WorldWideScience

Sample records for atomic structure

  1. Atomic Structure Theory Lectures on Atomic Physics

    CERN Document Server

    Johnson, Walter R

    2007-01-01

    Atomic Structure Theory is a textbook for students with a background in quantum mechanics. The text is designed to give hands-on experience with atomic structure calculations. Material covered includes angular momentum methods, the central field Schrödinger and Dirac equations, Hartree-Fock and Dirac-Hartree-Fock equations, multiplet structure, hyperfine structure, the isotope shift, dipole and multipole transitions, basic many-body perturbation theory, configuration interaction, and correlation corrections to matrix elements. Numerical methods for solving the Schrödinger and Dirac eigenvalue problems and the (Dirac)-Hartree-Fock equations are given as well. B-spline basis sets are used to carry out sums arising in higher-order many-body calculations. Illustrative problems are provided, together with solutions. FORTRAN programs implementing the numerical methods in the text are included.

  2. 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.

  3. Can atom-surface potential measurements test atomic structure models?

    Science.gov (United States)

    Lonij, Vincent P A; Klauss, Catherine E; Holmgren, William F; Cronin, Alexander D

    2011-06-30

    van der Waals (vdW) atom-surface potentials can be excellent benchmarks for atomic structure calculations. This is especially true if measurements are made with two different types of atoms interacting with the same surface sample. Here we show theoretically how ratios of vdW potential strengths (e.g., C₃(K)/C₃(Na)) depend sensitively on the properties of each atom, yet these ratios are relatively insensitive to properties of the surface. We discuss how C₃ ratios depend on atomic core electrons by using a two-oscillator model to represent the contribution from atomic valence electrons and core electrons separately. We explain why certain pairs of atoms are preferable to study for future experimental tests of atomic structure calculations. A well chosen pair of atoms (e.g., K and Na) will have a C₃ ratio that is insensitive to the permittivity of the surface, whereas a poorly chosen pair (e.g., K and He) will have a ratio of C₃ values that depends more strongly on the permittivity of the surface.

  4. Electronic structure interpolation via atomic orbitals.

    Science.gov (United States)

    Chen, Mohan; Guo, G-C; He, Lixin

    2011-08-17

    We present an efficient scheme for accurate electronic structure interpolation based on systematically improvable optimized atomic orbitals. The atomic orbitals are generated by minimizing the spillage value between the atomic basis calculations and the converged plane wave basis calculations on some coarse k-point grid. They are then used to calculate the band structure of the full Brillouin zone using the linear combination of atomic orbitals algorithms. We find that usually 16-25 orbitals per atom can give an accuracy of about 10 meV compared to the full ab initio calculations, and the accuracy can be systematically improved by using more atomic orbitals. The scheme is easy to implement and robust, and works equally well for metallic systems and systems with complicated band structures. Furthermore, the atomic orbitals have much better transferability than Shirley's basis and Wannier functions, which is very useful for perturbation calculations.

  5. Atomic Structure Calculations for Neutral Oxygen

    OpenAIRE

    Norah Alonizan; Rabia Qindeel; Nabil Ben Nessib

    2016-01-01

    Energy levels and oscillator strengths for neutral oxygen have been calculated using the Cowan (CW), SUPERSTRUCTURE (SS), and AUTOSTRUCTURE (AS) atomic structure codes. The results obtained with these atomic codes have been compared with MCHF calculations and experimental values from the National Institute of Standards and Technology (NIST) database.

  6. Introduction to Atomic Structure: Demonstrations and Labs.

    Science.gov (United States)

    Ciparick, Joseph D.

    1988-01-01

    Demonstrates a variety of electrical phenomena to help explain atomic structure. Topics include: establishing electrical properties, electrochemistry, and electrostatic charges. Recommends demonstration equipment needed and an explanation of each. (MVL)

  7. 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.

  8. Direct atomic structure determination by the inspection of structural phase.

    Science.gov (United States)

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne

    2013-08-27

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

  9. Quantum Structures of the Hydrogen Atom

    CERN Document Server

    Jeknic-Dugic, J; Francom, A; Arsenijevic, M

    2012-01-01

    Modern quantum theory introduces quantum structures (decompositions into subsystems) as a new discourse that is not fully comparable with the classical-physics counterpart. To this end, so-called Entanglement Relativity appears as a corollary of the universally valid quantum mechanics that can provide for a deeper and more elaborate description of the composite quantum systems. In this paper we employ this new concept to describe the hydrogen atom. We offer a consistent picture of the hydrogen atom as an open quantum system that naturally answers the following important questions: (a) how do the so called "quantum jumps" in atomic excitation and de-excitation occur? and (b) why does the classically and seemingly artificial "center-of-mass + relative degrees of freedom" structure appear as the primarily operable form in most of the experimental reality of atoms?

  10. Semiempirical studies of atomic structure

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, L.J.

    1992-01-01

    The energy level structure, transition probabilities, and general spectroscopic properties of highly-ionized many-electron systems are studied through the combined use of sensitive semiempirical data systematizations, selected precision experimental measurements, and specialized theoretical computations. Measurements are made primarily through the use of fast ion beam excitation methods, which are combined with available data from laser- and tokamak-produced plasmas, astrophysical sources, and conventional light sources. The experimental studies are strengthened through large scale ab initio calculations. Large blocks of data are predictively systematized and parameterized along isoelectric, homologous, isoionic, Rydberg, and yrast series, to provide a comprehensive and reliable data base.

  11. Atomic vapor spectroscopy in integrated photonic structures

    CERN Document Server

    Ritter, Ralf; Pernice, Wolfram; Kübler, Harald; Pfau, Tilman; Löw, Robert

    2015-01-01

    We investigate an integrated optical chip immersed in atomic vapor providing several waveguide geometries for spectroscopy applications. The narrow-band transmission through a silicon nitride waveguide and interferometer is altered when the guided light is coupled to a vapor of rubidium atoms via the evanescent tail of the waveguide mode. We use grating couplers to couple between the waveguide mode and the radiating wave, which allow for addressing arbitrary coupling positions on the chip surface. The evanescent atom-light interaction can be numerically simulated and shows excellent agreement with our experimental data. This work demonstrates a next step towards miniaturization and integration of alkali atom spectroscopy and provides a platform for further fundamental studies of complex waveguide structures.

  12. Atomic Structure of Graphene Subnanometer Pores.

    Science.gov (United States)

    Robertson, Alex W; Lee, Gun-Do; He, Kuang; Gong, Chuncheng; Chen, Qu; Yoon, Euijoon; Kirkland, Angus I; Warner, Jamie H

    2015-12-22

    The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert.

  13. Imaging DNA Structure by Atomic Force Microscopy.

    Science.gov (United States)

    Pyne, Alice L B; Hoogenboom, Bart W

    2016-01-01

    Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometre resolution. For biological applications, one of its key advantages is its ability to visualize substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine superstructure and secondary structure of surface-bound DNA. The method is also readily applicable to probe DNA-DNA interactions and DNA-protein complexes.

  14. 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.

  15. Local Atomic Structure of Piperidyl Nd Dithiocarbamate

    Institute of Scientific and Technical Information of China (English)

    吴忠华; 李前树; 等

    1999-01-01

    The atomic structure of a novel rare earth complex consisting of Nd and the sulfur-containing ligand pipdtc (C5H10NCS2-) has been studied with extended x-ray absortpiton fine structure(EXAFS) and x-ray diffraction techniques.The complex of formula Nd(pipdtc)4N(CH3)4 crystallizaes in the monoclinic space group P21/n with the following lattice parameters,a=22.685(2),b=20.332(2),c=17.1270(10)A,β=100.570(10)°.Z=8,the calculated density is 1.47g/cm3,A new derivative method is used to remove the piost-edge absorption background including the multielectron excitation effect.The EXAFS results demonstrate that there are about eight S and four O atoms around Nd with the Nd-S bond length of 2.916A and the Nd-O bond length of 2.415A,respectively.This implies that the powder of this complex is not stable and is easy to oxidize in air.The possible change of structure before and after oxidation is discussed.

  16. 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.

  17. Local atomic structure in cubic stabilized zirconia

    Energy Technology Data Exchange (ETDEWEB)

    Villella, P.; Conradson, S. D.; Espinosa-Faller, F. J.; Foltyn, S. R.; Sickafus, K. E.; Valdez, J. A.; Degueldre, C. A.

    2001-09-01

    X-ray-absorption fine structure measurements have been used to elucidate the local atomic structure of quaternary Zr, Y, Er, Ce/U cubic stabilized zirconia. These compounds display more complicated local environments than those reported for simpler binary systems. While the shortest cation-O distances are similar to those found in the binary cubic stabilized compounds, responding to the different sizes of the cations, we have identified large distortions in the first-shell oxygen distribution involving long, 2.8--3.2 {angstrom} cation-O distances that are similar to those found in the amorphous phase of zirconium. The cation-cation distributions are also found to be quite complicated (non-Gaussian) and element specific. The U-near neighbor distances are expanded relative to the Ce ions for which it substitutes, consistent with the larger size of the actinide, and the U-cation distribution is also more complicated. In terms of the effects of this substitution on the other cation sites, the local environment around Y is altered while the Zr and Er local environments remain unchanged. These results point out the importance of collective and correlated interactions between the different pairs of cations and the host lattice that are mediated by the local strain fields generated by the different cations. The presence of pair-specific couplings has not been commonly included in previous analyses and may have implications for the stabilization mechanisms of cubic zirconia.

  18. 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).

  19. 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.

  20. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

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

    2005-01-01

    We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

  1. 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.

  2. 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…

  3. 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.

  4. Update on nuclear structure effects in light muonic atoms

    Science.gov (United States)

    Hernandez, Oscar Javier; Dinur, Nir Nevo; Ji, Chen; Bacca, Sonia; Barnea, Nir

    2016-12-01

    We present calculations of the nuclear structure corrections to the Lamb shift in light muonic atoms, using state-of-the-art nuclear potentials. We outline updated results on finite nucleon size contributions.

  5. Update on nuclear structure effects in light muonic atoms

    CERN Document Server

    Hernandez, Oscar Javier; Ji, Chen; Bacca, Sonia; Barnea, Nir

    2016-01-01

    We present calculations of the nuclear structure corrections to the Lamb shift in light muonic atoms, using state-of-the-art nuclear potentials. We outline updated results on finite nucleon size contributions.

  6. Atomic structure of graphene on SiO2.

    Science.gov (United States)

    Ishigami, Masa; Chen, J H; Cullen, W G; Fuhrer, M S; Williams, E D

    2007-06-01

    We employ scanning probe microscopy to reveal atomic structures and nanoscale morphology of graphene-based electronic devices (i.e., a graphene sheet supported by an insulating silicon dioxide substrate) for the first time. Atomic resolution scanning tunneling microscopy images reveal the presence of a strong spatially dependent perturbation, which breaks the hexagonal lattice symmetry of the graphitic lattice. Structural corrugations of the graphene sheet partially conform to the underlying silicon oxide substrate. These effects are obscured or modified on graphene devices processed with normal lithographic methods, as they are covered with a layer of photoresist residue. We enable our experiments by a novel cleaning process to produce atomically clean graphene sheets.

  7. Toward the Atomic Structure of PrPSc.

    Science.gov (United States)

    Rodriguez, Jose A; Jiang, Lin; Eisenberg, David S

    2017-01-17

    In this review, we detail our current knowledge of PrP(Sc) structure on the basis of structural and computational studies. We discuss the progress toward an atomic resolution description of PrP(Sc) and results from the broader field of amyloid studies that may further inform our knowledge of this structure. Moreover, we summarize work that investigates the role of PrP(Sc) structure in its toxicity, transmissibility, and species specificity. We look forward to an atomic model of PrP(Sc), which is expected to bring diagnostics and/or therapeutics to the field of prion disease.

  8. 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,…

  9. Interface Structure and Atomic Bonding Characteristics in Silicon Nitride Ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Ziegler, A; Idrobo, J C; Cinibulk, M K; Kisielowski, C; Browning, N D; Ritchie, R O

    2004-10-12

    This investigation examines the interface atomic structure and bonding characteristics in an advanced ceramic, obtaining new and unique experimental information that will help to understand and improve the properties of ceramics. Unique direct atomic resolution images have been obtained that illustrate how a range of rare-earth atoms bond to the interface between the intergranular phase and the matrix grains in an advanced silicon nitride ceramic. It has been found that each rare-earth atom bonds to the interface at a different location, depending on atom size, electronic configuration and the presence of oxygen at the interface. This is the key factor to understanding the origin of the mechanical properties in these ceramics and will enable precise tailoring in the future to critically improve the materials performance in wide-ranging applications.

  10. Probing atomic structure and Majorana wavefunctions in mono-atomic Fe chains on superconducting Pb surface

    Science.gov (United States)

    Pawlak, Rémy; Kisiel, Marcin; Klinovaja, Jelena; Meier, Tobias; Kawai, Shigeki; Glatzel, Thilo; Loss, Daniel; Meyer, Ernst

    2016-11-01

    Motivated by the striking promise of quantum computation, Majorana bound states (MBSs) in solid-state systems have attracted wide attention in recent years. In particular, the wavefunction localisation of MBSs is a key feature and is crucial for their future implementation as qubits. Here we investigate the spatial and electronic characteristics of topological superconducting chains of iron atoms on the surface of Pb(110) by combining scanning tunnelling microscopy and atomic force microscopy. We demonstrate that the Fe chains are mono-atomic, structured in a linear manner and exhibit zero-bias conductance peaks at their ends, which we interpret as signature for a MBS. Spatially resolved conductance maps of the atomic chains reveal that the MBSs are well localised at the chain ends (≲25 nm), with two localisation lengths as predicted by theory. Our observation lends strong support to use MBSs in Fe chains as qubits for quantum-computing devices.

  11. 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.

  12. 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.

  13. Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

    Science.gov (United States)

    Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

    2016-10-01

    Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

  14. Atomic and electronic structure of twin growth defects in magnetite.

    Science.gov (United States)

    Gilks, Daniel; Nedelkoski, Zlatko; Lari, Leonardo; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Kepaptsoglou, Demie; Ramasse, Quentin; Evans, Richard; McKenna, Keith; Lazarov, Vlado K

    2016-02-15

    We report the existence of a stable twin defect in Fe3O4 thin films. By using aberration corrected scanning transmission electron microscopy and spectroscopy the atomic structure of the twin boundary has been determined. The boundary is confined to the (111) growth plane and it is non-stoichiometric due to a missing Fe octahedral plane. By first principles calculations we show that the local atomic structural configuration of the twin boundary does not change the nature of the superexchange interactions between the two Fe sublattices across the twin grain boundary. Besides decreasing the half-metallic band gap at the boundary the altered atomic stacking at the boundary does not change the overall ferromagnetic (FM) coupling between the grains.

  15. 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...

  16. 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)

  17. 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.

  18. 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.

  19. 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

  20. Energetics of atomic scale structure changes in graphene.

    Science.gov (United States)

    Skowron, Stephen T; Lebedeva, Irina V; Popov, Andrey M; Bichoutskaia, Elena

    2015-05-21

    The presence of defects in graphene has an essential influence on its physical and chemical properties. The formation, behaviour and healing of defects are determined by energetic characteristics of atomic scale structure changes. In this article, we review recent studies devoted to atomic scale reactions during thermally activated and irradiation-induced processes in graphene. The formation energies of vacancies, adatoms and topological defects are discussed. Defect formation, healing and migration are quantified in terms of activation energies (barriers) for thermally activated processes and by threshold energies for processes occurring under electron irradiation. The energetics of defects in the graphene interior and at the edge is analysed. The effects of applied strain and a close proximity of the edge on the energetics of atomic scale reactions are overviewed. Particular attention is given to problems where further studies are required.

  1. 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.

  2. 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

    2016-02-18

    A twist in bi- or few-layer graphene breaks the local symmetry, introducing a number of intriguing physical properties such as opening new bandgaps. Therefore, determining the twisted atomic structure is critical to understanding and controlling the functional properties of graphene. Combining low-angle annular dark-field electron microscopy with image simulations, we directly determine the atomic structure of twisted few-layer graphene in terms of a moiré superstructure which is parameterized by a single twist angle and lattice constant. This method is shown to be a powerful tool for accurately determining the atomic structure of two-dimensional materials such as graphene, even in the presence of experimental errors. Using coincidence-site-lattice and displacement-shift-complete theories, we show that the in-plane translation state between layers is not a significant structure parameter, explaining why the present method is adequate not only for bilayer graphene but also a few-layered twisted graphene.

  3. 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.

  4. 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

    2016-02-01

    A twist in bi- or few-layer graphene breaks the local symmetry, introducing a number of intriguing physical properties such as opening new bandgaps. Therefore, determining the twisted atomic structure is critical to understanding and controlling the functional properties of graphene. Combining low-angle annular dark-field electron microscopy with image simulations, we directly determine the atomic structure of twisted few-layer graphene in terms of a moiré superstructure which is parameterized by a single twist angle and lattice constant. This method is shown to be a powerful tool for accurately determining the atomic structure of two-dimensional materials such as graphene, even in the presence of experimental errors. Using coincidence-site-lattice and displacement-shift-complete theories, we show that the in-plane translation state between layers is not a significant structure parameter, explaining why the present method is adequate not only for bilayer graphene but also a few-layered twisted graphene.

  5. 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)

  6. Atomic structure of the amorphous nonstoichiometric silicon oxides and nitrides

    Energy Technology Data Exchange (ETDEWEB)

    Gritsenko, V A [Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)

    2008-07-31

    In addition to amorphous SiO{sub 2} and Si{sub 3}N{sub 4}, the two key dielectric film materials used in modern silicon devices, the fabrication technology of nonstoichiometric SiO{sub x}N{sub y}, SiN{sub x}, and SiO{sub x} compounds is currently under development. Varying the chemical composition of these compounds allows a wide range of control over their physical - specifically, optical and electrical - properties. The development of technology for synthesizing such films requires a detailed understanding of their atomic structure. Current views on the atomic structure of nonstoichiometric silicon nitrides and oxides are reviewed and summarized. (reviews of topical problems)

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

    Energy Technology Data Exchange (ETDEWEB)

    Kąc, M., E-mail: malgorzata.kac@ifj.edu.pl [The Henryk Niewodniczański Institute of Nuclear Physics PAN, ul. Radzikowskiego 152, 31-342 Kraków (Poland); Morgiel, J. [Institute of Metallurgy and Materials Science PAN, 25 Reymonta St., 30-059 Kraków (Poland); Polit, A.; Zabila, Y.; Marszałek, M. [The Henryk Niewodniczański Institute of Nuclear Physics PAN, ul. Radzikowskiego 152, 31-342 Kraków (Poland)

    2014-06-01

    Fe/Cr multilayers were deposited by molecular beam epitaxy on the MgO(1 0 0) substrate. Structural properties of the samples were analyzed by low energy electron diffraction, high resolution transmission electron microscopy (HRTEM), as well as by X-ray reflectivity, conversion electron Mössbauer spectroscopy (CEMS) and Auger electron spectroscopy. Investigations revealed multilayered system built of well-ordered Fe and Cr thin films with (1 0 0) orientation. A high geometrical perfection of the system, i.e. planar form of interfaces and reproducible thickness of layers, was also proven. Fe/Cr interface roughness was determined to be 2–3 atomic layers. CEMS studies allowed to analyze at atomic scale the structure of buried Fe/Cr interfaces, as well as to distinguish origin of interface roughness. Roughnesses resulting from interface corrugations and from the Fe–Cr interdiffusion at interfaces were observed. Fe/Cr multilayers showed strong antiferromagnetic coupling of Fe layers.

  8. 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.

  9. 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.

  10. Ground-state structures of atomic metallic hydrogen.

    Science.gov (United States)

    McMahon, Jeffrey M; Ceperley, David M

    2011-04-22

    Ab initio random structure searching using density functional theory is used to determine the ground-state structures of atomic metallic hydrogen from 500 GPa to 5 TPa. Including proton zero-point motion within the harmonic approximation, we estimate that molecular hydrogen dissociates into a monatomic body-centered tetragonal structure near 500 GPa (r(s)=1.23) that remains stable to 1 TPa (r(s)=1.11). At higher pressures, hydrogen stabilizes in an …ABCABC… planar structure that is similar to the ground state of lithium, but with a different stacking sequence. With increasing pressure, this structure compresses to the face-centered cubic lattice near 3.5 TPa (r(s)=0.92).

  11. 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.

  12. Deciphering Adsorption Structure on Insulators at the Atomic Scale

    Energy Technology Data Exchange (ETDEWEB)

    Thurmer, Konrad [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Materials Physics; Feibelman, Peter J. [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Integrated Nanotechnologies

    2014-09-01

    We applied Scanning Probe Microscopy and Density Functional Theory (DFT) to discover the basics of how adsorbates wet insulating substrates, addressing a key question in geochemistry. To allow experiments on insulating samples we added Atomic Force Microscopy (AFM) capability to our existing UHV Scanning Tunneling Microscope (STM). This was accomplished by integrating and debugging a commercial qPlus AFM upgrade. Examining up-to-40-nm-thick water films grown in vacuum we found that the exact nature of the growth spirals forming around dislocations determines what structure of ice, cubic or hexagonal, is formed at low temperature. DFT revealed that wetting of mica is controlled by how exactly a water layer wraps around (hydrates) the K+ ions that protrude from the mica surface. DFT also sheds light on the experimentally observed extreme sensitivity of the mica surface to preparation conditions: K atoms can easily be rinsed off by water flowing past the mica surface.

  13. 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.

  14. Atomic structure of anthrax protective antigen pore elucidates toxin translocation.

    Science.gov (United States)

    Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed.

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

    OpenAIRE

    Hyun-Kyung Chung; Per Jönsson; Alexander Kramida

    2013-01-01

    Atomic structure and transition probabilities are fundamental physical data required in many fields of science and technology. Atomic physics codes are freely available to other community users to generate atomic data for their interest, but the quality of these data is rarely verified. This special issue addresses estimation of uncertainties in atomic structure and transition probability calculations, and discusses methods and strategies to assess and ensure the quality of theoretical atomic...

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

    CERN Document Server

    Riedel, F; Schröter, W

    2002-01-01

    Defects in silicon like dislocations, grain boundaries, silicide precipitates, etc. are spatially extended and associated with a large number of electronic states in the band gap. Our knowledge on the relation between atomic structure and electronic states of these extended defects presently starts to grow by applying high-resolution electron microscopy (HRTEM) and deep level transient spectroscopy (DLTS) in combination with numerical simulations. While by means of HRTEM details of structure can be studied, DLTS has been shown to allow for a classification of extended defect states into bandlike and localized. Moreover, this method opens the perspective to distinguish between trap-like and recombination-like electrical activity. In this paper, we emphasize the particular role of nickel and copper silicide precipitates, since in their cases structural features could be successfully related to specific DLTS line characteristics. Rapid quenching from high diffusion temperatures prevents decoration of platelet-sh...

  17. Ordering of carbon atoms in boron carbide structure

    Energy Technology Data Exchange (ETDEWEB)

    Ponomarev, V. I., E-mail: i2212@yandex.ru; Kovalev, I. D.; Konovalikhin, S. V.; Vershinnikov, V. I. [Russian Academy of Sciences, Institute of Structural Macrokinetics and Materials Science (Russian Federation)

    2013-05-15

    Boron carbide crystals have been obtained in the entire compositional range according to the phase diagram by self-propagating high-temperature synthesis (SHS). Based on the results of X-ray diffraction investigations, the samples were characterized by the unit-cell metric and reflection half-width in the entire range of carbon concentrations. A significant spread in the boron carbide unit-cell parameters for the same carbon content is found in the data in the literature; this spread contradicts the structural concepts for covalent compounds. The SHS samples have not revealed any significant spread in the unit-cell parameters. Structural analysis suggests that the spread of parameters in the literary data is related to the unique process of ordering of carbon atoms in the boron carbide structure.

  18. 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.

  19. Editorial . Quantum fluctuations and coherence in optical and atomic structures

    Science.gov (United States)

    Eschner, Jürgen; Gatti, Alessandra; Maître, Agnès; Morigi, Giovanna

    2003-03-01

    From simple interference fringes, over molecular wave packets, to nonlinear optical patterns - the fundamental interaction between light and matter leads to the formation of structures in many areas of atomic and optical physics. Sophisticated technology in experimental quantum optics, as well as modern computational tools available to theorists, have led to spectacular achievements in the investigation of quantum structures. This special issue is dedicated to recent developments in this area. It presents a selection of examples where quantum dynamics, fluctuations, and coherence generate structures in time or in space or where such structures are observed experimentally. The examples range from coherence phenomena in condensed matter, over atoms in optical structures, entanglement in light and matter, to quantum patterns in nonlinear optics and quantum imaging. The combination of such seemingly diverse subjects formed the basis of a successful European TMR network, "Quantum Structures" (visit http://cnqo.phys.strath.ac.uk/~gianluca/QSTRUCT/). This special issue partly re.ects the results and collaborations of the network, going however well beyond its scope by including contributions from a global community and from many related topics which were not addressed directly in the network. The aim of this issue is to present side by side these di.erent topics, all of which are loosely summarized under quantum structures, to highlight their common aspects, their di.erences, and the progress which resulted from the mutual exchange of results, methods, and knowledge. To guide the reader, we have organized the articles into subsections which follow a rough division into structures in material systems and structures in optical .elds. Nevertheless, in the following introduction we point out connections between the contributions which go beyond these usual criteria, thus highlighting the truly interdisciplinary nature of quantum structures. Much of the progress in atom optics

  20. Local atomic structures of single-component metallic glasses

    Science.gov (United States)

    Trady, Salma; Hasnaoui, Abdellatif; Mazroui, M.'hammed; Saadouni, Khalid

    2016-10-01

    In this study we examine the structural properties of single-component metallic glasses of aluminum. We use a molecular dynamics simulation based on semi-empirical many-body potential, derived from the embedded atom method (EAM). The radial distribution function (RDF), common neighbors analysis method (CNA), coordination number analysis (CN) and Voronoi tessellation are used to characterize the metal's local structure during the heating and cooling (quenching). The simulation results reveal that the melting temperature depends on the heating rate. In addition, atomic visualization shows that the structure of aluminum after fast quenching is in a glassy state, confirmed quantitatively by the splitting of the second peak of the radial distribution function, and by the appearance of icosahedral clusters observed via CNA technique. On the other hand, the Wendt-Abraham parameters are calculated to determine the glass transition temperature (Tg), which depends strongly on the cooling rate; it increases while the cooling rate increases. On the basis of CN analysis and Voronoi tessellation, we demonstrate that the transition from the Al liquid to glassy state is mainly due to the formation of distorted and perfect icosahedral clusters.

  1. Chaotic dynamics and fractal structures in experiments with cold atoms

    Science.gov (United States)

    Daza, Alvar; Georgeot, Bertrand; Guéry-Odelin, David; Wagemakers, Alexandre; Sanjuán, Miguel A. F.

    2017-01-01

    We use tools from nonlinear dynamics for the detailed analysis of cold-atom experiments. A powerful example is provided by the recent concept of basin entropy, which allows us to quantify the final-state unpredictability that results from the complexity of the phase-space geometry. We show here that this enables one to reliably infer the presence of fractal structures in phase space from direct measurements. We illustrate the method with numerical simulations in an experimental configuration made of two crossing laser guides that can be used as a matter-wave splitter.

  2. Atomic structure prediction of nanostructures, clusters and surfaces

    CERN Document Server

    Ciobanu, Cristian V; Ho, Kai-Ming

    2013-01-01

    This work fills the gap for a comprehensive reference conveying the developments in global optimization of atomic structures using genetic algorithms. Over the last few decades, such algorithms based on mimicking the processes of natural evolution have made their way from computer science disciplines to solid states physics and chemistry, where they have demonstrated their versatility and predictive power for many materials. Following an introduction and historical perspective, the text moves on to provide an in-depth description of the algorithm before describing its applications to crystal s

  3. 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.

  4. 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

    2016-08-03

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

  5. Constraints on proton structure from precision atomic physics measurements

    Energy Technology Data Exchange (ETDEWEB)

    Brodsky, S

    2004-08-10

    The ground-state hyperfine splittings in hydrogen and muonium are extremely well measured. The difference between them, after correcting for the different magnetic moments of the muon and proton and for reduced mass effects, is due solely to the structure of the proton - the large QED contributions for a pointlike nucleus essentially cancel. A major contribution to the rescaled hyperfine difference is proportional to the Zemach radius, a fundamental measure of the proton which can be computed as an integral over the product of the elastic electric and magnetic form factors of the proton. The remaining proton structure corrections, the polarization contribution from inelastic states in the spin-dependent virtual Compton amplitude and the proton size dependence of the relativistic recoil corrections, have small uncertainties. The resulting high precision determination of the Zemach radius (1.013 {+-} 0.016) fm from atomic physics provides an important constraint on fits to accelerator measurements of the proton electric and magnetic form factors. Conversely, the authors use the muonium data to extract an 'experimental' value for the QED corrections to the hyperfine splitting of hydrogenic atoms. There is a significant discrepancy between measurement and theory which is in the same direction as a corresponding discrepancy in positronium.

  6. Constraints on proton structure from precision atomic physics measurements

    CERN Document Server

    Brodsky, S J; Hiller, J R; Hwang, D S

    2004-01-01

    The ground-state hyperfine splittings in hydrogen and muonium are extremely well measured. The difference between them, after correcting for the different magnetic moments of the muon and proton and for reduced mass effects, is due solely to the structure of the proton - the large QED contributions for a pointlike nucleus essentially cancel. A major contribution to the rescaled hyperfine difference is proportional to the Zemach radius, a fundamental measure of the proton which can be computed as an integral over the product of the elastic electric and magnetic form factors of the proton. The remaining proton structure corrections, the polarization contribution from inelastic states in the spin-dependent virtual Compton amplitude and the proton size dependence of the relativistic recoil corrections, have small uncertainties. The resulting high precision determination of the Zemach radius (1.013 +/- 0.016) fm from atomic physics provides an important constraint on fits to accelerator measurements of the proton ...

  7. 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.

  8. 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.

  9. Photonic Band Gap Structures with Periodically Arranged Atoms in a Two-Dimensional Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    LI Zhi-Yu; CHEN Fang; ZHOU Jian-Ying

    2005-01-01

    @@ Linear transmission, reflection and absorption spectra for a new two-dimensional photonic crystal with periodically arranged resonant atoms are examined. Numerical results show that a twin-gap structure with forbidden bands displaced from a non-doped bandgap structure can be produced as a result of atomic polarization. The absorption spectrum is also significantly altered compared to the single atom entity.

  10. 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. [...

  11. 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.

  12. An atomic force microscopy investigation of cyanophage structure.

    Science.gov (United States)

    Kuznetsov, Yurii G; Chang, Sheng-Chieh; Credaroli, Arielle; Martiny, Jennifer; McPherson, Alexander

    2012-12-01

    Marine viruses have only relatively recently come to the attention of molecular biologists, and the extraordinary diversity of potential host organisms suggests a new wealth of genetic and structural forms. A promising technology for characterizing and describing the viruses structurally is atomic force microscopy (AFM). We provide examples here of some of the different architectures and novel structural features that emerge from even a very limited investigation, one focused on cyanophages, viruses that infect cyanobacteria (blue-green algae). These were isolated by phage selection of viruses collected from California coastal waters. We present AFM images of tailed, spherical, filamentous, rod shaped viruses, and others of eccentric form. Among the tailed phages numerous myoviruses were observed, some having long tail fibers, some other none, and some having no visible baseplate. Syphoviruses and a podovirus were also seen. We also describe a unique structural features found on some tailed marine phages that appear to have no terrestrial homolog. These are long, 450 nm, complex helical tail fibers terminating in a unique pattern of 3+1 globular units made up of about 20 small proteins.

  13. Electronic Structure of Helium Atom in a Quantum Dot

    Science.gov (United States)

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

    2016-03-01

    Bound and resonance states of helium atom have been investigated inside a quantum dot by using explicitly correlated Hylleraas type basis set within the framework of stabilization method. To be specific, precise energy eigenvalues of bound 1sns (1Se) (n = 1-6) states and the resonance parameters i.e. positions and widths of 1Se states due to 2sns (n = 2-5) and 2pnp (n = 2-5) configurations of confined helium below N = 2 ionization threshold of He+ have been estimated. The two-parameter (Depth and Width) finite oscillator potential is used to represent the confining potential due to the quantum dot. It has been explicitly demonstrated that the electronic structural properties become sensitive functions of the dot size. It is observed from the calculations of ionization potential that the stability of an impurity ion within a quantum dot may be manipulated by varying the confinement parameters. A possibility of controlling the autoionization lifetime of doubly excited states of two-electron ions by tuning the width of the quantum cavity is also discussed here. TKM Gratefully Acknowledges Financial Support under Grant No. 37(3)/14/27/2014-BRNS from the Department of Atomic Energy, BRNS, Government of India. SB Acknowledges Financial Support under Grant No. PSW-160/14-15(ERO) from University Grants Commission, Government of India

  14. 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.

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2016-04-01

    Atomic scale details of surface structure play a crucial role for solid-liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces.Atomic scale details of surface structure play a crucial role for solid-liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all

  18. On the atomic structure of cocaine in solution.

    Science.gov (United States)

    Johnston, Andrew J; Busch, Sebastian; Pardo, Luis Carlos; Callear, Samantha K; Biggin, Philip C; McLain, Sylvia E

    2016-01-14

    Cocaine is an amphiphilic drug which has the ability to cross the blood-brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ∼5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Å of cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function.

  19. 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

  20. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    Science.gov (United States)

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

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

  1. 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.

  2. 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

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

    OpenAIRE

    Zhang, Chi; Liu, Song; Zhou, Hongyi; Zhou, Yaoqi

    2004-01-01

    An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, low-sequence-identity structural databases of 333 α-proteins and 271 β-proteins were built for examining the database dependence of three all-atom statistical energy functions. They are RAPDF (residue-specific all-atom conditional probability discriminatory function), atomic KBP ...

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

    Science.gov (United States)

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

    2016-04-21

    Atomic scale details of surface structure play a crucial role for solid-liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces.

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

    CERN Document Server

    Pawlak, Remy; Klinovaja, Jelena; Meier, Tobias; Kawai, Shigeki; Glatzel, Thilo; Loss, Daniel; Meyer, Ernst

    2015-01-01

    Motivated by the striking promise of quantum computation, Majorana bound states (MBSs) in solid-state systems have attracted wide attention in recent years. In particular, the wavefunction localization of MBSs is a key feature and crucial for their future implementation as qubits. Here, we investigate the spatial and electronic characteristics of topological superconducting chains of iron atoms on the surface of Pb(110) by combining scanning tunneling microscopy (STM) and atomic force microscopy (AFM). We demonstrate that the Fe chains are mono-atomic, structured in a linear fashion, and exhibit zero-bias conductance peaks at their ends which we interprete as signature for a Majorana bound state. Spatially resolved conductance maps of the atomic chains reveal that the MBSs are well localized at the chain ends (below 25 nm), with two localization lengths as predicted by theory. Our observation lends strong support to use MBSs in Fe chains as qubits for quantum computing devices.

  6. 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

  7. 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.

  8. 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.

  9. Atomic structure of water/Au, Ag, Cu and Pt atomic junctions.

    Science.gov (United States)

    Li, Yu; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

    2017-02-08

    Much progress has been made in understanding the transport properties of atomic-scale conductors. We prepared atomic-scale metal contacts of Cu, Ag, Au and Pt using a mechanically controllable break junction method at 10 K in a cryogenic vacuum. Water molecules were exposed to the metal atomic contacts and the effect of molecular adsorption was investigated by electronic conductance measurements. Statistical analysis of the electronic conductance showed that the water molecule(s) interacted with the surface of the inert Au contact and the reactive Cu ant Pt contacts, where molecular adsorption decreased the electronic conductance. A clear conductance signature of water adsorption was not apparent at the Ag contact. Detailed analysis of the conductance behaviour during a contact-stretching process indicated that metal atomic wires were formed for the Au and Pt contacts. The formation of an Au atomic wire consisting of low coordination number atoms leads to increased reactivity of the inert Au surface towards the adsorption of water.

  10. 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.

  11. Ab initio calculations and modelling of atomic cluster structure

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter

    2004-01-01

    framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....

  12. The cytotoxicity of organobismuth compounds with certain molecular structures can be diminished by replacing the bismuth atom with an antimony atom in the molecules.

    Science.gov (United States)

    Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki

    2015-06-01

    Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.

  13. 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.

  14. Unveiling the atomic structure and electronic properties of atomically thin boron sheets on an Ag(111) surface.

    Science.gov (United States)

    Shu, Haibo; Li, Feng; Liang, Pei; Chen, Xiaoshuang

    2016-09-15

    Two-dimensional (2D) boron sheets (i.e., borophene) have a huge potential as a basic building block in nanoelectronics and optoelectronics; such a situation is greatly promoted by recent experiments on fabrication of borophene on silver substrates. However, the fundamental atomic structure of borophene on the Ag substrate is still under debate, which greatly impedes further exploration of its properties. Herein, the atomic structure and electronic properties of borophene on an Ag(111) surface have been studied using first-principles calculations and ab initio molecular dynamics simulations. Our results reveal that there exist three energetically favorable borophene structures (β5, χ1, and χ2) on the Ag(111) surface and their simulated STM images are in good agreement with experimental results, suggesting the coexistence of boron phases during the growth. All these stable borophene structures have a planar structure with slight surface buckling (∼0.15 Å) and relatively high hexagonal vacancy density (1/6 and 1/5) and exhibit typical metallic conductivity. These findings not only can be applied to solve the experimental controversies about the atomic structure of borophene on the Ag substrate but also provide a theoretical basis for exploring the fundamental properties and applications of 2D boron sheets.

  15. 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.

  16. 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)

  17. Similarity recognition of molecular structures by optimal atomic matching and rotational superposition.

    Science.gov (United States)

    Helmich, Benjamin; Sierka, Marek

    2012-01-15

    An algorithm for similarity recognition of molecules and molecular clusters is presented which also establishes the optimum matching among atoms of different structures. In the first step of the algorithm, a set of molecules are coarsely superimposed by transforming them into a common reference coordinate system. The optimum atomic matching among structures is then found with the help of the Hungarian algorithm. For this, pairs of structures are represented as complete bipartite graphs with a weight function that uses intermolecular atomic distances. In the final step, a rotational superposition method is applied using the optimum atomic matching found. This yields the minimum root mean square deviation of intermolecular atomic distances with respect to arbitrary rotation and translation of the molecules. Combined with an effective similarity prescreening method, our algorithm shows robustness and an effective quadratic scaling of computational time with the number of atoms.

  18. Structure of the electron momentum density of atomic systems

    Energy Technology Data Exchange (ETDEWEB)

    Romera, E.; Dehesa, J.S. [Granada Univ. (Spain). Dept. de Fisica Moderna; Koga, T. [Department of Applied Chemistry, Muroran Institute of Technology, Muroran, Hokkaido 050 (Japan)

    1997-12-01

    The present paper addresses the controversial problem on the nonmonotonic behavior of the spherically-averaged momentum density {gamma}(p) observed previously for some ground-state atoms based on the Roothaan-Hartree-Fock (RHF) wave functions of Clementi and Roetti. Highly accurate RHF wave functions of Koga et al. are used to study the existence of extrema in the momentum density {gamma}(p) of all the neutral atoms from hydrogen to xenon. Three groups of atoms are clearly identified according to the nonmonotonicity parameter {mu}, whose value is either equal to, larger, or smaller than unity. Additionally, it is found that the function p{sup -{alpha}} {gamma}(p) is (i) monotonically decreasing from the origin for {alpha}{>=}0.75, (ii) convex for {alpha}{>=}1.35, and (iii) logarithmically convex for {alpha}{>=}3.64 for all the neutral atoms with nuclear charges Z = 1-54. Finally, these monotonicity properties are applied to derive simple yet general inequalities which involve three momentum moments left angle p{sup t} right angle. These inequalities not only generalize similar inequalities reported so far but also allow us to correlate some fundamental atomic quantities, such as the electron-electron repulsion energy and the peak height of Compton profile, in a simple manner. (orig.) 40 refs.

  19. Structure and atomic vibrations in bimetallic Ni13 - n Al n clusters

    Science.gov (United States)

    Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.

    2015-04-01

    The binding energy, equilibrium geometry, and vibration frequencies in bimetallic clusters Ni13 - n Al n ( n = 0-13) have been calculated using the embedded atom method potentials. It has been shown that the icosahedral structure is the most stable in monoatomic and bimetallic clusters. A tendency of Al atoms to segregate on the cluster surface has been revealed in agreement with the experimental data. The calculations of the atomic vibrations have shown the nonmonotonic dependence of the minimum and maximum vibration frequencies of cluster atoms on its composition and the coupling of their extreme values with the most stable atomic configuration. The increase in the number of Al atoms leads to the shift of the frequency spectrum and the substantial redistribution of the localization of vibrations on the cluster atoms.

  20. 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

  1. 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.

  2. Characteristics of Spontaneous Emission of Polarized Atoms in Metal-Dielectric Multiple Layer Structures

    Institute of Scientific and Technical Information of China (English)

    ZHAO Li-Ming; GU Ben-Yuan; ZHOU Yun-Song

    2007-01-01

    The spontaneous emission (SE) progress of polarized atoms in a stratified structure ofair-dielectric(D0)-metal(M)-dielectric(D1)-air can be controlled effectively by changing the thickness of the D1 layer and rotating the polarized direction of atoms. It is found that the normalized SE rate of atoms located inside the D0 layer crucially depends on the atomic position and the thickness of the D1 layer. When the atom is located near the D0-M interface, the normalized atomic SE rate as a function of the atomic position is abruptly onset for the thin D1 layer. However, with the increasing thickness of the D1 layer, the corresponding curve profile exhibits plateau and stays nearly unchanged. The substantial change of the SE rate stems from the excitation of the surface plasmon polaritons in metal-dielectric interface, and the feature crucially depends on the thickness of D1 layer. If atoms are positioned near the D0-air interface, the substantial variation of the normalized SE rate appears when rotating the polarized direction of atoms. These findings manifest that the atomic SE processes can be flexibly controlled by altering the thickness of the dielectric layer D1 or rotating the orientation of the polarization of atoms.

  3. 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

    2014-01-28

    A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs.

  4. Fine structure in a strong magnetic field: Paschen-Back effect reconsidered in Rydberg atoms

    Science.gov (United States)

    Liu, Wenyu; Gu, Sihong; Li, Baiwen

    1996-05-01

    Using a kind of potential model wave function for alkali metal atoms, we nonperturbatively study the effect of fine structure on the Rydberg spectra of Cs atom in a strong magnetic field. Our numerical results reveal spectral structure dramatically different from the well-established Paschen-Back effect, and we argue that the fine structure of the Rydberg Cs atom cannot be neglected even in a magnetic field as strong as several teslas. We also give an error estimate of our results and a word on possible experimental verification.

  5. Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite.

    Science.gov (United States)

    Chin, Yiing; Panduwinata, Dwi; Sintic, Maxine; Sum, Tze Jing; Hush, Noel S; Crossley, Maxwell J; Reimers, Jeffrey R

    2011-01-20

    The atomic structure of the chains of an alkyl porphyrin (5,10,15,20-tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for porphyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible. A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and, of the many possible atomic structures modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.

  6. 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

    2012-05-02

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

  7. 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…

  8. 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'…

  9. Probing Structure and Composition of Nickel/Titanium Carbide Hybrid Interfaces at the Atomic Scale (Preprint)

    Science.gov (United States)

    2010-01-01

    The transition in structure and composition across the titanium carbide /nickel hybrid interface has been determined at near atomic resolution by...coupling high-resolution transmission electron microscopy with three-dimensional atom probe tomography. The titanium carbide phase adopts a rocksalt-type

  10. In situ chemical and structural investigations of the oxidation of Ge(001) substrates by atomic oxygen

    Science.gov (United States)

    Molle, Alessandro; Bhuiyan, Md. Nurul Kabir; Tallarida, Grazia; Fanciulli, Marco

    2006-08-01

    The exposure of Ge(001) substrates to atomic oxygen was studied in situ to establish the stability of the germanium oxide. After preparing chemically clean and atomically flat Ge(001) surfaces, the Ge samples were exposed to atomic oxygen in a wide temperature range from room temperature to 400°C. The chemical composition of the so-formed oxides was studied by means of x-ray photoelectron spectroscopy, while the structure was observed by reflection high energy electron diffraction. At low substrate temperatures the atomic oxygen is efficiently chemisorbed and suboxides coexist with the dioxide, which in turn is remarkably promoted in the high temperature range.

  11. Structure and transport properties of atomic chains and molecules

    DEFF Research Database (Denmark)

    Strange, Mikkel

    2008-01-01

    to describe tip-suspended atomically thin chains between macroscopic size electrodes. It has been tested with the use of DFT calculations on metal chains for which good agreement with experiments was obtained. To ensure the correctness of the DFT based transport calculations presented here, and in more...... as the Siesta basis is enlarged. Overall, we find that a double zeta polarized atomic basis is generally sufficient, and in some cases necessary, to ensure quantitative agreement with the plane-wave calculation. In a detailed DFT study of the carbon monoxide molecule between Pt electrodes, a particularly stable...... with experiments is obtained. A study of CO in Au, Cu and Ni, reveals that the conductance for CO in the tilted bridge configuration for Ni is 0.5G0, in agreement with experiments [5]. For Au/CO and Cu/CO we find the effect of CO compared to the homogenous metal contacts is much smaller, in qualitative agreement...

  12. X-ray structure refinement using aspherical atomic density functions obtained from quantum-mechanical calculations.

    Science.gov (United States)

    Jayatilaka, Dylan; Dittrich, Birger

    2008-05-01

    An approach is outlined for X-ray structure refinement using atomic density fragments obtained by Hirshfeld partitioning of quantum-mechanical density fragments. Results are presented for crystal structure refinements of urea and benzene using these 'Hirshfeld atoms'. Using this procedure, the quantum-mechanical non-spherical electron density is taken into account in the structural model based on the conformation found in the crystal. Contrary to current consensus in structure refinement, the anisotropic displacement parameters of H atoms can be reproduced from neutron diffraction measurements simply from a least-squares fit using the Hirshfeld atoms derived from the BLYP level of theory and including a simple point-charge model to treat the crystal environment.

  13. 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.

  14. Validation methods for low-resolution fitting of atomic structures to electron microscopy data

    OpenAIRE

    Xu, Xiao-Ping; Volkmann, Niels

    2015-01-01

    Fitting of atomic-resolution structures into reconstructions from electron cryo-microscopy is routinely used to understand the structure and function of macromolecular machines. Despite the fact that a plethora of fitting methods has been developed over recent years, standard protocols for quality assessment and validation of these fits have not been established. Here, we present the general concepts underlying current validation ideas as they relate to fitting of atomic-resolution models int...

  15. 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).

  16. 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.

  17. Reconstructing Polyatomic Structures from Discrete X-Rays: NP-Completeness Proof for Three Atoms

    OpenAIRE

    Durr, Christoph; Chrobak, Marek

    1999-01-01

    We address a discrete tomography problem that arises in the study of the atomic structure of crystal lattices. A polyatomic structure T can be defined as an integer lattice in dimension D>=2, whose points may be occupied by $c$ distinct types of atoms. To ``analyze'' T, we conduct ell measurements that we call_discrete X-rays_. A discrete X-ray in direction xi determines the number of atoms of each type on each line parallel to xi. Given ell such non-parallel X-rays, we wish to reconstruct T....

  18. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water.

    Science.gov (United States)

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-08-19

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry.

  19. 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.

  20. 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).

  1. Atomic structure and properties of grain boundaries in ceramics through Z-contrast electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Pennycook, S.J.; Nellist, P.D. [Oak Ridge National Lab., TN (United States); Browning, N.D. [Illinois Univ., Chicago, IL (United States). Dept. of Physics

    1996-08-01

    The bulk properties of a large range of materials are controlled by the atomic structure and chemistry of grain boundaries, but how this occurs, at the fundamental atomic level, remains poorly understood. This is due largely to the many degrees of freedom associated with grain boundaries - five geometrical degrees of freedom along with a myriad of possibilities involving impurity segregation. Based on Z- contrast electron microscopy, a method have been developed for determining grain boundary atomic structure and chemistry directly from experimental data. The method utilizes the incoherent nature of the Z-contrast image; as there is no phase problem associated with an incoherent image, it represents a compositionally sensitive structure image which may be directly inverted to give atomic column positions. This method extracts the column locations to an accuracy of {+-}0.2 {Angstrom}, while preserving the intensity information. The procedure has been applied to SrTiO{sub 3} and YBCO.

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

    Science.gov (United States)

    Lin, Yuyuan; Wu, Zili; Wen, Jianguo; Ding, Kunlun; Yang, Xiaoyun; Poeppelmeier, Kenneth R; Marks, Laurence D

    2015-08-12

    We report an aberration-corrected electron microscopy analysis of the adhesion and atomic structures of gold nanoparticle catalysts supported on ceria nanocubes and nanorods. Under oxidative conditions, the as-prepared gold nanoparticles on the ceria nanocubes have extended atom layers at the metal-support interface. In contrast, regular gold nanoparticles and rafts are present on the ceria nanorod supports. Under the reducing conditions of water-gas shift reaction, the extended gold atom layers and rafts vanish. In addition, the gold particles on the nanocubes change in morphology and increase in size while those on the nanorods are almost unchanged. The size, morphology, and atomic interface structures of gold strongly depend on the surface structures of ceria supports ((100) surface versus (111) surface) and the reaction environment (reductive versus oxidative). These findings provide insights into the deactivation mechanisms and the shape-dependent catalysis of oxide supported metal catalysts.

  3. 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.

  4. 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.

  5. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.

    Science.gov (United States)

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira

    2014-07-01

    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

  6. The structure of filled skutterudites and the local vibration behavior of the filling atom

    Science.gov (United States)

    Zhou, Xiaojuan; Zong, Peng-an; Chen, Xihong; Tao, Juzhou; Lin, He

    2017-02-01

    Both of atomic pair distribution function (PDF) and extended x-ray absorption fine structure (EXAFS) experiments have been carried out on unfilled and Yb-filled skutterudites YbxCo4Sb12 (x=0, 0.15, 0.2 and 0.25) samples. The structure refinements on PDF data confirm the large amplitude vibration of Yb atom and the dependence of Yb vibration amplitude on the filling content. Temperature dependent EXAFS experiment on filled skutterudites have been carried out at Yb LⅢ-edge in order to explore the local vibration behavior of filled atom. EXAFS experiments show that the Einstein temperature of the filled atom is very low (70.9 K) which agrees with the rattling behavior.

  7. 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.

  8. 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.

  9. 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

    2016-09-21

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

  10. 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

  11. Knee structure in double ionization of noble atoms in circularly polarized laser fields

    Science.gov (United States)

    Chen, Xiang; Wu, Yan; Zhang, Jingtao

    2017-01-01

    Nonsequential double ionization is characterized by a knee structure in the plot of double-ionization probability versus laser intensity. In circularly polarized (CP) laser fields, this structure has only been observed for Mg atoms. By choosing laser fields according to a scaling law, we exhibit the knee structure in CP laser fields for Ar and He atoms. The collision of the ionized electron with the core enhances the ionization of the second electron and forms the knee structure. The electron recollision is universal in CP laser fields, but the ionization probability in the knee region decreases as the wavelength of the driven field increases. For experimental observations, it is beneficial to use target atoms with small ionization potentials and laser fields with short wavelengths.

  12. Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion plus Selected Inversion

    OpenAIRE

    Lin, Lin

    2012-01-01

    We describe how to apply the recently developed pole expansion plus selected inversion (PEpSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating charge density, total energy, Helmholtz free energy and atomic forces without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham...

  13. 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.

  14. 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.

  15. Near-Origin Structure of the Hooke's Atoms%Near-Origin Structure of the Hooke's Atoms

    Institute of Scientific and Technical Information of China (English)

    王雪梅

    2012-01-01

    The Hooke's atoms with two or more than two electrons give rise to an interesting quantum mechanical model with valuable practical applications. In this work, we study the electronic properties near the origin of the harmonic potential. It is seen that the spherically averaged density, ~, exhibits an interesting character -- it has only even order terms in its small r expansion. The spherical average of the Hartree potential, ~, and the spherical average of the Kohn-Sham exchange-correlation potential, 9~c, are also shown to have the same property -- all odd order terms in their expansions vanish. F~rthermore, the analysis and results extend also to the case of two-dimensional models. While only models interacting via. the Coulomb potential are primarily considered in the article, the results also extend to models interacting via. other potentials (viz. Van der Waals potential).

  16. Getting CAD in shape: the atomic structure of human dihydroorotase domain.

    Science.gov (United States)

    Hermoso, Juan A

    2014-02-04

    CAD is a large multifunctional polypeptide that initiates and controls the de novo biosynthesis of pyrimidines in animals. In this issue of Structure, Grande-García and colleagues provide the first atomic information of this antitumoral target by reporting the crystal structure of the dihydroorotase domain of human CAD.

  17. 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…

  18. Ultrathin film of nickel on the Cu (100) surface: Atomic structure and phonons

    Energy Technology Data Exchange (ETDEWEB)

    Borisova, Svetlana D., E-mail: svbor@ispms.tsc.ru, E-mail: rusina@ispms.tsc.ru, E-mail: rusina-g@mail.ru; Rusina, Galina G., E-mail: svbor@ispms.tsc.ru, E-mail: rusina@ispms.tsc.ru, E-mail: rusina-g@mail.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055, Russia and National Research Tomsk State University, Tomsk, 634050 (Russian Federation)

    2014-11-14

    We investigated the structural and vibrational properties of the Cu (100) surface covered with ultrathin (1-5 ML) Ni films using interaction potential from the embedded atom method. The surface relaxation, dispersion relation and polarization of vibrational modes are discussed. Our calculated structural parameters are in good agreement with experimental results. The obtained vibrational frequencies compare well with the available experimental data.

  19. 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...

  20. 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 ...

  1. Atomic and electronic structure of MoS2 nanoparticles

    DEFF Research Database (Denmark)

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

    2003-01-01

    at the edges. The electronic structure of the edge states is studied and we discuss their influence on the chemical properties of the edges. In particular, we study the reactivity towards hydrogen and show that hydrogen may form stable chemical bonds with both the two low-Miller indexed edges of MoS2. A model...

  2. 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.

  3. Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator.

    Science.gov (United States)

    Zhang, Zhe; Chen, Jue

    2016-12-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues. A single gate near the extracellular surface closes the channel. The regulatory domain, dephosphorylated, is located in the intracellular opening between the two nucleotide-binding domains (NBDs), preventing NBD dimerization and channel opening. The structure also reveals why many cystic-fibrosis-causing mutations would lead to defects either in folding, ion conduction, or gating and suggests new avenues for therapeutic intervention.

  4. 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.

  5. Electron-Hole Counting Approach to Surface Atomic Structure

    Science.gov (United States)

    Chadi, D. J.

    The observed reconstructions of III-V semiconductor surfaces are shown to be consistent with constraints imposed by a simple "electron-hole" counting rule proposed by Pashley. The rule ensures that the predicted surfaces are nonmetallic, nonpolar, and at least, metastable since the compensation of the "donor" electrons leaves no occupied states in the upper part of the band gap which can easily induce other reconstructions. Applications of the method to the problem of surface structure and passivation are examined.

  6. 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.

  7. 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...

  8. 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.

  9. Structured mirror array for two-dimensional collimation of a chromium beam in atom lithography

    Institute of Scientific and Technical Information of China (English)

    Zhang Wan-Jing; Ma Yan; Li Tong-Bao; Zhang Ping-Ping; Deng Xiao; Chen Sheng; Xiao Sheng-Wei

    2013-01-01

    Direct-write atom lithography,one of the potential nanofabrication techniques,is restricted by some difficulties in producing optical masks for the deposition of complex structures.In order to make further progress,a structured mirror array is developed to transversely collimate the chromium atomic beam in two dimensions.The best collimation is obtained when the laser red detunes by natural line-width of transition 7S3 → 7P40 of the chromium atom.The collimation ratio is 0.45 vertically (in x axis),and it is 0.55 horizontally (in y axis).The theoretical model is also simulated,and success of our structured mirror array is achieved.

  10. Atomic resolution structure of serine protease proteinase K at ambient temperature

    Science.gov (United States)

    Masuda, Tetsuya; Suzuki, Mamoru; Inoue, Shigeyuki; Song, Changyong; Nakane, Takanori; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Mikami, Bunzo; Nureki, Osamu; Numata, Keiji; Iwata, So; Sugahara, Michihiro

    2017-01-01

    Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites. PMID:28361898

  11. 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.

  12. Spatially localized structures and oscillons in atomic Bose-Einstein condensates confined in optical lattices

    Science.gov (United States)

    Charukhchyan, M. V.; Sedov, E. S.; Arakelian, S. M.; Alodjants, A. P.

    2014-06-01

    We consider the problem of formation of small-amplitude spatially localized oscillatory structures for atomic Bose-Einstein condensates confined in two- and three-dimensional optical lattices, respectively. Our approach is based on applying the regions with different signs of atomic effective masses where an atomic system exhibits effective hyperbolic dispersion within the first Brillouin zone. By using the kp method we have demonstrated mapping of the initial Gross-Pitaevskii equation on nonlinear Klein-Gordon and/or Ginzburg-Landau-Higgs equations, which is inherent in matter fields within ϕ4-field theories. Formation of breatherlike oscillating localized states—atomic oscillons—as well as kink-shaped states have been predicted in this case. Apart from classical field theories atomic field oscillons occurring in finite lattice structures possess a critical number of particles for their formation. The obtained results pave the way to simulating some analogues of fundamental cosmological processes occurring during our Universe's evolution and to modeling nonlinear hyperbolic metamaterials with condensed matter (atomic) systems.

  13. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up.

    Science.gov (United States)

    Hoelz, André; Glavy, Joseph S; Beck, Martin

    2016-07-01

    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.

  14. Atomic structure of solid and liquid polyethylene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, J.A.; Saboungi, M.; Price, D.L.; Ansell, S. [Argonne National Laboratory, Argonne, Illinois 60439 (United States); Russell, T.P. [Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Halley, J.W.; Nielsen, B. [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    1998-10-01

    The structure of polyethylene oxide (PEO) was investigated by neutron scattering in both semicrystalline and liquid states. Deuterated samples were studied in addition to the protonated ones in order to avoid the large incoherent scattering of hydrogen and identify features in the pair correlation functions attributable to C{endash}H pairs. Analysis of the deuterated sample gave additional information on the C{endash}O and C{endash}C pairs. The results are compared with molecular-dynamics simulations of liquid PEO. {copyright} {ital 1998 American Institute of Physics.}

  15. 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

  16. 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...

  17. The influence of the atomic structure of basal planes on interplanar distance in pyrolytic carbon materials

    Science.gov (United States)

    Borgardt, N. I.; Prihodko, A. S.; Seibt, M.

    2016-12-01

    The atomic structure of carbon materials is studied using the example of pyrocarbon and boronrich pyrocarbon by means of the method of reconstruction of the wave function in transmission electron microscopy. It is shown that the digital processing of the phase distributions of these functions allows us to find the average distance between the basal planes. Using the method of molecular dynamics for the formation of the test structures and obtaining for them the calculated phase distributions, the effect of depletion of the basal planes of the carbon atoms on the interplanar distance in the pyrocarbon materials is quantified.

  18. Extended x-ray absorption fine structure studies of the atomic structure of nanoparticles in different metallic matrices.

    Science.gov (United States)

    Baker, S H; Roy, M; Gurman, S J; Binns, C

    2009-05-06

    It has been appreciated for some time that the novel properties of particles in the size range 1-10 nm are potentially exploitable in a range of applications. In order to ultimately produce commercial devices containing nanosized particles, it is necessary to develop controllable means of incorporating them into macroscopic samples. One way of doing this is to embed the nanoparticles in a matrix of a different material, by co-deposition for example, to form a nanocomposite film. The atomic structure of the embedded particles can be strongly influenced by the matrix. Since some of the key properties of materials, including magnetism, strongly depend on atomic structure, the ability to determine atomic structure in embedded nanoparticles is very important. This review focuses on nanoparticles, in particular magnetic nanoparticles, embedded in different metal matrices. Extended x-ray absorption fine structure (EXAFS) provides an excellent means of probing atomic structure in nanocomposite materials, and an overview of this technique is given. Its application in probing catalytic metal clusters is described briefly, before giving an account of the use of EXAFS in determining atomic structure in magnetic nanocomposite films. In particular, we focus on cluster-assembled films comprised of Fe and Co nanosized particles embedded in various metal matrices, and show how the crystal structure of the particles can be changed by appropriate choice of the matrix material. The work discussed here demonstrates that combining the results of structural and magnetic measurements, as well as theoretical calculations, can play a significant part in tailoring the properties of new magnetic cluster-assembled materials.

  19. 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.)

  20. Energetic Stabilities, Structural and Electronic Properties of Monolayer Graphene Doped with Boron and Nitrogen Atoms

    Directory of Open Access Journals (Sweden)

    Seba Sara Varghese

    2016-12-01

    Full Text Available The structural, energetic, and electronic properties of single-layer graphene doped with boron and nitrogen atoms with varying doping concentrations and configurations have been investigated here via first-principles density functional theory calculations. It was found that the band gap increases with an increase in doping concentration, whereas the energetic stability of the doped systems decreases with an increase in doping concentration. It was observed that both the band gaps and the cohesive energies also depend on the atomic configurations considered for the substitutional dopants. Stability was found to be higher in N-doped graphene systems as compared to B-doped graphene systems. The electronic structures of B- and N-doped graphene systems were also found to be strongly influenced by the positioning of the dopant atoms in the graphene lattice. The systems with dopant atoms at alternate sublattices have been found to have the lowest cohesive energies and therefore form the most stable structures. These results indicate an ability to adjust the band gap as required using B and N atoms according to the choice of the supercell, i.e., the doping density and substitutional dopant sites, which could be useful in the design of graphene-based electronic and optical devices.

  1. 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.

  2. Time-Resolved Diffraction Profiles and Atomic Dynamics in Short-Pulse Laser-Induced Structural Transformations: Molecular Dynamics Study

    Science.gov (United States)

    2006-05-16

    clearly reflected in the evolution of the structure function. In just 3–4 ps the peaks characteristic of the fcc structure dis- appear and the structure...apparent in the figure. The diffraction peaks from 111 and 311 atomic planes, present in the original fcc structure , shift in the direction of smaller Q...the fcc crystalline structure. Each peak in Gr corresponds to a specific interatomic distance between a pair of atoms in a perfect fcc structure . For

  3. An Analysis of Taiwanese Eighth Graders' Science Achievement, Scientific Epistemological Beliefs and Cognitive Structure Outcomes After Learning Basic Atomic Theory.

    Science.gov (United States)

    Tsai, Chin-Chung

    1998-01-01

    Explores the interrelationships between students' general science achievement, scientific epistemological beliefs, and cognitive structure outcomes derived from instruction of basic atomic theory. Contains 19 references. (DDR)

  4. 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…

  5. 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)

  6. 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…

  7. 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.

  8. 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.

  9. 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.

  10. Electronic structure of atomically coherent square semiconductor superlattices with dimensionality below two

    NARCIS (Netherlands)

    Kalesaki, E.; Evers, W.H.; Vanmaekelbergh, D.; Delerue, C.

    2013-01-01

    The electronic structure of recently synthesized square superlattices with atomic coherence composed of PbSe, CdSe, or CdTe nanocrystals (NCs) attached along {100} facets is investigated using tight-binding calculations. In experimental realizations of these systems [W. H. Evers et al., Nano Lett. 1

  11. 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.

  12. 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

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

    Science.gov (United States)

    Campbellová, Anna; Ondráček, Martin; Pou, Pablo; Pérez, Rubén; Klapetek, Petr; Jelínek, Pavel

    2011-07-22

    A Si adatom on a Si(111)-(7 × 7) reconstructed surface is a typical atomic feature that can rather easily be imaged by a non-contact atomic force microscope (nc-AFM) and can be thus used to test the atomic resolution of the microscope. Based on our first principles density functional theory (DFT) calculations, we demonstrate that the structure of the termination of the AFM tip plays a decisive role in determining the appearance of the adatom image. We show how the AFM image changes depending on the tip-surface distance and the composition of the atomic apex at the end of the tip. We also demonstrate that contaminated tips may give rise to image patterns displaying so-called 'sub-atomic' features even in the attractive force regime.

  15. Paschen-Back effect involving atomic fine and hyperfine structure states

    Science.gov (United States)

    Sowmya, K.; Nagendra, K. N.; Sampoorna, M.; Stenflo, J. O.

    2015-10-01

    The linear polarization in spectral lines produced by coherent scattering is significantly modified by the quantum interference between the atomic states in the presence of a magnetic field. When magnetic fields produce a splitting which is of the order of or greater than the fine or hyperfine structure splittings, we enter the Paschen-Back effect (PBE) regime, in which the magnetic field dependence of the Zeeman splittings and transition amplitudes becomes non-linear. In general, PBE occurs for sufficiently strong fields when the fine structure states are involved and for weak fields in the case of hyperfine structure states. In this work, we apply the recently developed theory of PBE in the atomic fine and hyperfine structure states including the effects of partial frequency redistribution to the case of Li i 6708 Å doublet. We explore the signatures of PBE in a single scattering event and their applicability to the solar magnetic field diagnostics.

  16. 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.

  17. Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy.

    Science.gov (United States)

    Pyne, Alice; Thompson, Ruth; Leung, Carl; Roy, Debdulal; Hoogenboom, Bart W

    2014-08-27

    Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.

  18. Nanoscale structure and atomic disorder in the iron-based chalcogenides.

    Science.gov (United States)

    Saini, Naurang Lal

    2013-02-01

    The multiband iron-based superconductors have layered structure with a phase diagram characterized by a complex interplay of charge, spin and lattice excitations, with nanoscale atomic structure playing a key role in their fundamental electronic properties. In this paper, we briefly review nanoscale structure and atomic disorder in iron-based chalcogenide superconductors. We focus on the Fe(Se,S)1-x Te x (11-type) and K0.8Fe1.6Se2 (122-type) systems, discussing their local structure obtained by extended x-ray absorption fine structure. Local structure studies on the Fe(Se,S)1-x Te x system reveal clear nanoscale phase separation characterized by coexisting components of different atomic configurations, similar to the case of random alloys. In fact, the Fe-Se/S and Fe-Te distances in the ternary Fe(Se,S)1-x Te x are found to be closer to the respective distances in the binary FeSe/FeS and FeTe systems, showing significant divergence of the local structure from the average one. The observed features are characteristic of ternary random alloys, indicating breaking of the local symmetry in these materials. On the other hand, K0.8Fe1.6Se2 is known for phase separation in an iron-vacancy ordered phase and an in-plane compressed lattice phase. The local structure of these 122-type chalcogenides shows that this system is characterized by a large local disorder. Indeed, the experiments suggest a nanoscale glassy phase in K0.8Fe1.6Se2, with the superconductivity being similar to the granular materials. While the 11-type structure has no spacer layer, the 122-type structure contains intercalated atoms unlike the 1111-type REFeAsO (RE = rare earth) oxypnictides, having well-defined REO spacer layers. It is clear that the interlayer atomic correlations in these iron-based superconducting structures play an important role in structural stability as well as superconductivity and magnetism.

  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. Atomic structure and handedness of the building block of a biological assembly.

    Science.gov (United States)

    Loquet, Antoine; Habenstein, Birgit; Chevelkov, Veniamin; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Lange, Adam

    2013-12-26

    Noncovalent supramolecular assemblies possess in general several unique subunit-subunit interfaces.The basic building block of such an assembly consists of several subunits and contains all unique interfaces. Atomic-resolution structures of monomeric subunits are typically accessed by crystallography or solution NMR and fitted into electron microscopy density maps. However, the structure of the intact building block in the assembled state remains unknown with this hybrid approach. Here, we present the solid-state NMR atomic structure of the building block of the type III secretion system needle. The building block structure consists of a homotetrameric subunit complex with three unique supramolecular interfaces. Side-chain positions at the interfaces were solved at atomic detail. The high-resolution structure reveals unambiguously the helical handedness of the assembly, determined to be right-handed for the type III secretion system needle.Additionally, the axial rise per subunit could be extracted from the tetramer structure and independently validated by mass-per-length measurements.

  1. 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.

  2. 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.

  3. Structure and energetics of Ni clusters with up to 150 atoms

    CERN Document Server

    Grigoryan, V G

    2003-01-01

    We present a method (the Aufbau/Abbau method) for optimizing the structure of a whole series of clusters without making any assumptions on the structure. Subsequently, the method is combined with the embedded-atom method in determining the structure of the two energetically lowest isomers of Ni_N clusters with N up to 150. Finally, various analytical descriptors are introduced that are used in studying the overall shape of the clusters, their structure and stability, and possible growth and dissociation processes.

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

    DEFF Research Database (Denmark)

    Martinez, Jose Ignacio; Alonso, J.A.

    2008-01-01

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

  5. 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.……

  6. Quantum spacetime fluctuations: Lamb Shift and hyperfine structure of the hydrogen atom

    CERN Document Server

    Rivas, Juan Israel; Goeklue, Ertan

    2011-01-01

    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. In addition, we analyze the corresponding Lamb shift effect emerging from these fluctuations of spacetime. Once again, we will set a bound to these oscillations resorting to the current experimental outcomes

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

    DEFF Research Database (Denmark)

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

    2000-01-01

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

  8. 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.

  9. 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.

  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. Structural, magnetic and electronic properties of single Iron atom at graphene edges

    Science.gov (United States)

    Zhang, Junfeng; Hao, Yanjun; Xu, Xiaohong

    2017-02-01

    A systemic theoretical study of one iron atom on graphene ribbon edges (Fe/GR) has been carried out by using density functional theory. Thermodynamic stabilities, electronic and magnetic properties of Fe/GR with different edge types and adsorption locations were investigated. According to the Clar's aromatic sextet rule, the formation energies and density of states of Fe atom are found to rely tightly on the ribbon's periodic length. Moreover, Fe atoms on reconstructed zz edges are also stable with low formation energies and semiconducting properties. Finally, the magnetic properties are found sensitive with the structural details, especially the local bond environment. The present theoretical results constitute a useful picture for the deep comprehending on the interface details of the lateral Fe/graphene heterostructures.

  12. Diffraction of helium atom beams from a micro-structured reflection grating

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Bum Suk; Meijer, Gerard; Schoellkopf, Wieland [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin (Germany); Schulz, Stephan [Universitaet Ulm (Germany). Institut fuer Quanteninformationsverarbeitung

    2008-07-01

    We have observed high-resolution diffraction patterns of a thermal-energy helium-atom beam reflected from a micro-structured surface grating at grazing incidence. The grating has a periodicity of 20 {mu}m and consists of 10-{mu}m-wide Cr stripes patterned on a quartz substrate. Fully-resolved diffraction peaks up to the 7-th order are observed at grazing incidence angles up to 20 mrad. With changes in de Broglie wavelength or incidence angle the relative diffraction intensities show significant variations which are attributed to the atom-surface Casimir-van der Waals potential. In addition, the overall probability of coherent reflection is found to increase with increasing de Broglie wavelength and decreasing incidence angle. We discuss whether this behavior indicates quantum reflection at the long-range attractive branch of the atom-surface potential.

  13. TUNABLE Band Structures of 2d Multi-Atom Archimedean-Like Phononic Crystals

    Science.gov (United States)

    Xu, Y. L.; Chen, C. Q.; Tian, X. G.

    2012-06-01

    Two dimensional multi-atom Archimedean-like phononic crystals (MAPCs) can be obtained by adding "atoms" at suitable positions in primitive cells of traditional simple lattices. Band structures of solid-solid and solid-air MAPCs are computed by the finite element method in conjunction with the Bloch theory. For the solid-solid system, our results show that the MAPCs can be suitably designed to split and shift band gaps of the corresponding traditional simple phononic crystal (i.e., with only one scatterer inside a primitive cell). For the solid-air system, the MAPCs have more and wider band gaps than the corresponding traditional simple phononic crystal. Numerical calculations for both solid-solid and solid-air MAPCs show that the band gap of traditional simple phononic crystal can be tuned by appropriately adding "atoms" into its primitive cell.

  14. Hierarchical surface atomic structure of a manganese-based spinel cathode for lithium-ion batteries.

    Science.gov (United States)

    Lee, Sanghan; Yoon, Gabin; Jeong, Minseul; Lee, Min-Joon; Kang, Kisuk; Cho, Jaephil

    2015-01-19

    The increasing use of lithium-ion batteries (LIBs) in high-power applications requires improvement of their high-temperature electrochemical performance, including their cyclability and rate capability. Spinel lithium manganese oxide (LiMn2O4) is a promising cathode material because of its high stability and abundance. However, it exhibits poor cycling performance at high temperatures owing to Mn dissolution. Herein we show that when stoichiometric lithium manganese oxide is coated with highly doped spinels, the resulting epitaxial coating has a hierarchical atomic structure consisting of cubic-spinel, tetragonal-spinel, and layered structures, and no interfacial phase is formed. In a practical application of the coating to doped spinel, the material retained 90% of its capacity after 800 cycles at 60 °C. Thus, the formation of an epitaxial coating with a hierarchical atomic structure could enhance the electrochemical performance of LIB cathode materials while preventing large losses in capacity.

  15. Temperature effects on the atomic structure and kinetics in single crystal electrochemistry

    Science.gov (United States)

    Gründer, Yvonne; Markovic, Nenad M.; Thompson, Paul; Lucas, Christopher A.

    2015-01-01

    The influence of temperature on the atomic structure at the electrochemical interface has been studied using in-situ surface x-ray scattering (SXS) during the formation of metal monolayers on a Au(111) electrode. For the surface reconstruction of Au(111), higher temperatures increase the mobility of surface atoms in the unreconstructed phase which then determines the surface ordering during the formation of the reconstruction. For the underpotential deposition (UPD) systems, the surface diffusion of the depositing metal adatoms is significantly reduced at low temperatures which results in the frustration of ordered structures in the case of Cu UPD, occurring on a Br-modified surface, and in the formation of a disordered Ag monolayer during Ag UPD. The results indicate that temperature changes affect the mass transport and diffusion of metal adatoms on the electrode surface. This demonstrates the importance of including temperature as a variable in studying surface structure and reactions at the electrochemical interface.

  16. 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

    2015-03-03

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

  17. Vapour phase growth and grain boundary structure of molybdenum disulphide atomic layers.

    Science.gov (United States)

    Najmaei, Sina; Liu, Zheng; Zhou, Wu; Zou, Xiaolong; Shi, Gang; Lei, Sidong; Yakobson, Boris I; Idrobo, Juan-Carlos; Ajayan, Pulickel M; Lou, Jun

    2013-08-01

    Single-layered molybdenum disulphide with a direct bandgap is a promising two-dimensional material that goes beyond graphene for the next generation of nanoelectronics. Here, we report the controlled vapour phase synthesis of molybdenum disulphide atomic layers and elucidate a fundamental mechanism for the nucleation, growth, and grain boundary formation in its crystalline monolayers. Furthermore, a nucleation-controlled strategy is established to systematically promote the formation of large-area, single- and few-layered films. Using high-resolution electron microscopy imaging, the atomic structure and morphology of the grains and their boundaries in the polycrystalline molybdenum disulphide atomic layers are examined, and the primary mechanisms for grain boundary formation are evaluated. Grain boundaries consisting of 5- and 7- member rings are directly observed with atomic resolution, and their energy landscape is investigated via first-principles calculations. The uniformity in thickness, large grain sizes, and excellent electrical performance signify the high quality and scalable synthesis of the molybdenum disulphide atomic layers.

  18. Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion plus Selected Inversion

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Lin; Chen, Mohan; Yang, Chao; He, Lixin

    2012-02-10

    We describe how to apply the recently developed pole expansion plus selected inversion (PEpSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating charge density, total energy, Helmholtz free energy and atomic forces without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEpSI is that it has a much lower computational complexity than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEpSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEpSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundreds. Both the wall clock time and the memory requirement of PEpSI is modest. This makes it even possible to perform Kohn-Sham DFT calculations for 10,000-atom nanotubes on a single processor. We also show that the use of PEpSI does not lead to loss of accuracy required in a practical DFT calculation.

  19. Atomic and electronic structure of both perfect and nanostructured Ni(111) surfaces: First-principles calculations

    Energy Technology Data Exchange (ETDEWEB)

    Piskunov, Sergei, E-mail: piskunov@lu.l [Faculty of Computing, University of Latvia, 19 Raina blvd., Riga LV-1586 (Latvia); Faculty of Physics and Mathematics, University of Latvia, 8 Zellu Str., Riga LV-1002 (Latvia); Zvejnieks, Guntars; Zhukovskii, Yuri F. [Institute for Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia); Bellucci, Stefano [INFN-Laboratori Nazionali di Frascati, Via Enrico Fermi 40, I-00044, Frascati (Italy)

    2011-03-31

    In this study, we perform first principles simulations on both atomically smooth and nanostructured Ni(111) slabs. The latter contains periodically distributed nickel nanoclusters atop a thin metal film gradually growing from adatoms and serving as a promising catalyst. Applying the generalized gradient approximation within the formalism of the density functional theory we compare the atomic and electronic structures of Ni bulk, as well as both perfect and nanostructured (111) surfaces obtained using two different ab initio approaches: (i) the linear combination of atomic orbitals and (ii) the projector augmented plane waves. The most essential inter-atomic forces between the Ni adatoms upon the substrate have been found to be formed via: (i) attractive pair-wise interactions, (ii) repulsive triple-wise interactions within a triangle and (iii) attractive triple-wise interactions within a line between the nearest adatoms. The attractive interactions surmount the repulsive forces, hence resulting in the formation of stable clusters from Ni adatoms. The magnetic moment and the effective charge (within both Mulliken and Bader approaches) of the outer atoms in Ni nanoparticles increase as compared to those for the smooth Ni(111) surface. The calculated electronic charge redistribution in the Ni nanoclusters features them as possible adsorption centers with increasing catalytic activity, e.g., for further synthesis of carbon nanotubes.

  20. 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.

  1. Enhanced water removal in a fuel cell stack by droplet atomization using structural and acoustic excitation

    Science.gov (United States)

    Palan, Vikrant; Shepard, W. Steve

    This work examines new methods for enhancing product water removal in fuel cell stacks. Vibration and acoustic based methods are proposed to atomize condensed water droplets in the channels of a bipolar plate or on a membrane electrode assembly (MEA). The vibration levels required to atomize water droplets of different sizes are first examined using two different approaches: (1) exciting the droplet at the same energy level required to form that droplet; and (2) by using a method called 'vibration induced droplet atomization', or VIDA. It is shown analytically that a 2 mm radius droplet resting on a bipolar-like plate can be atomized by inducing acceleration levels as low as 250 g at a certain frequency. By modeling the direct structural excitation of a simplified bipolar plate using a realistic source, the response levels that can be achieved are then compared with those required levels. Furthermore, a two-cell fuel cell finite element model and a boundary element model of the MEA were developed to demonstrate that the acceleration levels required for droplet atomization may be achieved in both the bipolar plate as well as the MEA through proper choice of excitation frequency and source strength.

  2. Enhanced water removal in a fuel cell stack by droplet atomization using structural and acoustic excitation

    Energy Technology Data Exchange (ETDEWEB)

    Palan, Vikrant; Shepard, W. Steve [Department of Mechanical Engineering, The University of Alabama, 290 Hardaway Hall, Box 870276, Tuscaloosa, AL 35487 (United States)

    2006-09-22

    This work examines new methods for enhancing product water removal in fuel cell stacks. Vibration and acoustic based methods are proposed to atomize condensed water droplets in the channels of a bipolar plate or on a membrane electrode assembly (MEA). The vibration levels required to atomize water droplets of different sizes are first examined using two different approaches: (1) exciting the droplet at the same energy level required to form that droplet; and (2) by using a method called 'vibration induced droplet atomization', or VIDA. It is shown analytically that a 2mm radius droplet resting on a bipolar-like plate can be atomized by inducing acceleration levels as low as 250g at a certain frequency. By modeling the direct structural excitation of a simplified bipolar plate using a realistic source, the response levels that can be achieved are then compared with those required levels. Furthermore, a two-cell fuel cell finite element model and a boundary element model of the MEA were developed to demonstrate that the acceleration levels required for droplet atomization may be achieved in both the bipolar plate as well as the MEA through proper choice of excitation frequency and source strength. (author)

  3. Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.

    Science.gov (United States)

    Chae, Myong-Ho; Krull, Florian; Knapp, Ernst-Walter

    2015-05-01

    The DOcking decoy-based Optimized Potential (DOOP) energy function for protein structure prediction is based on empirical distance-dependent atom-pair interactions. To optimize the atom-pair interactions, native protein structures are decomposed into polypeptide chain segments that correspond to structural motives involving complete secondary structure elements. They constitute near native ligand-receptor systems (or just pairs). Thus, a total of 8609 ligand-receptor systems were prepared from 954 selected proteins. For each of these hypothetical ligand-receptor systems, 1000 evenly sampled docking decoys with 0-10 Å interface root-mean-square-deviation (iRMSD) were generated with a method used before for protein-protein docking. A neural network-based optimization method was applied to derive the optimized energy parameters using these decoys so that the energy function mimics the funnel-like energy landscape for the interaction between these hypothetical ligand-receptor systems. Thus, our method hierarchically models the overall funnel-like energy landscape of native protein structures. The resulting energy function was tested on several commonly used decoy sets for native protein structure recognition and compared with other statistical potentials. In combination with a torsion potential term which describes the local conformational preference, the atom-pair-based potential outperforms other reported statistical energy functions in correct ranking of native protein structures for a variety of decoy sets. This is especially the case for the most challenging ROSETTA decoy set, although it does not take into account side chain orientation-dependence explicitly. The DOOP energy function for protein structure prediction, the underlying database of protein structures with hypothetical ligand-receptor systems and their decoys are freely available at http://agknapp.chemie.fu-berlin.de/doop/.

  4. Real-Space Imaging of the Atomic Structure of Organic-Inorganic Perovskite.

    Science.gov (United States)

    Ohmann, Robin; Ono, Luis K; Kim, Hui-Seon; Lin, Haiping; Lee, Michael V; Li, Youyong; Park, Nam-Gyu; Qi, Yabing

    2015-12-30

    Organic-inorganic perovskite is a promising class of materials for photovoltaic applications and light emitting diodes. However, so far commercialization is still impeded by several drawbacks. Atomic-scale effects have been suggested to be possible causes, but an unequivocal experimental view at the atomic level is missing. Here, we present a low-temperature scanning tunneling microscopy study of single crystal methylammonium lead bromide CH3NH3PbBr3. Topographic images of the in situ cleaved perovskite surface reveal the real-space atomic structure. Compared to the bulk we observe modified arrangements of atoms and molecules on the surface. With the support of density functional theory we explain these by surface reconstruction and a substantial interplay of the orientation of the polar organic cations (CH3NH3)(+) with the position of the hosting anions. This leads to structurally and electronically distinct domains with ferroelectric and antiferroelectric character. We further demonstrate local probing of defects, which may also impact device performance.

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

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob;

    2002-01-01

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

  6. Atomic structure and electronic properties of the two-dimensional (Au ,Al )/Si (111 )2 ×2 compound

    Science.gov (United States)

    Gruznev, D. V.; Bondarenko, L. V.; Matetskiy, A. V.; Tupchaya, A. Y.; Chukurov, E. N.; Hsing, C. R.; Wei, C. M.; Eremeev, S. V.; Zotov, A. V.; Saranin, A. A.

    2015-12-01

    A combination of scanning tunneling microscopy, angle-resolved photoelectron spectroscopy, ab initio random structure searching, and density functional theory electronic structure calculations was applied to elucidate the atomic arrangement and electron band structure of the (Au ,Al )/Si (111 )2 ×2 two-dimensional compound formed upon Al deposition onto the mixed 5 ×2 /√{3 }×√{3 } Au/Si(111) surface. It was found that the most stable 2 ×2 -(Au, Al) compound incorporates four Au atoms, three Al atoms, and two Si atoms per 2 ×2 unit cell. Its atomic arrangement can be visualized as an array of meandering Au atomic chains with two-thirds of the Al atoms incorporated into the chains and one-third of the Al atoms interconnecting the chains. The compound is metallic and its electronic properties can be controlled by appropriate Al dosing since energetic location of the bands varies by ˜0.5 eV during increasing of Al contents. The 2 ×2 -(Au, Al) structure appears to be lacking the C3 v symmetry typical for the hexagonal lattices. The consequence of the peculiar atomic structure of the two-dimensional alloy is spin splitting of the metallic states, which should lead to anisotropy of the current-induced in-plane spin polarization.

  7. 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.

  8. Optically excited structural transition in atomic wires on surfaces at the quantum limit.

    Science.gov (United States)

    Frigge, T; Hafke, B; Witte, T; Krenzer, B; Streubühr, C; Samad Syed, A; Mikšić Trontl, V; Avigo, I; Zhou, P; Ligges, M; von der Linde, D; Bovensiepen, U; Horn-von Hoegen, M; Wippermann, S; Lücke, A; Sanna, S; Gerstmann, U; Schmidt, W G

    2017-03-29

    Transient control over the atomic potential-energy landscapes of solids could lead to new states of matter and to quantum control of nuclear motion on the timescale of lattice vibrations. Recently developed ultrafast time-resolved diffraction techniques combine ultrafast temporal manipulation with atomic-scale spatial resolution and femtosecond temporal resolution. These advances have enabled investigations of photo-induced structural changes in bulk solids that often occur on timescales as short as a few hundred femtoseconds. In contrast, experiments at surfaces and on single atomic layers such as graphene report timescales of structural changes that are orders of magnitude longer. This raises the question of whether the structural response of low-dimensional materials to femtosecond laser excitation is, in general, limited. Here we show that a photo-induced transition from the low- to high-symmetry state of a charge density wave in atomic indium (In) wires supported by a silicon (Si) surface takes place within 350 femtoseconds. The optical excitation breaks and creates In-In bonds, leading to the non-thermal excitation of soft phonon modes, and drives the structural transition in the limit of critically damped nuclear motion through coupling of these soft phonon modes to a manifold of surface and interface phonons that arise from the symmetry breaking at the silicon surface. This finding demonstrates that carefully tuned electronic excitations can create non-equilibrium potential energy surfaces that drive structural dynamics at interfaces in the quantum limit (that is, in a regime in which the nuclear motion is directed and deterministic). This technique could potentially be used to tune the dynamic response of a solid to optical excitation, and has widespread potential application, for example in ultrafast detectors.

  9. Protein structure prediction by all-atom free-energy refinement

    Directory of Open Access Journals (Sweden)

    Wenzel Wolfgang

    2007-03-01

    Full Text Available Abstract Background The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01 that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure prediction purposes. We therefore investigate here a low-cost free-energy relaxation protocol for protein structure prediction that combines heuristic methods for model generation with all-atom free-energy relaxation in PFF01. Results We use PFF01 to rank and cluster the conformations for 32 proteins generated by ROSETTA. For 22/10 high-quality/low quality decoy sets we select near-native conformations with an average Cα root mean square deviation of 3.03 Å/6.04 Å. The protocol incorporates an inherent reliability indicator that succeeds for 78% of the decoy sets. In over 90% of these cases near-native conformations are selected from the decoy set. This success rate is rationalized by the quality of the decoys and the selectivity of the PFF01 forcefield, which ranks near-native conformations an average 3.06 standard deviations below that of the relaxed decoys (Z-score. Conclusion All-atom free-energy relaxation with PFF01 emerges as a powerful low-cost approach toward generic de-novo protein structure prediction. The approach can be applied to large all-atom decoy sets of any origin and requires no preexisting structural information to identify the native conformation. The study provides evidence that a large class of proteins may be foldable by PFF01.

  10. On the hyperfine structure of the triplet $n^{3}S-$states of the four-electron atoms and ions

    CERN Document Server

    Frolov, Alexei M

    2016-01-01

    Hyperfine structures of the triplet $n^3S-$states in the four-electron Be-atom(s) and Be-like ions are considered. It is shown that to determine the hyperfine structure splitting in such atomic systems one needs to know the triplet electron density at the central atomic nucleus $\\rho_T(0)$. We have developed the procedure which allows allows one to determine the triplet electron density $\\rho_T(0)$ for arbitrary four-electron atoms and ions.

  11. 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.

  12. Atomic and Electronic Structures of Cd0.96Zn0.04Te(110) Surface

    Institute of Scientific and Technical Information of China (English)

    ZHA Gang-Qiang; JIE Wan-Qi; ZHANG Wen-Hua; LI Qiang; XU Fa-Qiang

    2005-01-01

    @@ X-Ray diffraction is used to analyse the lattice structure of Cd0.96Zn0.04Te (CZT), and the lattice constant is measured to be 0.647nm. The atomic structure of the clean CZT(110) surface obtained by Ar+ etching in vacuum is observed by low-energy electron diffraction, where no surface reconstruction is discovered. Angleresolved photoemission spectroscopy was used to characterize the surface state of the clean CZT (110) surface,by which we find a 1.5-eV-wide surface band with the peak at 0.9eV below the Fermi energy containing about6.9 × 1014 electrons/cm2, approximately one electron per surface atom.

  13. Atomic structure and phonons of a Pb ultrathin film on the Al(100) surface

    Science.gov (United States)

    Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.

    2014-10-01

    The atomic and phonon structures of a Pb ultrathin film on the Al(100) surface have been theoretically studied. Surface relaxation, local density of vibrational states, and polarization of the phonon modes of adatoms and atoms of a substrate have been discussed. It has been shown that the adsorption of Pb results in the oscillating relaxation of the surface of the substrate and warping of the structure in subsurface layers. Comparative analysis of the vibrational characteristics of the pure surface of the substrate and the surface with adatoms has shown that the adsorptive interaction in the system and its dynamic stability are governed by new vibrational modes that are not inherent in pure Al and Pb surfaces.

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

    Energy Technology Data Exchange (ETDEWEB)

    Latychevskaia, Tatiana; Fink, Hans-Werner [Physics Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich (Switzerland)

    2015-01-12

    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.

  15. 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.

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

    CERN Document Server

    Emmert, Andreas; Brune, Michel; Raimond, Jean-Michel; Haroche, Serge; Nogues, Gilles

    2009-01-01

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

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

    Science.gov (United States)

    Emmert, A.; Lupaşcu, A.; Brune, M.; Raimond, J.-M.; Haroche, S.; Nogues, G.

    2009-12-01

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

  18. 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.

  19. Deformation behavior of metallic glasses with shear band like atomic structure: a molecular dynamics study.

    Science.gov (United States)

    Zhong, C; Zhang, H; Cao, Q P; Wang, X D; Zhang, D X; Ramamurty, U; Jiang, J Z

    2016-08-02

    Molecular dynamics simulations were employed to investigate the plastic deformation within the shear bands in three different metallic glasses (MGs). To mimic shear bands, MG specimens were first deformed until flow localization occurs, and then the volume of the material within the localized regions was extracted and replicated. Homogeneous deformation that is independent of the size of the specimen was observed in specimens with shear band like structure, even at a temperature that is far below the glass transition temperature. Structural relaxation and rapid cooling were employed to examine the effect of free volume content on the deformation behavior. This was followed by detailed atomic structure analyses, employing the concepts of Voronoi polyhedra and "liquid-like" regions that contain high fraction of sub-atomic size open volumes. Results suggest that the total fraction of atoms in liquid-like regions is a key parameter that controls the plastic deformation in MGs. These are discussed in the context of reported experimental results and possible strategies for synthesizing monolithic amorphous materials that can accommodate large tensile plasticity are suggested.

  20. Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR.

    Science.gov (United States)

    Shi, Chaowei; Fricke, Pascal; Lin, Lin; Chevelkov, Veniamin; Wegstroth, Melanie; Giller, Karin; Becker, Stefan; Thanbichler, Martin; Lange, Adam

    2015-12-01

    Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the species Caulobacter crescentus is not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR-derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

  1. The Relationship Between Atomic Structure and Strain Distribution of Misfit Dislocation Cores at Cubic Heteroepitaxial Interfaces.

    Science.gov (United States)

    Wen, Cai

    2017-03-09

    The atomic reconstruction of a misfit dislocation (MD) core causes change in the strain distribution around the core. Several MD cores at the AlSb/GaAs (001) cubic zincblende interface, including a symmetrical glide set Lomer dislocation (LD), a left-displaced glide set LD, a glide set LD with an atomic step, a symmetrical shuffle set LD, and a 60° dislocation pair, were studied using simulated projected potential and aberration-corrected transmission electron microscope images. Image deconvolution was also used to restore structure images from nonoptimum-defocus images. The corresponding biaxial strain maps, ε xx (in-plane) and ε yy (out-of-plane), were obtained by geometric phase analysis using the GaAs substrate as the reference lattice. The results show that atomic structure characteristics of MD cores can be revealed by the strain maps. The strain maps should be measured from optimum-defocus images or restored structure images. Furthermore, the ε xx strain map has been found more accurate than the ε yy strain map for MD cores, and the specimen thickness should be below the critical thickness due to the influence of dynamical scattering.

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

    Science.gov (United States)

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

    2016-02-01

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

  3. Investigation of organic films by atomic force microscopy: Structural, nanotribological and electrical properties

    Science.gov (United States)

    Qi, Yabing

    2011-11-01

    Atomic force microscopy (AFM) has found its applications in a wide range of research fields. In this review, we show by examples that atomic force microscopy is a powerful technique to investigate structural, mechanical and electrical properties of organic films. We start with an introduction of AFM instrumentation highlighting AFM developments that are of direct relevance to organic films. Next, we review AFM studies on organic films according to their preparation methods: self-assembly, the Langmuir-Blodgett technique, solution preparation, and thermal evaporation. In the discussion on self-assembled monolayers, we focus on aspects such as structural evolution, load-induced molecular tilting, annealing, and incorporation of conjugated groups. For solution prepared organic films, we stress annealing-induced structural evolution as well as the effects of phase separation/segregation. We also briefly summarize the progress of AFM investigation on Langmuir-Blodgett films and thermally evaporated organic films. We conclude the review by providing some thoughts for future exploration. In particular, atomic force microscopy combined with ultra-flat coplanar nano-electrodes provides a promising platform to isolate single or a small number of molecular features (e.g. vacancies, defects, grain boundaries) in organic films as well as to identify the role of these features at the nanometer scale.

  4. 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

    2016-06-02

    Peptide coated gold nanoclusters (AuNCs) have a precise molecular formula and atomic structure, which are critical for their unique applications in targeting specific proteins either for protein analysis or drug design. To date, a study of the crystal structure of peptide coated AuNCs is absent primarily due to the difficulty of obtaining their crystalline phases in an experiment. Here we study a typical peptide coated AuNC (Au24Peptide8, Peptide = H2N-CCYKKKKQAGDV-COOH, Anal. Chem., 2015, 87, 2546) to figure out its atomic structure and electronic structure using a theoretical method for the first time. In this work, we identify the explicit configuration of the essential structure of Au24Peptide8, Au24(Cys-Cys)8, using density functional theory (DFT) computations and optical spectroscopic experiments, where Cys denotes cysteine without H bonded to S. As the first multidentate ligand binding AuNC, Au24(Cys-Cys)8 is characterized as a distorted Au13 core with Oh symmetry covered by two Au(Cys-Cys) and three Au3(Cys-Cys)2 staple motifs in its atomic structure. The most stable configuration of Au24(Cys-Cys)8 is confirmed by comparing its UV-vis absorption spectrum from time-dependent density-functional theory (TDDFT) calculations with optical absorption measurements, and these results are consistent with each other. Furthermore, we carry out frontier molecular orbital (FMO) calculations to elucidate that the electronic structure of Au24(Cys-Cys)8 is different from that of Au24(SR)20 as they have a different Au/S ratio, where SR represents alkylthiolate. Importantly, the different ligand coatings, Cys-Cys and SR, in Au24(Cys-Cys)8 and Au24(SR)20 cause the different Au/S ratios in the coated Au24. The reason is that the Au/S ratio is crucial in determining the size of the Au core of the ligand protected AuNC, and the size of the Au core corresponds to a specific electronic structure. By the adjustment of ligand coatings from alkylthiolate to peptide, the Au/S ratio

  5. Effects of atomic grain boundary structures on primary radiation damage in α-Fe

    Energy Technology Data Exchange (ETDEWEB)

    Esfandiarpour, A. [Department of Physics, Payame Noor University (PNU), P.O. BOX 19395-3697, Tehran (Iran, Islamic Republic of); Feghhi, S.A.H., E-mail: a.feghhi@gmail.com [Department of Radiation Application, Shahid Beheshti University G.C., Tehran (Iran, Islamic Republic of); Shokri, A.A. [Department of Physics, Payame Noor University (PNU), P.O. BOX 19395-3697, Tehran (Iran, Islamic Republic of)

    2015-11-01

    In this paper, we used five different grain boundary (GB) structures including two twists, two symmetric tilts and one asymmetric tilt for α-Fe, in order to study the influence of different GB structures on the production and time evolution of defects. Energetic behavior of point defects near GBs is investigated and analyzed using Molecular Static (MS) method to calculate and compare the “defect absorbency” of each structure. The primary radiation damage state near each GB structure is simulated using Molecular Dynamic (MD) method for 3 keV and 6 keV primary-knocked on atom (PKA) with velocity vector perpendicular to the GB plane at various distances in 300 K. We found that all five GB structures can decrease the defect number in bulk region, if cascade center locates on the GB plane (prefect overlap) and increase the vacancy number, if the overlap is imperfect. This depends on the energy of PKA and its distance from GB plane. Also, the results proved that the magnitude of the observed variations depends on the atomic structure of GB. Furthermore, the GBs that have stronger “interstitial absorbency” produce an excess concentration of vacancies in the bulk region, while the edge of the cascades overlaps with GB plane. This is the result of bigger “interstitial absorbency” of GBs in comparison with vacancies.

  6. 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.

  7. Effect of hydrogen atoms on the structures of trinuclear metal carbonyl clusters: trinuclear manganese carbonyl hydrides.

    Science.gov (United States)

    Liu, Xian-mei; Wang, Chao-yang; Li, Qian-shu; Xie, Yaoming; King, R Bruce; Schaefer, Henry F

    2009-05-18

    The structures of the trinuclear manganese carbonyl hydrides H(3)Mn(3)(CO)(n) (n = 12, 11, 10, 9) have been investigated by density functional theory (DFT). Optimization of H(3)Mn(3)(CO)(12) gives the experimentally known structure in which all carbonyl groups are terminal and each edge of a central Mn(3) equilateral triangle is bridged by a single hydrogen atom. This structure establishes the canonical distance 3.11 A for the Mn-Mn single bond satisfying the 18-electron rule. The central triangular (mu-H)(3)Mn(3) unit is retained in the lowest energy structure of H(3)Mn(3)(CO)(11), which may thus be derived from the H(3)Mn(3)(CO)(12) structure by removal of a carbonyl group with concurrent conversion of one of the remaining carbonyl groups into a semibridging carbonyl group to fill the resulting hole. The potential energy surface of H(3)Mn(3)(CO)(10) is relatively complicated with six singlet and five triplet structures. One of the lower energy H(3)Mn(3)(CO)(10) structures has one of the hydrogen atoms bridging the entire Mn(3) triangle and the other two hydrogen atoms bridging Mn-Mn edges. This H(3)Mn(3)(CO)(10) structure achieves the favored 18-electron configuration with a very short MnMn triple bond of 2.36 A. The other low energy H(3)Mn(3)(CO)(10) structure retains the (mu-H)(3)Mn(3) core of H(3)Mn(3)(CO)(12) but has a unique six-electron donor eta(2)-mu(3) carbonyl group bridging the entire Mn(3) triangle similar to the unique carbonyl group in the known compound Cp(3)Nb(3)(CO)(6)(eta(2)-mu(3)-CO). For H(3)Mn(3)(CO)(9) a structure with a central (mu(3)-H)(2)Mn(3) trigonal bipyramid lies >20 kcal/mol below any of the other structures. Triplet structures were found for the unsaturated H(3)Mn(3)(CO)(n) (n = 11, 10, 9) systems but at significantly higher energies than the lowest lying singlet structures.

  8. Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion plus Selected Inversion

    CERN Document Server

    Lin, Lin; Yang, Chao; He, Lixin

    2012-01-01

    We describe how to apply the recently developed pole expansion plus selected inversion (PEpSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating charge density, total energy, Helmholtz free energy and atomic forces without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEpSI is that it has a much lower computational complexity than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEpSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEpSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundr...

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

    Directory of Open Access Journals (Sweden)

    ANDREY A. TOROPOV

    2005-04-01

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

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

    CERN Document Server

    Esfeld, Michael; Oldofredi, Andrea

    2015-01-01

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

  11. 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

  12. Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction.

    Science.gov (United States)

    Yan, Chengfei; Xu, Xianjin; Zou, Xiaoqin

    2016-10-04

    Protein-peptide interactions play an important role in many cellular processes. In silico prediction of protein-peptide complex structure is highly desirable for mechanistic investigation of these processes and for therapeutic design. However, predicting all-atom structures of protein-peptide complexes without any knowledge about the peptide binding site and the bound peptide conformation remains a big challenge. Here, we present a docking-based method for predicting protein-peptide complex structures, referred to as MDockPeP, which starts with the peptide sequence and globally docks the all-atom, flexible peptide onto the protein structure. MDockPeP was tested on the peptiDB benchmarking database using both bound and unbound protein structures. The results show that MDockPeP successfully generated near-native peptide binding modes in 95.0% of the bound docking cases and in 92.2% of the unbound docking cases. The performance is significantly better than other existing docking methods. MDockPeP is computationally efficient and suitable for large-scale applications.

  13. Atomic Structure and Doping Response of Grain Boundary in Transition Metal Ni

    Institute of Scientific and Technical Information of China (English)

    王崇愚; 于涛

    1994-01-01

    Based on the coincidence site lattice model and by use of the molecular dynamics method, the relaxation calculations on the atomic structures of the grain boundaries of various generating functions (∑3,∑5,…, ∑19,…,∑33) in the transition metal Ni are performed. The features of atomic structures corresponding to the grain boundaries and the effects of the pre-parameter on the interface structures are given. To study the doping response relating to the properties of materials, the 23 tilt grain boundary is selected. Based on the interstice and vacancy mechanisms, the interface responses doping boron, nitrogen and phosphorus for the grain boundary are investigated. According to the criterion of the energy in molecular dynamics simulation, the most probable positions of doping impurities and effect of doping impurities on the interface structure are given, and the dependence of the fine structure on doping type and the order of the impurity amount are obtained. The analysis of the local energy for the

  14. Fine- and hyperfine structure investigations of even configuration system of atomic terbium

    Science.gov (United States)

    Stefanska, D.; Elantkowska, M.; Ruczkowski, J.; Furmann, B.

    2017-03-01

    In this work a parametric study of the fine structure (fs) and the hyperfine structure (hfs) for the even-parity configurations of atomic terbium (Tb I) is presented, based in considerable part on the new experimental results. Measurements on 134 spectral lines were performed by laser induced fluorescence (LIF) in a hollow cathode discharge lamp; on this basis, the hyperfine structure constants A and B were determined for 52 even-parity levels belonging to the configurations 4f85d6s2, 4f85d26s or 4f96s6p; in all the cases those levels were involved in the transitions investigated as the lower levels. For 40 levels the hfs was examined for the first time, and for the remaining 12 levels the new measurements supplement our earlier results. As a by-product, also preliminary values of the hfs constants for 84 odd-parity levels were determined (the investigations of the odd-parity levels system in the terbium atom are still in progress). This huge amount of new experimental data, supplemented by our earlier published results, were considered for the fine and hyperfine structure analysis. A multi-configuration fit of 7 configurations was performed, taking into account second-order of perturbation theory, including the effects of closed shell-open shell excitations. Predicted values of the level energies, as well as of magnetic dipole and electric quadrupole hyperfine structure constants A and B, are quoted in cases when no experimental values are available. By combining our experimental data with our own semi-empirical procedure it was possible to identify correctly the lower and upper level of the line 544.1440 nm measured by Childs with the use of the atomic-beam laser-rf double-resonance technique (Childs, J Opt Soc Am B 9;1992:191-6).

  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.

  16. 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

    2016-06-03

    Extended defects are of considerable importance in determining the electronic properties of semiconductors, especially in photovoltaics (PVs), due to their effects on electron-hole recombination. We employ model systems to study the effects of dislocations in CdTe by constructing grain boundaries using wafer bonding. Atomic-resolution scanning transmission electron microscopy (STEM) of a [1-10]/(110) 4.8° tilt grain boundary reveals that the interface is composed of three distinct types of Lomer dislocations. Geometrical phase analysis is used to map strain fields, while STEM and density functional theory (DFT) modeling determine the atomic structure at the interface. The electronic structure of the dislocation cores calculated using DFT shows significant mid-gap states and different charge-channeling tendencies. Cl-doping is shown to reduce the midgap states, while maintaining the charge separation effects. This report offers novel avenues for exploring grain boundary effects in CdTe-based solar cells by fabricating controlled bicrystal interfaces and systematic atomic-scale analysis.

  17. Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle.

    Science.gov (United States)

    Sener, Melih K; Olsen, John D; Hunter, C Neil; Schulten, Klaus

    2007-10-02

    The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.

  18. 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.

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

    Science.gov (United States)

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

    2014-07-01

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

  20. 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.

  1. Reduction of graphene oxide to graphene, A study of changes in the atomic structure

    Science.gov (United States)

    Mittal, A.; Wagner, A.; Mattevi, C.; Chov, A.; Liao, K.; Macosko, C.; Chhowalla, M.; Mkhoyan, K. A.

    2012-02-01

    An economic method for large scale production of graphene is based on exfoliation of graphite into 1-atom thick sheets by oxidation, creating graphene oxide (GO) and subsequent reduction of GO into graphene. Reduced GO sheets approach the highly desired properties of graphene, such as electrical conductivity and mechanical strength, to various degrees, but not completely. To understand why, we must understand the nanostructure of the sheets. Different methods of reduction result in products that are similar to graphene, but these products retain some oxidized areas or contain regions with sp^3 bonded carbon. The concentration and distribution of these defects on the reduced GO sheet affect the properties of the 2D material. Here, we have characterized the atomic structure of GO and reduced GO via high resolution transmission electron microscopy, electron diffraction, and electron energy loss spectroscopy. Spectroscopic data taken during thermal reduction of GO shows changes in the fine structure of carbon K-edge as the carbon changes from an oxidized form to elemental amorphous carbon to graphite like form, clearly delineating the process of reduction of GO to graphene. Products of several other reduction methods are also characterized revealing information on electronic environment surrounding carbon atoms, distribution of crystalline areas, and oxygen removal from GO.

  2. A simple atomic-level hydrophobicity scale reveals protein interfacial structure.

    Science.gov (United States)

    Kapcha, Lauren H; Rossky, Peter J

    2014-01-23

    Many amino acid residue hydrophobicity scales have been created in an effort to better understand and rapidly characterize water-protein interactions based only on protein structure and sequence. There is surprisingly low consistency in the ranking of residue hydrophobicity between scales, and their ability to provide insightful characterization varies substantially across subject proteins. All current scales characterize hydrophobicity based on entire amino acid residue units. We introduce a simple binary but atomic-level hydrophobicity scale that allows for the classification of polar and non-polar moieties within single residues, including backbone atoms. This simple scale is first shown to capture the anticipated hydrophobic character for those whole residues that align in classification among most scales. Examination of a set of protein binding interfaces establishes good agreement between residue-based and atomic-level descriptions of hydrophobicity for five residues, while the remaining residues produce discrepancies. We then show that the atomistic scale properly classifies the hydrophobicity of functionally important regions where residue-based scales fail. To illustrate the utility of the new approach, we show that the atomic-level scale rationalizes the hydration of two hydrophobic pockets and the presence of a void in a third pocket within a single protein and that it appropriately classifies all of the functionally important hydrophilic sites within two otherwise hydrophobic pores. We suggest that an atomic level of detail is, in general, necessary for the reliable depiction of hydrophobicity for all protein surfaces. The present formulation can be implemented simply in a manner no more complex than current residue-based approaches.

  3. Correlation of atomic structure and photoluminescence of the same quantum dot: pinpointing surface and internal defects that inhibit photoluminescence.

    Science.gov (United States)

    Orfield, Noah J; McBride, James R; Keene, Joseph D; Davis, Lloyd M; Rosenthal, Sandra J

    2015-01-27

    In a size regime where every atom counts, rational design and synthesis of optimal nanostructures demands direct interrogation of the effects of structural divergence of individuals on the ensemble-averaged property. To this end, we have explored the structure-function relationship of single quantum dots (QDs) via precise observation of the impact of atomic arrangement on QD fluorescence. Utilizing wide-field fluorescence microscopy and atomic number contrast scanning transmission electron microscopy (Z-STEM), we have achieved correlation of photoluminescence (PL) data and atomic-level structural information from individual colloidal QDs. This investigation of CdSe/CdS core/shell QDs has enabled exploration of the fine structural factors necessary to control QD PL. Additionally, we have identified specific morphological and structural anomalies, in the form of internal and surface defects, that consistently vitiate QD PL.

  4. Topological Structures and Membrane Nanostructures of Erythrocytes after Splenectomy in Hereditary Spherocytosis Patients via Atomic Force Microscopy

    OpenAIRE

    Li, Ying; Lu, Liyuan; Li, Juan

    2016-01-01

    Hereditary spherocytosis is an inherited red blood cell membrane disorder resulting from mutations of genes encoding erythrocyte membrane and cytoskeletal proteins. Few equipments can observe the structural characteristics of hereditary spherocytosis directly expect for atomic force microscopy In our study, we proved atomic force microscopy is a powerful and sensitive instrument to describe the characteristics of hereditary spherocytosis. Erythrocytes from hereditary spherocytosis patients we...

  5. 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...... terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive...

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

    DEFF Research Database (Denmark)

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

    1998-01-01

    We have simulated the mechanical deformation of atomic-scale metallic contacts under tensile strain using molecular dynamics and effective medium theory potentials. The evolution of the structure of the contacts and the underlying deformation mechanisms are described along with the calculated...... electronic conductance. Various defects such as intersecting stacking faults, local disorder, and vacancies are created during the deformation. Disordered regions act as weak spots that reduce the strength of the contacts. The disorder tends to anneal out again during the subsequent atomic rearrangements......, but vacancies can be permanently present. The transition states and energies for slip mechanisms have been determined using the nudged elastic band method, and we find a size-dependent crossover from a dislocation-mediated slip to a homogeneous slip when the contact diameter becomes less than a few nm. We show...

  7. 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.

  8. 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.

  9. 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

  10. Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

    Science.gov (United States)

    Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

    2016-12-13

    Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

  11. Quantum Yield Heterogeneity among Single Nonblinking Quantum Dots Revealed by Atomic Structure-Quantum Optics Correlation.

    Science.gov (United States)

    Orfield, Noah J; McBride, James R; Wang, Feng; Buck, Matthew R; Keene, Joseph D; Reid, Kemar R; Htoon, Han; Hollingsworth, Jennifer A; Rosenthal, Sandra J

    2016-02-23

    Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. Herein, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking "giant" CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging, rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive "dark" fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be "dark". Therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.

  12. 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.

  13. 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.

  14. 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)

  15. 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.

  16. 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....

  17. Atom type preferences, structural diversity, and property profiles of known drugs, leads, and nondrugs: a comparative assessment.

    Science.gov (United States)

    Viswanadhan, Vellarkad N; Rajesh, Hariharan; Balaji, Vitukudi N

    2011-05-09

    A new characterization of known drug, lead, and representative nondrug databases was performed taking into account several properties at the atomic and molecular levels. This characterization included atom type preferences, intrinsic structural diversity (Atom Type Diversity, ATD), and other well-known physicochemical properties, as an approach for rapid assessment of druglikeness for small molecule libraries. To characterize ATD, an elaborate united atom classification, UALOGP (United Atom Log P), with 148 atom types, was developed along with associated atomic physicochemical parameters. This classification also enabled an analysis of atom type and physicochemical property distributions (for calculated log P, molar refractivity, molecular weight, total atom count, and ATD) of drug, lead, and nondrug databases, a reassessment of the Ro5 (Rule of Five) and GVW (Ghose−Viswanadhan−Wendoloski) criteria, and development of new criteria and ranges more accurately reflecting the chemical space occupied by small molecule drugs. A relative druglikeness parameter was defined for atom types in drugs, identifying the most preferred types. The present work demonstrates that drug molecules are constitutionally more diverse relative to nondrugs, while being less diverse than leads.

  18. GENERAL REGULARITIES OF FORMATION OF CRYSTAL STRUCTURES OF ELEMENTS DEPENDING ON ELECTRON STRUCTURE OF ATOMS (OBSHCHILE ZAKONOMERNOSTI OBRAZOVANIYA KRISTALLICHESKIKH STRUKTUR ELEMENTOV V ZAVISIMOSTI OT ELEKTRONNOGO STROENIYA ATOMOV),

    Science.gov (United States)

    A table is given showing the dependence of crystalline structures of elements on the number of electrons in the incompleted electronic subshells of...its atoms. The conclusion is drawn that the types of crystalline structures of the elements depend on the configuration of the outer electronic...subshells acquired by the atoms prior to crystallization. Crystalline structures of elements not governed by the 8 - N rule are determined by one or both

  19. 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.

  20. Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

    Science.gov (United States)

    Dostál, Jiří; Pecina, Adam; Hrušková-Heidingsfeldová, Olga; Marečková, Lucie; Pichová, Iva; Řezáčová, Pavlina; Lepšík, Martin; Brynda, Jiří

    2015-12-01

    The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized.

  1. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

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

    Energy Technology Data Exchange (ETDEWEB)

    Devaud, G. (Department of Physics, University of Colorado, Boulder, Colorado 80309 (United States)); Furcinitti, P.S. (Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309 (United States)); Fleming, J.C.; Lyon, M.K.; Douglas, K. (Department of Physics, University of Colorado, Boulder, Colorado 80309 (United States))

    1992-09-01

    We have examined the structure of S-layers isolated from {ital Sulfolobus} {ital acidocaldarius} using atomic force microscopy (AFM) and transmission electron microscopy (TEM). From the AFM images, we were able to directly observe individual dimers of the crystal, defects in the crystal structure, and twin boundaries. We have identified two types of boundaries, one defined by a mirror plane and the other by a glide plane. This work shows that twin boundaries are highly structured regions that are directly related to the organization of units within each crystal domain. Projection maps from TEM images have shown that there are significant differences in the final average maps, depending on which side of the sample is adsorbed to the carbon support film. Comparison of AFM images to TEM projection maps has allowed us to relate high magnification views obtained by AFM to the relatively high resolution information obtained by electron microscopy and image processing.

  3. 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.

  4. Local atomic and magnetic structure of dilute magnetic semiconductor (Ba,K)(Zn,Mn)$_2$As$_2$

    OpenAIRE

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

    2016-01-01

    We have studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba,K)(Zn,Mn)$_2$As$_2$ 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-def...

  5. Interfacial engineering of two-dimensional nano-structured materials by atomic layer deposition

    Science.gov (United States)

    Zhuiykov, Serge; Kawaguchi, Toshikazu; Hai, Zhenyin; Karbalaei Akbari, Mohammad; Heynderickx, Philippe M.

    2017-01-01

    Atomic Layer Deposition (ALD) is an enabling technology which provides coating and material features with significant advantages compared to other existing techniques for depositing precise nanometer-thin two-dimensional (2D) nanostructures. It is a cyclic process which relies on sequential self-terminating reactions between gas phase precursor molecules and a solid surface. ALD is especially advantageous when the film quality or thickness is critical, offering ultra-high aspect ratios. ALD provides digital thickness control to the atomic level by depositing film one atomic layer at a time, as well as pinhole-free films even over a very large and complex areas. Digital control extends to sandwiches, hetero-structures, nano-laminates, metal oxides, graded index layers and doping, and it is perfect for conformal coating and challenging 2D electrodes for various functional devices. The technique's capabilities are presented on the example of ALD-developed ultra-thin 2D tungsten oxide (WO3) over the large area of standard 4" Si substrates. The discussed advantages of ALD enable and endorse the employment of this technique for the development of hetero-nanostructure 2D semiconductors with unique properties.

  6. 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.

  7. Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures.

    Science.gov (United States)

    Huang, Sheng-You; Zou, Xiaoqin

    2011-09-01

    In this study, we have developed a statistical mechanics-based iterative method to extract statistical atomic interaction potentials from known, nonredundant protein structures. Our method circumvents the long-standing reference state problem in deriving traditional knowledge-based scoring functions, by using rapid iterations through a physical, global convergence function. The rapid convergence of this physics-based method, unlike other parameter optimization methods, warrants the feasibility of deriving distance-dependent, all-atom statistical potentials to keep the scoring accuracy. The derived potentials, referred to as ITScore/Pro, have been validated using three diverse benchmarks: the high-resolution decoy set, the AMBER benchmark decoy set, and the CASP8 decoy set. Significant improvement in performance has been achieved. Finally, comparisons between the potentials of our model and potentials of a knowledge-based scoring function with a randomized reference state have revealed the reason for the better performance of our scoring function, which could provide useful insight into the development of other physical scoring functions. The potentials developed in this study are generally applicable for structural selection in protein structure prediction.

  8. Atomic structures suggest determinants of transmission barriers in mammalian prion disease.

    Science.gov (United States)

    Apostol, Marcin I; Wiltzius, Jed J W; Sawaya, Michael R; Cascio, Duilio; Eisenberg, David

    2011-04-05

    Prion represents a unique class of pathogens devoid of nucleic acid. The deadly diseases transmitted by it between members of one species and, in certain instances, to members of other species present a public health concern. Transmissibility and the barriers to transmission between species have been suggested to arise from the degree to which a pathological protein conformation from an individual of one species can seed a pathological conformation in another species. However, this hypothesis has never been illustrated at an atomic level. Here we present three X-ray atomic structures of the same segment from human, mouse, and hamster PrP, which is critical for forming amyloid and confers species specificity in PrP seeding experiments. The structures reveal that different sequences encode different steric zippers and suggest that the degree of dissimilarity of these zipper structures gives rise to transmission barriers in prion disease, such as those that protect humans from acquiring bovine spongiform encephalopathy (BSE) and chronic wasting disease (CWD).

  9. 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.

  10. Structure and analysis of atomic vibrations in clusters of Cu n ( n ≤ 20)

    Science.gov (United States)

    Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.

    2013-02-01

    The binding energy, equilibrium geometry, and vibration frequencies of free clusters Cu n (2 ≤ n ≤ 20) are calculated using the potentials of interatomic interactions found using the tight-binding approximation. The nonmonotonic dependence of the clusters' minimum vibration frequency on their sizes and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 is demonstrated. It is noted that this result agrees with the theoretical and experimental data on stable structures of small and medium metallic clusters.

  11. 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.

  12. 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.

  13. Growth and atomic structure of tellurium thin films grown on Bi2Te3

    Science.gov (United States)

    Okuyama, Yuma; Sugiyama, Yuya; Ideta, Shin-ichiro; Tanaka, Kiyohisa; Hirahara, Toru

    2017-03-01

    We have grown tellurium (Te) thin films on Bi2Te3 and investigated the atomic structure. From low-energy electron diffraction (LEED) measurements, we found that the Te films are [10 1 bar0]-oriented with six domains. A detailed analysis of the reflection high-energy electron diffraction (RHEED) pattern revealed that the films are strained with the in-plane lattice constant compressed by ∼1.5% compared to the bulk value due to the epitaxy between Te and Bi2Te3. These films will be interesting systems to investigate the predicted topological phases that occur in strained Te.

  14. 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

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

  15. 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.

  16. The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.

    Science.gov (United States)

    Snyder, David A; Grullon, Jennifer; Huang, Yuanpeng J; Tejero, Roberto; Montelione, Gaetano T

    2014-02-01

    Maximizing the scientific impact of NMR-based structure determination requires robust and statistically sound methods for assessing the precision of NMR-derived structures. In particular, a method to define a core atom set for calculating superimpositions and validating structure predictions is critical to the use of NMR-derived structures as targets in the CASP competition. FindCore (Snyder and Montelione, Proteins 2005;59:673-686) is a superimposition independent method for identifying a core atom set and partitioning that set into domains. However, as FindCore optimizes superimposition by sensitively excluding not-well-defined atoms, the FindCore core may not comprise all atoms suitable for use in certain applications of NMR structures, including the CASP assessment process. Adapting the FindCore approach to assess predicted models against experimental NMR structures in CASP10 required modification of the FindCore method. This paper describes conventions and a standard protocol to calculate an "Expanded FindCore" atom set suitable for validation and application in biological and biophysical contexts. A key application of the Expanded FindCore method is to identify a core set of atoms in the experimental NMR structure for which it makes sense to validate predicted protein structure models. We demonstrate the application of this Expanded FindCore method in characterizing well-defined regions of 18 NMR-derived CASP10 target structures. The Expanded FindCore protocol defines "expanded core atom sets" that match an expert's intuition of which parts of the structure are sufficiently well defined to use in assessing CASP model predictions. We also illustrate the impact of this analysis on the CASP GDT assessment scores.

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

    Science.gov (United States)

    Valentin, Jan B; Andreetta, Christian; Boomsma, Wouter; Bottaro, Sandro; Ferkinghoff-Borg, Jesper; Frellsen, Jes; Mardia, Kanti V; Tian, Pengfei; Hamelryck, Thomas

    2014-02-01

    We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive the parameters of the nonlocal model from the native structure without loss of generality. The local and nonlocal models are combined using the reference ratio method, which is a well-justified probabilistic construction. For evaluation, we use the resulting joint models to predict the structure of four proteins. The results indicate that the proposed method and the probabilistic models show considerable promise for probabilistic protein structure prediction and related applications.

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

    Science.gov (United States)

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

    2016-01-01

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

  19. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    Science.gov (United States)

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  20. Structure and dynamics of interfaces in organic and inorganic materials using atomic level simulation

    Science.gov (United States)

    Lee, Donghwa

    Interfaces in materials play a key role for industrial applications. The structures and dynamics at various interfaces including ferroelectric domain walls, gas-organic interface, organic-semiconductor interface and metal-gas interface are investigated with different atomic levels of simulation approaches. Ferroelectricity: Due to their unique ferroelectric and nonlinear optical properties, trigonal ferroelectrics such as LiNbO3 and LiTaO 3, are of wide interest for their potential applications in optoelectronics and nonlinear optics. The properties of these materials are heavily influenced by the shape of ferroelectric domains and domain walls. Therefore, investigation of the local structure and energetics of the ferroelectric domain walls and their interaction with defects on atomic scales, which is not clearly understood, is extremely important. The structure and energetics of ferroelectric domain walls in LiNbO 3 are examined using density functional theory (DFT) and molecular dynamics (MD) methods. The energetically favorable structures of 180° domain walls and the activation energy for domain wall motion are determined by atomic level simulations. The variation of polarization due to the presence of domain walls is also discussed. Defects can be pinned by domain walls. Various defects-domain walls interactions and the effects on domain wall motion are described using atomic level simulation methods. Although the structure of LiTaO3 is very similar with LiNbO3, it has been said experimentally that the shapes of domain walls are different with the presence of particular defects. Using both DFT and a newly developed interatomic potential for LiTaO 3, the differences in domain wall structure are understood in terms of the difference in energetics of domain walls between two materials. Polymerization: Surface polymerization by ion-assisted deposition (SPIAD) enables the control of thin film chemistry and morphology on the nanoscale during growth of conductive

  1. 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.

  2. 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

    2015-08-07

    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 methods

  3. 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

  4. 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

    2016-07-12

    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.

  5. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, H. L.; Han, Y. F., E-mail: yfhan@sjtu.edu.cn, E-mail: bdsun@sjtu.edu.cn; Zhou, W.; Dai, Y. B. [Shanghai Key Laboratory of Advanced High-temperature Materials and Precision Forming, Shanghai Jiao Tong University, No. 800, Dongchuan Road, Shanghai 200240 (China); Wang, J.; Sun, B. D., E-mail: yfhan@sjtu.edu.cn, E-mail: bdsun@sjtu.edu.cn [Shanghai Key Laboratory of Advanced High-temperature Materials and Precision Forming, Shanghai Jiao Tong University, No. 800, Dongchuan Road, Shanghai 200240 (China); State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, No. 800, Dongchuan Road, Shanghai 200240 (China)

    2015-01-26

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

  7. 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

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lobato, I; Rojas, J [Instituto Peruano de EnergIa Nuclear, Avenida Canada 1470, Lima 41 (Peru); Landauro, C V; Torres, J [Facultad de Ciencias Fisicas, Universidad Nacional Mayor de San Marcos, P.O. box 14-0149, Lima 14 (Peru)], E-mail: jrojast@unmsm.edu.pe

    2009-02-04

    The structural evolution and dynamics of silver nanodrops Ag{sub 2869} (4.4 nm in diameter) under rapid cooling conditions have been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modelled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique are used to reveal the structural transition in the process of solidification. It is shown that Ag nanoparticles evolve into different nanostructures under different cooling processes. At a cooling rate of 1.5625 x 10{sup 13} K s{sup -1} the nanoparticles preserve an amorphous-like structure containing a large amount of 1551 and 1541 pairs which correspond to icosahedral symmetry. For a lower cooling rate (1.5625 x 10{sup 12} K s{sup -1}), the nanoparticles transform into a crystal-like structure consisting mainly of 1421 and 1422 pairs which correspond to the face centred cubic and hexagonal close packed structures, respectively. The variations of the electronic density of states for the differently cooled nanoparticles are small, but in correspondence with the structural changes.

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

    Science.gov (United States)

    Lobato, I.; Rojas, J.; Landauro, C. V.; Torres, J.

    2009-02-01

    The structural evolution and dynamics of silver nanodrops Ag2869 (4.4 nm in diameter) under rapid cooling conditions have been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modelled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique are used to reveal the structural transition in the process of solidification. It is shown that Ag nanoparticles evolve into different nanostructures under different cooling processes. At a cooling rate of 1.5625 × 1013 K s-1 the nanoparticles preserve an amorphous-like structure containing a large amount of 1551 and 1541 pairs which correspond to icosahedral symmetry. For a lower cooling rate (1.5625 × 1012 K s-1), the nanoparticles transform into a crystal-like structure consisting mainly of 1421 and 1422 pairs which correspond to the face centred cubic and hexagonal close packed structures, respectively. The variations of the electronic density of states for the differently cooled nanoparticles are small, but in correspondence with the structural changes.

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

    DEFF Research Database (Denmark)

    Levermann, A.H.; Howes, P.B.; Edwards, K.A.

    1996-01-01

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

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

    Science.gov (United States)

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

    2015-03-01

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

  13. Role of atomic multiplets in the electronic structure of rare-earth semiconductors and semimetals.

    Science.gov (United States)

    Pourovskii, Leonid V; Delaney, Kris T; Van de Walle, Chris G; Spaldin, Nicola A; Georges, Antoine

    2009-03-06

    We present a study of the effects of strong correlations in rare-earth pnictides, in which localized 4f states simultaneously retain atomiclike character and strongly influence the free-electron-like valence electron states. Using erbium arsenide as our example, we use a modern implementation of dynamical mean-field theory to obtain the atomic multiplet structure of the Er3+ 4f shell, as well as its unusually strong coupling to the electronic Fermi surfaces; these types of behavior are not correctly described within conventional electronic-structure methods. We are then able to explain the long-standing theoretical question of the quasisaturation of magnetization in an applied magnetic field, and to obtain the first quantitative agreement with experimental Shubnikov-de Haas frequencies of the Fermi-surface sheets.

  14. 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.

  15. Trends of structural and electrical properties in atomic layer deposited HfO{sub 2} films

    Energy Technology Data Exchange (ETDEWEB)

    Scarel, G.; Spiga, S.; Wiemer, C.; Tallarida, G.; Ferrari, S.; Fanciulli, M

    2004-06-15

    Understanding and optimizing electrical and structural properties of high-{kappa} oxides are key steps in view of their application as SiO{sub 2} substitutes in CMOS devices. In this work, we address the effects of growth temperature (T{sub g},) post-deposition annealing and substrate preparation on the structural, compositional, and electrical properties of thin films ({approx}13 nm thick), deposited on p-type Si(1 0 0)/SiO{sub 2} (chemical oxide) by atomic layer deposition (ALD). In particular, we investigate the effects of: (1) different T{sub g} (150, 250 and 350 deg. C); (2) rapid thermal annealing at 950 deg. C in N{sub 2} for 60 s; and (3) substrate in situ heat treatment before growth and longer pulses at the beginning of the deposition.

  16. A standard format for reporting atomic positions in measured or calculated surface structures: The CIF file

    Science.gov (United States)

    Marks, Laurence D.

    2010-06-01

    In his editorial in this issue, the editor-in-chief emphasizes the editorial policy that any paper which involves a crystallographic structure (whether experimentally measured or theoretically calculated) must also include a complete listing of all the atomic positions within the crystal structure, either as supporting information or directly within the paper itself. He also strongly recommends that the complete crystallographic data set be included as supporting information. At the request of the editor-in-chief, I outline here the reasons why this is scientifically desirable. Furthermore, I propose here that the Surface Science community adopt the same standard format for reporting these as is already widely used in bulk crystallography publications, namely the inclusion of a Crystallographic Information Format file (or CIF file) as supporting information. Finally, I describe the details of this specific file format, with illustrative examples.

  17. Topography and Atomic Structure Investigations Of (100 Cleavage Surface of In4Se3 Layered Crystals

    Directory of Open Access Journals (Sweden)

    P.V. Galiy

    2014-06-01

    Full Text Available The atomic microstructure and crystallography of (100 surfaces of In4Se3 layered crystals obtained by cleavage in situ were studied by the methods of scanning tunneling and atomic force microscopies (STM, AFM and low energy electron diffraction (LEED for reflection. The obtained results indicate the existence of periodic corrugated structures on the cleavage surface. It is shown that (100 In4Se3 cleavage surface is structurally stable and doesn't undergo reconstruction in a wide temperature range of 77-295 K. The anisotropy of thermal expansion along the main crystallography directions in the (100 In4Se3 cleavage plane has been shown. The evaluation of the two-dimensional lattice constant in the cleavage (100 surface plane of orthorhombic In4Se3 layered crystal was done. The calculated values of the lattice constants in consequence of LEED study, such as b  11,475 Å and c  3,734 Å, coincide well with those obtained by the AFM and STM (b  13-14 Å and c  4 Å, and correlate, within the errors limits, with the corresponding values obtained by X-ray diffraction (b  12,308(1 Å and c  4,0810(5 Å. Besides, the obtained results of cleavage surface structure studies show the correctness of filtering application concerning topography images and indicate the adequacy of the model used for calculations of the cleavage (100 surfaces lattice constants of In4Se3 in accordance with the LEED results. The influence of the LEED experimental module structure on the results has been considered.

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

    Science.gov (United States)

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

    2014-04-30

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

  19. 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...

  20. Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.

    Science.gov (United States)

    Organtini, Lindsey J; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E; Makhov, Alexander M; Conway, James F; Parrish, Colin R; Hafenstein, Susan

    2016-11-01

    Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM.

  1. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    Science.gov (United States)

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  2. 2D Tl-Pb compounds on Ge(1 1 1) surface: atomic arrangement and electronic band structure.

    Science.gov (United States)

    Gruznev, D V; Bondarenko, L V; Tupchaya, A Y; Eremeev, S V; Mihalyuk, A N; Chou, J P; Wei, C M; Zotov, A V; Saranin, A A

    2017-01-25

    Structural transformations and evolution of the electron band structure in the (Tl, Pb)/Ge(1 1 1) system have been studied using low-energy electron diffraction, scanning tunneling microscopy, angle-resolved photoelectron spectroscopy and density functional theory calculations. The two 2D Tl-Pb compounds on Ge(1 1 1), [Formula: see text]-(Tl, Pb) and [Formula: see text]-(Tl, Pb), have been found and their composition, atomic arrangement and electron properties has been characterized. The (Tl, Pb)/Ge(1 1 1)[Formula: see text] compound is almost identical to the alike (Tl, Pb)/Si(1 1 1)[Formula: see text] system from the viewpoint of its atomic structure and electronic properties. They contain 1.0 ML of Tl atoms arranged into a honeycomb network of chained trimers and 1/3 ML of Pb atoms occupying the centers of the honeycomb units. The (Tl, Pb)/Ge(1 1 1)[Formula: see text] compound contains six Tl atoms and seven Pb atoms per [Formula: see text] unit cell (i.e.  ∼0.67 ML Tl and  ∼0.78 ML Pb). Its atomic structure can be visualized as consisting of Pb hexagons surrounded by Tl trimers. The (Tl, Pb)/Ge(1 1 1)[Formula: see text] and (Tl, Pb)/Ge(1 1 1)[Formula: see text] compounds are metallic and their band structures contain spin-split surface-state bands. By analogy with the (Tl, Pb)/Si(1 1 1)[Formula: see text], these (Tl, Pb)/Ge(1 1 1) compounds are believed to be promising objects for prospective studies of superconductivity in one-atom-layer systems.

  3. 2D Tl-Pb compounds on Ge(1 1 1) surface: atomic arrangement and electronic band structure

    Science.gov (United States)

    Gruznev, D. V.; Bondarenko, L. V.; Tupchaya, A. Y.; Eremeev, S. V.; Mihalyuk, A. N.; Chou, J. P.; Wei, C. M.; Zotov, A. V.; Saranin, A. A.

    2017-01-01

    Structural transformations and evolution of the electron band structure in the (Tl, Pb)/Ge(1 1 1) system have been studied using low-energy electron diffraction, scanning tunneling microscopy, angle-resolved photoelectron spectroscopy and density functional theory calculations. The two 2D Tl-Pb compounds on Ge(1 1 1), \\sqrt{3}× \\sqrt{3} -(Tl, Pb) and 3× 3 -(Tl, Pb), have been found and their composition, atomic arrangement and electron properties has been characterized. The (Tl, Pb)/Ge(1 1 1)\\sqrt{3}× \\sqrt{3} compound is almost identical to the alike (Tl, Pb)/Si(1 1 1)\\sqrt{3}× \\sqrt{3} system from the viewpoint of its atomic structure and electronic properties. They contain 1.0 ML of Tl atoms arranged into a honeycomb network of chained trimers and 1/3 ML of Pb atoms occupying the centers of the honeycomb units. The (Tl, Pb)/Ge(1 1 1)3× 3 compound contains six Tl atoms and seven Pb atoms per 3× 3 unit cell (i.e.  ˜0.67 ML Tl and  ˜0.78 ML Pb). Its atomic structure can be visualized as consisting of Pb hexagons surrounded by Tl trimers. The (Tl, Pb)/Ge(1 1 1)\\sqrt{3}× \\sqrt{3} and (Tl, Pb)/Ge(1 1 1)3× 3 compounds are metallic and their band structures contain spin-split surface-state bands. By analogy with the (Tl, Pb)/Si(1 1 1)\\sqrt{3}× \\sqrt{3} , these (Tl, Pb)/Ge(1 1 1) compounds are believed to be promising objects for prospective studies of superconductivity in one-atom-layer systems.

  4. The first principle study on the atomic and electronic structure of GaN(101-bar 0) surface

    Energy Technology Data Exchange (ETDEWEB)

    Li Yonghua [Structure Research Laboratory, University of Science and Technology of China, Academia Sinica, Hefei 230026 (China); NSRL, University of Science and Technology of China, Hefei 230029 (China); Xu Pengshou [Structure Research Laboratory, University of Science and Technology of China, Academia Sinica, Hefei 230026 (China) and NSRL, University of Science and Technology of China, Hefei 230029 (China)]. E-mail: psxu@ustc.edu.cn; Pan Haibin [NSRL, University of Science and Technology of China, Hefei 230029 (China); Xu Faqiang [NSRL, University of Science and Technology of China, Hefei 230029 (China)

    2005-06-15

    In this paper, we have calculated the atomic and electronic structure of GaN(101-bar 0) surface using an augmented plane wave plus local orbital (APW+lo) method. It is found that the surface is characterized by a top-layer bond-length-contracting rotation relaxation. The surface Ga atom moves towards the substrate and tends to form a planar sp{sup 2}-like bonding. While the surface N atom tends to a p{sup 3}-like bonding. Surface relaxation induces the transformation from metallic to semiconducting characterization.

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

    Energy Technology Data Exchange (ETDEWEB)

    Babilas, Rafał, E-mail: rafal.babilas@polsl.pl

    2015-09-15

    The atomic structure of Fe{sub 70}Nb{sub 10}B{sub 20} alloy in “as-cast” state and after annealing was investigated using high-energy X-ray diffraction (XRD), Mössbauer spectroscopy (MS) and high resolution transmission electron microscopy (HRTEM). The HRTEM observations allowed to indicate some medium-range order (MRO) regions about 2 nm in size and formation of some kinds of short-range order (SRO) structures represented by atomic clusters with diameter ca. 0.5 nm. The Reverse Monte Carlo (RMC) method basing on the results of XRD measurements was used in modeling the atomic structure of Fe-based alloy. The structural model was described by peak values of partial pair correlation functions and coordination numbers determined by Mössbauer spectroscopy investigations. The three-dimensional configuration box of atoms was obtained from the RMC simulation and the representative Fe-centered clusters were taken from the calculated structure. According to the Gonser et al. approach, the measured spectra of alloy studied were decomposed into 5 subspectra representing average Fe–Fe coordination numbers. Basing on the results of disaccommodation of magnetic permeability, which is sensitive to the short order of the random packing of atoms, it was stated that an occurrence of free volume is not detected after nanocrystallization process. - Highlights: • Atomic cluster model of amorphous structure was proposed for studied glassy alloy. • Short range order (ca. 0.5 nm) regions interpreted as clusters were identified by HREM. • Clusters correspond to coordination numbers (N = 4,6,8,9) calculated by using Gonser approach. • Medium-range order (ca. 2 nm) could be referred to few atomic clusters. • SRO regions are able to grow up as nuclei of crystalline bcc Fe and iron borides. • Crystalline particles have spherical morphology with an average diameter of 20 nm.

  6. Effect of interface atomic structure on the electronic properties of nano-sized metal-oxide interfaces.

    Science.gov (United States)

    Qin, Wei; Hou, Jiechang; Bonnell, Dawn A

    2015-01-14

    We report that the size dependence of electronic properties at nanosized metal-semiconducting oxide interfaces is significantly affected by the interface atomic structure. The properties of interfaces with two orientations are compared over size range of 20-200 nm. The difference in interface atomic structure leads to electronic structure differences that alter electron transfer paths. Specifically, interfaces with a higher concentration of undercoordinated Ti result in enhanced tunneling due to the presence of defect states or locally reduced tunnel barrier widths. This effect is superimposed on the mechanisms of size dependent properties at such small scales.

  7. 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.

  8. The atomic structure of ternary amorphous TixSi1-xO2 hybrid oxides.

    Science.gov (United States)

    Landmann, M; Köhler, T; Rauls, E; Frauenheim, T; Schmidt, W G

    2014-06-25

    Atomic length-scale order characteristics of binary and ternary amorphous oxides are presented within the framework of ab initio theory. A combined numerically efficient density functional based tight-binding molecular dynamics and density functional theory approach is applied to model the amorphous (a) phases of SiO2 and TiO2 as well as the amorphous phase of atomically mixed TixSi1-xO2 hybrid-oxide alloys over the entire composition range. Short and mid-range order in the disordered material phases are characterized by bond length and bond-angle statistics, pair distribution function analysis, coordination number and coordination polyhedra statistics, as well as ring statistics. The present study provides fundamental insights into the order characteristics of the amorphous hybrid-oxide frameworks formed by versatile types of TiOn and SiOm coordination polyhedra. In a-SiO2 the fourfold crystal coordination of Si ions is almost completely preserved and the atomic structure is widely dominated by ring-like mid-range order characteristics. In contrast, the structural disorder of a-TiO2 arises from short-range disorder in the local coordination environment of the Ti ion. The coordination number analysis indicates a large amount of over and under-coordinated Ti ions (coordination defects) in a-TiO2. Aside from the ubiquitous distortions of the crystal-like coordinated polyhedra, even the basic coordination-polyhedra geometry type changes for a significant fraction of TiO6 units (geometry defects). The combined effects of topological and chemical disorder in a-TixSi1-xO2 alloys lead to a continuos increase in both the Si as well as the Ti coordination number with the chemical composition x. The important roles of intermediate fivefold coordination states of Ti and Si cations are highlighted for ternary a-TixSi1-xO2 as well as for binary a-TiO2. The continuous decrease in ring size with increasing Ti content reflects the progressive loss of mid-range order structure

  9. 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.

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

    Science.gov (United States)

    Xu, Haijiao; Su, Weiheng; Cai, Mingjun; Jiang, Junguang; Zeng, Xianlu; Wang, Hongda

    2013-01-01

    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.

  11. 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.

  12. The Asymmetrical Structure of Golgi Apparatus Membranes Revealed by In situ Atomic Force Microscope

    Science.gov (United States)

    Xu, Haijiao; Su, Weiheng; Cai, Mingjun; Jiang, Junguang; Zeng, Xianlu; Wang, Hongda

    2013-01-01

    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. PMID:23613878

  13. Atomic Structure of Pt3Ni Nanoframe Electrocatalysts by in Situ X-ray Absorption Spectroscopy.

    Science.gov (United States)

    Becknell, Nigel; Kang, Yijin; Chen, Chen; Resasco, Joaquin; Kornienko, Nikolay; Guo, Jinghua; Markovic, Nenad M; Somorjai, Gabor A; Stamenkovic, Vojislav R; Yang, Peidong

    2015-12-23

    Understanding the atomic structure of a catalyst is crucial to exposing the source of its performance characteristics. It is highly unlikely that a catalyst remains the same under reaction conditions when compared to as-synthesized. Hence, the ideal experiment to study the catalyst structure should be performed in situ. Here, we use X-ray absorption spectroscopy (XAS) as an in situ technique to study Pt3Ni nanoframe particles which have been proven to be an excellent electrocatalyst for the oxygen reduction reaction (ORR). The surface characteristics of the nanoframes were probed through electrochemical hydrogen underpotential deposition and carbon monoxide electrooxidation, which showed that nanoframe surfaces with different structure exhibit varying levels of binding strength to adsorbate molecules. It is well-known that Pt-skin formation on Pt-Ni catalysts will enhance ORR activity by weakening the binding energy between the surface and adsorbates. Ex situ and in situ XAS results reveal that nanoframes which bind adsorbates more strongly have a rougher Pt surface caused by insufficient segregation of Pt to the surface and consequent Ni dissolution. In contrast, nanoframes which exhibit extremely high ORR activity simultaneously demonstrate more significant segregation of Pt over Ni-rich subsurface layers, allowing better formation of the critical Pt-skin. This work demonstrates that the high ORR activity of the Pt3Ni hollow nanoframes depends on successful formation of the Pt-skin surface structure.

  14. 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.

  15. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

    Science.gov (United States)

    Davis, Ian W; Leaver-Fay, Andrew; Chen, Vincent B; Block, Jeremy N; Kapral, Gary J; Wang, Xueyi; Murray, Laura W; Arendall, W Bryan; Snoeyink, Jack; Richardson, Jane S; Richardson, David C

    2007-07-01

    MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

  16. 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.

  17. 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

  18. Semiempirical studies of atomic structure. Progress report, 1 July 1991--1 October 1993

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, L.J.

    1993-10-01

    Atomic structure/properties of highly ionized many-electron systems are studied using sensitive semiempirical data systematization, experiment, and theory. Measurements are made using fast ion beams, combined with data from laser- and tokamak-produced plasmas, astrophysical sources, and light sources. Results during this 3-y period are discussed under the following headings: Invited review article (decay rates in systems of negative ions to very heavy one-electron ions), fast ion beam lifetime measurements (Pt sequence, neutral carbon, Na sequence), multiplexed decay curve measurements, multiplexed decay curve measurements (lifetimes of alkali-like resonance transitions, spin-forbidden intercombination lines), lifetimes in Ne sequence, lifetimes for H and He sequences, data-based semiempirical formulations, calculations, and accelerator studies.

  19. 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.

  20. sp(4,R)-systematics of atomic nuclei. F-multiplets and nuclear structure

    CERN Document Server

    Drenska, S B; Minkov, N

    2007-01-01

    A systematics of the atomic nuclei in the frame of the nucleon number $A = Z + N$ and the proton-neutron difference $F = Z - N$ is considered. The classification scheme is provided by means of the non-compact algebra $sp(4,R)$. In this scheme the nuclei are ordered into isobaric multiplets, for which $A={fix}$, as well as in F-multiplets, for which $F={fix}$. The dependence of the mass excess $\\Delta$, the first exited states $E_{2^+}$ and the ratio $R_2=E_{4^+}/E_{2^+}$ on the nucleon number $A$ is empirically investigated within the $F$-multiplets. Appropriate filters are used to study the properties of the mass excess. Many structural effects are observed. The mirror symmetry is clearly indicated for the energy levels of the nuclei with the same value of $A$ and opposite $F$-values.

  1. Atomic and electronic structure of silicon nanocrystals embedded in a silica matrix

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Ngoc Bich; Dufour, Christian [Centre de Recherche sur les Ions, les Materiaux et la Photonique, 6 boulevard Marechal Juin, 14050 Caen Cedex (France); Petit, Sebastien [Laboratoire de Cristallographie et Sciences des Materiaux, 6 boulevard Marechal Juin, 14050 Caen Cedex (France)

    2008-11-12

    The atomic structures and the optical and electronic properties of silicon nanocrystals (nc-Si) in a {beta} cristobalite matrix are studied using DFT calculations provided by the AIMPRO code. Five atomic models are considered (two nanocrystal diameters of 5.6 and 11 A with and without interface defects). After total relaxation, the mean Si-Si distances in nc-Si are found to be 6% higher than those in perfect bulk silicon. The optical and electronic properties are influenced by many parameters, among which are the nanograin density and size. The quantum confinement effect is demonstrated by the increase of energy gap when decreasing nanograin size. The energy gap of nc-Si is adjusted by using B3LYP functional calculations; the energy gap of 5.6 A nc-Si is found to be equal to 3.4 eV while that of 11 A nc-Si is equal to 3.1 eV. In the band structure, the levels due to nc-Si appear in the forbidden band of SiO{sub 2}. The electronic density of these levels is presented in 3D. A redshift is observed in the optical absorption spectrum as the nc-Si size increases, and the absorbance of nc-Si/SiO{sub 2} is proportional to the nanograin density. The system is more stable as the distance between nanograins increases. We have also studied two kinds of nc-Si/SiO{sub 2} interface defects (Si-O-Si and Si = O bonds). It is found that the Si-O-Si bridge bond leads to the most stable configuration. The presence of Si = O double bonds reduces the nc-Si energy gap and leads to a redshift in the absorption spectrum. The Si-O-Si bonds produce the inverse effect, i.e. an energy gap increase associated with a blueshift in the absorption spectrum.

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

    NARCIS (Netherlands)

    Gross, L.; Mohn, F.; Moll, N.; Liljeroth, P.|info:eu-repo/dai/nl/314007423; 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

  3. 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).

  4. 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.

  5. Synthesis of two-dimensional Tl(x)Bi(1-x) compounds and Archimedean encoding of their atomic structure.

    Science.gov (United States)

    Gruznev, Dimitry V; Bondarenko, Leonid V; Matetskiy, Andrey V; Mihalyuk, Alexey N; Tupchaya, Alexandra Y; Utas, Oleg A; Eremeev, Sergey V; Hsing, Cheng-Rong; Chou, Jyh-Pin; Wei, Ching-Ming; Zotov, Andrey V; Saranin, Alexander A

    2016-01-19

    Crystalline atomic layers on solid surfaces are composed of a single building block, unit cell, that is copied and stacked together to form the entire two-dimensional crystal structure. However, it appears that this is not an unique possibility. We report here on synthesis and characterization of the one-atomic-layer-thick Tl(x)Bi(1-x) compounds which display quite a different arrangement. It represents a quasi-periodic tiling structures that are built by a set of tiling elements as building blocks. Though the layer is lacking strict periodicity, it shows up as an ideally-packed tiling of basic elements without any skips or halting. The two-dimensional Tl(x)Bi(1-x) compounds were formed by depositing Bi onto the Tl-covered Si(111) surface where Bi atoms substitute appropriate amount of Tl atoms. Atomic structure of each tiling element as well as arrangement of Tl(x)Bi(1-x) compounds were established in a detail. Electronic properties and spin texture of the selected compounds having periodic structures were characterized. The shown example demonstrates possibility for the formation of the exotic low-dimensional materials via unusual growth mechanisms.

  6. Synthesis of two-dimensional TlxBi1−x compounds and Archimedean encoding of their atomic structure

    Science.gov (United States)

    Gruznev, Dimitry V.; Bondarenko, Leonid V.; Matetskiy, Andrey V.; Mihalyuk, Alexey N.; Tupchaya, Alexandra Y.; Utas, Oleg A.; Eremeev, Sergey V.; Hsing, Cheng-Rong; Chou, Jyh-Pin; Wei, Ching-Ming; Zotov, Andrey V.; Saranin, Alexander A.

    2016-01-01

    Crystalline atomic layers on solid surfaces are composed of a single building block, unit cell, that is copied and stacked together to form the entire two-dimensional crystal structure. However, it appears that this is not an unique possibility. We report here on synthesis and characterization of the one-atomic-layer-thick TlxBi1−x compounds which display quite a different arrangement. It represents a quasi-periodic tiling structures that are built by a set of tiling elements as building blocks. Though the layer is lacking strict periodicity, it shows up as an ideally-packed tiling of basic elements without any skips or halting. The two-dimensional TlxBi1−x compounds were formed by depositing Bi onto the Tl-covered Si(111) surface where Bi atoms substitute appropriate amount of Tl atoms. Atomic structure of each tiling element as well as arrangement of TlxBi1−x compounds were established in a detail. Electronic properties and spin texture of the selected compounds having periodic structures were characterized. The shown example demonstrates possibility for the formation of the exotic low-dimensional materials via unusual growth mechanisms. PMID:26781340

  7. Synthesis of two-dimensional TlxBi1-x compounds and Archimedean encoding of their atomic structure

    Science.gov (United States)

    Gruznev, Dimitry V.; Bondarenko, Leonid V.; Matetskiy, Andrey V.; Mihalyuk, Alexey N.; Tupchaya, Alexandra Y.; Utas, Oleg A.; Eremeev, Sergey V.; Hsing, Cheng-Rong; Chou, Jyh-Pin; Wei, Ching-Ming; Zotov, Andrey V.; Saranin, Alexander A.

    2016-01-01

    Crystalline atomic layers on solid surfaces are composed of a single building block, unit cell, that is copied and stacked together to form the entire two-dimensional crystal structure. However, it appears that this is not an unique possibility. We report here on synthesis and characterization of the one-atomic-layer-thick TlxBi1-x compounds which display quite a different arrangement. It represents a quasi-periodic tiling structures that are built by a set of tiling elements as building blocks. Though the layer is lacking strict periodicity, it shows up as an ideally-packed tiling of basic elements without any skips or halting. The two-dimensional TlxBi1-x compounds were formed by depositing Bi onto the Tl-covered Si(111) surface where Bi atoms substitute appropriate amount of Tl atoms. Atomic structure of each tiling element as well as arrangement of TlxBi1-x compounds were established in a detail. Electronic properties and spin texture of the selected compounds having periodic structures were characterized. The shown example demonstrates possibility for the formation of the exotic low-dimensional materials via unusual growth mechanisms.

  8. Impact of Atomic Structure on Absolute Energy Levels of Methylammonium Lead Iodide Perovskite

    Science.gov (United States)

    Choi, Joshua

    2015-03-01

    There has been a staggeringly rapid increase in the photovoltaic performance of methylammonium lead iodide (MAPbI3) perovskite - greater than 19 percent solar cell power conversion efficiency has been reported in less than five years since the first report in 2009. Despite the progress in device performance, structure-property relationships in MAPbI3 are still poorly understood. I will present our recent findings on the impact of changing the Pb-I bond length and Pb-I-Pb bond angle on the electronic structure of MAPbI3. By using the combination of temperature dependent X-ray scattering, ultraviolet photoelectron spectroscopy, absorbance and PL spectroscopy, we show that the energy levels of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) shift in the same direction as MAPbI3 goes through tetragonal-to-cubic structural phase transition wherein the rotational angle of PbI6 octahedra is the order parameter of the transition. Our experimental results are corroborated by density functional theory calculations which show that the lattice expansion and bond angle distortion cause different degree of orbital overlap between the Pb and I atoms and the anti-bonding orbital nature of both HOMO and LUMO results in the same direction of their shift. Moreover, through pair distribution function analysis of X-ray scattering, we discovered that the majority of MAPbI3 in thin film solar cell layer has highly disordered structure with a coherence range of only 1.4 nm. The nanostructuring correlates with a blueshift of the absorption onset and increases the photoluminescence. Our results underscore the importance of understanding the structure-property relationships in order to improve the device performance of metal-organic perovskites.

  9. 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.

  10. Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase.

    Science.gov (United States)

    Nishimasu, Hiroshi; Ishitani, Ryuichiro; Yamashita, Koki; Iwashita, Chikako; Hirata, Akira; Hori, Hiroyuki; Nureki, Osamu

    2009-05-19

    tRNAs from all 3 phylogenetic domains have a 5-methyluridine at position 54 (T54) in the T-loop. The methyl group is transferred from S-adenosylmethionine by TrmA methyltransferase in most Gram-negative bacteria and some archaea and eukaryotes, whereas it is transferred from 5,10-methylenetetrahydrofolate (MTHF) by TrmFO, a folate/FAD-dependent methyltransferase, in most Gram-positive bacteria and some Gram-negative bacteria. However, the catalytic mechanism remains unclear, because the crystal structure of TrmFO has not been solved. Here, we report the crystal structures of Thermus thermophilus TrmFO in its free form, tetrahydrofolate (THF)-bound form, and glutathione-bound form at 2.1-, 1.6-, and 1.05-A resolutions, respectively. TrmFO consists of an FAD-binding domain and an insertion domain, which both share structural similarity with those of GidA, an enzyme involved in the 5-carboxymethylaminomethylation of U34 of some tRNAs. However, the overall structures of TrmFO and GidA are basically different because of their distinct domain orientations, which are consistent with their respective functional specificities. In the THF complex, the pteridin ring of THF is sandwiched between the flavin ring of FAD and the imidazole ring of a His residue. This structure provides a snapshot of the folate/FAD-dependent methyl transfer, suggesting that the transferring methylene group of MTHF is located close to the redox-active N5 atom of FAD. Furthermore, we established an in vitro system to measure the methylation activity. Our TrmFO-tRNA docking model, in combination with mutational analyses, suggests a catalytic mechanism, in which the methylene of MTHF is directly transferred onto U54, and then the exocyclic methylene of U54 is reduced by FADH(2).

  11. 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.

  12. 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.

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

    CERN Document Server

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

    2008-01-01

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

  14. All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Wen-juan Wu; Jing-man Huang; Xin Meng

    2011-01-01

    All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution.Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis.Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network.Moreover,temperature-dependent NMR are used to compare with the results of the MD simulations.The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution.And the NMR results show agreement with the MD simulations.All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.

  15. 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.

  16. On the influence of the internal structure of the atom on Bose-Einstein condensation in an ideal gas of hydrogenlike atoms

    Science.gov (United States)

    Slyusarenko, Yu. V.; Sotnikov, A. G.

    2007-01-01

    The features of Bose condensation in an equilibrium ideal gas consisting of two types of charged fermions and their bound states—hydrogenlike atoms—in the presence of equilibrium between the photons and matter are investigated. It is shown that under such conditions the main influence on the Bose-Einstein condensation comes from the existence of levels concerned with the hyperfine splitting of the ground state of the hydrogenlike atom. The critical temperature and condensate density as functions of magnetic field are determined by considering effects due to the additional splitting of the levels of the hyperfine structure of the ground state in an external uniform static magnetic field (the Zeeman and Paschen-Back effects). It is found that under conditions of total statistical equilibrium in the system, a condensate is formed only by atoms found in the lowest energy state. It is shown that in the absence of equilibrium between radiation and matter, in the region of ultralow temperatures and low densities, the system can be treated as a multicomponent ideal gas of hydrogenlike atoms. The existence of a hierarchy of individual transition temperatures of each of the samples to the state with Bose-Einstein condensation is established. Expressions are found for the critical temperatures and number densities of particles in the condensate for each of the system components.

  17. Lifetime analysis of individual-atom contacts and crossover to geometric-shell structures in unstrained silver nanowires

    Directory of Open Access Journals (Sweden)

    Christian Obermair

    2011-11-01

    Full Text Available We study the crossover of quantum point contacts from (i individual-atom contacts to (ii electronic-shell effects and finally to (iii geometric-shell effects in electrochemically deposited silver contacts. The method allows the fabrication of mechanically unstrained structures, which is a requirement for determining the individual atomic configuration by means of a detailed lifetime analysis of their conductance. Within the geometric-shell model, the sequence of conductance maxima is explained quantitatively based on the crystal structure data of silver, and the growth mechanism of the nanowires is discussed.

  18. Is the Oxygen Atom Static or Dynamic? The Effect of Generating Animations on Students' Mental Models of Atomic Structure

    Science.gov (United States)

    Akaygun, Sevil

    2016-01-01

    Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…

  19. Structure-dependent behaviours of skin layers studied by atomic force microscopy.

    Science.gov (United States)

    Chang, A C; Liu, B H; Shao, P L; Liao, J D

    2017-03-23

    The multilayer skin provides the physical resistance and strength against the environmental attacks, and consequently plays a significant role in maintaining the mammalian health. Currently, optical microscopy (OM) is the most common method for the research related to skin tissues while with the drawbacks including the possibility of changing the native morphology of the sample with the addition of the chemical or immunological staining and the restricted resolution of images for the direct observation of the tissue structures. To investigate if the function of each tissue is structure-dependent and the how the injured skin returns to the intact condition, we applied atomic force microscopy (AFM) on the sectioned mice-skin to reveal the tissue structures with a nanoscale resolution. From the outermost stratum to the inner layer of the skin tissue, the respectively laminated, fibrous, and brick-like structures were observed and corresponded to various functions. Due to the mechanical differences between the tissue constituents and their boundaries, the sizes and arrangements of the components were characterised and quantified by the mechanical mapping of AFM, which enabled the analytical comparisons between tissue layers. For the wound model, the skin tissues were examined with the initial formation of blood vessels and type-I collagen, which agreed with the stage of healing process estimated by OM but showed more detail information about the evolution of proteins among the skin. In conclusion, the characterisation of the components that consist of skin tissue by AFM enables the connection of the tissue function to the corresponded ultrastructure.

  20. 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

  1. Surface structure of anatase TiO{sub 2}(001): Reconstruction, atomic steps, and domains

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yong; Gan, Shupan; Chambers, Scott A.; Altman, Eric I.

    2001-06-15

    The surface structure of anatase TiO{sub 2}(001) was investigated using scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy (XPS), reflection high-energy electron diffraction (RHEED), and low-energy electron diffraction (LEED). A two-domain (1{times}4)/(4{times}1) reconstruction, similar to those previously reported in LEED and ion scattering studies, was observed by STM and RHEED. This reconstruction was found to be stable not only from room temperature to 850{degree}C in ultrahigh vacuum and oxygen-rich environments, but also during the anatase film growth. High-resolution STM images obtained at positive sample biases revealed two types of atomic row within each surface unit cell, indicating different Ti-derived states at the surface. At the same time, XPS of the reconstructed surfaces showed no evidence of Ti{sup 3+}. Based on the STM, XPS, RHEED, and LEED results, an {open_quotes}added{close_quotes}-and-{open_quotes}missing{close_quotes}-row model is proposed to account for the (1{times}4) reconstruction. Atomic steps and their relationship to the population of (1{times}4) and (4{times}1) domains were also investigated. The results showed that for vicinal surfaces the domain population depended strongly on the overall surface step orientation. While populations of the (1{times}4) and the (4{times}1) domains were nearly equal on flat (001) surfaces, they became significantly lopsided on a surface with its normal 2{degree} away from the (001) direction, demonstrating a strong correlation between surface steps and domain population on vicinal surfaces.

  2. Surface Structure of Anatase TiO{sub 2}(001): Reconstruction, Atomic Steps, and Domains

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yong; Gan, Shupan; Chambers, Scott A.; Altman, Eric I.

    2001-06-15

    The surface structure of anatase TiO{sub 2}(001) was investigated using scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy (XPS), reflection high energy electron diffraction (RHEED), and low energy electron diffraction (LEED). A two-domain (1 x 4)/(4 x 1) reconstruction, similar to those previously reported in LEED and ion scattering studies, was observed by STM and RHEED. This reconstruction was found to be stable not only from room temperature to 850 C in ultra-high vacuum and oxygen rich environments, but also during the anatase film growth. High-resolution STM images obtained at positive sample biases revealed two types of atomic rows within each surface unit cell, indicating different Ti-derived states at the surface. At the same time, XPS of the reconstructed surfaces showed no evidence of Ti{sup 3+}. Based on the STM, XPS, RHEED, and LEED results, an ''added''-and-''missing''-row model is proposed to account for the (1 x 4) reconstruction. Atomic steps and their relationship to the population of (1 x 4) and (4 x 1) domains were also investigated. Results showed that for vicinal surfaces, the domain population depended strongly on the overall surface step orientation. While populations of the (1 x 4) and the (4 x 1) domains were nearly equal on the flat (001) surfaces, they became significantly lopsided on the surface with its normal 2{sup o} away from the (001) direction, demonstrating a strong correlation between surface steps and domain population on vicinal surfaces.

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

    Science.gov (United States)

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

    2016-08-09

    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.

  4. A Near-Atomic Structure of the Dark Apoptosome Provides Insight into Assembly and Activation.

    Science.gov (United States)

    Cheng, Tat Cheung; Akey, Ildikó V; Yuan, Shujun; Yu, Zhiheng; Ludtke, Steven J; Akey, Christopher W

    2017-01-03

    In Drosophila, the Apaf-1-related killer (Dark) forms an apoptosome that activates procaspases. To investigate function, we have determined a near-atomic structure of Dark double rings using cryo-electron microscopy. We then built a nearly complete model of the apoptosome that includes 7- and 8-blade β-propellers. We find that the preference for dATP during Dark assembly may be governed by Ser325, which is in close proximity to the 2' carbon of the deoxyribose ring. Interestingly, β-propellers in V-shaped domains of the Dark apoptosome are more widely separated, relative to these features in the Apaf-1 apoptosome. This wider spacing may be responsible for the lack of cytochrome c binding to β-propellers in the Dark apoptosome. Our structure also highlights the roles of two loss-of-function mutations that may block Dark assembly. Finally, the improved model provides a framework to understand apical procaspase activation in the intrinsic cell death pathway.

  5. 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

    2013-10-09

    We use scanning tunneling microscopy and X-ray spectroscopy to characterize the atomic and electronic structure of boron-doped and nitrogen-doped graphene created by chemical vapor deposition on copper substrates. Microscopic measurements show that boron, like nitrogen, incorporates into the carbon lattice primarily in the graphitic form and contributes ~0.5 carriers into the graphene sheet per dopant. Density functional theory calculations indicate that boron dopants interact strongly with the underlying copper substrate while nitrogen dopants do not. The local bonding differences between graphitic boron and nitrogen dopants lead to large scale differences in dopant distribution. The distribution of dopants is observed to be completely random in the case of boron, while nitrogen displays strong sublattice clustering. Structurally, nitrogen-doped graphene is relatively defect-free while boron-doped graphene films show a large number of Stone-Wales defects. These defects create local electronic resonances and cause electronic scattering, but do not electronically dope the graphene film.

  6. 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.

  7. Advances in research on structural characterisation of agricultural products using atomic force microscopy.

    Science.gov (United States)

    Liu, Dongli; Cheng, Fang

    2011-03-30

    Atomic force microscopy (AFM) has many unique features compared with other conventional microscopies, such as high magnification with high resolution, minimal sample preparation, acquiring 2D and 3D images at the same time, observing ongoing processes directly, the possibility of manipulating macromolecules, etc. As a nanotechnology tool, AFM has been used to investigate the nanostructure of materials in many fields. This mini-review focuses mainly on its latest application to characterise the macromolecular nanostructure and surface topography of agricultural products. First the fundamentals of AFM are briefly explained. Then the macromolecular nanostructure information on agricultural products from AFM images is introduced by exploring the structure-function relationship in three aspects: agricultural product processing, agricultural product ripening and storage, and genetic and environmental factors. The surface topography characterisation of agricultural products using AFM is also discussed. The results reveal that AFM could be a powerful nanotechnology tool to acquire a deeper understanding of the mechanisms of structure and quality variations of agricultural products, which could be instructive in improving processing and storage technologies, and AFM is also helpful to reveal the essential nature of a product at nanoscale.

  8. 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.

  9. Regulating infrared photoresponses in reduced graphene oxide phototransistors by defect and atomic structure control.

    Science.gov (United States)

    Chang, Haixin; Sun, Zhenhua; Saito, Mitsuhiro; Yuan, Qinghong; Zhang, Han; Li, Jinhua; Wang, Zhongchang; Fujita, Takeshi; Ding, Feng; Zheng, Zijian; Yan, Feng; Wu, Hongkai; Chen, Mingwei; Ikuhara, Yuichi

    2013-07-23

    Defects play significant roles in properties of graphene and related device performances. Most studies of defects in graphene focus on their influences on electronic or luminescent optical properties, while controlling infrared optoelectronic performance of graphene by defect engineering remains a challenge. In the meantime, pristine graphene has very low infrared photoresponses of ~0.01 A/W due to fast photocarrier dynamics. Here we report regulating infrared photoresponses in reduced graphene oxide phototransistors by defect and atomic structure control for the first time. The infrared optoelectronic transport and photocurrent generation are significantly influenced and well controlled by oxygenous defects and structures in reduced graphene oxide. Moreover, remarkable infrared photoresponses are observed in photoconductor devices based on reduced graphene oxide with an external responsivity of ~0.7 A/W, at least over one order of magnitude higher than that from pristine graphene. External quantum efficiencies of infrared devices reach ultrahigh values of ~97%, which to our knowledge is one of the best efficiencies for infrared photoresponses from nonhybrid, pure graphene or graphene-based derivatives. The flexible infrared photoconductor devices demonstrate no photoresponse degradation even after 1000 bending tests. The results open up new routes to control optoelectronic behaviors of graphene for high-performance devices.

  10. 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.

  11. 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.

  12. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    Science.gov (United States)

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.

  13. The effect of atomic-scale defects and dopants on graphene electronic structure

    OpenAIRE

    Martinazzo, Rocco; Casolo, Simone; Tantardini, Gian Franco

    2011-01-01

    Graphene, being one-atom thick, is extremely sensitive to the presence of adsorbed atoms and molecules and, more generally, to defects such as vacancies, holes and/or substitutional dopants. This property, apart from being directly usable in molecular sensor devices, can also be employed to tune graphene electronic properties. Here we briefly review the basic features of atomic-scale defects that can be useful for material design. After a brief introduction on isolated $p_z$ defects, we analy...

  14. 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.

  15. Local atomic structure of solid solutions with overlapping shells by EXAFS: The regularization method

    Energy Technology Data Exchange (ETDEWEB)

    Babanov, Yu.A., E-mail: babanov@imp.uran.ru [M.N. Miheev Institute of Metal Physics, Ural Branch, Russian Academy of Sciences, Ekaterinburg 620990 (Russian Federation); Ponomarev, D.A.; Ustinov, V.V. [M.N. Miheev Institute of Metal Physics, Ural Branch, Russian Academy of Sciences, Ekaterinburg 620990 (Russian Federation); Baranov, A.N. [M.V. Lomonosov Moscow State University, Moscow 119991 (Russian Federation); Zubavichus, Ya.V. [Russian Research Centre “Kurchatov Institute”, 123182 Moscow (Russian Federation)

    2016-08-15

    Highlights: • A method for determining bond lengths from combined EXAFS spectra for solid oxide solutions is proposed. • We have demonstrated a high resolution in r-space of close spacing atoms in the Periodical Table. • These results were obtained without any assumptions concerning interatomic distances for multi-component systems. • Coordinates ions for the solid solution with rock salt structure are determined. - Abstract: The regularization method of solving ill-posed problem is used to determine five partial interatomic distances on the basis of combined two EXAFS spectra. Mathematical algorithm and experimental results of the EXAFS analysis for Ni{sub c}Zn{sub 1−c}O (c = 0.0, 0.3, 0.5, 0.7, 1.0) solid solutions with the rock salt (rs) crystal structure are discussed. Samples were synthesized from the binary oxide powders at pressure of 7.7 GPa and temperatures 1450–1650 K. The measurements were performed using synchrotron facilities (Russian Research Centre “Kurchatov Institute”, Moscow). The Ni and Zn K absorption spectra were recorded in transmission mode under room temperature. It is shown, the ideal rock salt lattice is distorted and long-range order exists only in the average (Vegard law). In order to determine coordinates ions for the solid solution with rock salt structure, we used the Pauling model. The simulation is performed for 343,000 cluster of oxide ions. The distribution functions for ions (Ni−O, Ni−Ni, Ni−Zn, Zn−Zn, Zn−O, O−O) depending on the distance are obtained. The width of the Gaussian distribution function is determined by the difference of the radii of the metal ions. The results are consistent with the data both X-ray diffraction and the EXAFS spectroscopy.

  16. Origin of the catalytic activity of face-centered-cubic ruthenium nanoparticles determined from an atomic-scale structure.

    Science.gov (United States)

    Kumara, L S R; Sakata, Osami; Kohara, Shinji; Yang, Anli; Song, Chulho; Kusada, Kohei; Kobayashi, Hirokazu; Kitagawa, Hiroshi

    2016-11-09

    The 3-dimensional (3D) atomic-scale structure of newly discovered face-centered cubic (fcc) and conventional hexagonal close packed (hcp) type ruthenium (Ru) nanoparticles (NPs) of 2.2 to 5.4 nm diameter were studied using X-ray pair distribution function (PDF) analysis and reverse Monte Carlo (RMC) modeling. Atomic PDF based high-energy X-ray diffraction measurements show highly diffuse X-ray diffraction patterns for fcc- and hcp-type Ru NPs. We here report the atomic-scale structure of Ru NPs in terms of the total structure factor and Fourier-transformed PDF. It is found that the respective NPs have substantial structural disorder over short- to medium-range order atomic distances from the PDF analysis. The first-nearest-neighbor peak analyses show a significant size dependence for the fcc-type Ru NPs demonstrating the increase in the peak height due to an increase in the number density as a function of particle size. The bond angle and coordination number (CN) distribution for the RMC-simulated fcc- and hcp-type Ru NP models indicated inherited structural features from their bulk counterparts. The CN analysis of the whole NP and surface of each RMC model of Ru NPs show the low activation energy packing sites on the fcc-type Ru NP surface atoms. Finally, our newly defined order parameters for RMC simulated Ru NP models suggested that the enhancement of the CO oxidation activity of fcc-type NPs was due to a decrease in the close packing ordering that resulted from the increased NP size. These structural findings could be positively supported for synthesized low-cost and high performance nano-sized catalysts and have potential application in fuel-cell systems and organic synthesis.

  17. Atomic-scale structure evolution in a quasi-equilibrated electrochemical process of electrode materials for rechargeable batteries.

    Science.gov (United States)

    Gu, Lin; Xiao, Dongdong; Hu, Yong-Sheng; Li, Hong; Ikuhara, Yuichi

    2015-04-01

    Lithium-ion batteries have proven to be extremely attractive candidates for applications in portable electronics, electric vehicles, and smart grid in terms of energy density, power density, and service life. Further performance optimization to satisfy ever-increasing demands on energy storage of such applications is highly desired. In most of cases, the kinetics and stability of electrode materials are strongly correlated to the transport and storage behaviors of lithium ions in the lattice of the host. Therefore, information about structural evolution of electrode materials at an atomic scale is always helpful to explain the electrochemical performances of batteries at a macroscale. The annular-bright-field (ABF) imaging in aberration-corrected scanning transmission electron microscopy (STEM) allows simultaneous imaging of light and heavy elements, providing an unprecedented opportunity to probe the nearly equilibrated local structure of electrode materials after electrochemical cycling at atomic resolution. Recent progress toward unraveling the atomic-scale structure of selected electrode materials with different charge and/or discharge state to extend the current understanding of electrochemical reaction mechanism with the ABF and high angle annular dark field STEM imaging is presented here. Future research on the relationship between atomic-level structure evolution and microscopic reaction mechanisms of electrode materials for rechargeable batteries is envisaged.

  18. 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…

  19. Soluble model of Bose-atoms with two level internal structure: non-conventional Bose-Einstein condensation

    Directory of Open Access Journals (Sweden)

    M. Corgini

    2010-01-01

    Full Text Available For a Bose atom system whose energy operator is diagonal in the so-called number operators and its ground state has an internal two-level structure with negative energies, exact expressions for the limit free canonical energy and pressure are obtained. The existence of non-conventional Bose-Einstein condensation has been also proved.

  20. 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…

  1. Atomic structure of screw dislocations intersecting the Au(111) surface: A combined scanning tunneling microscopy and molecular dynamics study

    DEFF Research Database (Denmark)

    Engbæk, Jakob; Schiøtz, Jakob; Dahl-Madsen, Bjarke;

    2006-01-01

    The atomic-scale structure of naturally occurring screw dislocations intersecting a Au(111) surface has been investigated both experimentally by scanning tunneling microscopy (STM) and theoretically using molecular dynamics (MD) simulations. The step profiles of 166 dislocations were measured usi...

  2. 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…

  3. 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)

  4. The Effect of Boron Addition on the Atomic Structure and Microwave Magnetic Properties of FeGaB Thin Films

    Energy Technology Data Exchange (ETDEWEB)

    Gao, J.; Yang, A; Chen, Y; Kirkland, J; Lou, J; Sun, N; Vittoria, C; Harris, V

    2009-01-01

    Varying amounts of boron were added to the host FeGa alloy to investigate its impact upon local atomic structure and magnetic and microwave properties. The impact of B upon the local atomic structure in FeGaB films was investigated by extended x-ray absorption fine structure (EXAFS) analysis. The EXAFS fitting results revealed a contraction of lattice parameters with the introduction of B. The Debye-Waller factor determined from EXAFS fitting increases as a function of boron addition and abruptly changes during the structural evolution from crystalline to amorphous that occurs near 9% B. Upon the onset of this transition the static and microwave magnetic properties became exceptionally soft, with values of coercivity and ferromagnetic linewidth reducing to less than 1 Oe and 25 Oe, respectively.

  5. Segregation and temperature effect on the atomic structure of Bi{sub 30}Ga{sub 70} liquid alloy

    Energy Technology Data Exchange (ETDEWEB)

    Sbihi, D Es; Grosdidier, B; Gasser, J-G [Laboratoire de Physique des Milieux Denses, Institut de Chimie Physique et Materiaux, Universite Paul Verlaine-Metz, 1 Boulevard Arago 57078 Metz Cedex 3 (France); Kaban, I; Gruner, S; Hoyer, W [Institute of Physics, Chemnitz University of Technology, D-09107 Chemnitz (Germany)], E-mail: grosdidi@univ-metz.fr

    2009-06-17

    We investigate the structure of liquid monotectic alloy Bi{sub 30}Ga{sub 70} above and below the critical point. The three-dimensional structure at 265 deg. C is modelled by means of the reverse Monte Carlo simulation technique using neutron and x-ray diffraction experimental data. It is shown that atomic segregation on the short-range scale exists in the liquid Bi{sub 30}Ga{sub 70} slightly above the critical temperature (T{sub C} = 262 deg. C). We present also the structure factors of Bi{sub 30}Ga{sub 70} liquid alloy under the critical point at 240 and 230 deg.C obtained with neutron diffraction to highlight the temperature effect in the atomic structure.

  6. 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.

  7. 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.

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

    Science.gov (United States)

    Jarvis, Samuel Paul

    2015-01-01

    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. PMID:26307976

  9. Structural and electrical properties of ultrathin niobium nitride films grown by atomic layer deposition

    Science.gov (United States)

    Linzen, S.; Ziegler, M.; Astafiev, O. V.; Schmelz, M.; Hübner, U.; Diegel, M.; Il’ichev, E.; Meyer, H.-G.

    2017-03-01

    We studied and optimised the properties of ultrathin superconducting niobium nitride films fabricated with a plasma-enhanced atomic layer deposition (PEALD) process. By adjusting process parameters, the chemical embedding of undesired oxygen into the films was minimised and a film structure consisting of mainly polycrystalline niobium nitride with a small fraction of amorphous niobium oxide and niobium oxo-nitrides were formed. For this composition a critical temperature of 13.8 K and critical current densities of 7 × 106 A cm–2 at 4.2 K were measured on 40 nm thick films. A fundamental correlation between these superconducting properties and the crystal lattice size of the cubic δ-niobium-nitride grains were found. Moreover, the film thickness variation between 40 and 2 nm exhibits a pronounced change of the electrical conductivity at room temperature and reveals a superconductor–insulator-transition in the vicinity of 3 nm film thickness at low temperatures. The thicker films with resistances up to 5 kΩ per square in the normal state turn to the superconducting one at low temperatures. The perfect thickness control and film homogeneity of the PEALD growth make such films extremely promising candidates for developing novel devices on the coherent quantum phase slip effect.

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

    Science.gov (United States)

    Jarvis, Samuel Paul

    2015-08-21

    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.

  11. First-principles study of atomic and electronic structures of kaolinite in soft rock

    Institute of Scientific and Technical Information of China (English)

    He Man-Chao; Zhao Jian; Fang Zhi-Jie

    2012-01-01

    Kaolinite is a kind of clay mineral which often causes large deformations in soft-rock tunnel engineering and thus causes safety issues.To deal with these engineering safety issues,the physical/chemical properties of the kaolinite should be studied from basic viewpoints.By using the density-functional theory,in this paper,the atomic and the electronic structures of the kaolinite are studied within the local-density approximation (LDA).It is found that the kaolinite has a large indirect band gap with the conduction band minimum (CBM) and the valence band maximum (VBM) being at the T and the B points,respeetively.The chemical bonding between the cation and the oxygen anion in kaolinite is mainly ionic,accompanied by a minor covalent component.It is pointed that the VBM and the CBM of kaolinite consist of oxygen 2p and cation s states,respectively.The bond lengths between different cations and anions,as well as of the different OH groups,are also compared.

  12. 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.

  13. Structure of various K L1 x-ray satellite lines of heavy atoms

    Science.gov (United States)

    Polasik, Marek; Lewandowska-Robak, Maja

    2004-11-01

    Multiconfiguration Dirac-Fock calculations with the inclusion of the transverse (Breit) interaction and QED corrections have been carried out for Pd, Sn, Tb, Ta, Pb, and Th in order to obtain positions and intensities of various electric dipole, electric quadrupole, and magnetic dipole K x-ray diagram lines and of their KL1 satellites. Theoretically constructed stick spectra have been presented together with synthesized spectra (the sum of the Lorentzian natural line shapes) for each studied element. Taking into account the existence of an L -shell hole in the 2s or 2p subshell, the effect of additional L -shell ionization on the shapes and structure of the K x-ray spectra has been examined. It has been observed that generally with increasing atomic number Z the shapes of particular satellite line groups tend to become smoother and to differ less from the shapes of appropriate diagram lines. Relations between the values of energy shifts of various satellite lines for each element and the changes of these relations with Z have also been studied. Additionally, the relations between the intensities of different diagram lines for each element have been systematically analyzed, likewise the changes with Z of the role of particular diagram lines. This study can be helpful in reliable and quantitative interpretation of many experimental K x-ray spectra of Pd, Sn, Tb, Ta, Pb, and Th induced in collisions with various projectiles.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mättö, Laura [Department of Physics, University of Jyväskylä, P.O. Box 35 (YFL), FI-40014 (Finland); Szilágyi, Imre M., E-mail: imre.szilagyi@mail.bme.hu [Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest H-1111 (Hungary); MTA-BME Technical Analytical Research Group, Szent Gellért tér 4, Budapest H-1111 (Hungary); Department of Chemistry, University of Helsinki, P.O. Box 55, Helsinki FI-00014 (Finland); Laitinen, Mikko [Department of Physics, University of Jyväskylä, P.O. Box 35 (YFL), FI-40014 (Finland); Ritala, Mikko; Leskelä, Markku [Department of Chemistry, University of Helsinki, P.O. Box 55, Helsinki FI-00014 (Finland); Sajavaara, Timo [Department of Physics, University of Jyväskylä, P.O. Box 35 (YFL), FI-40014 (Finland)

    2016-10-01

    In this study flexible TiO{sub 2} 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 TiO{sub 2} films were deposited into the pores of the Kapton membranes by atomic layer deposition using Ti({sup i}OPr){sub 4} and water as precursors at 250 °C. The TiO{sub 2} 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. - Highlights: • Porous Kapton membranes were obtained by ion track technology and chemical etching. • TiO{sub 2} films were deposited by ALD into the pores of the Kapton membranes. • TiO{sub 2} nanotube array was prepared by removing the polymer core. • MCP structures were obtained from the coated membranes. • Electron multiplication was achieved using the ALD-coated Kapton foils.

  15. 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.

  16. 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.

  17. 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...

  18. Water replacement hypothesis in atomic detail--factors determining the structure of dehydrated bilayer stacks.

    Science.gov (United States)

    Golovina, Elena A; Golovin, Andrey V; Hoekstra, Folkert A; Faller, Roland

    2009-07-22

    According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail. The starting conformation of a palmitoyloleolylphosphatidylcholine lipid bilayer in excess water was been obtained by self-assembly. A series of molecular-dynamics simulations of palmitoyloleolylphosphatidylcholine with different degrees of dehydration (28.5, 11.7, and 5.4 waters per lipid) and different molar trehalose/lipid ratios (1:1) were carried out in the NPT ensemble. Water removal causes the formation of multilamellar "stacks" through periodic boundary conditions. The headgroups reorient from pointing outward to inward with dehydration. This causes changes in the electrostatic interactions between interfaces, resulting in interface interpenetration. Interpenetration creates self-spacing of the bilayers and prevents gel-phase formation. At lower concentrations, trehalose does not separate the interfaces, and acting together with self-spacing, it causes a considerable increase of APL. APL decreases at higher trehalose concentrations when the layer of sugar physically separates the interfaces. When interfaces are separated, the model confirms the water replacement hypothesis.

  19. Water Replacement Hypothesis in Atomic Detail—Factors Determining the Structure of Dehydrated Bilayer Stacks

    Science.gov (United States)

    Golovina, Elena A.; Golovin, Andrey V.; Hoekstra, Folkert A.; Faller, Roland

    2009-01-01

    Abstract According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail. The starting conformation of a palmitoyloleolylphosphatidylcholine lipid bilayer in excess water was been obtained by self-assembly. A series of molecular-dynamics simulations of palmitoyloleolylphosphatidylcholine with different degrees of dehydration (28.5, 11.7, and 5.4 waters per lipid) and different molar trehalose/lipid ratios (1:1) were carried out in the NPT ensemble. Water removal causes the formation of multilamellar “stacks” through periodic boundary conditions. The headgroups reorient from pointing outward to inward with dehydration. This causes changes in the electrostatic interactions between interfaces, resulting in interface interpenetration. Interpenetration creates self-spacing of the bilayers and prevents gel-phase formation. At lower concentrations, trehalose does not separate the interfaces, and acting together with self-spacing, it causes a considerable increase of APL. APL decreases at higher trehalose concentrations when the layer of sugar physically separates the interfaces. When interfaces are separated, the model confirms the water replacement hypothesis. PMID:19619463

  20. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Jayachandran, Suseendran, E-mail: suseendran.jayachandran@imec.be [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Metallurgy and Materials, Castle Arenberg 44, B-3001 Leuven (Belgium); Billen, Arne [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven (Belgium); Douhard, Bastien; Conard, Thierry; Meersschaut, Johan; Moussa, Alain; Caymax, Matty; Bender, Hugo [Imec, Kapeldreef 75, 3001 Leuven (Belgium); Vandervorst, Wilfried [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Physics and Astronomy, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Heyns, Marc [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Metallurgy and Materials, Castle Arenberg 44, B-3001 Leuven (Belgium); Delabie, Annelies [Imec, Kapeldreef 75, 3001 Leuven (Belgium); KU Leuven (University of Leuven), Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven (Belgium)

    2016-10-30

    Highlights: • O{sub 3} or O{sub 2} exposures on H-Si(100) result in O ALs with different surface structures. • Si-EPI on O AL using O{sub 3} process is by direct epitaxial growth mechanism. • Si-EPI on O AL using O{sub 2} process is by epitaxial lateral overgrowth mechanism. • Distortions by O AL, SiH{sub 4} flux rate and Si thickness has an impact on Si-EPI quality. - Abstract: 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 (O{sub 3}) or oxygen (O{sub 2}) exposure on H-terminated Si at 50 °C and 300 °C respectively. Epitaxial Si is deposited by chemical vapor deposition using silane (SiH{sub 4}) at 500 °C. After O{sub 3} 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 SiH{sub 4} reactants, allowing more time for surface diffusion. After O{sub 2} exposure, the O atoms are present in the form of SiO{sub x} clusters. Regions of hydrogen-terminated Si remain present between the SiO{sub x} 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.

  2. 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...

  3. Atomically resolved tomography to directly inform simulations for structure-property relationships

    Science.gov (United States)

    Moody, Michael P.; Ceguerra, Anna V.; Breen, Andrew J.; Cui, Xiang Yuan; Gault, Baptiste; Stephenson, Leigh T.; Marceau, Ross K. W.; Powles, Rebecca C.; Ringer, Simon P.

    2014-11-01

    Microscopy encompasses a wide variety of forms and scales. So too does the array of simulation techniques developed that correlate to and build upon microstructural information. Nevertheless, a true nexus between microscopy and atomistic simulations is lacking. Atom probe has emerged as a potential means of achieving this goal. Atom probe generates three-dimensional atomistic images in a format almost identical to many atomistic simulations. However, this data is imperfect, preventing input into computational algorithms to predict material properties. Here we describe a methodology to overcome these limitations, based on a hybrid data format, blending atom probe and predictive Monte Carlo simulations. We create atomically complete and lattice-bound models of material specimens. This hybrid data can then be used as direct input into density functional theory simulations to calculate local energetics and elastic properties. This research demonstrates the role that atom probe combined with theoretical approaches can play in modern materials engineering.

  4. 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.

  5. Atomic structure of a stable high-index Ge surface: G2(103)-(4x1)

    DEFF Research Database (Denmark)

    Seehofer, L.; Bunk, O.; Falkenberg, G.

    1997-01-01

    Based on scanning tunneling microscopy and surface X-ray diffraction, we propose a complex structural model for the Ge(103)-(4 x 1) reconstruction. Each unit cell contains two (103) double steps, which gives rise to the formation of stripes of Ge atoms oriented in the [] direction....... The stripes and the spaces between them are covered with threefold-coordinated Ge adatoms. Charge is transferred from the bulk-like edge atoms of the double steps to the adatoms. The formation of the reconstruction can be explained in terms of stress relief, charge transfer, and minimization of the dangling...

  6. Watching Silica's Dance: Imaging the Structure and Dynamics of the Atomic (Re-) Arrangements in 2D Glass

    Science.gov (United States)

    Muller, David

    2014-03-01

    Even though glasses are almost ubiquitous--in our windows, on our iPhones, even on our faces--they are also mysterious. Because glasses are notoriously difficult to study, basic questions like: ``How are the atoms arranged? Where and how do glasses break?'' are still under contention. We use aberration corrected transmission electron microscopy (TEM) to image the atoms in a new two-dimensional phase of silica glass - freestanding it becomes the world's thinnest pane of glass at only 3-atoms thick, and take a unique look into these questions. Using atom-by-atom imaging and spectroscopy, we are able to reconstruct the full structure and bonding of this 2D glass and identify it as a bi-tetrahedral layer of SiO2. Our images also strikingly resemble Zachariasen's original cartoon models of glasses, drawn in 1932. As such, our work realizes an 80-year-old vision for easily understandable glassy systems and introduces promising methods to test theoretical predictions against experimental data. We image atoms in the disordered solid and track their motions in response to local strain. We directly obtain ring statistics and pair distribution functions that span short-, medium-, and long-range order, and test these against long-standing theoretical predictions of glass structure and dynamics. We use the electron beam to excite atomic rearrangements, producing surprisingly rich and beautiful videos of how a glass bends and breaks, as well as the exchange of atoms at a solid/liquid interface. Detailed analyses of these videos reveal a complex dance of elastic and plastic deformations, phase transitions, and their interplay. These examples illustrate the wide-ranging and fundamental materials physics that can now be studied at atomic-resolution via transmission electron microscopy of two-dimensional glasses. Work in collaboration with: S. Kurasch, U. Kaiser, R. Hovden, Q. Mao, J. Kotakoski, J. S. Alden, A. Shekhawat, A. A. Alemi, J. P. Sethna, P. L. McEuen, A.V. Krasheninnikov

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Atomic fingers, bridges and slingshots: formation of exotic surface structures during ion irradiation of heavy metals

    Energy Technology Data Exchange (ETDEWEB)

    Nordlund, K. E-mail: kai.nordlund@helsinki.fi; Tarus, J.; Keinonen, J.; Donnelly, S.E.; Birtcher, R.C

    2003-05-01

    Recent experiments on ion irradiation of heavy metals such as gold and silver have shown that very unusual surface configurations can be produced by the irradiation. Typically, the surface damage has the shape of a crater, similar to those produced by meteorite impacts. The crater shapes are, however, often highly asymmetric and can show extended adatom ridges extending far from the crater well. Using molecular dynamics simulations we show how such exotic atom arrangements are produced. We describe atomic bridges over a crater and illustrate a slingshot-like effect which can propel atom clusters far from an impact position to produce isolated adatom islands.

  13. 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

    2015-12-07

    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

  14. Study of hyperfine structure in simple atoms and precision tests of the bound state QED

    Energy Technology Data Exchange (ETDEWEB)

    Karshenboim, S.G. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); D.I. Mendeleev Institute for Metrology (VNIIM), St. Petersburg 190005 (Russian Federation); Eidelman, S.I. [Budker Institute for Nuclear Physics and Novosibirsk State University, Novosibirsk, 630090 (Russian Federation); Fendel, P. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ivanov, V.G. [Pulkovo Observatory, St. Petersburg 196140 (Russian Federation); Kolachevsky, N.N. [P.N. Lebedev Physics Institute, Moscow, 119991 (Russian Federation); Shelyuto, V.A. [D.I. Mendeleev Institute for Metrology (VNIIM), St. Petersburg 190005 (Russian Federation); Haensch, T.W. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany)

    2006-12-15

    We consider the most accurate tests of bound state QED, precision theory of simple atoms, related to the hyperfine splitting in light hydrogen-like atoms. We discuss the HFS interval of the 1s state in muonium and positronium and of the 2s state in hydrogen, deuterium and helium-3 ion. We summarize their QED theory and pay attention to involved effects of strong interactions. We also consider recent optical measurements of the 2s HFS interval in hydrogen and deuterium.

  15. Study of hyperfine structure in simple atoms and precision tests of the bound state QED

    CERN Document Server

    Karshenboim, S G; Fendel, P; Ivanov, V G; Kolachevsky, N N; Shelyuto, V A; Hänsch, T W

    2006-01-01

    We consider the most accurate tests of bound state QED, precision theory of simple atoms, related to the hyperfine splitting in light hydrogen-like atoms. We discuss the HFS interval of the 1s state in muonium and positronium and of the 2s state in hydrogen, deuterium and helium-3 ion. We summarize their QED theory and pay attention to involved effects of strong interactions. We also consider recent optical measurements of the 2s HFS interval in hydrogen and deuterium.

  16. Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy

    Science.gov (United States)

    Yehl, Jenna; Kudryashova, Elena; Reisler, Emil; Kudryashov, Dmitri; Polenova, Tatyana

    2017-01-01

    Cellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin’s involvement in these processes is mediated by many actin-binding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin. PMID:28303963

  17. Operando atomic structure and active sites of TiO2(110)-supported gold nanoparticles during carbon monoxide oxidation.

    Science.gov (United States)

    Saint-Lager, Marie-Claire; Laoufi, Issam; Bailly, Aude

    2013-01-01

    It is well known that gold nanoparticles supported on TiO2 act as a catalyst for CO oxidation, even below room temperature. Despite extensive studies, the origin of this catalytic activity remains under debate. Indeed, when the particle size decreases, many changes may occur; thus modifying the nanoparticles' electronic properties and consequently their catalytic performances. Thanks to a state-of-the-art home-developed setup, model catalysts can be prepared in ultra-high vacuum and their morphology then studied in operando conditions by Grazing Incidence Small Angle X-ray Scattering, as well as their atomic structure by Grazing Incidence X-ray Diffraction as a function of their catalytic activity. We previously reported on the existence of a catalytic activity maximum observed for three-dimensional gold nanoparticles with a diameter of 2-3 nm and a height of 6-7 atomic planes. In the present work we correlate this size dependence of the catalytic activity to the nanoparticles' atomic structure. We show that even when their size decreases below the optimum diameter, the gold nanoparticles keep the face-centered cubic structure characteristic of bulk gold. Nevertheless, for these smallest nanoparticles, the lattice parameter presents anisotropic strains with a larger contraction in the direction perpendicular to the surface. Moreover a careful analysis of the atomic-scale morphology around the catalytic activity maximum tends to evidence the role of sites with a specific geometry at the interface between the nanoparticles and the substrate. This argues for models where atoms at the interface periphery act as catalytically active sites for carbon monoxide oxidation.

  18. Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

    Science.gov (United States)

    Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

    2014-11-01

    Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin.

  19. A DFT study of atomic structure and adhesion at the Fe(BCC)/Fe3O4 interfaces

    Science.gov (United States)

    Forti, M. D.; Alonso, P. R.; Gargano, P. H.; Balbuena, P. B.; Rubiolo, G. H.

    2016-05-01

    The adhesion at Fe/Fe3O4 interface is one of the critical pieces of information that is often lacking upon designing the protective magnetite layer on the inner surfaces of carbon steel piping or upon modeling the scale removal mechanism for optimization of industrial descaling of the wire or strip surface of carbon steel after hot rolling process. In this context, we have performed ab initio DFT calculations to determine the atomic structure, work of separation (γ), and bonding character of the Fe(001)/Fe3O4(001) interface. Three candidate interface geometries were considered, including Fe and FeO2 terminations of the oxide. The minimization of the forces resulted in substantial changes to the atomic structure of the metal and oxide layer at both side of the interface, and also of the subsurface layer of the oxide in the case of Fe-terminated oxide slab. Moreover, the relaxation of the geometry in one of the two considered Fe-terminated oxide interface leads to completely unstable interface structures. By applying several methods of analysis, we have thoroughly characterized the electronic structure and have determined that the dominant bonding mechanism is the metallic-ionic interaction between the iron atoms of both metal and oxide slabs. Our calculations predict γ ≈ 1.42 J/m2 regardless of the interfacial stoichiometry.

  20. 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.

  1. 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.

  2. Molecular Dynamics Study on Interfacial Energy and Atomic Structure of Ag/Ni and Cu/Ni Heterophase System

    Institute of Scientific and Technical Information of China (English)

    Haijiang LIU; Shaoqing WANG; An DU; Caibei ZHANG

    2004-01-01

    The results of molecular dynamics calculations on the interfacial energies and atomic structures of Ag/Ni and Cu/Ni interaces are presented. Calculation on Ag/Ni interfaces with low-index planes shows that those containing the (111) plane have the lowest energies, which is in agreement with the experiments. Comparing surface energy with interracial energy, it is found the order of the interfacial energies of Ag/Ni and Cu/Ni containing the planes fall in the same order as solid-vapor surface energies of Ag, Cu and Ni. In this MD simulation, the relaxed atomic structure and dislocation network of (110)Ag||(110)Ni interface are coincident to HREM observations.

  3. 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.

  4. Theory for the atomic shell structure of the cluster magnetic moment and magnetoresistance of a cluster ensemble

    Science.gov (United States)

    Jensen, P. J.; Bennemann, K. H.

    1995-12-01

    We present a simple theory for the cluster size dependence of the average cluster magnetic moment of transition metal clusters. Assuming a local environmental dependence of the atomic magnetic moments, the cluster magnetization exhibits a magnetic shell structure, reflecting the atomic structure of the cluster. Thus, the observed oscillations of the average cluster magnet moment may serve as a fingerprint of the cluster geometry. We also discuss the giant magnetoresistance (GMR) exhibited by an ensemble of magnetic clusters embedded in a metallic matrix. It is shown that the magnetic anisotropy affects strongly the magnetization of the cluster ensemble under certain conditions. Since the GMR depends on the cluster ensemble magnetization, it can be used to determine the cluster magnetic anisotropy energy.

  5. Hybrid-structure atomic models for HED laboratory plasma diagnostics and simulations

    Science.gov (United States)

    Hansen, Stephanie

    2010-03-01

    While theoretical atomic physics calculations are well developed for isolated atoms and have been thoroughly benchmarked against low-density laboratory sources such as electron beam ion traps and tokamak plasmas, the high energy density (HED) regime offers significant challenges for atomic physics and spectroscopic modeling. High plasma densities lead to collective effects such as continuum lowering, line broadening, and significant populations in multiply excited atomic states. These effects change the plasma equation of state and the character of emission and absorption spectra and must be accounted for in order to accurately simulate radiative transfer in and apply spectroscopic diagnostics to HED plasmas. Modeling complex mid- and high-Z ions in the HED regime is a particular challenge because exponential growth in accessible configuration space overwhelms the reduction of the Rydberg levels through continuum lowering. This talk will discuss one approach to generating a tractable spectroscopic-quality atomic kinetics model and describe its application to HED laboratory plasmas produced on Sandia's Z facility. [4pt] Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  6. Topological Structures and Membrane Nanostructures of Erythrocytes after Splenectomy in Hereditary Spherocytosis Patients via Atomic Force Microscopy.

    Science.gov (United States)

    Li, Ying; Lu, Liyuan; Li, Juan

    2016-09-01

    Hereditary spherocytosis is an inherited red blood cell membrane disorder resulting from mutations of genes encoding erythrocyte membrane and cytoskeletal proteins. Few equipments can observe the structural characteristics of hereditary spherocytosis directly expect for atomic force microscopy In our study, we proved atomic force microscopy is a powerful and sensitive instrument to describe the characteristics of hereditary spherocytosis. Erythrocytes from hereditary spherocytosis patients were small spheroidal, lacking a well-organized lattice on the cell membrane, with smaller cell surface particles and had reduced valley to peak distance and average cell membrane roughness vs. those from healthy individuals. These observations indicated defects in the certain cell membrane structural proteins such as α- and β-spectrin, ankyrin, etc. Until now, splenectomy is still the most effective treatment for symptoms relief for hereditary spherocytosis. In this study, we further solved the mysteries of membrane nanostructure changes of erythrocytes before and after splenectomy in hereditary spherocytosis by atomic force microscopy. After splenectomy, the cells were larger, but still spheroidal-shaped. The membrane ultrastructure was disorganized and characterized by a reduced surface particle size and lower than normal Ra values. These observations indicated that although splenectomy can effectively relieve the symptoms of hereditary spherocytosis, it has little effect on correction of cytoskeletal membrane defects of hereditary spherocytosis. We concluded that atomic force microscopy is a powerful tool to investigate the pathophysiological mechanisms of hereditary spherocytosis and to monitor treatment efficacy in clinical practices. To the best of our knowledge, this is the first report to study hereditary spherocytosis with atomic force microscopy and offers important mechanistic insight into the underlying role of splenectomy.

  7. 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.

  8. Atomic-Scale Structure and Local Chemistry of CoFeB-MgO Magnetic Tunnel Junctions.

    Science.gov (United States)

    Wang, Zhongchang; Saito, Mitsuhiro; McKenna, Keith P; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi

    2016-03-09

    Magnetic tunnel junctions (MTJs) constitute a promising building block for future nonvolatile memories and logic circuits. Despite their pivotal role, spatially resolving and chemically identifying each individual stacking layer remains challenging due to spatially localized features that complicate characterizations limiting understanding of the physics of MTJs. Here, we combine advanced electron microscopy, spectroscopy, and first-principles calculations to obtain a direct structural and chemical imaging of the atomically confined layers in a CoFeB-MgO MTJ, and clarify atom diffusion and interface structures in the MTJ following annealing. The combined techniques demonstrate that B diffuses out of CoFeB electrodes into Ta interstitial sites rather than MgO after annealing, and CoFe bonds atomically to MgO grains with an epitaxial orientation relationship by forming Fe(Co)-O bonds, yet without incorporation of CoFe in MgO. These findings afford a comprehensive perspective on structure and chemistry of MTJs, helping to develop high-performance spintronic devices by atomistic design.

  9. Relating Electronic and Geometric Structure of Atomic Layer Deposited BaTiO3 to its Electrical Properties.

    Science.gov (United States)

    Torgersen, Jan; Acharya, Shinjita; Dadlani, Anup Lal; Petousis, Ioannis; Kim, Yongmin; Trejo, Orlando; Nordlund, Dennis; Prinz, Fritz B

    2016-04-21

    Atomic layer deposition allows the fabrication of BaTiO3 (BTO) ultrathin films with tunable dielectric properties, which is a promising material for electronic and optical technology. Industrial applicability necessitates a better understanding of their atomic structure and corresponding properties. Through the use of element-specific X-ray absorption near edge structure (XANES) analysis, O K-edge of BTO as a function of cation composition and underlying substrate (RuO2 and SiO2) is revealed. By employing density functional theory and multiple scattering simulations, we analyze the distortions in BTO's bonding environment captured by the XANES spectra. The spectral weight shifts to lower energy with increasing Ti content and provides an atomic scale (microscopic) explanation for the increase in leakage current density. Differences in film morphologies in the first few layers near substrate-film interfaces reveal BTO's homogeneous growth on RuO2 and its distorted growth on SiO2. This work links structural changes to BTO thin-film properties and provides insight necessary for optimizing future BTO and other ternary metal oxide-based thin-film devices.

  10. 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

    2016-03-07

    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.

  11. Atomic force microscopic study of the structure of high-density polyethylene deformed in liquid medium by crazing mechanism.

    Science.gov (United States)

    Bagrov, D V; Yarysheva, A Y; Rukhlya, E G; Yarysheva, L M; Volynskii, A L; Bakeev, N F

    2014-02-01

    A procedure has been developed for the direct atomic force microscopic (AFM) examination of the native structure of high-density polyethylene (HDPE) deformed in an adsorption-active liquid medium (AALM) by the crazing mechanism. The AFM investigation has been carried out in the presence of a liquid medium under conditions preventing deformed films from shrinkage. Deformation of HDPE in AALM has been shown to proceed through the delocalized crazing mechanism and result in the development of a fibrillar-porous structure. The structural parameters of the crazed polymer have been determined. The obtained AFM images demonstrate a nanosized nonuniformity of the deformation and enable one to observe the structural rearrangements that take place in the deformed polymer after removal of the liquid medium and stress relaxation. A structural similarity has been revealed between HDPE deformed in the AALM and hard elastic polymers.

  12. Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale.

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-19

    Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

  13. Strain and Structure Heterogeneity in MoS2 Atomic Layers Grown by Chemical Vapour Deposition

    Science.gov (United States)

    2014-11-18

    with second-layer MoS2 stripes grown along the GBs, indicated by the white arrows. Scale bar, 5 mm. (e) Annular dark-field scanning TEM image of defect...lattice of monolayer MoS2 (Fig. 1e) can be seen from the annular dark field scanning TEM imaging. The brighter atomic sites are Mo atoms, while the...strains in MoS2 layer as a function of the applied strain on PDMS are shown in Fig. 4i, where a linear relationship is predicted within the range of 5

  14. 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.

  15. 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

    2016-05-04

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

  16. Atomic structure of the vimentin central α-helical domain and its implications for intermediate filament assembly.

    Science.gov (United States)

    Chernyatina, Anastasia A; Nicolet, Stefan; Aebi, Ueli; Herrmann, Harald; Strelkov, Sergei V

    2012-08-21

    Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) "rod" domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.

  17. 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.

  18. Finite-Temperature Atomic Structure of 180^o Ferroelectric Domain Walls in PbTiO3

    OpenAIRE

    Angoshtari, Arzhang; Yavari, Arash

    2010-01-01

    In this letter we obtain the finite-temperature structure of 180^o domain walls in PbTiO3 using a quasi-harmonic lattice dynamics approach. We obtain the temperature dependence of the atomic structure of domain walls from 0K up to room temperature. We also show that both Pb-centered and Ti-centered 180^o domain walls are thicker at room temperature; domain wall thickness at T=300K is about three times larger than that of T=0K. Our calculations show that Ti-centered domain walls have a lower f...

  19. 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....... The electronic density of states is metal-like in both the crystalline and the liquid phases, but it exhibits a pseudogap at the Fermi level in the amorphous phase, reflecting the strong abundance of fourfold coordinated Si in the amorphous phase....

  20. Surface modelling on heavy atom crystalline compounds: HfO{sub 2} and UO{sub 2} fluorite structures

    Energy Technology Data Exchange (ETDEWEB)

    Evarestov, Robert [Department of Quantum Chemistry, St. Petersburg State University, 26 Universitetsky Prospect, Peterhof, St. Petersburg 198504 (Russian Federation)], E-mail: re1973@re1973.spb.edu; Bandura, Andrei; Blokhin, Eugeny [Department of Quantum Chemistry, St. Petersburg State University, 26 Universitetsky Prospect, Peterhof, St. Petersburg 198504 (Russian Federation)

    2009-01-15

    The study of the bulk and surface properties of cubic (fluorite structure) HfO{sub 2} and UO{sub 2} was performed using the hybrid Hartree-Fock density functional theory linear combination of atomic orbitals simulations via the CRYSTAL06 computer code. The Stuttgart small-core pseudopotentials and corresponding basis sets were used for the core-valence interactions. The influence of relativistic effects on the structure and properties of the systems was studied. It was found that surface properties of Mott-Hubbard dielectric UO{sub 2} differ from those found for other metal oxides with the closed-shell configuration of d-electrons.

  1. c(4 × 2) and related structural units on the SrTiO3(001) surface: scanning tunneling microscopy, density functional theory, and atomic structure.

    Science.gov (United States)

    Becerra-Toledo, A E; Marshall, M S J; Castell, M R; Marks, L D

    2012-06-07

    Density functional theory is used to simulate high-bias, constant-current scanning tunneling micrographs for direct comparison with experimental images. Coupled to previous spectroscopic data, these simulations are used to determine the atomic structure of Ti-rich nanostructures on strontium titanate (001) surfaces. These nanostructures have three consecutive TiO(x) surface layers and exploit the distinctive structural motif of the c(4 × 2) reconstruction as their main building block. A structural model of a characteristic triline defect is also proposed.

  2. 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.

  3. The effect of the electronic structure, phase transition, and localized dynamics of atoms in the formation of tiny particles of gold

    Science.gov (United States)

    Ali, Mubarak; Lin, I.-Nan

    2017-01-01

    In addition to self-governing properties, tiny-sized particles of metallic colloids are the building blocks of large-sized particles; thus, their study has been the subject of a large number of publications. In the present work, it has been discussed that geometry structure of tiny particle made through atom-to-atom amalgamation depends on attained dynamics of gold atoms along with protruded orientations. The localized process conditions direct two-dimensional structure of a tiny particle at atomically flat air-solution interface while heating locally dynamically approached atoms, thus, negate the role of van der Waals interactions. At electronphoton-solution interface, impinging electrons stretch or deform atoms of tiny particles depending on the mechanism of impingement. In addition, to strike regular grid of electrons ejected on split of atoms not executing excitations and de-excitations of their electrons, atoms of tiny particles also deform or stretch while occupying various sites depending on the process of synergy. Under suitable impinging electron streams, those tiny particles in monolayer two-dimensional structure electron states of their atoms are diffused in the direction of transferred energy, thus, coincide to the next adjacent atoms in each one-dimensional array dealing the same sort of behavior. Instantaneously, photons of adequate energy propagate on the surfaces of such electronic structures and modify those into smooth elements, thus, disregard the phenomenon of localized surface plasmons. This study highlights the fundamental process of formation of tiny particles where the role of localized dynamics of atoms and their electronic structure along with interaction to light are discussed. Such a tool of processing materials, in nonequilibrium pulse-based process, opens a number of possibilities to develop engineered materials with specific chemical, optical, and electronic properties.

  4. Everyone Wants to Be a Model Teacher: Part III: Extensions to Atomic Structures and Bonding.

    Science.gov (United States)

    Schrader, C. L.

    1985-01-01

    Describes activities in which students: (1) propose creative atomic models that account for observed properties and predict additional experimental data; (2) calculate empirical formulas for 27 binary compounds; (3) propose a model to explain why certain elements have certain valences; and (4) arrange hypothetical elements into a periodic chart.…

  5. Hybrid platforms of graphane–graphene 2D structures: prototypes for atomically precise nanoelectronics

    OpenAIRE

    Mota,F.B.; Rivelino, R.; Medeiros, P.V.C.; Mascarenhas, A.J.S.; de Castilho, C. M. C.

    2014-01-01

    p.23558-23563 First-principles calculations demonstrate that line/ribbon defects, resulting from a controlled dehydrogenation in graphane, lead to the formation of low-dimensional electron-rich tracks in a monolayer. The present simulations point out that hybrid graphane–graphene nanostructures exhibit important elements, greatly required for the fabrication of efficient electronic circuits at the atomic level.

  6. Structural and chemical evolution of single-wall carbon nanotubes under atomic and molecular deuterium interaction

    NARCIS (Netherlands)

    Lisowski, W.; Keim, E.G.; Berg, van den A.H.J.; Smithers, M.A.

    2005-01-01

    The interaction of atomic (D) and molecular (D2) deuterium, as present in a (D + D2) gas mixture, with single-wall carbon nanotubes (SWNTs) has been studied by means of a combination of scanning electron microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy. The SWNT samp

  7. Atomic and Electronic Structure of Quantum Dots Measured with Scanning Probe Techniques

    NARCIS (Netherlands)

    Sun, Z.

    2012-01-01

    This thesis deals with low temperature scanning tunneling microscopy/spectroscopy and atomic force microscopy (LT-STM/STS and AFM) studies on colloidal semiconductor and graphene quantum dots (g-QDs). These nanostructures are interesting because they show tunable electrical and optical properties du

  8. Structural and Theoretical Evidence of the Depleted Proton Affinity of the N3-Atom in Acyclovir

    Directory of Open Access Journals (Sweden)

    Esther Vílchez-Rodríguez

    2016-10-01

    Full Text Available The hydronium salt (H3O2[Cu(N7–acv2(H2O2(SO42]·2H2O (1, acv = acyclovir has been synthesized and characterized by single-crystal X-ray diffraction and spectral methods. Solvated Cu(OH2 is a by-product of the synthesis. In the all-trans centrosymmetric complex anion, (a the Cu(II atom exhibits an elongated octahedral coordination; (b the metal-binding pattern of acyclovir (acv consists of a Cu–N7(acv bond plus an (aquaO–H···O6(acv interligand interaction; and (c trans-apical/distal sites are occupied by monodentate O-sulfate donor anions. Neutral acyclovir and aqua-proximal ligands occupy the basal positions, stabilizing the metal binding pattern of acv. Each hydronium(1+ ion builds three H-bonds with O–sulfate, O6(acv, and O–alcohol(acv from three neighboring complex anions. No O atoms of solvent water molecules are involved as acceptors. Theoretical calculations of molecular electrostatic potential surfaces and atomic charges also support that the O-alcohol of the N9(acv side chain is a better H-acceptor than the N3 or the O-ether atoms of acv.

  9. 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…

  10. Atomic structure solution of the complex quasicrystal approximant Al77Rh15Ru8 from electron diffraction data.

    Science.gov (United States)

    Samuha, Shmuel; Mugnaioli, Enrico; Grushko, Benjamin; Kolb, Ute; Meshi, Louisa

    2014-12-01

    The crystal structure of the novel Al77Rh15Ru8 phase (which is an approximant of decagonal quasicrystals) was determined using modern direct methods (MDM) applied to automated electron diffraction tomography (ADT) data. The Al77Rh15Ru8 E-phase is orthorhombic [Pbma, a = 23.40 (5), b = 16.20 (4) and c = 20.00 (5) Å] and has one of the most complicated intermetallic structures solved solely by electron diffraction methods. Its structural model consists of 78 unique atomic positions in the unit cell (19 Rh/Ru and 59 Al). Precession electron diffraction (PED) patterns and high-resolution electron microscopy (HRTEM) images were used for the validation of the proposed atomic model. The structure of the E-phase is described using hierarchical packing of polyhedra and a single type of tiling in the form of a parallelogram. Based on this description, the structure of the E-phase is compared with that of the ε6-phase formed in Al-Rh-Ru at close compositions.

  11. 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.

  12. Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.

    Science.gov (United States)

    Zhou, Mengying; Li, Yini; Hu, Qi; Bai, Xiao-Chen; Huang, Weiyun; Yan, Chuangye; Scheres, Sjors H W; Shi, Yigong

    2015-11-15

    The apoptotic protease-activating factor 1 (Apaf-1) controls the onset of many known forms of intrinsic apoptosis in mammals. Apaf-1 exists in normal cells as an autoinhibited monomer. Upon binding to cytochrome c and dATP, Apaf-1 oligomerizes into a heptameric complex known as the apoptosome, which recruits and activates cell-killing caspases. Here we present an atomic structure of an intact mammalian apoptosome at 3.8 Å resolution, determined by single-particle, cryo-electron microscopy (cryo-EM). Structural analysis, together with structure-guided biochemical characterization, uncovered how cytochrome c releases the autoinhibition of Apaf-1 through specific interactions with the WD40 repeats. Structural comparison with autoinhibited Apaf-1 revealed how dATP binding triggers a set of conformational changes that results in the formation of the apoptosome. Together, these results constitute the molecular mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.

  13. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

    Science.gov (United States)

    Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L; Meiler, Jens

    2012-03-07

    Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.

  14. Probing the dynamic structure factor of a neutral Fermi superfluid along the BCS-BEC crossover using atomic impurity qubits

    Science.gov (United States)

    Mitchison, Mark T.; Johnson, Tomi H.; Jaksch, Dieter

    2016-12-01

    We study an impurity atom trapped by an anharmonic potential, immersed within a cold atomic Fermi gas with attractive interactions that realizes the crossover from a Bardeen-Cooper-Schrieffer superfluid to a Bose-Einstein condensate. Considering the qubit comprising the lowest two vibrational energy eigenstates of the impurity, we demonstrate that its dynamics probes the equilibrium density fluctuations encoded in the dynamic structure factor of the superfluid. Observing the impurity's evolution is thus shown to facilitate nondestructive measurements of the superfluid order parameter and the contact between collective and single-particle excitation spectra. Our setup constitutes a model of an open quantum system interacting with a thermal reservoir, the latter supporting both bosonic and fermionic excitations that are also coupled to each other.

  15. Electronic and atomic structures of the Sr3Ir4Sn13 single crystal: A possible charge density wave material

    Science.gov (United States)

    Wang, H.-T.; Srivastava, M. K.; Wu, C.-C.; Hsieh, S.-H.; Wang, Y.-F.; Shao, Y.-C.; Liang, Y.-H.; Du, C.-H.; Chiou, J.-W.; Cheng, C.-M.; Chen, J.-L.; Pao, C.-W.; Lee, J.-F.; Kuo, C. N.; Lue, C. S.; Wu, M.-K.; Pong, W.-F.

    2017-01-01

    X-ray scattering (XRS), x-ray absorption near-edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) spectroscopic techniques were used to study the electronic and atomic structures of the high-quality Sr3Ir4Sn13 (SIS) single crystal below and above the transition temperature (T* ≈ 147 K). The evolution of a series of modulated satellite peaks below the transition temperature in the XRS experiment indicated the formation of a possible charge density wave (CDW) in the (110) plane. The EXAFS phase derivative analysis supports the CDW-like formation by revealing different bond distances [Sn1(2)-Sn2] below and above T* in the (110) plane. XANES spectra at the Ir L3-edge and Sn K-edge demonstrated an increase (decrease) in the unoccupied (occupied) density of Ir 5d-derived states and a nearly constant density of Sn 5p-derived states at temperatures T atomic structures and the CDW-like phase in the SIS single crystal. PMID:28106144

  16. 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 ...

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Structure determination of adipokinetic hormones using fast atom bombardment tandem mass spectrometry; An unknown adipokinetic hormone (AKH-III) from Locusta migratoria

    Energy Technology Data Exchange (ETDEWEB)

    Heerma, W.; Versluis, C.; Lankhof, H. (Utrecht University (Netherlands). Faculty of Chemistry, Department of Analytical Molecular Spectrometry); Oudejans, R.C.H.M.; Kooiman, F.P.; Beenakkers, A.M.T. (Utrecht University (Netherlands). Department of Experimental Zoology)

    1991-08-01

    Fast atom bombardment mass spectrometry combined with various tandem mass spectrometric techniques and accurate mass measurement were used to elucidate the structure of an unknown biologically active peptide isolated from Locusa migratoria. (author). 23 refs.; 6 figs.; 2 schemes.

  4. Atomic resolution transmission electron microscopy of the intergranular structure of a Y{sub 2}O{sub 3}-silicon nitride ceramic

    Energy Technology Data Exchange (ETDEWEB)

    Ziegler, A.; Kisielowski, C.; Hoffmann, M.J.; Ritchie, R.O.

    2002-05-01

    High-resolution transmission electron microscopy (HRTEM) employing focus-variation phase-reconstruction methods is used to image the atomic structure of grain boundaries in a silicon nitride ceramic at a resolution of 0.8 Angstrom

  5. Two-photon photoemission study of the coverage-dependent electronic structure of chemisorbed alkali atoms on a Ag(111) surface.

    Science.gov (United States)

    Wang, Lei-Ming; Sametoglu, Vahit; Winkelmann, Aimo; Zhao, Jin; Petek, Hrvoje

    2011-09-01

    We report a systematic investigation of the electronic structure of chemisorbed alkali atoms (Li-Cs) on a Ag(111) surface by two-photon photoemission spectroscopy. Angle-resolved two-photon photoemission spectra are obtained for 0-0.1 monolayer coverage of alkali atoms. The interfacial electronic structure as a function of periodic properties and the coverage of alkali atoms is observed and interpreted assuming ionic adsorbate/substrate interaction. The energy of the alkali atom σ-resonance at the limit of zero coverage is primarily determined by the image charge interaction, whereas at finite alkali atom coverages, it follows the formation of a dipolar surface field. The coverage- and angle-dependent two-photon photoemission spectra provide information on the photoinduced charge-transfer excitation of adsorbates on metal surfaces. This work complements the previous work on alkali/Cu(111) chemisorption [Phys. Rev. B 2008, 78, 085419].

  6. The stability and electronic structures of Si/O/Al/P atom doped (5,0)boron nitrogen nanotubes with Stone-Wales defects: Density functional theory studies

    Science.gov (United States)

    Li, KeJing; Ye, JinQian; Zhang, Juan; Wang, XiYuan; Shao, QingYi

    2017-03-01

    Using density functional theory, we have investigated Si/O/Al/P atoms doped (5,0)BNNTs with SW defects. We have mainly found that Si/O/Al/P have improved the stability of (5,0)BNNTs with SW defects. In view of Mulliken charge, we have thought Si/O/Al/P atoms have donated electrons (charge +e state or charge -e state) to nanotubes, contributing BNNTs with SW defects to stable. Meanwhile, from the aspect of energy band structure and DOS, we have further explained the reason. We have considerred that stability of doped structures has related to hybridization between doped atom and BNNTs. The stability has changed with changing the degree of hybridization. Moreover, B atom can play a crucial role in the insertion of Si/O/Al/P atom into (5,0)BNNTs with SW defects.

  7. The structure and function of cell membranes examined by atomic force microscopy and single-molecule force spectroscopy.

    Science.gov (United States)

    Shan, Yuping; Wang, Hongda

    2015-06-07

    The cell membrane is one of the most complicated biological complexes, and long-term fierce debates regarding the cell membrane persist because of technical hurdles. With the rapid development of nanotechnology and single-molecule techniques, our understanding of cell membranes has substantially increased. Atomic force microscopy (AFM) has provided several unprecedented advances (e.g., high resolution, three-dimensional and in situ measurements) in the study of cell membranes and has been used to systematically dissect the membrane structure in situ from both sides of membranes; as a result, novel models of cell membranes have recently been proposed. This review summarizes the new progress regarding membrane structure using in situ AFM and single-molecule force spectroscopy (SMFS), which may shed light on the study of the structure and functions of cell membranes.

  8. Structural and chemical characteristics of atomically smooth GaN surfaces prepared by abrasive-free polishing with Pt catalyst

    Science.gov (United States)

    Murata, Junji; Sadakuni, Shun; Okamoto, Takeshi; Hattori, Azusa N.; Yagi, Keita; Sano, Yasuhisa; Arima, Kenta; Yamauchi, Kazuto

    2012-06-01

    This paper reports the structural and chemical characteristics of atomically flat gallium nitride (GaN) surfaces prepared by abrasive-free polishing with platinum (Pt) catalyst. Atomic force microscopy revealed regularly alternating wide and narrow terraces with a step height equivalent to that of a single bilayer on the flattened GaN surfaces, which originate from the differences in etching rate of two neighboring terraces. The material removal characteristics of the method for GaN surfaces were investigated in detail. We confirmed that an atomically smooth GaN surface with an extremely small number of surface defects, including pits and scratches, can be achieved, regardless of the growth method, surface polarity, and doping concentration. X-ray photoelectron spectroscopy showed that the flattening method produces clean GaN surfaces with only trace impurities such as Ga oxide and metallic Ga. Contamination with the Pt catalyst was also evaluated using total-reflection X-ray fluorescence analysis. A wet cleaning method with aqua regia is proposed, which markedly eliminates this Pt contamination without affecting the surface morphology.

  9. Carbon nanotubes randomly decorated with gold clusters: from nano{sup 2}hybrid atomic structures to gas sensing prototypes

    Energy Technology Data Exchange (ETDEWEB)

    Charlier, J-C; Zanolli, Z [Unite de Physico-Chimie et de Physique des Materiaux (PCPM), European Theoretical Spectroscopy Facility (ETSF), Universite Catholique de Louvain, Place Croix du Sud 1, B-1348 Louvain-la-Neuve (Belgium); Arnaud, L; Avilov, I V; Felten, A; Pireaux, J-J [Centre de Recherche en Physique de la Matiere et du Rayonnement (PMR-LISE), Facultes Universitaires Notre-Dame de la Paix, 61 Rue de Bruxelles, B-5000 Namur (Belgium); Delgado, M [Sensotran, s.l., Avenida Remolar 31, E-08820 El Prat de Llobregat, Barcelona (Spain); Demoisson, F; Reniers, F [Service de Chimie Analytique et Chimie des Interfaces (CHANI), Universite Libre de Bruxelles, Faculte des Sciences, CP255, Boulevard du Triomphe 2, B-1050 Bruxelles (Belgium); Espinosa, E H; Ionescu, R; Leghrib, R; Llobet, E [Department of Electronic Engineering, Universitat Rovira i Virgili, Avenida Paisos Catalans 26, E-43007 Tarragona (Spain); Ewels, C P; Suarez-Martinez, I [Institut des Materiaux Jean Rouxel (IMN), Universite de Nantes, 2 rue de la Houssiniere-BP 32229, F-44322 Nantes Cedex 3 (France); Guillot, J; Mansour, A; Migeon, H-N [Departement Science et Analyse des Materiaux, Centre de Recherche Public-Gabriel Lippmann, rue du Brill 41, L-4422 Belvaux (Luxembourg); Watson, G E, E-mail: jean-jacques.pireaux@fundp.ac.b [Vega Science Trust, Unit 118, Science Park SQ, Brighton, BN1 9SB (United Kingdom)

    2009-09-16

    Carbon nanotube surfaces, activated and randomly decorated with metal nanoclusters, have been studied in uniquely combined theoretical and experimental approaches as prototypes for molecular recognition. The key concept is to shape metallic clusters that donate or accept a fractional charge upon adsorption of a target molecule, and modify the electron transport in the nanotube. The present work focuses on a simple system, carbon nanotubes with gold clusters. The nature of the gold-nanotube interaction is studied using first-principles techniques. The numerical simulations predict the binding and diffusion energies of gold atoms at the tube surface, including realistic atomic models for defects potentially present at the nanotube surface. The atomic structure of the gold nanoclusters and their effect on the intrinsic electronic quantum transport properties of the nanotube are also predicted. Experimentally, multi-wall CNTs are decorated with gold clusters using (1) vacuum evaporation, after activation with an RF oxygen plasma and (2) colloid solution injected into an RF atmospheric plasma; the hybrid systems are accurately characterized using XPS and TEM techniques. The response of gas sensors based on these nano{sup 2}hybrids is quantified for the detection of toxic species like NO{sub 2}, CO, C{sub 2}H{sub 5}OH and C{sub 2}H{sub 4}.

  10. The X-like shaped spatiotemporal structure of the biphoton entangled state in a cold two-level atomic ensemble.

    Science.gov (United States)

    Zhang, Dasen; Zhang, Zhiming

    2017-02-20

    We study the spatiotemporal structure of the biphoton entangled state generated by the four-wave mixing (FWM) process in a cold two-level atomic ensemble. We analyze, for the first time, the X-like shaped structure of the biphoton entangled state and the geometry of the biphoton correlation for different lengths and densities of the cold atomic ensemble. The propagation equations of the photon pairs generated from FWM process are derived in a spatiotemporal framework. By means of the input-output relations of the propagation equations, the biphoton amplitude function is obtained in a spatiotemporal domain. In the given frequency range, the biphoton amplitude displays an X-like shaped geometry, nonfactorizable in the space-time domain. Such an X-like shaped spatiotemporal structure is caused by the phase matching and the FWM gain. The former leads to the X-like shaped envelope of the biphoton correlation, while the latter gives rise to the oscillations around the X-like shaped envelope.

  11. Element-resolved atomic structure imaging of rocksalt Ge2Sb2Te5 phase-change material

    Science.gov (United States)

    Zhang, Bin; Zhang, Wei; Shen, Zhenju; Chen, Yongjin; Li, Jixue; Zhang, Shengbai; Zhang, Ze; Wuttig, Matthias; Mazzarello, Riccardo; Ma, Evan; Han, Xiaodong

    2016-05-01

    Disorder-induced electron localization and metal-insulator transitions (MITs) have been a very active research field starting from the seminal paper by Anderson half a century ago. However, pure Anderson insulators are very difficult to identify due to ubiquitous electron-correlation effects. Recently, an MIT has been observed in electrical transport measurements on the crystalline state of phase-change GeSbTe compounds, which appears to be exclusively disorder driven. Subsequent density functional theory simulations have identified vacancy disorder to localize electrons at the Fermi level. Here, we report a direct atomic scale chemical identification experiment on the rocksalt structure obtained upon crystallization of amorphous Ge2Sb2Te5. Our results confirm the two-sublattice structure resolving the distribution of chemical species and demonstrate the existence of atomic disorder on the Ge/Sb/vacancy sublattice. Moreover, we identify a gradual vacancy ordering process upon further annealing. These findings not only provide a structural underpinning of the observed Anderson localization but also have implications for the development of novel multi-level data storage within the crystalline phases.

  12. The X-like shaped spatiotemporal structure of the biphoton entangled state in a cold two-level atomic ensemble

    Science.gov (United States)

    Zhang, Dasen; Zhang, Zhiming

    2017-01-01

    We study the spatiotemporal structure of the biphoton entangled state generated by the four-wave mixing (FWM) process in a cold two-level atomic ensemble. We analyze, for the first time, the X-like shaped structure of the biphoton entangled state and the geometry of the biphoton correlation for different lengths and densities of the cold atomic ensemble. The propagation equations of the photon pairs generated from FWM process are derived in a spatiotemporal framework. By means of the input-output relations of the propagation equations, the biphoton amplitude function is obtained in a spatiotemporal domain. In the given frequency range, the biphoton amplitude displays an X-like shaped geometry, nonfactorizable in the space-time domain. Such an X-like shaped spatiotemporal structure is caused by the phase matching and the FWM gain. The former leads to the X-like shaped envelope of the biphoton correlation, while the latter gives rise to the oscillations around the X-like shaped envelope. PMID:28218235

  13. Equilibrated Atomic Models of Outward-Facing P-glycoprotein and Effect of ATP Binding on Structural Dynamics

    Science.gov (United States)

    Pan, Lurong; Aller, Stephen G.

    2015-01-01

    P-glycoprotein (Pgp) is an ATP-binding cassette (ABC) transporter that alternates between inward- and outward-facing conformations to capture and force substrates out of cells like a peristaltic pump. The high degree of similarity in outward-facing structures across evolution of ABC transporters allowed construction of a high-confidence outward-facing Pgp atomic model based on crystal structures of outward-facing Sav1866 and inward-facing Pgp. The model adhered to previous experimentally determined secondary- and tertiary- configurations during all-atom molecular dynamics simulations in the presence or absence of MgATP. Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access. The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket. Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms. PMID:25600711

  14. Atomic layer deposition TiO{sub 2} coated porous silicon surface: Structural characterization and morphological features

    Energy Technology Data Exchange (ETDEWEB)

    Iatsunskyi, Igor, E-mail: igoyat@amu.edu.pl [NanoBioMedical Centre, Adam Mickiewicz University, 85 Umultowska str., 61-614, Poznan (Poland); Department of Experimental Physics, Odessa National I.I. Mechnikov University, 42, Pastera str., 65023 Odessa (Ukraine); Jancelewicz, Mariusz; Nowaczyk, Grzegorz [NanoBioMedical Centre, Adam Mickiewicz University, 85 Umultowska str., 61-614, Poznan (Poland); Kempiński, Mateusz [NanoBioMedical Centre, Adam Mickiewicz University, 85 Umultowska str., 61-614, Poznan (Poland); Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poland (Poland); Peplińska, Barbara [NanoBioMedical Centre, Adam Mickiewicz University, 85 Umultowska str., 61-614, Poznan (Poland); Department of Macromolecular Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland); Jarek, Marcin; Załęski, Karol [NanoBioMedical Centre, Adam Mickiewicz University, 85 Umultowska str., 61-614, Poznan (Poland); Jurga, Stefan [NanoBioMedical Centre, Adam Mickiewicz University, 85 Umultowska str., 61-614, Poznan (Poland); Department of Macromolecular Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland); Smyntyna, Valentyn [Department of Experimental Physics, Odessa National I.I. Mechnikov University, 42, Pastera str., 65023 Odessa (Ukraine)

    2015-08-31

    TiO{sub 2} thin films were grown on highly-doped p-Si (100) macro- and mesoporous structures by atomic layer deposition (ALD) using TiCl{sub 4} 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 TiO{sub 2} crystallites was determined by TEM, XRD and Raman spectroscopy. It was shown that the mean crystallite size and the crystallinity of the TiO{sub 2} 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 TiO{sub 2} and porous Si were established. • The approximate size of TiO{sub 2} nanocrystals was estimated. • The model of the atomic layer deposition coating in the porous Si was presented.

  15. 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.

  16. 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).

  17. Local atomic structural investigations of precursory phenomenon of the hydrogen release from LiAlD4

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Toyoto [ORNL; Tomiyasu, Dr. Keisuke [Tohoku University, Japan; Ikeda, Kazutaka [High Energy Accelerator Research Organization, KEK; Otomo, Toshiya [ORNL; Feygenson, Mikhail [ORNL; Neuefeind, Joerg C [ORNL; Yamada, Kazuyoshi [Institute for Materials Research, Tohoku University, Sendai, Japan; Orimo, Shin-ichi [Institute for Materials Research, Tohoku University, Sendai, Japan

    2013-01-01

    Local atomic structural investigations of LiAlD4, which is composed of Li+ and [AlD4], at 40 300 K were studied by total neutron scattering combined with pair distribution function (PDF) analysis for understanding of hydrogen release from LiAlD4. The results showed that the Al D pair distribution almost unchanged, while the Li D pair distribution clearly started to broaden and shrink above 200 250 K. The shrinking of the Li D pair distribution might lead to the local generation of LiD, which was speculated as the precursory phenomenon for the hydrogen release from LiAlD4.

  18. Selective spatial localization of the atom displacements in one-dimensional hybrid quasi-regular (Thue Morse and Rudin Shapiro)/periodic structures

    Science.gov (United States)

    Montalbán, A.; Velasco, V. R.; Tutor, J.; Fernández-Velicia, F. J.

    2007-06-01

    We have studied the vibrational frequencies and atom displacements of one-dimensional systems formed by combinations of Thue-Morse and Rudin-Shapiro quasi-regular stackings with periodic ones. The materials are described by nearest-neighbor force constants and the corresponding atom masses. These systems exhibit differences in the frequency spectrum as compared to the original simple quasi-regular generations and periodic structures. The most important feature is the presence of separate confinement of the atom displacements in one of the parts forming the total composite structure for different frequency ranges, thus acting as a kind of phononic cavity.

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

    OpenAIRE

    Borisyuk, P. V.; Vasilyev, O S; Krasavin, A.V.; Lebedinskii, Yu Yu; V. I. Troyan; Tkalya, E. V.

    2015-01-01

    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 ...

  20. 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.

  1. Modulation of the photonic band structure topology of a honeycomb lattice in an atomic vapor

    CERN Document Server

    Zhang, Yiqi; Belić, Milivoj R; Wu, Zhenkun; Zhang, Yanpeng

    2015-01-01

    In an atomic vapor, a honeycomb lattice can be constructed by utilizing the three-beam interference method. In the method, the interference of the three beams splits the dressed energy level periodically, forming a periodic refractive index modulation with the honeycomb profile. The energy band topology of the honeycomb lattice can be modulated by frequency detunings, thereby affecting the appearance (and disappearance) of Dirac points and cones in the momentum space. This effect can be usefully exploited for the generation and manipulation of topological insulators.

  2. Characterization of Atomic Structure, Relaxation and Phase Transformation Mechanisms in Bulk and Thin Film Amorphous Chalcogenides and Gallium Antimonide

    Science.gov (United States)

    Edwards, Trenton Gerard

    This dissertation details the characterization of the atomic structure, relaxation processes and phase transformation mechanisms in a variety of chalcogenide (selenides and tellurides) and other non-oxide (Ga-Sb alloys) glasses which are highly relevant to optoelectronic and phase change memory applications. One of the principal goals of these studies is to develop a fundamental, atomistic understanding of the structure-property relationships in these materials. Variable temperature Raman spectroscopy is used to the study the structure and its temperature dependent relaxation in GexSe100-x glasses and supercooled liquids with x ≤ 33.33 %. It is shown that the compositional dependence of the relative fractions of the edge- and corner-shared GeSe4 tetrahedra is fully consistent with a structural model based on random connectivity between the tetrahedral and chain elements. Temperature-dependent structural changes involve a progressive conversion of edge-shared to corner shared GeSe4 tetrahedra with decreasing equilibration temperature. The time scale of this structural conversion agrees with both enthalpy and shear relaxation near the glass transition. The temperature dependent change in the edge- vs. corner- sharing tetrahedral speciation is shown to be related to the production of configurational entropy, indicating a connection between structural relaxation, configurational entropy, and viscous flow. A combination of Raman and 77Se nuclear magnetic resonance (NMR) spectroscopy is applied to study the structure of a series of Se-deficient GexSe100-x glasses, with 42 ≥ x ≥ 33.33. Considerable violation of chemical order in the nearest-neighbor coordination environments of the constituent atoms is observed in the stoichiometric GeSe2 glass. On the other hand, the presence of a random distribution of Ge-Ge bonds can be inferred in the Se-deficient glasses. Furthermore, the results of this study conclusively indicate that the structure of these glasses is

  3. 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.

  4. 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.

  5. 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.

  6. Atomic and electronic structure of CdTe/metal (Cu, Al, Pt) interfaces and their influence to the Schottky barrier

    Science.gov (United States)

    Odkhuu, Dorj; Miao, Mao-sheng; Aqariden, F.; Grein, Christoph; Kioussis, Nicholas

    2016-11-01

    Schottky barrier heights (SBHs) and other features of the interfaces are determining factors for the performance of the CdTe based high-energy photon detectors. Although known for long time that SBH is sensitive to surface treatment and metal contact growth method, there is a lack of understanding of the effect of the atomic and electronic structures of CdTe/metal interface on the SBH. Employing first-principles electronic structure calculations, we have systematically studied the structural stability and electronic properties of a number of representing structures of Cd Terminated CdTe/metal (Cu, Pt, and Al) interfaces. Comparison of the total energies of the various optimized structural configurations allows to identify the existence of Te-metal alloy formation at the interface. The SBHs of Cu, Pt, and Al metal contacts with a number of stable interface structures are determined by aligning the band edges of bulk CdTe with the Fermi level of the metal/CdTe system. We find that the metal-induced states in the gap play an essential role in determining the SBH.

  7. 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.

  8. Dirac R-matrix calculations of photoionization cross sections of Ni XII and atomic structure data of Ni XIII

    Science.gov (United States)

    Nazir, R. T.; Bari, M. A.; Bilal, M.; Sardar, S.; Nasim, M. H.; Salahuddin, M.

    2017-02-01

    We performed R-matrix calculations for photoionization cross sections of the two ground state configuration 3s23p5 (^2P^o3/2,1/2) levels and 12 excited states of Ni XII using relativistic Dirac Atomic R-matrix Codes (DARC) across the photon energy range between the ionizations thresholds of the corresponding states and well above the thresholds of the last level of the Ni XIII target ion. Generally, a good agreement is obtained between our results and the earlier theoretical photoionization cross sections. Moreover, we have used two independent fully relativistic GRASP and FAC codes to calculate fine-structure energy levels, wavelengths, oscillator strengths, transitions rates among the lowest 48 levels belonging to the configuration (3s23p4, 3s3p5, 3p6, 3s23p33d) in Ni XIII. Additionally, radiative lifetimes of all the excited states of Ni XIII are presented. Our results of the atomic structure of Ni XIII show good agreement with other theoretical and experimental results available in the literature. A good agreement is found between our calculated lifetimes and the experimental ones. Our present results are useful for plasma diagnostic of fusion and astrophysical plasmas.

  9. Local atomic structural investigations of precursory phenomenon of the hydrogen release from LiAlD{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Toyoto, E-mail: toyoto@imr.tohoku.ac.jp [Institute for Materials Research, Tohoku University, Aoba-ku, Sendai 980-8577 (Japan); Tomiyasu, Keisuke [Department of Physics, Tohoku University, 6-3 Aoba, Aoba-ku, Sendai 980-8578 (Japan); Ikeda, Kazutaka; Otomo, Toshiya [Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801 (Japan); Feygenson, Mikhail; Neuefeind, Jörg [Chemical and Engineering Materials Division, Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Yamada, Kazuyoshi [Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801 (Japan); Orimo, Shin-ichi [Institute for Materials Research, Tohoku University, Aoba-ku, Sendai 980-8577 (Japan); WPI-Advanced Institute for Materials Research, Tohoku University, Aoba-ku, Sendai 980-8577 (Japan)

    2014-02-15

    Highlights: • Local atomic structural changes in LiAlD{sub 4} were investigated. • The Li–D pair distribution started to broaden and shrink above 200–250 K. • The Al–D pair distribution remained nearly constant below 300 K. -- Abstract: Local atomic structural investigations of LiAlD{sub 4}, which is composed of Li{sup +} and [AlD{sub 4}]{sup −}, at 40–300 K were studied by total neutron scattering combined with pair distribution function (PDF) analysis for understanding of hydrogen release from LiAlD{sub 4}. The results showed that the Al–D pair distribution almost unchanged, while the Li–D pair distribution clearly started to broaden and shrink above 200–250 K. The shrinking of the Li–D pair distribution might lead to the local generation of LiD, which was speculated as the precursory phenomenon for the hydrogen release from LiAlD{sub 4}.

  10. Optical processes of photonic band gap structure with dressing field in atomic system

    Science.gov (United States)

    Zhang, Yun-Zhe; Liu, Zhe; Cai, Kang-Ning; Zhong, Hua; Zhang, Wei-Tao; Liu, Jun-Feng; Zhang, Yan-Peng

    2016-12-01

    We experimentally investigate probe transmission signals (PTS), the four-wave mixing photonic band gap signal (FWM BGS), and the fluorescence signal (FLS) in an inverted Y-type four level atomic system. For the first time, we compare the FLS of the two ground-state hyperfine levels of Rb 85. In particular, the second-order and the fourth-order fluorescence signals perform dramatic dressing discrepancies under the two hyperfine levels. Moreover, we find that the dressing field has some dressing effects on three such types of signals. Therefore, we demonstrate that the characteristics of PTS, FWM BGS, and FLS can be controlled by frequency detunings, the powers or phases of the dressing field. Such research could have potential applications in optical diodes, amplifiers, and quantum information processing.

  11. 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.

  12. 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.

  13. 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

  14. Combining Theory and Experiment to Characterize the Atomic Structures of Surface-Deposited Au309 Clusters

    NARCIS (Netherlands)

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

    2007-01-01

    Gold clusters with icosahedral, decahedral, and cuboctahedral shell structures, have been studied using the Gupta many-body potential, to aid in the structural characterization of surface-deposited Au309 clusters using high-angle annular dark field-scanning transmission electron microscopy (HAADF-ST

  15. 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

  16. The atomic geometries of GaP(110) and ZnS(110) revisited - A structural ambiguity and its resolution

    Science.gov (United States)

    Duke, C. B.; Paton, A.; Kahn, A.

    1984-01-01

    The atomic geometries of GaP(110) and ZnS(110) are reexamined using the R-factor minimization procedure, developed for GaAs(110) and previously applied to GaSb(110), ZnTe(110), InAs(110), and AlP(110), to analyze experimental elastic low-energy electron diffraction intensities. Unlike most of the earlier cases, both GaP(110) and ZnS(110) exhibit two distinct minimum-Rx structures which cannot be distinguished by analysis of the shapes of the intensity profiles alone. One region of best-fit structures exhibits top-layer displacements normal to the surface characterized by a small bond-length-conserving, top-layer rotation (omega aproximately 2-3 deg), a small relaxation of the top layer away from the surface, and a 10 percent expansion of the top-layer bond length. The other region of best-fit structures is the conventional one: nearly bond-length-conserving rotations of omega = 26-28 deg in the top layer and a small (approximately 0.1 A) contraction of the uppermost layer spacing. This ambiguity may be removed, however, by consideration of the integrated beam intensities. The conventional region of structural parameters provides a decisively better description of the relative magnitudes of the integrated beam intensities and hence is the preferred structure.

  17. 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.

  18. 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.

  19. 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

  20. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser.

    Science.gov (United States)

    Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Bunker, Richard D; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P; Doak, R Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L; Wang, Dingjie; Weierstall, Uwe; White, Thomas A; Williams, Garth J; Zatsepin, Nadia A; Fromme, Petra; Spence, John C H; Goldie, Kenneth N; Jehle, Johannes A; Metcalf, Peter; Barty, Anton; Chapman, Henry N

    2017-02-28

    To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm(3) in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm(3) in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.

  1. Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution.

    Science.gov (United States)

    von der Ecken, Julian; Heissler, Sarah M; Pathan-Chhatbar, Salma; Manstein, Dietmar J; Raunser, Stefan

    2016-06-30

    The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated during a complex mechanochemical reaction cycle. Crystal structures of myosin in different states have provided important structural insights into the myosin motor cycle when myosin is detached from F-actin. The difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of actomyosin complexes. Thus, although structural models exist of F-actin in complex with various myosins, a high-resolution structure of the F-actin–myosin complex is missing. Here, using electron cryomicroscopy, we present the structure of a human rigor actomyosin complex at an average resolution of 3.9 Å. The structure reveals details of the actomyosin interface, which is mainly stabilized by hydrophobic interactions. The negatively charged amino (N) terminus of actin interacts with a conserved basic motif in loop 2 of myosin, promoting cleft closure in myosin. Surprisingly, the overall structure of myosin is similar to rigor-like myosin structures in the absence of F-actin, indicating that F-actin binding induces only minimal conformational changes in myosin. A comparison with pre-powerstroke and intermediate (Pi-release) states of myosin allows us to discuss the general mechanism of myosin binding to F-actin. Our results serve as a strong foundation for the molecular understanding of cytoskeletal diseases, such as autosomal dominant hearing loss and diseases affecting skeletal and cardiac muscles, in particular nemaline myopathy and hypertrophic cardiomyopathy.

  2. Atomic Structure of Clathrin: A β Propeller Terminal Domain Joins an α Zigzag Linker

    OpenAIRE

    ter Haar, Ernst; Musacchio, Andrea; Harrison, Stephen C.; Kirchhausen, Tomas

    1998-01-01

    Clathrin triskelions form the lattice that organizes recruitment of proteins to coated pits and helps drive vesiculation of the lipid bilayer. We report the crystal structure at 2.6 Å resolution of a 55 kDa N-terminal fragment from the 190 kDa clathrin heavy chain. The structure comprises the globular “terminal domain” and the linker that joins it to the end of a triskelion leg. The terminal domain is a seven-blade β propeller, a structure well adapted to interaction with multiple partners, s...

  3. 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

  4. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome.

    Science.gov (United States)

    Passos, Dario Oliveira; Li, Min; Yang, Renbin; Rebensburg, Stephanie V; Ghirlando, Rodolfo; Jeon, Youngmin; Shkriabai, Nikoloz; Kvaratskhelia, Mamuka; Craigie, Robert; Lyumkis, Dmitry

    2017-01-06

    Like all retroviruses, HIV-1 irreversibly inserts a viral DNA (vDNA) copy of its RNA genome into host target DNA (tDNA). The intasome, a higher-order nucleoprotein complex composed of viral integrase (IN) and the ends of linear vDNA, mediates integration. Productive integration into host chromatin results in the formation of the strand transfer complex (STC) containing catalytically joined vDNA and tDNA. HIV-1 intasomes have been refractory to high-resolution structural studies. We used a soluble IN fusion protein to facilitate structural studies, through which we present a high-resolution cryo-electron microscopy (cryo-EM) structure of the core tetrameric HIV-1 STC and a higher-order form that adopts carboxyl-terminal domain rearrangements. The distinct STC structures highlight how HIV-1 can use the common retroviral intasome core architecture to accommodate different IN domain modules for assembly.

  5. The atomic structure of polar and non-polar InGaN quantum wells and the green gap problem.

    Science.gov (United States)

    Humphreys, C J; Griffiths, J T; Tang, F; Oehler, F; Findlay, S D; Zheng, C; Etheridge, J; Martin, T L; Bagot, P A J; Moody, M P; Sutherland, D; Dawson, P; Schulz, S; Zhang, S; Fu, W Y; Zhu, T; Kappers, M J; Oliver, R A

    2017-02-03

    We have used high resolution transmission electron microscopy (HRTEM), aberration-corrected quantitative scanning transmission electron microscopy (Q-STEM), atom probe tomography (APT) and X-ray diffraction (XRD) to study the atomic structure of (0001) polar and (11-20) non-polar InGaN quantum wells (QWs). This paper provides an overview of the results. Polar (0001) InGaN in QWs is a random alloy, with In replacing Ga randomly. The InGaN QWs have atomic height interface steps, resulting in QW width fluctuations. The electrons are localised at the top QW interface by the built-in electric field and the well-width fluctuations, with a localisation energy of typically 20meV. The holes are localised near the bottom QW interface, by indium fluctuations in the random alloy, with a localisation energy of typically 60meV. On the other hand, the non-polar (11-20) InGaN QWs contain nanometre-scale indium-rich clusters which we suggest localise the carriers and produce longer wavelength (lower energy) emission than from random alloy non-polar InGaN QWs of the same average composition. The reason for the indium-rich clusters in non-polar (11-20) InGaN QWs is not yet clear, but may be connected to the lower QW growth temperature for the (11-20) InGaN QWs compared to the (0001) polar InGaN QWs.

  6. Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

    Science.gov (United States)

    Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

    2015-11-19

    The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).

  7. 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.

  8. 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.

  9. Correlating anomalous diffusion with lipid bilayer membrane structure using single molecule tracking and atomic force microscopy

    Science.gov (United States)

    Skaug, Michael J.; Faller, Roland; Longo, Marjorie L.

    2011-06-01

    Anomalous diffusion has been observed abundantly in the plasma membrane of biological cells, but the underlying mechanisms are still unclear. In general, it has not been possible to directly image the obstacles to diffusion in membranes, which are thought to be skeleton bound proteins, protein aggregates, and lipid domains, so the dynamics of diffusing particles is used to deduce the obstacle characteristics. We present a supported lipid bilayer system in which we characterized the anomalous diffusion of lipid molecules using single molecule tracking, while at the same time imaging the obstacles to diffusion with atomic force microscopy. To explain our experimental results, we performed lattice Monte Carlo simulations of tracer diffusion in the presence of the experimentally determined obstacle configurations. We correlate the observed anomalous diffusion with obstacle area fraction, fractal dimension, and correlation length. To accurately measure an anomalous diffusion exponent, we derived an expression to account for the time-averaging inherent to all single molecule tracking experiments. We show that the length of the single molecule trajectories is critical to the determination of the anomalous diffusion exponent. We further discuss our results in the context of confinement models and the generating stochastic process.

  10. Structural and optical properties of electrohydrodynamically atomized TiO{sub 2} nanostructured thin films

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Kyung-Hyun; Duraisamy, Navaneethan; Muhammad, Nauman Malik [Jeju National University, School of Mechatronics Engineering, Jeju (Korea, Republic of); Kim, Inyoung; Jo, Jeongdai [Korea Institute of Machinery and Materials (KIMM), Printed Electronics Research Center, Daejeon (Korea, Republic of); Choi, Hyunseok [Korea Institute of Industrial Technology (KITECH), Cheonan, Chungcheongnam-do (Korea, Republic of)

    2012-06-15

    In this paper, we report an alternate technique for the deposition of nanostructured TiO{sub 2} thin films using the electrohydrodynamic atomization (EHDA) technique using polyvinylpyrrolidone (PVP) as a stabilizer. The required parameters for achieving uniform TiO{sub 2} films using EHDA are also discussed in detail. X-ray diffraction results confirm that the TiO{sub 2} films were oriented in the anatase phase. Scanning electron microscope studies revealed the uniform deposition of the TiO{sub 2}. The purity of the films is characterized by using Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS), confirming the presence of Ti-O bonding in the films without any organic residue. The optical properties of the TiO{sub 2} films were measured by UV-visible spectroscopy, which shows that the transparency of the films is nearly 85% in the visible region. The current-voltage (I-V) curve of the TiO{sub 2} thin films shows a nearly linear behavior with 45 m{omega} cm of electrical resistivity. These results suggest that TiO{sub 2} thin films deposited via the EHDA method possess promising applications in optoelectronic devices. (orig.)

  11. 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.

  12. Evaluation of the interactions between polymeric chains and surfaces with different structures performed by an atomic force microscope

    Directory of Open Access Journals (Sweden)

    Oréfice Rodrigo Lambert

    1998-01-01

    Full Text Available Interactions between polymers and inorganic surfaces are present in a series of phenomena involving processes such as coagulation and deffloculation of ceramic powder and adsorption of organic macromolecules on the surface of implants, among others. In this work, Atomic Force Microscopy (AFM was modified to allow the evaluation of interactions between polymeric chains and inorganic surfaces (silica with different structures. Polymers (sulfonated polysulfone were grafted onto AFM cantilevers. AFM force-distance curves were obtained for this modified tip against a series of substrates produced by depositing silica films on silicon wafers. The structure of the silica layer was modified by employing heat treatments at different temperatures. The results showed that the interactions between polymer and surfaces are dependent on the structure of the surfaces. Penetration of the polymeric chains can occur through a soft gel layer (substrates treated at low temperature, 110 °C. For surfaces with dense silica layers, the results showed that not only the concentration of hydroxy groups but also their spatial distribution along the surfaces are important in defining the magnitude of interactions between polymers and surfaces. A model involving a molecular recognition process, in which interactions are maximized for inorganic surfaces with structures that can match the chemical architecture of the polymer, was then used to explain the obtained results.

  13. Atomic structure and thermal stability of Pt-Fe bimetallic nanoparticles: from alloy to core/shell architectures.

    Science.gov (United States)

    Huang, Rao; Wen, Yu-Hua; Shao, Gui-Fang; Sun, Shi-Gang

    2016-06-22

    Bimetallic nanoparticles comprising noble metal and non-noble metal have attracted intense interest over the past few decades due to their low cost and significantly enhanced catalytic performances. In this article, we have explored the atomic structure and thermal stability of Pt-Fe alloy and core-shell nanoparticles by molecular dynamics simulations. In Fe-core/Pt-shell nanoparticles, Fe with three different structures, i.e., body-centered cubic (bcc), face-centered cubic (fcc), and amorphous phases, has been considered. Our results show that Pt-Fe alloy is the most stable configuration among the four types of bimetallic nanoparticles. It has been discovered that the amorphous Fe cannot stably exist in the core and preferentially transforms into the fcc phase. The phase transition from bcc to hexagonal close packed (hcp) has also been observed in bcc-Fe-core/Pt-shell nanoparticles. In contrast, Fe with the fcc structure is the most preferred as the core component. These findings are helpful for understanding the structure-property relationships of Pt-Fe bimetallic nanoparticles, and are also of significance to the synthesis and application of noble metal based nanoparticle catalysts.

  14. 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.

  15. a Proposal for a General Method for Determining Semi-Experimental Equilibrium Structures of Carbon Atom Backbones

    Science.gov (United States)

    Craig, Norman C.

    2010-06-01

    Semi-experimental equilibrium structures are determined from ground state rotational constants derived from the analysis of rotational transitions in high-resolution spectra and from the quantum chemical calculation of spectroscopic alphas. In the full application of this method, spectra of numerous isotopic species must be investigated. Most of these isotopic species require specialized synthesis. We now propose focusing on the carbon atoms, for which microwave spectroscopy routinely yields spectra for polar molecules with 13C substitution in natural abundance. Needed spectroscopic alphas can be computed with Gaussian software. Application of the Kraitchman substitution relationships gives Cartesian coordinates for the carbon atoms and thence bond parameters for the carbon backbone. This method will be evaluated with ethylene, 1,1-difluoroethylene, 1,1-difluorocyclopropane, propene, and butadiene. The method will then be applied to cis-hexatriene and the two conformers of glycidol. R. D. Suenram, B. H. Pate, A. Lessari, J. L. Neill, S. Shipman, R. A. Holmes, M. C. Leyden, and N. C. Craig, J. Phys. Chem. A 113, 1864-1868 (2009). A. R. Conrad, N. H. Teumelsan, P. E. Wang, and M. J. Tubergen, J. Phys. Chem. A 114, 336-342 (2010).

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

    Energy Technology Data Exchange (ETDEWEB)

    Widjaja, Hantarto [School of Engineering & Information Technology, Murdoch University, Murdoch, WA 6150 (Australia); Jiang, Zhong-Tao, E-mail: Z.Jiang@murdoch.edu.au [School of Engineering & Information Technology, Murdoch University, Murdoch, WA 6150 (Australia); Altarawneh, Mohammednoor [School of Engineering & Information Technology, Murdoch University, Murdoch, WA 6150 (Australia); Yin, Chun-Yang [School of Science and Engineering, Teesside University, Borough Road, Middlesbrough TS1 3BA (United Kingdom); Goh, Bee-Min [School of Chemistry, Bedson Building, Newcastle University, NE1 7RU United Kingdom (United Kingdom); Mondinos, Nicholas [School of Engineering & Information Technology, Murdoch University, Murdoch, WA 6150 (Australia); Amri, Amun [Department of Chemical Engineering, University of Riau, Pekanbaru (Indonesia); Dlugogorski, Bogdan Z. [School of Engineering & Information Technology, Murdoch University, Murdoch, WA 6150 (Australia)

    2016-06-15

    Highlights: • We examined the orientation (zigzag, armchair) effects of F/Cl-adsorbed graphene. • Both F/Cl-adsorbed graphene systems show contrasting adsorption trends. • F favours full and 25% adsorption coverage while Cl favours 25% adsorption coverage. - Abstract: 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.

  17. Simplified protein models can rival all atom simulations in predicting folding pathways and structure

    Science.gov (United States)

    Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    We demonstrate the ability of simultaneously determining a protein’s folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing native-like substructures or "foldons". Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R.O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that native-like propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the MD study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo. PMID:23889448

  18. 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.

  19. 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.

  20. 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.