, as well as surface chemistry engineering of porous solid materials are described.

  13. The Materials Chemistry of Atomic Oxygen with Applications to Anisotropic Etching of Submicron Structures in Microelectronics and the Surface Chemistry Engineering of Porous Solids

    Science.gov (United States)

    Koontz, Steve L.; Leger, Lubert J.; Wu, Corina; Cross, Jon B.; Jurgensen, Charles W.

    1994-01-01

    Neutral atomic oxygen is the most abundant component of the ionospheric plasma in the low Earth orbit environment (LEO; 200 to 700 kilometers altitude) and can produce significant degradation of some spacecraft materials. In order to produce a more complete understanding of the materials chemistry of atomic oxygen, the chemistry and physics of O-atom interactions with materials were determined in three radically different environments: (1) The Space Shuttle cargo bay in low Earth orbit (the EOIM-3 space flight experiment), (2) a high-velocity neutral atom beam system (HVAB) at Los Alamos National Laboratory (LANL), and (3) a microwave-plasma flowing-discharge system at JSC. The Space Shuttle and the high velocity atom beam systems produce atom-surface collision energies ranging from 0.1 to 7 eV (hyperthermal atoms) under high-vacuum conditions, while the flowing discharge system produces a 0.065 eV surface collision energy at a total pressure of 2 Torr. Data obtained in the three different O-atom environments referred to above show that the rate of O-atom reaction with polymeric materials is strongly dependent on atom kinetic energy, obeying a reactive scattering law which suggests that atom kinetic energy is directly available for overcoming activation barriers in the reaction. General relationships between polymer reactivity with O atoms and polymer composition and molecular structure have been determined. In addition, vacuum ultraviolet photochemical effects have been shown to dominate the reaction of O atoms with fluorocarbon polymers. Finally, studies of the materials chemistry of O atoms have produced results which may be of interest to technologists outside the aerospace industry. Atomic oxygen 'spin-off' or 'dual use' technologies in the areas of anisotropic etching in microelectronic materials and device processing, as well as surface chemistry engineering of porous solid materials are described.

  14. Adsorption of atomic oxygen, electron structure and elastic moduli of TiC(0 0 1) surface during its laser reconstruction: Ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Ilyasov, V.V., E-mail: viily@mail.ru; Pham, Khang D., E-mail: dinhkhang307@gmail.com; Holodova, O.M.; Ershov, I.V., E-mail: thijd@mail.ru

    2015-10-01

    We have performed ab initio simulation of oxygen atom adsorption on TiC(0 0 1) laser-reconstructed surface. Relaxed atomic structures of the O/Ti{sub x}C{sub y}(0 0 1) surface observed upon thermal impact have been studied. DFT calculations of their thermodynamic, electronic, and elastic properties have been carried out. For the first time we have established the bond length and adsorption energy for various reconstructions of the O/Ti{sub x}C{sub y}(0 0 1) surface atomic structure. We have examined the effects of the oxygen adatom upon the band and electron spectra of the O/TiC(0 0 1) surface in its various reconstructions. For the first time we have established a correlation between the energy level of flat bands (−5.4 eV and −5.8 eV) responsible for the doublet of singular peaks of partial densities of oxygen 2p electrons, and the adsorption energy of oxygen atom in non-stoichiometric O/TiC{sub y}(0 0 1) systems. Effective charges of titanium and carbon atoms surrounding the oxygen adatom in various reconstructions have been identified. We have established charge transfer from titanium atom to oxygen and carbon atoms determined by the reconstruction of local atomic and electron structures which correlate with atomic electronegativity values and chemisorption processes. Potential mechanisms for laser nanostructuring of titanium carbide surface have been suggested.

  15. Crystallization, phase evolution and corrosion of Fe-based metallic glasses: An atomic-scale structural and chemical characterization study

    International Nuclear Information System (INIS)

    Understanding phase changes, including their formation and evolution, is critical for the performance of functional as well as structural materials. We analyze in detail microstructural and chemical transformations of the amorphous steel Fe50Cr15Mo14C15B6 during isothermal treatments at temperatures ranging from 550 to 800 °C. By combining high-resolution transmission electron microscopy and Rietveld analyses of X-ray diffraction patterns together with the local chemical data obtained by atom probe tomography, this research provides relevant information at the atomic scale about the mechanisms of crystallization and the subsequent phases evolution. During the initial stages of crystallization a stable (Fe,Cr)23(C,B)6 precipitates as well as two metastable intermediates of M3(C,B) and the intermetallic χ-phase. When full crystallization is reached, only a percolated nano-scale Cr-rich (Fe,Cr)23(C,B)6 and Mo-rich η-Fe3Mo3C structure is detected, with no evidence to suggest that other phases appear at any subsequent time. Finally, the corrosion behavior of the developed phases is discussed from considerations of the obtained atomic information

  16. Variation of 3s photoionization resonance structures in a serial atomic number species Ar, K, and Ca

    International Nuclear Information System (INIS)

    Subvalence 3s-shell photoionization resonances of Ca were measured with monochromatized synchrotron radiation and photoion time-of-flight spectroscopy method. Charge resolved photoion yield spectra were obtained. Broad peak structures were found in the Ca+ spectrum and shallow window structures were found in the Ca2+ spectrum. We performed MCDF calculations to assign the resonance structures. The 3s-shell photoionization of Ar and K were also measured for comparison. A systematic increase was observed in Fano-Beutler parameter and in the resonance width along with the increase of atomic number from Z=18(Ar) to 20(Ca). We discuss also the spectral structures that could be of the 3p double-shake-up satellites, which are observed in the 3s photoionization region. (author)

  17. Ab initio study of the structural, magnetic, and electronic properties of copper and silver clusters and their alloys with one palladium atom

    Directory of Open Access Journals (Sweden)

    S. J Hashemifar

    2015-01-01

    Full Text Available In this paper, the structural, magnetic, and electronic properties of two- to nine-atom copper and silver clusters and their alloys with one palladium atom are investigated by using full-potential all-electron density functional computations. After calculating minimized energy of several structural isomers of every nanocluster, it is argued that the small size nanoclusters (up to size of 6, ‎ prefer planar structures, while by increasing size a 2D-3D structural transformation is observed. The structural transformation of pure and copper-palladium clusters occurs in the size of seven and that of silver-palladium cluster in happens at the size of six. The calculated second difference and dissociation energies confirm that the two- and eight- atom pure clusters and three- and seven- atom alloyed clusters are magic clusters. The electronic and magnetic properties of stable isomers are calculated and considered after applying many body based GW correction.

  18. Double-sided F and Cl adsorptions on graphene at various atomic ratios: Geometric, orientation and electronic structure aspects

    Science.gov (United States)

    Widjaja, Hantarto; Jiang, Zhong-Tao; Altarawneh, Mohammednoor; Yin, Chun-Yang; Goh, Bee-Min; Mondinos, Nicholas; Amri, Amun; Dlugogorski, Bogdan Z.

    2016-06-01

    Elemental adsorption on graphene offers an effective procedure in fine-tuning electronic and mechanical properties of graphene. The effects of dopants depend on adsorption site, the degree of coverage as well as on the configuration of the deployed supercell. In this contribution, the density functional theory (DFT) calculations were performed to investigate the electronic structures of F and Cl adsorption (double-sided, top site) on graphene in terms of adsorption orientation, atomic ratios, i.e., from C:F/Cl = 18:2 to C:F/Cl = 2:2. Despite being members of the halogens group, F- and Cl-adsorbed on graphene show contrasting trends. F is adsorbed to graphene more strongly than Cl. F favours full and 25% adsorption coverage, while Cl favours 25% coverage. Both F and Cl cases open band gap (at Fermi energy) at certain atomic concentration coverage, but none creates magnetization.

  19. Effects of atomic oxygen treatment on structures, morphologies and electrical properties of ZnO:Al films

    International Nuclear Information System (INIS)

    ZnO:Al (ZAO) film has a potential application in providing spacecrafts the protection against atomic oxygen (AO) erosion. To advance the understanding of the AO resisting mechanisms and the relationships between the structures, morphologies and conductive properties of ZAO film, direct current magnetron sputtered ZAO films with different thicknesses were treated with AO in a ground-based simulation facility. The microstructure, surface chemical state, morphologies and electrical properties of pristine films and irradiated ones were characterized by X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, atomic force microscopy and Hall measurement. It is found that AO exposure produces novel, oriented recrystallization of the surface particles. It also increases the content of oxygen ions in fully oxidized stoichiometric surroundings on the surface, resulting in the decrease of the conductivity. As the thickness of ZAO film increases, the crystallinity, conductivity and resistance to AO erosion are all improved.

  20. A systematic study of coordinate precision in X-ray structure analyses. Pt. 2. Predictive estimates of E.S.D.'s for the general-atom case

    International Nuclear Information System (INIS)

    The relationship between the mean isotropic e.s.d. anti σ(A)o of any element type A in a crystal structure and the R factor and atomic constitution of that structure is explored for 124 905 element-type occurrences calculated from 33 955 entries in the Cambridge Structural Database. On the basis of the work of Cruickshank [Acta Cryst. (1960), 13, 774-777], it is shown that anti σ(A)p values can be estimated by equations of the form anti σ(A)p = KRN1/2c/ZA where Nc is taken as ΣZ2i/Z2C, the Zi are atomic numbers and the summation is over all atoms in the asymmetric unit. Values of K were obtained by regression techniques using the anti σ(A)o as basis. The constant Knc for noncentrosymmetric structures is found to be larger than Kc for centrosymmetric structures by a factor of ∼21/2, as predicted by Cruickshank (1960). Two predictive equations are generated, one for first-row elements and the second for elements with ZA > 10. The relationship between the different constants K that arise in these two situations is linked to shape differentials in scattering-factor (fi) curves for light and heavy atoms. It is found that predictive equations in which the Zi are selectively replaced by fi at a constant sinθ/λ of 0.30 A-1 generate closely similar values of K for the light-atom and heavy-atom subsets. The overall analysis indicates that atomic e.s.d.'s may be seriously underestimated in the more precise structure determinations, that e.s.d.'s for the heaviest atoms may be less reliable than those for lighter atoms and that e.s.d.'s in noncentrosymmetric structures may be less accurate than those in centrosymmetric structures. (orig.)

  1. Characterization of atomic structure of oxide films on carbon steel in simulated concrete pore solutions using EELS

    Science.gov (United States)

    Gunay, H. Burak; Ghods, Pouria; Isgor, O. Burkan; Carpenter, Graham J. C.; Wu, Xiaohua

    2013-06-01

    The atomic structure of oxide films formed on carbon steel that are exposed to highly alkaline simulated concrete pore solutions was investigated using Electron Energy Loss Spectroscopy (EELS). In particular, the effect of chloride exposure on film structure was studied in two types of simulated pore solutions: saturated calcium hydroxide (CH) and a solution prepared to represent typical concrete pore solutions (CP). It was shown that the films that form on carbon steel in simulated concrete pore solutions contained three indistinct layers. The inner oxide film had a structure similar to that of FeIIO, which is known to be unstable in the presence of chlorides. The outer oxide film mainly resembled Fe3O4 (FeIIO·Fe2IIIO3) in the CH solution and α-Fe2IIIO3/Fe3O4 in the CP solution. The composition of the transition layer between the inner and outer layers of the oxide film was mainly composed of Fe3O4 (FeIIO·Fe2IIIO3). In the presence of chloride, the relative amount of the FeIII/FeII increased, confirming that chlorides induce valence state transformation of oxides from FeII to FeIII, and the difference between the atomic structures of oxide film layers diminished.

  2. Weak links between fast mobility and local structure in molecular and atomic liquids

    CERN Document Server

    Bernini, S; Leporini, D

    2016-01-01

    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 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 characteristic of small $n$-alkanes and $n$-alcohols. Possible links between the fast mobility and ...

  3. Sensing and atomic-scale structure analysis of single nuclear spin clusters in diamond

    OpenAIRE

    Shi, Fazhan; Kong, Xi; Wang, Pengfei; Kong, Fei; Zhao, Nan; Liu, Ren-Bao; Du, Jiangfeng

    2013-01-01

    Single-molecule nuclear magnetic resonance (NMR) is a crown-jewel challenge in the field of magnetic resonance spectroscopy and has important applications in chemical analysis and in quantum computing. Recently, it becomes possible to tackle this grand challenge thanks to experimental advances in preserving quantum coherence of nitrogen-vacancy (NV) center spins in diamond as a sensitive probe and theoretical proposals on atomic-scale magnetometry via dynamical decoupling control. Through dec...

  4. Atomic layer deposition of ZnO thin films and dot structures

    International Nuclear Information System (INIS)

    Successful growth of thin films and quantum dots of ZnO by atomic layer deposition (ALD) is reported. Properties of ZnO films produced by four different ALD-procedures and by oxidation of ALD-grown ZnS films are discussed. The use of thin ZnO films as buffer layers for GaN deposition is also shortly described. (author)

  5. Using Xe as a heavy atom for phase determination of protein trichosanthin structure

    International Nuclear Information System (INIS)

    Under gas pressures of 1-3 MPa, xenon can be bound to discrete sites in hydrophobic cavities of protein, so as to use Xe as a heavy atom for determining phases in protein crystallography. Using single anomalous scattering diffraction method, we demonstrate that an interpretable electron density map can be obtained for protein trichosanthin from a single xenon derivative. We found, for the first time, a pre-existing hydrophobic cavity just under the protein surface of trichosanthin. (authors)

  6. Phase space structures and ionization dynamics of hydrogen atom in elliptically polarized microwaves

    OpenAIRE

    Shchekinova, Elena; Chandre, Cristel; Uzer, Turgay

    2006-01-01

    International audience The multiphoton ionization of hydrogen atoms in a strong elliptically polarized microwave field exhibits complex features that are not observed for ionization in circular and linear polarized fields. Experimental data reveal high sensitivity of ionization dynamics to the small changes of the field polarization. The multidimensional nature of the problem makes widely used diagnostics of dynamics, such as Poincaré surfaces of section, impractical. We analyze the phase ...

  7. Excess-photon ionization spectra and atomic structure in intense laser fields

    International Nuclear Information System (INIS)

    Floquet states represent intrinsic modes of ionization of an atom in a monochromatic field of constant intensity. To describe atomic wave packets evolving in realistic laser pulses, linear superpositions of Floquet states are required ('multistate Floquet theory'). This gives the possibility of following the evolution of wave packets in terms of the Floquet states that are populated during the pulse. We study here the way in which the Floquet states present in the representation of the wave packet manifest themselves in the excess-photon ionization spectra (EPI/ATI). For the purpose of illustration we choose a 1D atomic model with a soft-core Coulomb potential. We calculate the totality of the Floquet states, at all intensities needed, and generate the corresponding 'Floquet map'. We then calculate the EPI spectra for wave packets evolving from the ground state under different types of pulses. By analyzing the location of the lines in the spectrum, and their shapes, we show that they can be associated, in a clear cut and predictable way, to Floquet states responsible for the emission. The understanding of the underlying physics can lead to tailoring laser pulses, such as to obtain EPI signals in a controlled way. Whereas our analysis is applied to theoretical spectra, it would apply, just as well, to experimental ones

  8. Spray structure of a pressure-swirl atomizer for combustion applications

    Directory of Open Access Journals (Sweden)

    Jicha Miroslav

    2012-04-01

    Full Text Available In the present work, global as well as spatially resolved parameters of a spray produced by a pressure-swirl atomizer are obtained. Small pressure-swirl atomizer for aircraft combustion chambers was run on a newly designed test bench with Jet A-1 kerosene type aviation fuel. The atomizer was tested in four regimes based on typical operation conditions of the engine. Spray characteristics were studied using two optical measurement systems, Particle Image velocimetry (PIV and Phase-Doppler Particle Analyzer (P/DPA. The results obtained with P/DPA include information about Sauter Mean Diameter of droplets and spray velocity profiles in one plane perpendicular to the spray axis. Velocity magnitudes of droplets in an axial section of the spray were obtained using PIV. The experimental outputs also show a good confirmation of velocity profiles obtained with both instruments in the test plane. These data together will elucidate impact of the spray quality on the whole combustion process, its efficiency and exhaust gas emissions.

  9. Towards hybrid quantum systems: Trapping a single atom near a nanoscale solid-state structure

    Directory of Open Access Journals (Sweden)

    Tiecke T.G.

    2013-08-01

    Full Text Available We describe and demonstrate a method to deterministically trap single atoms near nanoscale solid-state objects. The trap is formed by the interference of an optical tweezer and its reflection from the nano object, creating a one-dimensional optical lattice where the first lattice site is at z0 ∼ λ/4 from the surface. Using a tapered optical fiber as the nanoscopic object, we characterize the loading into different lattice sites by means of the AC-Stark shift induced by a guided fiber mode. We demonstrate a loading efficiency of 94(6% into the first lattice site, and measure the cooperativity for the emission of the atom into the guided mode of the nanofiber. We show that by tailoring the dimensions of the nanofiber the distance of the trap to the surface can be adjusted. This method is applicable to a large variety of nanostructures and represents a promising starting point for interfacing single atoms with arbitrary nanoscale solid-state systems.

  10. Atomic Structure and Biochemical Characterization of an RNA Endonuclease in the N Terminus of Andes Virus L Protein.

    Directory of Open Access Journals (Sweden)

    Yaiza Fernández-García

    2016-06-01

    Full Text Available Andes virus (ANDV is a human-pathogenic hantavirus. Hantaviruses presumably initiate their mRNA synthesis by using cap structures derived from host cell mRNAs, a mechanism called cap-snatching. A signature for a cap-snatching endonuclease is present in the N terminus of hantavirus L proteins. In this study, we aimed to solve the atomic structure of the ANDV endonuclease and characterize its biochemical features. However, the wild-type protein was refractory to expression in Escherichia coli, presumably due to toxic enzyme activity. To circumvent this problem, we introduced attenuating mutations in the domain that were previously shown to enhance L protein expression in mammalian cells. Using this approach, 13 mutant proteins encompassing ANDV L protein residues 1-200 were successfully expressed and purified. Protein stability and nuclease activity of the mutants was analyzed and the crystal structure of one mutant was solved to a resolution of 2.4 Å. Shape in solution was determined by small angle X-ray scattering. The ANDV endonuclease showed structural similarities to related enzymes of orthobunya-, arena-, and orthomyxoviruses, but also differences such as elongated shape and positively charged patches surrounding the active site. The enzyme was dependent on manganese, which is bound to the active site, most efficiently cleaved single-stranded RNA substrates, did not cleave DNA, and could be inhibited by known endonuclease inhibitors. The atomic structure in conjunction with stability and activity data for the 13 mutant enzymes facilitated inference of structure-function relationships in the protein. In conclusion, we solved the structure of a hantavirus cap-snatching endonuclease, elucidated its catalytic properties, and present a highly active mutant form, which allows for inhibitor screening.

  11. Atomic Structure and Biochemical Characterization of an RNA Endonuclease in the N Terminus of Andes Virus L Protein.

    Science.gov (United States)

    Fernández-García, Yaiza; Reguera, Juan; Busch, Carola; Witte, Gregor; Sánchez-Ramos, Oliberto; Betzel, Christian; Cusack, Stephen; Günther, Stephan; Reindl, Sophia

    2016-06-01

    Andes virus (ANDV) is a human-pathogenic hantavirus. Hantaviruses presumably initiate their mRNA synthesis by using cap structures derived from host cell mRNAs, a mechanism called cap-snatching. A signature for a cap-snatching endonuclease is present in the N terminus of hantavirus L proteins. In this study, we aimed to solve the atomic structure of the ANDV endonuclease and characterize its biochemical features. However, the wild-type protein was refractory to expression in Escherichia coli, presumably due to toxic enzyme activity. To circumvent this problem, we introduced attenuating mutations in the domain that were previously shown to enhance L protein expression in mammalian cells. Using this approach, 13 mutant proteins encompassing ANDV L protein residues 1-200 were successfully expressed and purified. Protein stability and nuclease activity of the mutants was analyzed and the crystal structure of one mutant was solved to a resolution of 2.4 Å. Shape in solution was determined by small angle X-ray scattering. The ANDV endonuclease showed structural similarities to related enzymes of orthobunya-, arena-, and orthomyxoviruses, but also differences such as elongated shape and positively charged patches surrounding the active site. The enzyme was dependent on manganese, which is bound to the active site, most efficiently cleaved single-stranded RNA substrates, did not cleave DNA, and could be inhibited by known endonuclease inhibitors. The atomic structure in conjunction with stability and activity data for the 13 mutant enzymes facilitated inference of structure-function relationships in the protein. In conclusion, we solved the structure of a hantavirus cap-snatching endonuclease, elucidated its catalytic properties, and present a highly active mutant form, which allows for inhibitor screening. PMID:27300328

  12. Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and Its Precursors on Metal Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, George W [Columbia University

    2015-02-16

    Executive Summary of Final Report for Award DE-FG02-88ER13937 Project Title: Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and its Precursors on Metal Surfaces Applicant/Institution: Columbia University Principal Investigator: George W. Flynn Objectives: The objectives of this project were to reveal the mechanisms and reaction processes that solid carbon materials undergo when combining with gases such as oxygen, water vapor and hydrocarbons. This research was focused on fundamental chemical events taking place on single carbon sheets of graphene, a two-dimensional, polycyclic carbon material that possesses remarkable chemical and electronic properties. Ultimately, this work is related to the role of these materials in mediating the formation of polycyclic aromatic hydrocarbons (PAH’s), their reactions at interfaces, and the growth of soot particles. Our intent has been to contribute to a fundamental understanding of carbon chemistry and the mechanisms that control the formation of PAH’s, which eventually lead to the growth of undesirable particulates. We expect increased understanding of these basic chemical mechanisms to spur development of techniques for more efficient combustion of fossil fuels and to lead to a concomitant reduction in the production of undesirable solid carbon material. Project Description: Our work treated specifically the surface chemistry aspects of carbon reactions by using proximal probe (atomic scale imaging) techniques to study model systems of graphene that have many features in common with soot forming reactions of importance in combustion flames. Scanning tunneling microscopy (STM) is the main probe technique that we used to study the interfacial structure and chemistry of graphene, mainly because of its ability to elucidate surface structure and dynamics with molecular or even atomic resolution. Scanning tunneling spectroscopy (STS), which measures the local density of quantum states over a single

  13. Structure and property of metal melt Ⅱ—Evolution of atomic clusters in the not high temperature range above liquidus

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Based on the theory of micro-inhomogeneity of liquid metal,a calculation model is established for the quantitative description of the structural information of metal melts.Only by thermophysical property parameters and basic structural parameters of solid metal,can this model produce the main information of melt structure,including the relative concentration of active atoms,size of atomic clusters and number of short-range order atoms.Based on this model,the main structural information of Al and Ni melts in the not high range above the liquidus is calculated,with results in good agreement with experimental values.Besides,analyzed is the influence of superheating temperature and atomic number on the melt structural information of the first (IA) and second main group (IIA) elements.With temperature increasing,melt structural information regularly changes for both IA and IIA elements.With the atomic number increasing,melt structural information of IA elements changes regularly,for the crystal structures of the IA elements are all of bcc lattice type.However,no notable regular change of melt structural information for IIA elements has been found,mainly because the lattice type of IIA elements is of hcp-fcc-bcc transition.The present work presents an effective way for better understanding metal melt structure and for forecasting the change of the physical property of metal melts.

  14. Influence of transition metal atoms doping on structural, electronic and nonlinear optical properties of Mg12O12 nanoclusters: A DFT study

    Science.gov (United States)

    Shamlouei, Hamid Reza; Nouri, Amin; Mohammadi, Asghar; Tehrani, Abbas Dadkhah

    2016-03-01

    Using density functional theory, we investigated the effect of transition metal doping on structural, electronic, energetic, linear and nonlinear optical properties of Mg12O12 nanocluster. The result revealed that transition metal atoms doping lead to reduce the Eg and increase the dipole moment. The doping of transition metal atom on Mg12O12 nanocluster enhances its polarizability value. Also polarizability values for doped nanoclusters decrease as the atomic number of transition metal increase. The first hyperpolarizability value dramatically increases as substitute a magnesium atom with a transition metal atom. Among the transition metal atom doped nanocage, scandium has the largest first hyperpolarizability value (β◦≈47,872 au). The stability and remarkable values of β◦ (for Sc, Ti and V doped of nanocage) suggest that these compounds may be applicable as NLO material in industrial.

  15. Unique Electronic Structure in a Porous Ga-In Bimetallic Oxide Nano-Photocatalyst with Atomically Thin Pore Walls.

    Science.gov (United States)

    Chen, Hui; Yu, Guangtao; Li, Guo-Dong; Xie, Tengfeng; Sun, Yuanhui; Liu, Jingwei; Li, Hui; Huang, Xuri; Wang, Dejun; Asefa, Tewodros; Chen, Wei; Zou, Xiaoxin

    2016-09-12

    A facile synthetic route is presented that produces a porous Ga-In bimetallic oxide nanophotocatalyst with atomically thin pore walls. The material has an unprecedented electronic structure arising from its ultrathin walls. The bottom of the conduction band and the top of the valence band of the material are distributed on two opposite surfaces separated with a small electrostatic potential difference. This not only shortens the distance by which the photogenerated charges travel from the sites where they are generated to the sites where they catalyze the reactions, but also facilitates charge separations in the material. The porous structure within the walls results in a large density of exposed surface reactive/catalytic sites. Because of these optimized electronic and surface structures, the material exhibits superior photocatalytic activity toward the hydrogen evolution reaction (HER). PMID:27529769

  16. Structural, elastic, and electronic properties of sodium atoms encapsulated type-I silicon-clathrate compound under high pressure

    Science.gov (United States)

    Zhang, Wei; Chen, Qing-Yun; Zeng, Zhao-Yi; Cai, Ling-Cang

    2015-10-01

    We calculated the structural, elastic, and electronic properties of alkali metal Na atoms doped type-I silicon-clathrate compound (Na8Si46) under pressure using first-principles methods. The obtained dependencies of bond lengths and bond angles on pressure show heterogeneous behaviors which may bring out a structural transition. By using the elastic stability criteria from the calculated elastic constants, we confirm that the Na8Si46 is elastically unstable under high pressure. Some of the mechanical and thermal quantities include bulk modulus, shear modulus, Young’s modulus, Debye temperature, sound velocity, melting point, and hardness, which are also derived from the elastic constants. The calculated total and partial electron densities of states of Na8Si46 indicate a weak interaction between the encapsulated Na atoms and the silicon framework. Moreover, the effect of pressure on its electronic structure is also investigated, which suggests that pressure is not a good choice to enhance the thermoelectricity performance of Na8Si46. Project supported by National Natural Science Foundation of China (Grant Nos. 11347134 and 11304254) and the Doctor Foundation of Southwest University of Science and Technology, China (Grant No. 13zx7125).

  17. Structural, elastic, and electronic properties of sodium atoms encapsulated type-I silicon-clathrate compound under high pressure

    Institute of Scientific and Technical Information of China (English)

    张伟; 陈青云; 曾召益; 蔡灵仓

    2015-01-01

    We calculated the structural, elastic, and electronic properties of alkali metal Na atoms doped type-I silicon–clathrate compound (Na8Si46) under pressure using first-principles methods. The obtained dependencies of bond lengths and bond angles on pressure show heterogeneous behaviors which may bring out a structural transition. By using the elastic stability criteria from the calculated elastic constants, we confirm that the Na8Si46 is elastically unstable under high pressure. Some of the mechanical and thermal quantities include bulk modulus, shear modulus ,Young’s modulus, Debye temperature, sound velocity, melting point, and hardness, which are also derived from the elastic constants. The calculated total and partial electron densities of states of Na8Si46 indicate a weak interaction between the encapsulated Na atoms and the silicon framework. Moreover, the effect of pressure on its electronic structure is also investigated, which suggests that pressure is not a good choice to enhance the thermoelectricity performance of Na8Si46.

  18. Atomic transition frequencies, isotope shifts, and sensitivity to variation of the fine structure constant for studies of quasar absorption spectra

    CERN Document Server

    Berengut, J C; Flambaum, V V; King, J A; Kozlov, M G; Murphy, M T; Webb, J K

    2010-01-01

    Theories unifying gravity with other interactions suggest spatial and temporal variation of fundamental "constants" in the Universe. A change in the fine structure constant, alpha, could be detected via shifts in the frequencies of atomic transitions in quasar absorption systems. Recent studies using 140 absorption systems from the Keck telescope and 153 from the Very Large Telescope, suggest that alpha varies spatially. That is, in one direction on the sky alpha seems to have been smaller at the time of absorption, while in the opposite direction it seems to have been larger. To continue this study we need accurate laboratory measurements of atomic transition frequencies. The aim of this paper is to provide a compilation of transitions of importance to the search for alpha variation. They are E1 transitions to the ground state in several different atoms and ions, with wavelengths ranging from around 900 - 6000 A, and require an accuracy of better than 10^{-4} A. We discuss isotope shift measurements that are...

  19. Complete-active-space multiconfiguration Dirac-Hartree-Fock calculations of hyperfine-structure constants of the gold atom

    International Nuclear Information System (INIS)

    The multiconfiguration Dirac-Hartree-Fock model has been employed to calculate the expectation values for the hyperfine splittings of the 5d96s22D3/2 and 5d96s22D5/2 levels of atomic gold. One-, two-, and three-body electron correlation effects involving all 79 electrons have been included in a systematic manner. The approximation employed in this study is equivalent to a complete-active-space approach. Calculated electric field gradients, together with experimental values of the electric quadrupole hyperfine-structure constants, allow us to extract a nuclear electric quadrupole moment Q(197Au)=521.5(5.0) mb.

  20. Crystal structure of post-perovskite-type CaIrO3 reinvestigated: new insights into atomic thermal vibration behaviors

    OpenAIRE

    Akihiko Nakatsuka; Kazumasa Sugiyama; Akira Yoneda; Keiko Fujiwara; Akira Yoshiasa

    2015-01-01

    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 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...

  1. X-ray diffraction study of atomic structure features of amorphous carbon containing materials of nature and synthetic origin

    International Nuclear Information System (INIS)

    The atomic structure of amorphous carbon-containing materials such as carbon glass, spectroscopically pure carbon, schungite and anthracite is investigated using X ray diffraction analysis and computerized simulation. In computerized simulation of model gratings packing into packets an interlayer distance and a number of layer in a packet varied and a gratings turn is predetermined randomly. The quantity of gratings in a packet is shown to vary between four for anthracite and six for spectroscopically pure coal. The interlayer distance for all amorphous carbonaceous materials is above 3.35 A which is typical for graphite

  2. Atomic Transition Frequencies, Isotope Shifts, and Sensitivity to Variation of the Fine Structure Constant for Studies of Quasar Absorption Spectra

    Science.gov (United States)

    Berengut, J. C.; Dzuba, V. A.; Flambaum, V. V.; King, J. A.; Kozlov, M. G.; Murphy, M. T.; Webb, J. K.

    Theories unifying gravity with other interactions suggest spatial and temporal variation of fundamental "constants" in the Universe. A change in the fine structure constant, α = {e}2/hslash c , could be detected via shifts in the frequencies of atomic transitions in quasar absorption systems. Recent studies using 140 absorption systems from the Keck telescope and 153 from the Very Large Telescope, suggest that α varies spatially (61). That is, in one direction on the sky α seems to have been smaller at the time of absorption, while in the opposite direction it seems to have been larger.

  3. Determination of the fine structure constant based on BLOCH oscillations of ultracold atoms in a vertical optical lattice.

    Science.gov (United States)

    Cladé, Pierre; de Mirandes, Estefania; Cadoret, Malo; Guellati-Khélifa, Saïda; Schwob, Catherine; Nez, François; Julien, Lucile; Biraben, François

    2006-01-27

    We report an accurate measurement of the recoil velocity of 87Rb atoms based on Bloch oscillations in a vertical accelerated optical lattice. We transfer about 900 recoil momenta with an efficiency of 99.97% per recoil. A set of 72 measurements of the recoil velocity, each one with a relative uncertainty of about 33 ppb in 20 min integration time, leads to a determination of the fine structure constant with a statistical relative uncertainty of 4.4 ppb. The detailed analysis of the different systematic errors yields to a relative uncertainty of 6.7 ppb. The deduced value of alpha-1 is 137.035 998 78(91).

  4. Atomic structure and growth mechanism of T1 precipitate in Al–Cu–Li–Mg–Ag alloy

    International Nuclear Information System (INIS)

    The atomic structure of a 0.94-nm-thick T1 precipitate in an Al–Cu–Li–Mg–Ag alloy is investigated by combining aberration-corrected scanning transmission electron microscopy (STEM) and energy-dispersive X-ray spectroscopy (EDX). Ag segregates at the first layer of the T1 precipitate interface, revealing a significant compositional variation of Ag throughout the interface. Moreover, the T1 precipitate thickened from 0.94 nm with successive stacking of identical 0.94 nm thick layers

  5. Study on the local atomic structure of germanium in organic germanium compounds by EXAFS

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Organic germanium compounds have been extensively applied in medicine as tonics,In this paper,the local structures of two organic germanium compounds,carboxyethylgermanium sesquioxide and polymeric germanium glutamate,were determined by EXAFS.The structure parameters including coordination numbers and bond lengths were reported,and possible structure patterns were discussed.

  6. Quantum mechanical theory of a structured atom-diatom collision system - A + BC/1-Sigma/

    Science.gov (United States)

    Devries, P. L.; George, T. F.

    1977-01-01

    The problem of a 2-p state atom colliding with a singlet sigma state diatom, which involves multiple potential surfaces, is investigated. Within a diabatic representation for the electronic degrees of freedom (plus spin-orbit interaction), coupled scattering equations are derived in both space-fixed and body-fixed coordinate systems. Coefficients, analogous to Percival-Seaton coefficients, are obtained. Approximations to the exact equations, including angular momenta decoupling approximations, are discussed for both the space-fixed and body-fixed formalisms.

  7. Localized positronium atoms in porous structures studied by 2D-ACAR

    International Nuclear Information System (INIS)

    The localization of positronium (PS) atoms was studied by measurements of two-dimensional angular correlation of positron annihilation radiation (2D-ACAR) for porous glasses. Annihilations of positron-electron pairs with a large anisotropy were found in 2D-ACAR spectra. This fact can be attributed to the momentum uncertainty due to the localization of Ps in a finite dimension of pores. The present investigation showed the possibility of the detection of microstructures in amorphous materials by the 2D-ACAR technique. (orig.)

  8. Local atomic structure in (Zr{sub 1-x}U{sub x})N

    Energy Technology Data Exchange (ETDEWEB)

    Walter, M. [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, D-76125 Karlsruhe (Germany)], E-mail: marcus.walter@ec.europa.eu; Somers, J.; Fernandez-Carretero, A. [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, D-76125 Karlsruhe (Germany); Rothe, J. [Forschungszentrum Karlsruhe, Institut fuer Nukleare Entsorgung (INE), P.O. Box 3640, D-76021 Karlsruhe (Germany)

    2008-02-15

    (Zr{sub 1-x}U{sub x})N solid solutions were prepared for EXAFS measurements by a sol-gel route combined with infiltration and carbothermic reduction. The lattice parameter and the more distant coordination shells (Me{sub 2} and Me{sub 3}) around the Zr and U atoms follow the Vegard law. In the first coordination shell, the U-N distance also follows the Vegard law. Though the Zr-N bond distance increases with the lattice expansion caused by increasing U content, it remains constant at 232-235 pm in U-rich (Zr{sub 1-x}U{sub x})N (x > 0.6). The measurements indicate that U accommodates the lattice contraction with increasing Zr content, whereas Zr is able to expand its Zr-N bond only at lower U content. In the composition range of transmutation fuels, (Zr{sub 1-x}U{sub x})N is homogeneous at the local atomic scale.

  9. Effects of rapid thermal annealing on the structural and local atomic properties of ZnO: Ge nanocomposite thin films

    Energy Technology Data Exchange (ETDEWEB)

    Ceylan, Abdullah, E-mail: aceylanabd@yahoo.com; Ozcan, Sadan [SNTG Laboratory, Department of Physics Engineering, Hacettepe University, 06800 Ankara (Turkey); Rumaiz, Abdul K. [National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973 (United States); Caliskan, Deniz [Nanotechnology Research Center, Bilkent University, 06800 Ankara (Turkey); Ozbay, Ekmel [Nanotechnology Research Center, Bilkent University, 06800 Ankara (Turkey); Department of Physics, Bilkent University, 06800 Ankara (Turkey); Department of Electrical and Electronics Engineering, Bilkent University, 06800 Ankara (Turkey); Woicik, J. C. [National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States)

    2015-03-14

    We have investigated the structural and local atomic properties of Ge nanocrystals (Ge-ncs) embedded ZnO (ZnO: Ge) thin films. The films were deposited by sequential sputtering of ZnO and Ge thin film layers on z-cut quartz substrates followed by an ex-situ rapid thermal annealing (RTA) at 600 °C for 30, 60, and 90 s under forming gas atmosphere. Effects of RTA time on the evolution of Ge-ncs were investigated by x-ray diffraction (XRD), scanning electron microscopy (SEM), hard x-ray photoelectron spectroscopy (HAXPES), and extended x-ray absorption fine structure (EXAFS). XRD patterns have clearly shown that fcc diamond phase Ge-ncs of sizes ranging between 18 and 27 nm are formed upon RTA and no Ge-oxide peak has been detected. However, cross-section SEM images have clearly revealed that after RTA process, Ge layers form varying size nanoclusters composed of Ge-ncs regions. EXAFS performed at the Ge K-edge to probe the local atomic structure of the Ge-ncs has revealed that as prepared ZnO:Ge possesses Ge-oxide but subsequent RTA leads to crystalline Ge structure without the oxide layer. In order to study the occupied electronic structure, HAXPES has been utilized. The peak separation between the Zn 2p and Ge 3d shows no significant change due to RTA. This implies little change in the valence band offset due to RTA.

  10. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

    Science.gov (United States)

    Mohammadiarani, Hossein; Vashisth, Harish

    2016-01-01

    The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID

  11. Unraveling the Architecture and Structural Dynamics of Pathogens by High-Resolution in vitro Atomic Force Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Malkin, A J; Plomp, M; Leighton, T J; McPherson, A; Wheeler, K E

    2005-04-12

    Progress in structural biology very much depends upon the development of new high-resolution techniques and tools. Despite decades of study of viruses, bacteria and bacterial spores and their pressing importance in human medicine and biodefense, many of their structural properties are poorly understood. Thus, characterization and understanding of the architecture of protein surface and internal structures of pathogens is critical to elucidating mechanisms of disease, immune response, physicochemical properties, environmental resistance and development of countermeasures against bioterrorist agents. Furthermore, even though complete genome sequences are available for various pathogens, the structure-function relationships are not understood. Because of their lack of symmetry and heterogeneity, large human pathogens are often refractory to X-ray crystallographic analysis or reconstruction by cryo-electron microscopy (cryo-EM). An alternative high-resolution method to examine native structure of pathogens is atomic force microscopy (AFM), which allows direct visualization of macromolecular assemblies at near-molecular resolution. The capability to image single pathogen surfaces at nanometer scale in vitro would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, specific cellular processes, environmental dynamics and biotransformation.

  12. An X-ray absorption spectroscopy investigation of the local atomic structure in Cu-Ni-Si alloy after severe plastic deformation and ageing

    Science.gov (United States)

    Azzeddine, H.; Harfouche, M.; Hennet, L.; Thiaudiere, D.; Kawasaki, M.; Bradai, D.; Langdon, T. G.

    2015-08-01

    The local atomic structure of Cu-Ni-Si alloy after severe plastic deformation (SPD) processing and the decomposition of supersaturated solid solution upon annealing were investigated by means of X-ray absorption spectroscopy. The coordination number and interatomic distances were obtained by analyzing experimental extend X-ray absorption fine structure data collected at the Ni K-edge. Results indicate that the environment of Ni atoms in Cu-Ni-Si alloy is strongly influenced by the deformation process. Moreover, ageing at 973 K affects strongly the atomic structure around the Ni atoms in Cu-Ni-Si deformed by equal channel angular pressing and high pressure torsion. This influence is discussed in terms of changes and decomposition features of the Cu-Ni-Si solid solution.

  13. Pressure Effects on the Atomic and Electronic Structure of Aligned Small Diameter Carbon Nanotubes

    OpenAIRE

    Saxena, Sumit; Trevor A. Tyson

    2008-01-01

    Density functional methods have been used to calculate the electronic properties of aligned smalldiameter single-walled carbon nanotubes under hydrostatic pressures. Abrupt pressure induced semiconductor-metal and metal-semiconductor transitions concomitant with changes in structure are observed. Novel and unexpected unit cell nanotube cross-sections are found. These tubes are observed to form interlinking structures at very high pressures. The large changes in electronic structure and the ab...

  14. Atomic structure of Mn-rich nanocolumns probed by x-ray absorption spectroscopy

    Science.gov (United States)

    Rovezzi, M.; Devillers, T.; Arras, E.; d'Acapito, F.; Barski, A.; Jamet, M.; Pochet, P.

    2008-06-01

    In this letter, we have used the extended x-ray-absorption fine-structure (EXAFS) technique to investigate the structure of Mn-rich self-organized nanocolumns grown by low temperature molecular beam epitaxy. The EXAFS analysis has shown that Mn-rich nanocolumns exhibit a complex local structure that cannot be described by a simple substitutional model. Additional interatomic distances had to be considered in the EXAFS model which are in excellent agreement with the structure of a Ge-3Mn building block tetrahedron of Ge3Mn5.

  15. Atomic Scale Interface Manipulation, Structural Engineering, and Their Impact on Ultrathin Carbon Films in Controlling Wear, Friction, and Corrosion.

    Science.gov (United States)

    Dwivedi, Neeraj; Yeo, Reuben J; Yak, Leonard J K; Satyanarayana, Nalam; Dhand, Chetna; Bhat, Thirumaleshwara N; Zhang, Zheng; Tripathy, Sudhiranjan; Bhatia, Charanjit S

    2016-07-13

    Reducing friction, wear, and corrosion of diverse materials/devices using systems. Here, we present a novel approach based on atomic scale interface manipulation to engineer and control the friction, wear, corrosion, and structural characteristics of 0.7-1.7 nm carbon-based films on CoCrPt:oxide-based magnetic media. We demonstrate that when an atomically thin (∼0.5 nm) chromium nitride (CrNx) layer is sandwiched between the magnetic media and an ultrathin carbon overlayer (1.2 nm), it modifies the film-substrate interface, creates various types of interfacial bonding, increases the interfacial adhesion, and tunes the structure of carbon in terms of its sp(3) bonding. These contribute to its remarkable functional properties, such as stable and lowest coefficient of friction (∼0.15-0.2), highest wear resistance and better corrosion resistance despite being only ∼1.7 nm thick, surpassing those of ∼2.7 nm thick current commercial carbon overcoat (COC) and other overcoats in this work. While this approach has direct implications for advancing current magnetic storage technology with its ultralow thickness, it can also be applied to advance the protective and barrier capabilities of other ultrathin materials for associated technologies. PMID:27267790

  16. Simple Nuclear Structure in (111-129)Cd from Atomic Isomer Shifts.

    Science.gov (United States)

    Yordanov, D T; Balabanski, D L; Bissell, M L; Blaum, K; Budinčević, I; Cheal, B; Flanagan, K; Frömmgen, N; Georgiev, G; Geppert, Ch; Hammen, M; Kowalska, M; Kreim, K; Krieger, A; Meng, J; Neugart, R; Neyens, G; Nörtershäuser, W; Rajabali, M M; Papuga, J; Schmidt, S; Zhao, P W

    2016-01-22

    Isomer shifts have been determined in ^{111-129}Cd by high-resolution laser spectroscopy at CERN-ISOLDE. The corresponding mean square charge-radii changes, from the 1/2^{+} and the 3/2^{+} ground states to the 11/2^{-} isomers, have been found to follow a distinct parabolic dependence as a function of the atomic mass number. Since the isomers have been previously associated with simplicity due to the linear mass dependence of their quadrupole moments, the regularity of the isomer shifts suggests a higher order of symmetry affecting the ground states in addition. A comprehensive description assuming nuclear deformation is found to accurately reproduce the radii differences in conjunction with the known quadrupole moments. This intuitive interpretation is supported by covariant density functional theory. PMID:26849588

  17. Sub-cellular structure studied by combined atomic force-fluorescence microscopy

    Science.gov (United States)

    Trache, Andreea

    2009-03-01

    A novel experimental technique that integrates atomic force microscopy (AFM) with fluorescence imaging was used to study the role of extracellular matrix proteins in cellular organization. To understand the mechanism by which living cells sense mechanical forces, and how they respond and adapt to their environment, we developed a new technology able to investigate cellular behavior at sub-cellular level that integrates an AFM with total internal reflection fluorescence (TIRF) microscopy and fast-spinning disk (FSD) confocal microscopy. Live smooth muscle cells exhibited differences in focal adhesions and actin pattern depending on the extracellular matrix used for substrate coating. Data obtained by using the AFM-optical imaging integrated technique offer novel quantitative information that allows understanding the fundamental processes of cellular reorganization in response to extracellular matrix modulation. The integrated microscope presented here is broadly applicable across a wide range of molecular dynamic studies in any adherent live cells.

  18. Phase-space structures and ionization dynamics of the hydrogen atom in elliptically polarized microwaves

    Science.gov (United States)

    Shchekinova, E.; Chandre, C.; Uzer, T.

    2006-10-01

    The multiphoton ionization of hydrogen atoms in a strong elliptically polarized microwave field exhibits complex features that are not observed for ionization in circular and linear polarized fields. Experimental data reveal high sensitivity of ionization dynamics to the small changes of the field polarization. The multidimensional nature of the problem makes widely used diagnostics of dynamics, such as Poincaré surfaces of section, impractical. We analyze the phase-space dynamics using the finite time stability analysis rendered by the fast Lyapunov indicators technique. The concept of zero-velocity surface is used to initialize the calculations and visualize the dynamics. Our analysis provides stability maps calculated for the initial energy at the maximum and below the saddle of the zero-velocity surface. We estimate qualitatively the dependence of ionization thresholds on the parameters of the applied field, such as polarization and scaled amplitude.

  19. Atomically Thin Ordered Alloys of Transition Metal Dichalcogenides: Stability and Band Structures

    DEFF Research Database (Denmark)

    Pandey, Mohnish; Jacobsen, Karsten Wedel; Thygesen, Kristian Sommer

    2016-01-01

    to be close to zero for several alloys and below 20 meV/atom for all the alloys. We explore to what extent the electronic properties like the band gap and band edge positions of the alloy can be evaluated by taking the weighted average of the corresponding properties of the pristine systems. In general......, this approach works well with the only exception being Cr containing compounds. Because the calculated properties of the alloys are very similar to the weighted averages, we expect that the trends observed for the ordered alloys will also hold for more realistic disordered alloys......We explore the possibility of modulating the electronic band edges of the transition metal dichalcogenides (TMD) via alloying of different semiconductors within the same group (intra-group alloying). The stability of the ordered alloys is assessed from the calculated mixing enthalpy which is found...

  20. Coating and functionalization of high density ion track structures by atomic layer deposition

    Science.gov (United States)

    Mättö, Laura; Szilágyi, Imre M.; Laitinen, Mikko; Ritala, Mikko; Leskelä, Markku; Sajavaara, Timo

    2016-10-01

    In this study flexible TiO2 coated porous Kapton membranes are presented having electron multiplication properties. 800 nm crossing pores were fabricated into 50 μm thick Kapton membranes using ion track technology and chemical etching. Consecutively, 50 nm TiO2 films were deposited into the pores of the Kapton membranes by atomic layer deposition using Ti(iOPr)4 and water as precursors at 250 °C. The TiO2 films and coated membranes were studied by scanning electron microscopy (SEM), X-ray diffraction (XRD) and X-ray reflectometry (XRR). Au metal electrode fabrication onto both sides of the coated foils was achieved by electron beam evaporation. The electron multipliers were obtained by joining two coated membranes separated by a conductive spacer. The results show that electron multiplication can be achieved using ALD-coated flexible ion track polymer foils.

  1. In situ surface X-ray diffraction studies of the copper-electrolyte interface. Atomic structure and homoepitaxial grwoth

    Energy Technology Data Exchange (ETDEWEB)

    Golks, Frederik

    2011-05-19

    Copper electrodeposition is the predominantly used technique for on-chip wiring in the fabrication of ultra-large scale integrated (ULSI) microchips. In this 'damascene copper electroplating' process, multicomponent electrolytes containing organic additives realize void-free filling of trenches with high aspect ratio ('superconformal deposition'). Despite manifold studies, motivated by the continuous trend to shrink wiring dimensions and thus the demand of optimized plating baths, detailed knowledge on the growth mechanism - in presence and absence of additives - is still lacking. Using a recently developed hanging meniscus X-ray transmission cell, brilliant synchrotron x-rays and a fast, one-dimensional detector system, unique real-time in situ surface X-ray diffraction studies of copper electrodeposition were performed under realistic reaction conditions, approaching rates of technological relevance. Preparatory measurements of the electrochemical dissolution of Au(001) in chloride-containing electrolyte demonstrated the capability of this powerful technique, specifically the possibility to follow atomic-scale deposition or dissolution processes with a time resolution down to five milliseconds. The electrochemical as well as structural characterization of the Cu(001)- and Cu(111)-electrolyte interfaces provided detailed insight into the complex atomic-scale structures in presence of specifically adsorbed chloride on these surfaces. The interface of Cu(001) in chloride-containing electrolyte exhibits a continuous surface phase transition of a disordered Cl adlayer to a c(2 x 2) Cl adlayer with increasing potential. The latter was found to induce a small vertical corrugation of substrate atoms, which can be ascribed to lattice relaxations induced by the presence of coadsorbed water molecules and cations in the outer part of the electrochemical double layer. The study of the specific adsorption of chloride on Cu(111) from acidic aqueous

  2. Colloidal PbSe/CdSe Heteronanocrystals. Atomic configuration, electronic structure and optical properties

    NARCIS (Netherlands)

    Grodzinska, D.

    2012-01-01

    This thesis focuses on the structural characterization and the opto-electronic properties of PbSe/CdSe core/shell QDs and on the structural and morphological evolution of PbSe/CdSe core/shell QDs upon thermal annealing under vacuum.

  3. Three-dimensional atomic-scale structure of size-selected gold nanoclusters

    NARCIS (Netherlands)

    Li, Z.; Young, N.P.; Di Vece, M.; Palomba, S.; Palmer, R.E.; Bleloch, A.l.; Curley, B.C.; Johnston, R.L.; Jiang, J.; Yuan, J.

    2008-01-01

    An unambiguous determination of the three-dimensional structure of nanoparticles is challenging1. Electron tomography requires a series of images taken for many different specimen orientations2. This approach is ideal for stable and stationary structures3. But ultrasmall nanoparticles are intrinsica

  4. Effect of additional elements on compositional modulated atomic layered structure of hexagonal Co80Pt20 alloy films with superlattice diffraction

    Directory of Open Access Journals (Sweden)

    Shintaro Hinata

    2016-05-01

    Full Text Available The effect of additional element on compositionally modulated atomic layered structure of hexagonal Co80Pt20 alloy films with superlattice diffraction was investigated. In this study it is found that the addition of Cr or W element to Co80Pt20 alloy film shows less deterioration of hcp stacking structure and compositionally modulated atomic layer stacking structure as compared to Si or Zr or Ti with Ku of around 1.4 or 1.0 × 107 erg/cm3 at 5 at.% addition. Furthermore, for O2 addition of O2 ≥ 5.0 × 10−3 Pa to CoPt alloy, compositionally modulated atomic layer stacking structure will be deteriorated with enhancement of formation of hcp stacking structure which leads higher Ku of 1.0 × 107 erg/cm3.

  5. Origin of structural analogies and differences between the atomic structures of GeSe4 and GeS4 glasses: A first principles study

    International Nuclear Information System (INIS)

    First-principles molecular dynamics simulations based on density functional theory are employed for a comparative study of structural and bonding properties of two stoichiometrically identical chalcogenide glasses, GeSe4 and GeS4. Two periodic cells of 120 and 480 atoms are adopted. Both glasses feature a coexistence of Ge-centered tetrahedra and Se(S) homopolar connections. Results obtained for N = 480 indicate substantial differences at the level of the Se(S) environment, since Ge–Se–Se connections are more frequent than the corresponding Ge–S–S ones. The presence of a more prominent first sharp diffraction peak in the total neutron structure factor of glassy GeS4 is rationalized in terms of a higher number of large size rings, accounting for extended Ge–Se correlations. Both the electronic density of states and appropriate electronic localization tools provide evidence of a higher ionic character of Ge–S bonds when compared to Ge–Se bonds. An interesting byproduct of these investigations is the occurrence of discernible size effects that affect structural motifs involving next nearest neighbor distances, when 120 or 480 atoms are used

  6. Origin of structural analogies and differences between the atomic structures of GeSe{sub 4} and GeS{sub 4} glasses: A first principles study

    Energy Technology Data Exchange (ETDEWEB)

    Bouzid, Assil; Le Roux, Sébastien; Ori, Guido; Boero, Mauro; Massobrio, Carlo [Institut de Physique et de Chimie des Matériaux de Strasbourg, Université de Strasbourg and CNRS UMR 7504, 23 rue du Loess, BP43, F-67034 Strasbourg Cedex 2 (France)

    2015-07-21

    First-principles molecular dynamics simulations based on density functional theory are employed for a comparative study of structural and bonding properties of two stoichiometrically identical chalcogenide glasses, GeSe{sub 4} and GeS{sub 4}. Two periodic cells of 120 and 480 atoms are adopted. Both glasses feature a coexistence of Ge-centered tetrahedra and Se(S) homopolar connections. Results obtained for N = 480 indicate substantial differences at the level of the Se(S) environment, since Ge–Se–Se connections are more frequent than the corresponding Ge–S–S ones. The presence of a more prominent first sharp diffraction peak in the total neutron structure factor of glassy GeS{sub 4} is rationalized in terms of a higher number of large size rings, accounting for extended Ge–Se correlations. Both the electronic density of states and appropriate electronic localization tools provide evidence of a higher ionic character of Ge–S bonds when compared to Ge–Se bonds. An interesting byproduct of these investigations is the occurrence of discernible size effects that affect structural motifs involving next nearest neighbor distances, when 120 or 480 atoms are used.

  7. Atomic Structure of Defects in Anion-Deficient Perovskite-Based Ferrites with a Crystallographic Shear Structure

    OpenAIRE

    Batuk, Maria; Turner, Stuart; Abakumov, Artem M.; Batuk, Dmitry; Hadermann, Joke; Tendeloo, van, G.

    2014-01-01

    Abstract: Crystallographic shear (CS) planes provide a new structure-generation mechanism in the anion-deficient perovskites containing lone-pair cations. Pb2Sr2Bi2Fe6O16, a new n = 6 representative of the AnBnO3n2 homologous series of the perovskite-based ferrites with the CS structure, has been synthesized using the solid-state technique. The structure is built of perovskite blocks with a thickness of four FeO6 octahedra spaced by double columns of FeO5 edge-sharing distorted tetragonal pyr...

  8. X-ray absorption spectroscopy: EXAFS and XANES - A versatile tool to study the atomic and electronic structure of materials

    International Nuclear Information System (INIS)

    X-ray absorption spectroscopy (XAS) had been an essential tool to gather spectroscopic information about atomic energy level structure in the early decades of this century. The correct interpretation of the oscillatory structure in the x-ray absorption cross-section above the absorption edge has transformed XAS from a spectroscopic tool to a structural technique. EXAFS (Extended X-ray Absorption Fine Structure) yields information about the interatomic distances, near neighbor coordination numbers, and lattice dynamics. XANES (X-ray Absorption Near Edge Structure), on the other hand, gives information about the valence state, energy bandwidth and bond angles. Today, there are about 50 experimental stations in various synchrotrons around the world dedicated to collecting x-ray absorption data from the bulk and surfaces of solids and liquids. In this chapter, they will give the basic principles of XAS, explain the information content of essentially two different aspects of the absorption process leading to EXAFS and XANES, and discuss the source and sample limitations

  9. Atomic structure and stability of magnetite Fe3O4(001): An X-ray view

    Science.gov (United States)

    Arndt, Björn; Bliem, Roland; Gamba, Oscar; van der Hoeven, Jessi E. S.; Noei, Heshmat; Diebold, Ulrike; Parkinson, Gareth S.; Stierle, Andreas

    2016-11-01

    The structure of the Fe3O4(001) surface was studied using surface X-ray diffraction in both ultra-high vacuum, and higher-pressure environments relevant to water-gas shift catalysis. The experimental X-ray structure factors from the √{ 2 } x√{ 2 } R 45∘ reconstructed surface are found to be in excellent agreement with the recently proposed subsurface cation vacancy (SCV) model for this surface (Science 346 (2014), 1215). Further refinement of the structure results in small displacements of the iron atoms in the first three double layers compared to structural parameters deduced from LEED I-V experiments and DFT calculations. An alternative, previously proposed structure, based on a distorted bulk truncation (DBT), is conclusively ruled out. The lifting of the √{ 2 } ×√{ 2 } R 45∘ reconstruction upon exposure to water vapor in the mbar pressure regime was studied at different temperatures under flow conditions, and a roughening of the surface was observed. Addition of CO flow did not further change the roughness perpendicular to the surface but decreased the lateral correlations.

  10. Atomic and electronic structure of polar Fe2O3(0001)/MgO(111) interfaces

    Science.gov (United States)

    Pande, K.; Gajdardziska-Josifovska, M.; Weinert, M.

    2012-07-01

    We present a first-principles investigation of the structural, electronic, and magnetic properties of ultrathin Fe2O3(0001) films on a polar MgO(111) substrate. The results imply that the heterointerface is atomically abrupt with oxidelike stacking for film thicknesses between ˜1.5 and 8.5 Å. The Fe-Fe bilayer (nominal separation of 0.59 Å in Fe2O3) at the interface collapses into an “Fe2” monolayer. Both electronic polarization and structural relaxations effectively screen the dipole field of the polar interface system. The structural relaxations—consisting of interpenetration, separation, and merger of Fe and oxygen planes—are particularly drastic in the three- and four-bilayers-thick films, giving rise to barrierless movement of oxygen towards the surface and the formation of an “Fe2|FeO3” layer structure not seen in hematite. Comparisons to calculations of unsupported polar Fe2O3(0001) slabs demonstrate that these unusual changes in stacking sequence and electronic structure are associated with the polar nature of this oxide heterointerface.

  11. Three-dimensional holographic vector of atomic interaction field for quantitative structure-retention relationship of purine bases

    Institute of Scientific and Technical Information of China (English)

    TONG Jianbo; ZHOU Peng; ZHANG Shengwan; ZHOU Yuan; MEI Hu; ZENG Hui; LI Meiping; LI Zhiliang

    2006-01-01

    A newly developed descriptor, threedimensional holographic vector of atomic interaction field (3D-HoVAIF), was used to describe the chemical structures of purine bases. After variable screening by stepwise multiple regression (SMR) technique, a partial least square (PLS) regression model was built with 3D-HoVAIF. The model was satisfactory comparing to reference since correlation coefficients of molecular modeling ( R2cum), cross-validation (Q2cum)and standard deviation of estimation (SD) were 0.966,0.860 and 0.112, respectively, showing that the model had favorable estimation and prediction capabilities. It was illustrated that information related to retention data of purine bases could preferably be expressed by 3D-HoVAIF with definite physicochemical meanings and easy structural interpretation for purine bases. It was illustrated that 3D-HoVAIF was to preferably express retention data of purine bases and had definite physicochemical significance.So 3D-HoVAIF was a useful structural expression technique for quantitative structure activity (or property or retention) relationships (QSAR/QSPR/QSRR)study, such as structural characterization and chromatographic retention prediction.

  12. Embedded atom computer simulation of lattice distortion and dislocation core structure and mobility in Fe-Cr alloys

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D.; Schon, C.G.; Lima, M.S.F. de [Virginia Polytechnic Inst., Blacksburg, VA (United States). Dept. of Materials Science and Engineering; Goldenstein, H. [Escola Politecnica USP, Sao Paulo (Brazil). Dept. de Metalurgia

    1996-01-01

    The atomistic structure of dislocation cores of <111> screw dislocations in disordered Fe-Cr b.c.c. alloys was simulated using embedded atom method potentials and molecular statics computer simulation. The mixed Fe-Cr interatomic potentials used were derived by fitting to the thermodynamic data of the disordered system and the measured lattice parameter changes of Fe upon Cr additions. The potentials predict phase separation as the most stable configuration for the central region of the phase diagram. The next most stable situation is the disordered b.c.c. phase. The structure of the screw 1/2 <111> dislocation core was studied using atomistic computer simulation and an improved visualization method for the representation of the resulting structures. The structure of the dislocation core is different from that typical of 1/2 <111> dislocations in pure b.c.c. materials. The core structure in the alloy tends to lose the threefold symmetry seen in pure b.c.c. materials and the stress necessary to initiate dislocation motion increases with Cr content. The mobility of kinks in these screw dislocations was also simulated and it was found that while the critical stress for kink motion in pure Fe is extremely low, it increases significantly with the addition of Cr. The implications of these differences for mechanical behavior are discussed.

  13. What is atomic structures of (ZnO) 34 magic cluster?

    Science.gov (United States)

    Wang, Xiaoqiu; Wang, Baolin; Tang, Lingli; Sai, Linwei; Zhao, Jijun

    2010-01-01

    Recent experiment on the mass spectrum of ZnO clusters revealed a (ZnO) 34 magic cluster with enhanced stability [A. Dmytruk, et al., Microelect. J. 40 (2009) 218]. We have performed an extensive search for the most stable structure of (ZnO) 34 using gradient-corrected density-functional theory. Instead of the previously nominated onion-like nested cage of (ZnO) 6@(ZnO) 28, we found that the hollow cage structures satisfying the isolated six square rule constitute the most preferred structural motif for (ZnO) 34 cluster.

  14. dftatom: A robust and general Schrödinger and Dirac solver for atomic structure calculations

    Science.gov (United States)

    Čertík, Ondřej; Pask, John E.; Vackář, Jiří

    2013-07-01

    A robust and general solver for the radial Schrödinger, Dirac, and Kohn-Sham equations is presented. The formulation admits general potentials and meshes: uniform, exponential, or other defined by nodal distribution and derivative functions. For a given mesh type, convergence can be controlled systematically by increasing the number of grid points. Radial integrations are carried out using a combination of asymptotic forms, Runge-Kutta, and implicit Adams methods. Eigenfunctions are determined by a combination of bisection and perturbation methods for robustness and speed. An outward Poisson integration is employed to increase accuracy in the core region, allowing absolute accuracies of 10-8 Hartree to be attained for total energies of heavy atoms such as uranium. Detailed convergence studies are presented and computational parameters are provided to achieve accuracies commonly required in practice. Comparisons to analytic and current-benchmark density-functional results for atomic number Z=1-92 are presented, verifying and providing a refinement to current benchmarks. An efficient, modular Fortran 95 implementation, dftatom, is provided as open source, including examples, tests, and wrappers for interface to other languages; wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines. Program summaryProgram title:dftatom Catalogue identifier: AEPA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 14122 No. of bytes in distributed program, including test data, etc.: 157453 Distribution format: tar.gz Programming language: Fortran 95 with interfaces to Python and C. Computer: Any computer with a Fortran 95 compiler. Operating system: Any OS with a Fortran 95 compiler. RAM: 500 MB

  15. Impact of Biofield Treatment on Atomic and Structural Characteristics of Barium Titanate Powder

    OpenAIRE

    Trivedi, Mahendra; Nayak, Gopal

    2015-01-01

    Barium titanate, perovskite structure is known for its high dielectric constant and piezoelectric properties, which makes it interesting material for fabricating capacitors, transducer, actuator, and sensors. The perovskite crystal structure and lattice vibrations play a crucial role in its piezoelectric and ferroelectric behavior. In the present study, the barium titanate powder was subjected to biofield treatment. Further, the control and treated samples were characterized using X-ray diffr...

  16. Surface structures from low energy electron diffraction: Atoms, small molecules and an ordered ice film on metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Materer, N.F.

    1995-09-01

    We investigated the surface bonding of various adsorbates (0, S, C{sub 2}H{sub 3} and NO) along with the resulting relaxation of the Pt(111) surface using low energy electron diffiraction (LEED). LEED experiments have been performed on these ordered overlayers along with theoretical structural analysis using automated tensor LEED (ATLEED). The resulting surface structures of these ordered overlayers exhibit similar adsorbate-induced relaxations. In all cases the adsorbate occupies the fcc hollow site and induces an approximately 0.1 A buckling of the metal surface. The three metal atoms directly bonded to the adsorbate are ``pulled`` out of the surface and the metal atom that is not bound to the adsorbate is `pushed`` inward. In order to understand the reliability of such details, we have carried out a comprehensive study of various non-structural parameters used in a LEED computation. We also studied the adsorption of water on the Pt(lll) surface. We ordered an ultra thin ice film on this surface. The film`s surface is found to be the (0001) face of hexagonal ice. This surface is apparently terminated by a full-bilayer, in which the uppermost water molecules have large vibrational amplitudes even at temperatures as low as 90 K. We examined two other metal surfaces besides Pt(111): Ni(111) and Fe(lll). On Ni(111), we have studied the surface under a high coverage of NO. On both Ni(111) and Pt(111) NO molecules occupy the hollow sites and the N-0 bond distances are practically identical. The challenging sample preparation of an Fe(111) surface has been investigated and a successful procedure has been obtained. The small interlayer spacing found on Fe(111) required special treatment in the LEED calculations. A new ATLEED program has been developed to handle this surface.

  17. Molecule-optimized Basis Sets and Hamiltonians for Accelerated Electronic Structure Calculations of Atoms and Molecules

    CERN Document Server

    Gidofalvi, Gergely

    2014-01-01

    Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multi-referenced) electrons. We use a low-cost approximate solution of the anti-Hermitian contracted Schr{\\"o}dinger equation (ACSE) for the one- and two-electron reduced density matrices (RDMs) to generate an approximate set of natural orbitals for strongly correlated quantum systems. The natural-orbital basis set is truncated to generate a molecule-optimized basis set whose rank matches that of a standard correlation-consistent basis set optimized for the atoms. We show that basis-set truncation by approximate natural orbitals can be viewed as a one-electron unitary transformation of the Hamiltonian operator and suggest an extension of approximate natural-orbital truncations through two-electron unitary transformations of the Hamiltonian operator, such as those employed in the solution of the ACSE. The molecule-optimized basis set from the ACS...

  18. Influence of Sedimentation of Atoms on Structural and Thermoelectric Properties of Bi-Sb Alloys

    Science.gov (United States)

    Januszko, Kamila; Stabrawa, Artur; Ogata, Yudai; Tokuda, Makoto; Khandaker, Jahirur Islam; Wojciechowski, Krzysztof; Mashimo, Tsutomu

    2016-03-01

    Functionally graded thermoelectric materials (FGTMs) have been prepared by sedimentation of atoms under a strong gravitational field. Starting samples of Bi x Sb1- x alloys with different composition x were synthesized by melting of metals and subsequent annealing of quenched samples. The thermoelectric properties (Seebeck coefficient, electrical conductivity) of the starting materials were characterized over the temperature range from 300 K to 525 K. Strong gravity experiments were performed in a unique ultracentrifuge apparatus under acceleration of over 0.5 × 106 G at temperatures of 538 K and 623 K. Changes of the microstructure and chemical composition were analyzed using scanning electron microscopy with energy-dispersive x-ray spectroscopy analysis. The distribution of the Seebeck coefficient of the Bi-Sb alloys was characterized by scanning thermoelectric microprobe. As a result of sedimentation, large changes in chemical composition ( x = 0.45 to 1) were obtained. It was found that the changes in chemical composition were correlated with alterations of the Seebeck coefficient. The obtained experimental data allowed the development of a semiempirical model for the selection of optimal processing parameters for preparation of Bi-Sb alloys with required thermoelectric properties.

  19. Atomic and molecular physics, physicochemical properties of biologically important structure, and high-voltage research

    International Nuclear Information System (INIS)

    Research in atomic and molecular physics is reported. Studies included: experimental evidence for the existence of a Ramsauer-Townsend minimum in liquid methane and liquid argon; discovery of a Ramsauer-Townsend minimum in gaseous ethane and propane; motion of thermal electrons in n-alkane vapors; electron mobilities in high pressure gases; electron capture and drift in liquid media; electron attachment to molecules in dense gases; attachment of slow electrons to hexafluorobenzene; fragmentation of atmospheric halocarbons under electron impact; negative ion resonances and threshold electron excitation spectra of organic molecules; theoretical studies of negative-ion resonance states of organic molecules; kinetics of electron capture by sulfur hexafluoride in solution; interactions of slow electrons with benzene and benzene derivatives; Stokes and anti-Stokes fluorescence of 1 : 12-benzoperylene in solution; photoionization of molecules in liquid media; construction of high-voltage breakdown apparatus for gaseous insulation studies; measurements of the breakdown strengths of gaseous insulators and their relation to basic electron-collision processes; accuracy of the breakdown voltage measurements; and assembling basic data on electronegative gases of significance to breakdown

  20. Atomic structure of defects in GaN:Mg grown with Ga polarity

    International Nuclear Information System (INIS)

    Electron microscope phase images, produced by direct reconstruction of the scattered electron wave from a focal series of high-resolution images, were used to determine the nature of defects formed in GaN:Mg crystals. We studied bulk crystals grown from dilute solutions of atomic nitrogen in liquid gallium at high pressure and thin films grown by the MOCVD method. All the crystals were grown with Ga-polarity. In both types of samples the majority of defects were three dimensional Mg-rich hexagonal pyramids with bases on the (0001) plane and six walls on {11(und 2)3} planes seen in cross-section as triangulars. Some other defects appear in cross-section as trapezoidal (rectangular) defects as a result of presence of truncated pyramids. Both type of defects have hollow centers. They are decorated by Mg on all six side walls and a base. The GaN which grows inside on the defect walls shows polarity inversion. It is shown that change of polarity starts from the defect tip and propagates to the base, and that the stacking sequence changes from ab in the matrix to bc inside the defect. Exchange of the Ga sublattice with the N sublattice within the defect leads to 0.6 ± 0.2(angstrom) displacement between Ga sublattices outside and inside the defects. It is proposed that lateral overgrowth of the cavities formed within the defect takes place to restore matrix polarity on the defect base

  1. International Atomic Energy Agency specialist meeting on advances in structural analysis for LMFBR applications. Summary report

    International Nuclear Information System (INIS)

    After the first session on review of national positions in the subject field, the meeting was divided into five technical sections as follows: General methods of Structural Analysis for Elevated Temperatures; Inelastic Analysis Methods for Elevated Temperature; Effects of Cyclic loading; Design Codes and Criteria; Instability and Buckling - Piping Analysis in the Creep Range. The conclusions of the Meeting were summarised as follows. In view of the complexity of material behaviour and the variability of properties from cast to cast, continuing work is needed to develop simple constitutive relations which ensure an acceptable level of conservatism for design evaluations. It is recognized that simplified design methods require further development for the assessment of ratchetting and shakedown of high temperature structures. More development work is required in the areas of buckling elastic follow up weld factors and these developments should take account of the imperfections inherent in welded fabrications. There is a need for realistic tests on welded structural features to validate design methods. It is proposed that this subject would be the topic of a future specialists meeting. In several countries, organisations are now preparing Guides and Codes concerning Structural Assessment for LMFBR components. It seems that some of these Codes could be drafted within a few years. In order to make a more realistic assessment of LMFBR structures, defect assessment in elevated temperature range must be considered

  2. Construction aspects of containment structures of a typical large atomic power project

    International Nuclear Information System (INIS)

    The Containment Structure of a Reactor Building in a Nuclear Power Plant is a very important structure as it houses the main reactor. The containment system has to be designed and constructed to withstand high pressures and temperatures released during postulated accidents in case of any accidents and to act as a biological shield against leakage of radiation. Construction of the Containment structure, which is a safety-related structure, is a key activity in the overall project implementation of a Nuclear Power Project. Typically in India, the containment system consists of a double containment structure with a part-spherical dome on top. Usually the inner containment is in prestressed concrete and the outer containment is in reinforced concrete. Special types of concrete such as High Performance Concrete with temperature control and Heavy Concrete are used in the construction. The need for accurately positioning many special embedded parts and through pipes at various locations poses a challenge. The construction methodologies, techniques for prestressing, special formwork systems etc need special attention. Other techniques such as mechanisation, use of automated climbing formwork system, increase in height of concrete pours after mock-ups, use of threaded couplers for rebars, etc also merit attention. The paper also discusses the various safety, quality and construction management systems used at site for better implementation of the projects. (authors)

  3. Assembly of Complex Nano-Structure from Single Atoms —Chemical Identification, Manipulation and Assembly by AFM—

    Science.gov (United States)

    Morita, Seizo; Sugimoto, Yoshiaki; Ooyabu, Noriaki; Custance, Óscar; Abe, Masayuki; Pou, Pablo; Jelinek, Pavel; Pérez, Rubén

    An atomic force microscope (AFM) under noncontact and nearcontact regions operated at room-temperature (RT) in ultrahigh vacuum, is used as a tool for topography-based atomic discrimination and atomic-interchange manipulations of two intermixed atomic species on semiconductor surfaces. Noncontact AFM topography based site-specific force curves provide the chemical covalent bonding forces between the tip apex and the atoms at the surface. Here, we introduced an example related to topography-based atomic discrimination using selected Sn and Si adatoms in Sn/Si(111)-(√3 ×√3 ) surface. Recently, under nearcontact region, we found a lateral atom-interchange manipulation phenomenon at RT in Sn/Ge(111)-c(2×8) intermixed sample. This phenomenon can interchange an embedded Sn atom with a neighbor Ge atom at RT. Using the vector scan method under nearcontact region, we constructed “Atom Inlay”, that is, atom letters “Sn” consisted of 19 Sn atoms embedded in Ge(111)-c(2×8) substrate. Using these methods, now we can assemble compound semiconductor nanostructures atom-by-atom.

  4. First-principles study of atomic structure and electronic properties of Si and F doped anatase TiO2

    Directory of Open Access Journals (Sweden)

    Li Hongping

    2015-09-01

    Full Text Available Chemical doping represents one of the most effective ways in engineering electronic structures of anatase TiO2 for practical applications. Here, we investigate formation energies, geometrical structures, and electronic properties of Si-, F-doped and Si/F co-doped anatase TiO2 by using spin-polarized density functional theory calculation. We find that the co-doped TiO2 is thermodynamically more favorable than the Si- and F-doped TiO2- Structural analysis shows that atomic impurity varies crystal constants slightly. Moreover, all the three doped systems show a pronounced narrowing of band gap by 0.33 eV for the F-doped TiO2, 0.17 eV for the Si-doped TiO2, and 0.28 eV for the Si/F-co-doped TiO2, which could account for the experimentally observed redshift of optical absorption edge. Our calculations suggest that the Si/F-co-doping represents an effective way in tailoring electronic structure and optical properties of anatase TiO2.

  5. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Nalini; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, Shimla(HP)-171005 (India); Thakur, Anil [Department of Physics, Govt. P. G. College Solan (HP)-173212 (India)

    2015-05-15

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  6. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    International Nuclear Information System (INIS)

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys

  7. Fe{sub 2-x}Co{sub x}MnSi (x = 0, 1 and 2) Heusler alloys: Structural, magnetic and atomic site disorder properties

    Energy Technology Data Exchange (ETDEWEB)

    Bhatt, Harsh, E-mail: harsh.bhatt@cbs.ac.in [UM-DAE Centre for Excellence in Basic Sciences, Mumbai-400098 (India); Mukadam, M. D.; Meena, S. S.; Yusuf, S. M. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400085 (India)

    2015-06-24

    The Heusler alloy series Fe{sub 2-x}Co{sub x}MnSi (x = 0, 1 and 2) is theoretically predicted to be half metallic. We prepared the sample series and determined the structural and magnetic properties to check if these materials are suitable for spintronics applications. The Curie temperatures of two of the alloys have been found to be well above the room temperature. But the presence of elements with atoms of similar size leads to atomic site disorder in these alloys, which may destroy the half metallic nature. The atomic site disorder has been confirmed by Mössbauer spectroscopy.

  8. Local Atomic Structure of Semiconductor Alloys Using Pair Distribution Function Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Billinge, S.J.L.; Thorpe, M.F.

    2002-06-24

    We have been taking advantage of recent experimental developments, which involve utilizing diffraction data from x-rays or neutrons out to very large wave-vectors, to obtain a detailed structural characterization of semiconductor alloys. This approach allows an accurate Pair Distribution Function (PDF) to be obtained to 20A and beyond and reveals the local structure of the alloy directly. These data can be modeled explicitly to learn about local correlations and short-range order in materials. We are combining theory, modeling and experiments to study a range of materials from semiconductors to thermoelectrics and proton conductors.

  9. Atomic Structure and Energy Distribution of Collapsed Carbon Nanotubes of Different Chiralities

    Directory of Open Access Journals (Sweden)

    Julia A. Baimova

    2015-01-01

    Full Text Available For carbon nanotubes of sufficiently large diameter at sufficiently low temperature, due to the action of the van der Waals forces, the ground state is a bilayer graphene with closed edges, the so-called collapsed configuration. Molecular dynamics simulation of collapsed carbon nanotubes is performed. The effect of length, diameter, and chirality of the nanotubes on their properties is investigated. It is shown that collapsed nanotubes after relaxation have rippled structure which is strongly dependent on the nanotube chirality. The structural properties are studied by calculating the radial distribution function and energy distribution along various regions in the collapsed carbon nanotubes.

  10. Plasma out of thermodynamical equilibrium: influence of the plasma environment on atomic structure and collisional cross sections

    International Nuclear Information System (INIS)

    In hot dense plasmas, the free-electron and ion spatial distribution may strongly affect the atomic structure. To account for such effects we have implemented a potential correction based on the uniform electron gas model and on a Thomas-Fermi Approach in the Flexible Atomic Code (FAC). This code has been applied to obtain energies, wave-functions and radiative rates modified by the plasma environment. In hydrogen-like ions, these numerical results have been successfully compared to an analytical calculation based on first-order perturbation theory. In the case of multi-electron ions, we observe level crossings in agreement with another recent model calculation. Various methods for the collision cross-section calculations are reviewed. The influence of plasma environment on these cross-sections is analyzed in detail. Some analytical expressions are proposed for hydrogen-like ions in the limit where Born or Lotz approximations apply and are compared to the numerical results from the FAC code. Finally, from this work, we study the influence of the plasma environment on our collisional-radiative model so-called Foch. Because of this environment, the mean charge state of the ions increases. The line shift is observed on the bound-bound emission spectra. A good agreement is found between our work and experimental data on a Titanium plasma. (author)

  11. Atomic structure and thermal stability of interfaces between metallic glass and embedding nano-crystallites revealed by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gao, X.Z.; Yang, G.Q.; Xu, B.; Qi, C.; Kong, L.T., E-mail: konglt@sjtu.edu.cn; Li, J.F.

    2015-10-25

    Molecular dynamics simulations were performed to investigate the atomic structure and thermal stability of interfaces formed between amorphous Cu{sub 50}Zr{sub 50} matrix and embedding B2 CuZr nano-crystallites. The interfaces are found to be rather abrupt, and their widths show negligible dependence on the nano-crystallite size. Local atomic configuration in the interfacial region is dominated by geometry characterized by Voronoi polyhedra <0,5,2,6> and <0,4,4,6>, and the contents of these polyhedra also exhibit apparent size dependence, which in turn results in an increasing trend in the interfacial energy against the nano-crystallite size. Annealing of the interface models at elevated temperatures will also enrich these characterizing polyhedra. While when the temperature is as high as the glass transition temperature of the matrix, growth of the nano-crystallites will be appreciable. The growth activation energy also shows size dependence, which is lower for larger nano-crystallites, suggesting that large nano-crystallites are prone to grow upon thermal disturbance. - Highlights: • Special clusters characterizing the local geometry are abundant in the interfaces. • Their content varies with the size of the embedding nano-crystallite. • In turn, size dependences in interfacial thermodynamics and kinetics are observed.

  12. Effects of Atomic-Scale Structure on the Fracture Properties of Amorphous Carbon - Carbon Nanotube Composites

    Science.gov (United States)

    Jensen, Benjamin D.; Wise, Kristopher E.; Odegard, Gregory M.

    2015-01-01

    The fracture of carbon materials is a complex process, the understanding of which is critical to the development of next generation high performance materials. While quantum mechanical (QM) calculations are the most accurate way to model fracture, the fracture behavior of many carbon-based composite engineering materials, such as carbon nanotube (CNT) composites, is a multi-scale process that occurs on time and length scales beyond the practical limitations of QM methods. The Reax Force Field (ReaxFF) is capable of predicting mechanical properties involving strong deformation, bond breaking and bond formation in the classical molecular dynamics framework. This has been achieved by adding to the potential energy function a bond-order term that varies continuously with distance. The use of an empirical bond order potential, such as ReaxFF, enables the simulation of failure in molecular systems that are several orders of magnitude larger than would be possible in QM techniques. In this work, the fracture behavior of an amorphous carbon (AC) matrix reinforced with CNTs was modeled using molecular dynamics with the ReaxFF reactive forcefield. Care was taken to select the appropriate simulation parameters, which can be different from those required when using traditional fixed-bond force fields. The effect of CNT arrangement was investigated with three systems: a single-wall nanotube (SWNT) array, a multi-wall nanotube (MWNT) array, and a SWNT bundle system. For each arrangement, covalent bonds are added between the CNTs and AC, with crosslink fractions ranging from 0-25% of the interfacial CNT atoms. The SWNT and MWNT array systems represent ideal cases with evenly spaced CNTs; the SWNT bundle system represents a more realistic case because, in practice, van der Waals interactions lead to the agglomeration of CNTs into bundles. The simulation results will serve as guidance in setting experimental processing conditions to optimize the mechanical properties of CNT

  13. Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.

    Science.gov (United States)

    Sun, Siyang; Xiang, Ye; Akahata, Wataru; Holdaway, Heather; Pal, Pankaj; Zhang, Xinzheng; Diamond, Michael S; Nabel, Gary J; Rossmann, Michael G

    2013-04-02

    A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment. DOI:http://dx.doi.org/10.7554/eLife.00435.001.

  14. Atomic resolution structure of the E. coli YajR transporter YAM domain

    International Nuclear Information System (INIS)

    Highlights: • We report the crystal structure of the YAM domain of YajR transporter at 1.07 Å. • The YAM dimerization is related to the halogen-dependent high thermal stability. • A belt of poly-pentagonal water molecules was observed in the dimer interface. - Abstract: YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration

  15. Zeeman effects in the hyperfine structure of atomic iodine photodissociation laser emission.

    Science.gov (United States)

    Hwang, W. C.; Kasper, J. V. V.

    1972-01-01

    Observation of hyperfine structure in laser emission from CF3I and C2F5I photodissociation lasers. Constant magnetic fields affect the time behavior of the emission by changing the relative gains of the hyperfine transitions. Time-varying fields usually present in photodissociation lasers further complicate the emission.

  16. Atomic resolution structure of the E. coli YajR transporter YAM domain

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Daohua [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Zhao, Yan [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Fan, Junping; Liu, Xuehui; Wu, Yan; Feng, Wei [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); Zhang, Xuejun C., E-mail: zhangc@ibp.ac.cn [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China)

    2014-07-25

    Highlights: • We report the crystal structure of the YAM domain of YajR transporter at 1.07 Å. • The YAM dimerization is related to the halogen-dependent high thermal stability. • A belt of poly-pentagonal water molecules was observed in the dimer interface. - Abstract: YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration.

  17. 3D mechanical measurements with an atomic force microscope on 1D structures

    DEFF Research Database (Denmark)

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

    2012-01-01

    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...

  18. The role of adiabaticity in alkali atom-fine structure mixing

    Science.gov (United States)

    Eshel, Ben; Weeks, David E.; Perram, Glen P.

    2014-02-01

    Fine-structure mixing cross-sections for the alkalis in collisions with the rare gases are reviewed. Included in the review are all the rare gases in collisions with all of the first excited state of the alkalis, the second excited state for K, Rb and Cs and the third excited state for Rb and Cs. The cross-sections are converted to probabilities for energy transfer using a quantum-defect calculated cross-section and are then presented as a function of adiabaticity. The data shows a clear decreasing trend with adiabaticity but secondary factors prevent the probabilities from decreasing as quickly as expected. Polarizability is introduced as a proxy for the secondary influences on the data as it increases with both rare gas partner and alkali excited state. The polarizability is shown to cause the probability of fine structure transition to be higher than expected. An empirical model is introduced and fit to the data. Future work will develop a model using time-independent perturbation theory in order to further develop a physical rational for the dependence of fine structure cross sections on adiabaticity and to further understand the secondary influences on the probability for fine structure transition.

  19. Electronic instabilities and structural fluctuations in self-assembled atom wires

    NARCIS (Netherlands)

    Snijders, P.C.

    2006-01-01

    One-dimensional (1D) solid state systems can behave drastically different from their higher dimensional counterparts. Increased interactions can produce electronic and/or structural instabilities. In this respect, the following fundamental questions are important for a proper understanding of the p

  20. Quantum magnetism through atomic assembly

    NARCIS (Netherlands)

    Spinelli, A.

    2015-01-01

    This thesis presents an experimental study of magnetic structures, composed of only a few atoms. Those structures are first built atom-by-atom and then locally probed, both with a low-temperature STM. The technique that we use to assemble them is vertical atom manipulation, while to study their phy

  1. Structural stability and O2 dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study

    Directory of Open Access Journals (Sweden)

    Mingye Yang

    2015-06-01

    Full Text Available By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N4V 2 forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O2 dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N, the graphitic-N is more favorable to dissociate O2 molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.

  2. A comparative analysis of bleached and sound enamel structure through scanning electron microscopy and atomic force microscopy

    International Nuclear Information System (INIS)

    To analyze the effects of bleaching agent on enamel structure and to characterize the morphological and chemical changes in enamel due to bleaching. Study Design: Experimental study. Place and Duration of Study: School of Chemical and Material Engineering (SCME), NUST Islamabad from Feb to May 2013. Materials and Methods: Ten recently extracted pre molars between the 12-22 years age group were randomly assigned into two groups. Group one was a non-bleached control group with sound enamel. Group two was bleached with Everbrite In office tooth whitening system after specimen preparation, surface morphology was observed under SEM (scanned electron microscope) and AFM (Atomic force microscope). Results: The detrimental effects of hydrogen per-oxide on enamel were evident in bleached specimens under SEM, and AFM analysis. Conclusion: There were significant surface alterations found in the bleached specimens as compared to control group. However salivary buffering potentials could overcome the demineralizing effect of bleaching gel. (author)

  3. Crystal structure of post-perovskite-type CaIrO3 reinvestigated: new insights into atomic thermal vibration behaviors

    OpenAIRE

    Nakatsuka, Akihiko; Sugiyama, Kazumasa; Yoneda, Akira; Fujiwara, Keiko; Yoshiasa, Akira

    2015-01-01

    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 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 form...

  4. Local atomic structure and oxidation processes of Cu(I) binding site in amyloid beta peptide: XAS Study

    Science.gov (United States)

    Kremennaya, M. A.; Soldatov, M. A.; Stretsov, V. A.; Soldatov, A. V.

    2016-05-01

    There are two different motifs of X-ray absorption spectra for Cu(I) K-edge in amyloid-β peptide which could be due to two different configurations of local Cu(I) environment. Two or three histidine ligands can coordinate copper ion in varying conformations. On the other hand, oxidation of amyloid-β peptide could play an additional role in local copper environment. In order to explore the peculiarities of local atomic and electronic structure of Cu(I) binding sites in amyloid-β peptide the x-ray absorption spectra were simulated for various Cu(I) environments including oxidized amyloid-β and compared with experimental data.

  5. High-accuracy Complete Active Space multiconfiguration Dirac-Hartree-Fock calculations of hyperfine structure constants of the gold atom

    CERN Document Server

    Bierón, Jacek; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka

    2009-01-01

    The multiconfiguration Dirac-Hartree-Fock (MCDHF) model has been employed to calculate the expectation values for the hyperfine splittings of the 5d96s2 2D3/2 and 5d96s2 2D5/2 levels of atomic gold. One-, two-, and three-body electron correlation effects involving all 79 electrons have been included in a systematic manner. The approximation employed in this study is equivalent to a Complete Active Space (CAS) approach. Calculated electric field gradients, together with experimental values of the electric quadrupole hyperfine structure constants, allow us to extract a nuclear electric quadrupole moment Q(197Au)=521.5(5.0) mb.

  6. Arsenic Irradiation Induced Atomic Interdiffusion of InxGa1-xAs/InP Quantum Well Structures

    Directory of Open Access Journals (Sweden)

    P.L. Gareso,

    2012-12-01

    Full Text Available The atomic intermixing of InxGa1-xAs/InP quantum well structures induced by arsenic irradiation has been investigated using photoluminescence (PL measurement. The ion doses used were varried from 5x1011 As/cm2 to 1x1013 As/cm2. Also, the irradiation temperature were carried out from -200oC to 300oC. The samples were annealed under Argon flow in rapid thermal annealer (RTA at 750oC for 60 second. The photoluminescence result showed that there was increase in energy shift at lower doses. However, the energy shift was saturated at higher dose. At elevated temperature implantation showed that the energy shift did not change significantly for all the samples (LM, TS, CS. In additon to this, the higher energy shift was observed in the Compressive Strain (CS samples, but the lower of the energy shift was experienced in the Tensile Strain (TS samples

  7. Spectroscopic investigation of the electronic structure of thin atomic layer deposition HfO{sub 2} films

    Energy Technology Data Exchange (ETDEWEB)

    Corrêa, Silma Alberton, E-mail: silma.alberton@ufrgs.br; Brizzi, Simone; Schmeisser, Dieter [Applied Physics and Sensors, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 17, 03046 Cottbus (Germany)

    2016-01-15

    The electronic structure of HfO{sub 2} 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-HfO{sub 2} films are identified, pointing out that the amount of charges is essential to determine the accurate position of the surface potentials.

  8. BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement.

    Science.gov (United States)

    Woetzel, Nils; Lindert, Steffen; Stewart, Phoebe L; Meiler, Jens

    2011-09-01

    Cryo-electron microscopy (cryoEM) can visualize large macromolecular assemblies at resolutions often below 10Å and recently as good as 3.8-4.5 Å. These density maps provide important insights into the biological functioning of molecular machineries such as viruses or the ribosome, in particular if atomic-resolution crystal structures or models of individual components of the assembly can be placed into the density map. The present work introduces a novel algorithm termed BCL::EM-Fit that accurately fits atomic-detail structural models into medium resolution density maps. In an initial step, a "geometric hashing" algorithm provides a short list of likely placements. In a follow up Monte Carlo/Metropolis refinement step, the initial placements are optimized by their cross correlation coefficient. The resolution of density maps for a reliable fit was determined to be 10 Å or better using tests with simulated density maps. The algorithm was applied to fitting of capsid proteins into an experimental cryoEM density map of human adenovirus at a resolution of 6.8 and 9.0 Å, and fitting of the GroEL protein at 5.4 Å. In the process, the handedness of the cryoEM density map was unambiguously identified. The BCL::EM-Fit algorithm offers an alternative to the established Fourier/Real space fitting programs. BCL::EM-Fit is free for academic use and available from a web server or as downloadable binary file at http://www.meilerlab.org.

  9. Atomic and Electronic Structures of C_60+BN Nanopeapods from ab initio Pseudopotential Calculations

    Science.gov (United States)

    Trave, Andrea; Ribeiro, Filipe; Louie, Steven G.; Cohen, Marvin L.

    2004-03-01

    Nanopeapods are structures of nanometric size consisting of an external carbon nanotube encapsulating a chain or complex array of fullerenes. Recent calculations and experiments have proven that nanopeapods can be obtained assembling fullerenes within boron nitride nanotubes, creating novel materials of possible interest for electronic transport applications. To improve the understanding of the properties of these composite systems, as compared to empty nanotubes and carbon nanopeapods, ab-initio total energy calculations have been performed within the pseudopotential Density Functional Theory in local density approximation. Results of these calculations on the energetics and geometrical deformations involved in the encapsulation will be presented, followed by a discussion of the consequences on the electronic structures of these systems, with particular focus on aspects relevant to electronic transport phenomena. This work is supported by NFS (Grant DMR00-87088) and DOE (Contract DE-AC03-76SF00098), using computational resources at NERSC and NPACI.

  10. Atomic and molecular complex resonances from real eigenvalues using standard (hermitian) electronic structure calculations

    CERN Document Server

    Landau, Arie; Kaprálová-Žďánská, Petra Ruth; Moiseyev, Nimrod

    2015-01-01

    Complex eigenvalues, resonances, play an important role in large variety of fields in physics and chemistry. For example, in cold molecular collision experiments and electron scattering experiments, autoionizing and pre-dissociative metastable resonances are generated. However, the computation of complex resonance eigenvalues is difficult, since it requires severe modifications of standard electronic structure codes and methods. Here we show how resonance eigenvalues, positions and widths, can be calculated using the standard, widely used, electronic-structure packages. Our method enables the calculations of the complex resonance eigenvalues by using analytical continuation procedures (such as Pad\\'{e}). The key point in our approach is the existence of narrow analytical passages from the real axis to the complex energy plane. In fact, the existence of these analytical passages relies on using finite basis sets. These passages become narrower as the basis set becomes more complete, whereas in the exact limit,...

  11. Atomic structure of epitaxial graphene sidewall nanoribbons: flat graphene, miniribbons, and the confinement gap.

    Science.gov (United States)

    Palacio, Irene; Celis, Arlensiú; Nair, Maya N; Gloter, Alexandre; Zobelli, Alberto; Sicot, Muriel; Malterre, Daniel; Nevius, Meredith S; de Heer, Walt A; Berger, Claire; Conrad, Edward H; Taleb-Ibrahimi, Amina; Tejeda, Antonio

    2015-01-14

    Graphene nanoribbons grown on sidewall facets of SiC have demonstrated exceptional quantized ballistic transport up to 15 μm at room temperature. Angular-resolved photoemission spectroscopy (ARPES) has shown that the ribbons have the band structure of charge neutral graphene, while bent regions of the ribbon develop a bandgap. We present scanning tunneling microscopy and transmission electron microscopy of armchair nanoribbons grown on recrystallized sidewall trenches etched in SiC. We show that the nanoribbons consist of a single graphene layer essentially decoupled from the facet surface. The nanoribbons are bordered by 1-2 nm wide bent miniribbons at both the top and bottom edges of the nanoribbons. We establish that nanoscale confinement in the graphene miniribbons is the origin of the local large band gap observed in ARPES. The structural results presented here show how this gap is formed and provide a framework to help understand ballistic transport in sidewall graphene.

  12. Doping Cu{sub 2}O in Electrolyte Solution: Dopant Incorporation, Atomic Structures and Electrical Properties

    Energy Technology Data Exchange (ETDEWEB)

    Tao, Meng; Zhang, Qiming

    2013-11-24

    We have pursued a number of research activities between April 2010 and April 2011: A detailed study on n-type doping in Cu2O by Br; An analysis of natural resource limitations to terawatt-scale solar cells; Attempt to achieve a 1.4-eV direct band gap in Ni sulfides (NiSx); First-principles studies of doping in Cu2O and electronic structures of NiSx.

  13. Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili.

    Science.gov (United States)

    Xiao, Ke; Malvankar, Nikhil S; Shu, Chuanjun; Martz, Eric; Lovley, Derek R; Sun, Xiao

    2016-03-22

    The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics.

  14. Atomic force microscopy study of the structure function relationships of the biofilm-forming bacterium Streptococcus mutans

    Science.gov (United States)

    Cross, Sarah E.; Kreth, Jens; Zhu, Lin; Qi, Fengxia; Pelling, Andrew E.; Shi, Wenyuan; Gimzewski, James K.

    2006-02-01

    Atomic force microscopy (AFM) has garnered much interest in recent years for its ability to probe the structure, function and cellular nanomechanics inherent to specific biological cells. In particular, we have used AFM to probe the important structure-function relationships of the bacterium Streptococcus mutans. S. mutans is the primary aetiological agent in human dental caries (tooth decay), and is of medical importance due to the virulence properties of these cells in biofilm initiation and formation, leading to increased tolerance to antibiotics. We have used AFM to characterize the unique surface structures of distinct mutants of S. mutans. These mutations are located in specific genes that encode surface proteins, thus using AFM we have resolved characteristic surface features for mutant strains compared to the wild type. Ultimately, our characterization of surface morphology has shown distinct differences in the local properties displayed by various S. mutans strains on the nanoscale, which is imperative for understanding the collective properties of these cells in biofilm formation.

  15. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

    Science.gov (United States)

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-01

    In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties.

  16. Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili.

    Science.gov (United States)

    Xiao, Ke; Malvankar, Nikhil S; Shu, Chuanjun; Martz, Eric; Lovley, Derek R; Sun, Xiao

    2016-01-01

    The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics. PMID:27001169

  17. Atomic and Molecular Complex Resonances from Real Eigenvalues Using Standard (Hermitian) Electronic Structure Calculations.

    Science.gov (United States)

    Landau, Arie; Haritan, Idan; Kaprálová-Žd'ánská, Petra Ruth; Moiseyev, Nimrod

    2016-05-19

    Complex eigenvalues, resonances, play an important role in a large variety of fields in physics and chemistry. For example, in cold molecular collision experiments and electron scattering experiments, autoionizing and predissociative metastable resonances are generated. However, the computation of complex resonance requires modifications of standard electronic structure codes and methods, which are not always straightforward, in addition, application of complex codes requires more computational efforts. Here we show how resonance eigenvalues, positions and widths, can be calculated using the standard, widely used, electronic-structure packages. Our method enables the calculations of the complex resonance eigenvalues by using analytical continuation procedures (such as Padé). The key point in our approach is the existence of narrow analytical passages from the real axis to the complex energy plane. In fact, the existence of these analytical passages relies on using finite basis sets. These passages become narrower as the basis set becomes more complete, whereas in the exact limit, these passages to the complex plane are closed. As illustrative numerical examples we calculated the autoionization Feshbach resonances of helium, hydrogen anion, and hydrogen molecule. We show that our results are in an excellent agreement with the results obtained by other theoretical methods and with available experimental results. PMID:26677725

  18. Principle for possible memory structures with extra high density by using the electron sharing mechanisms of atoms in an inflective orbit

    Science.gov (United States)

    Sengor, T.

    2014-10-01

    Both of the qualitative and quantitative knowledge of electromagnetic fields in the inter-atomic scale bring useful applications. From this point of view, bringing some possible new sights and solutions to atom-electron-photon-atom and/or molecule interactions is aimed in the near-field at inter atomic scale and their potential applications. The electron sharing processes between neighbor atoms are considered as an inflective surface system and an inflective guiding processes. The critical pass and transition structures are derived. The structures involving trigging that transition mechanisms may be suitable to design extra high density and fast data storage processes. The electron sharing processes between two near atomic system are modelled with gate mechanisms involving two distinct passages: continuous pass and discontinuous pass. Even if the stochastic processes are applicable at these cases theoretical approach putting an influence like inner and external dipole mechanisms fits best to the situation and provides almost deterministic scheme, which has potential to estimate some processes being able to design new electronics structures and devices. We call orbitron all of such structures and/or devices. The boundary value problem of atomic system sharing an electron in the way of electron passage model is formulated in inflective spherical coordinate system. The wave phenomenon is studied near spherically inflection points. The analytical essentials are derived for the solution of Helmholtz's equation when inflective boundaries are included. The evaluation is obtained by the extracted separation method. The results are given by using the spherically inflective wave series. The method is reshaped for the solution of Schrödinger equation.

  19. Crystal structure of raw pure Mysore silk fibre based on (Ala-Gly)2-Ser-Gly peptide sequence using Linked-Atom-Least-Squares method

    Indian Academy of Sciences (India)

    Sangappa; S S Mahesh; R Somashekar

    2005-03-01

    We have carried out crystal structure analysis of raw pure Mysore silk fibers belonging to Bombyx mori on the basis of model parameters of Marsh et al using Linked-Atom-Least-Squares technique. The intensity of all the reflections were computed employing CCP13 software. We observe that the molecular modification is essentially same as -pleated structure with antipolar-antiparallel arrangements formed by hydrogen bonds. The essential differences observed in the structure are highlighted and discussed.

  20. Band structure and decay channels of thorium-229 low-lying isomeric state for ensemble of thorium atoms adsorbed on calcium fluoride

    International Nuclear Information System (INIS)

    The results are presented on the study of the electronic structure of thorium atoms adsorbed by the liquid atomic layer deposition from aqueous solution of thorium nitrate on the surface of CaF2. The chemical state of the atoms and the change of the band structure in the surface layers of Th/CaF2 system on CaF2 substrate were investigated by XPS and REELS techniques. It was found that REELS spectra for Th/CaF2 system include peaks in the region of low energy losses (3-7 eV) which are missing in the similar spectra for pure CaF2. It is concluded that the presence of the observed features in the REELS spectra is associated with the chemical state of thorium atoms and is caused by the presence of uncompensated chemical bonds at the Th/CaF2 interface, and, therefore, by the presence of unbound 6d- and 7s-electrons of thorium atoms. Assuming the equivalence of the electronic configuration of thorium-229 and thorium-232 atoms, an estimate was made on the time decay of the excited state of thorium-229 nuclei through the channel of the electron conversion. It was found that the relaxation time is about 40 μs for 6d-electrons, and about 1 μs for 7s-electrons. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)