WorldWideScience

Sample records for atomic structure

  1. Teach us atom structure

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Suh Yeon

    2006-08-15

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

  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. BOOK REVIEW: Computational Atomic Structure

    Science.gov (United States)

    Post, Douglass E.

    1998-02-01

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

  4. 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.

  5. Electronic structure of atoms: atomic spectroscopy information system

    Science.gov (United States)

    Kazakov, V. V.; Kazakov, V. G.; Kovalev, V. S.; Meshkov, O. I.; Yatsenko, A. S.

    2017-10-01

    The article presents a Russian atomic spectroscopy, information system electronic structure of atoms (IS ESA) (http://grotrian.nsu.ru), and describes its main features and options to support research and training. The database contains over 234 000 records, great attention paid to experimental data and uniform filling of the database for all atomic numbers Z, including classified levels and transitions of rare earth and transuranic elements and their ions. Original means of visualization of scientific data in the form of spectrograms and Grotrian diagrams have been proposed. Presentation of spectral data in the form of interactive color charts facilitates understanding and analysis of properties of atomic systems. The use of the spectral data of the IS ESA together with its functionality is effective for solving various scientific problems and training of specialists.

  6. Niels Bohr and the Atomic Structure

    Indian Academy of Sciences (India)

    IAS Admin

    Christien Bohr, was a professor of physiology in the Copenhagen. University. Niels received his education in Copenhagen, obtain- ing his masters degree in 1909, and the doctoral degree in 1911. M Durga Prasad ... Inelastic scattering of electrons from mercury atoms. 1914. J Franck, G Hertz. Interpretation of fine structure.

  7. Atomic Reference Data for Electronic Structure Calculations

    CERN Document Server

    Kotochigova, S; Shirley, E L

    We have generated data for atomic electronic structure calculations, to provide a standard reference for results of specified accuracy under commonly used approximations. Results are presented here for total energies and orbital energy eigenvalues for all atoms from H to U, at microHartree accuracy in the total energy, as computed in the local-density approximation (LDA) the local-spin-density approximation (LSD); the relativistic local-density approximation (RLDA); and scalar-relativistic local-density approximation (ScRLDA).

  8. Structure and properties of atomic nanoclusters

    CERN Document Server

    Alonso, Julio A

    2005-01-01

    Atomic clusters are the bridge between molecules and the bulk matter. Following two key experiments - the observation of electronic shells in metallic clusters and the discovery of the C60 fullerence - the field of atomic clusters has experienced a rapid growth, and is now considered a mature field. The electrons of the cluster are confined to a small volume, hence, quantum effects are manifested on many properties of the clusters. Another interesting feature is that the properties often change in a non-smooth way as the number of atoms in the cluster increases. This book provides an updated overview of the field, and presents a detailed description of the structure and electronic properties of different types of clusters: Van der Waals clusters, metallic clusters, clusters of ionic materials and network clusters. The assembling of clusters is also considered, since specially stable clusters are expected to play a role in the future design and synthesis of new materials.

  9. 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.

  10. 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.

  11. Structurally uniform and atomically precise carbon nanostructures

    Science.gov (United States)

    Segawa, Yasutomo; Ito, Hideto; Itami, Kenichiro

    2016-01-01

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

  12. MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES

    Energy Technology Data Exchange (ETDEWEB)

    D. M. PARKIN; L. CHEN; ET AL

    2000-09-01

    We explored both experimentally and theoretically the behavior of materials at stresses close to their theoretical strength. This involves the preparation of ultra fine scale structures by a variety of fabrication methods. In the past year work has concentrated on wire drawing of in situ composites such as Cu-Ag and Cu-Nb. Materials were also fabricated by melting alloys in glass and drawing them into filaments at high temperatures by a method known as Taylor wire technique. Cu-Ag microwires have been drawn by this technique to produce wires 10 {micro}m in diameter that consist of nanoscale grains of supersaturated solid solution. Organogels formed from novel organic gelators containing cholesterol tethered to squaraine dyes or trans-stilbene derivatives have been studied from several different perspectives. The two types of molecules are active toward several organic liquids, gelling in some cases at w/w percentages as low as 0.1. While relatively robust, acroscopically dry gels are formed in several cases, studies with a variety of probes indicate that much of the solvent may exist in domains that are essentially liquid-like in terms of their microenvironment. The gels have been imaged by atomic force microscopy and conventional and fluorescence microscopy, monitoring both the gelator fluorescence in the case of the stilbene-cholesterol gels and, the fluorescence of solutes dissolved in the solvent. Remarkably, our findings show that several of the gels are composed of similarly appearing fibrous structures visible at the nano-, micro-, and macroscale.

  13. 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).

  14. Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy.

    Science.gov (United States)

    Krivanek, Ondrej L; Chisholm, Matthew F; Nicolosi, Valeria; Pennycook, Timothy J; Corbin, George J; Dellby, Niklas; Murfitt, Matthew F; Own, Christopher S; Szilagyi, Zoltan S; Oxley, Mark P; Pantelides, Sokrates T; Pennycook, Stephen J

    2010-03-25

    Direct imaging and chemical identification of all the atoms in a material with unknown three-dimensional structure would constitute a very powerful general analysis tool. Transmission electron microscopy should in principle be able to fulfil this role, as many scientists including Feynman realized early on. It images matter with electrons that scatter strongly from individual atoms and whose wavelengths are about 50 times smaller than an atom. Recently the technique has advanced greatly owing to the introduction of aberration-corrected optics. However, neither electron microscopy nor any other experimental technique has yet been able to resolve and identify all the atoms in a non-periodic material consisting of several atomic species. Here we show that annular dark-field imaging in an aberration-corrected scanning transmission electron microscope optimized for low voltage operation can resolve and identify the chemical type of every atom in monolayer hexagonal boron nitride that contains substitutional defects. Three types of atomic substitutions were found and identified: carbon substituting for boron, carbon substituting for nitrogen, and oxygen substituting for nitrogen. The substitutions caused in-plane distortions in the boron nitride monolayer of about 0.1 A magnitude, which were directly resolved, and verified by density functional theory calculations. The results demonstrate that atom-by-atom structural and chemical analysis of all radiation-damage-resistant atoms present in, and on top of, ultra-thin sheets has now become possible.

  15. Revealing and exploiting hierarchical material structure through complex atomic networks

    Science.gov (United States)

    Ahnert, Sebastian E.; Grant, William P.; Pickard, Chris J.

    2017-08-01

    One of the great challenges of modern science is to faithfully model, and understand, matter at a wide range of scales. Starting with atoms, the vastness of the space of possible configurations poses a formidable challenge to any simulation of complex atomic and molecular systems. We introduce a computational method to reduce the complexity of atomic configuration space by systematically recognising hierarchical levels of atomic structure, and identifying the individual components. Given a list of atomic coordinates, a network is generated based on the distances between the atoms. Using the technique of modularity optimisation, the network is decomposed into modules. This procedure can be performed at different resolution levels, leading to a decomposition of the system at different scales, from which hierarchical structure can be identified. By considering the amount of information required to represent a given modular decomposition we can furthermore find the most succinct descriptions of a given atomic ensemble. Our straightforward, automatic and general approach is applied to complex crystal structures. We show that modular decomposition of these structures considerably simplifies configuration space, which in turn can be used in discovery of novel crystal structures, and opens up a pathway towards accelerated molecular dynamics of complex atomic ensembles. The power of this approach is demonstrated by the identification of a possible allotrope of boron containing 56 atoms in the primitive unit cell, which we uncover using an accelerated structure search, based on a modular decomposition of a known dense phase of boron, γ-B28.

  16. 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....

  17. Update on nuclear structure effects in light muonic atoms

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez, Oscar Javier, E-mail: javierh@triumf.ca; Dinur, Nir Nevo; Ji, Chen; Bacca, Sonia [TRIUMF (Canada); Barnea, Nir [The Hebrew University, Racah Institute of Physics (Israel)

    2016-12-15

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

  18. 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,…

  19. 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.

  20. Niels Bohr and the quantum atom the Bohr model of atomic structure 1913-1925

    CERN Document Server

    Kragh, Helge

    2012-01-01

    Niels Bohr and the Quantum Atom is the first book that focuses in detail on the birth and development of Bohr's atomic theory and gives a comprehensive picture of it. At the same time it offers new insight into Bohr's peculiar way of thinking, what Einstein once called his 'unique instinct and tact'. Contrary to most other accounts of the Bohr atom, the book presents it in a broader perspective which includes the reception among other scientists and the criticism launched against it by scientists of a more conservative inclination. Moreover, it discusses the theory as Bohr originally conceived it, namely, as an ambitious theory covering the structure of atoms as well as molecules. By discussing the theory in its entirety it becomes possible to understand why it developed as it did and thereby to use it as an example of the dynamics of scientific theories.

  1. 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.

  2. Atomic structure of clusters through chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Riley, S.J.

    1991-01-01

    Techniques for the probing of isolated metal cluster structure through adsorbate binding patterns will be described. The saturation of clusters with reagents such as ammonia and nitrogen provides information on the number of preferred binding sites for these reagents. The dependence of this number on cluster size can suggest particular structural themes. The equilibrium reaction with water can be used to identify cluster sizes having especially enhanced binding for the water molecule. Again, the sequence of cluster sizes showing such enhancement can point to specific cluster structure. The reaction with oxygen can identify cluster sizes having particularly high ionization potentials, and these can be compared to simple models for the electronic structure of metal clusters. Representative applications of these probes to iron, cobalt, nickel, and copper clusters will be discussed. 5 figs.

  3. ISOTROPIC INELASTIC COLLISIONS IN A MULTITERM ATOM WITH HYPERFINE STRUCTURE

    Energy Technology Data Exchange (ETDEWEB)

    Belluzzi, Luca [Istituto Ricerche Solari Locarno, CH-6605 Locarno Monti (Switzerland); Landi Degl’Innocenti, Egidio [Dipartimento di Fisica e Astronomia, Università di Firenze, I-50125 Firenze (Italy); Bueno, Javier Trujillo [Instituto de Astrofísica de Canarias, E-38205 La Laguna, Tenerife (Spain)

    2015-10-10

    A correct modeling of the scattering polarization profiles observed in some spectral lines of diagnostic interest, the sodium doublet being one of the most important examples, requires taking hyperfine structure (HFS) and quantum interference between different J-levels into account. An atomic model suitable for taking these physical ingredients into account is the so-called multiterm atom with HFS. In this work, we introduce and study the transfer and relaxation rates due to isotropic inelastic collisions with electrons, which enter the statistical equilibrium equations (SEE) for the atomic density matrix of this atomic model. Under the hypothesis that the electron–atom interaction is described by a dipolar operator, we provide useful relations between the rates describing the transfer and relaxation of quantum interference between different levels (whose numerical values are in most cases unknown) and the usual rates for the atomic level populations, for which experimental data and/or approximate theoretical expressions are generally available. For the particular case of a two-term atom with HFS, we present an analytical solution of the SEE for the spherical statistical tensors of the upper term, including both radiative and collisional processes, and we derive the expression of the emission coefficient in the four Stokes parameters. Finally, an illustrative application to the Na i D{sub 1} and D{sub 2} lines is presented.

  4. Single-atom based coherent quantum interference device structure.

    Science.gov (United States)

    Naydenov, Borislav; Rungger, Ivan; Mantega, Mauro; Sanvito, Stefano; Boland, John J

    2015-05-13

    We describe the fabrication, operation principles, and simulation of a coherent single-atom quantum interference device (QID) structure on Si(100) controlled by the properties of single atoms. The energy and spatial distribution of the wave functions associated with the device are visualized by scanning tunneling spectroscopy and the amplitude and phase of the evanescent wave functions that couple into the quantum well states are directly measured, including the action of an electrostatic gate. Density functional theory simulations were employed to simulate the electronic structure of the device structure, which is in excellent agreement with the measurements. Simulations of device transmission demonstrate that our coherent single-atom QID can have ON-OFF ratios in excess of 10(3) with potentially minimal power dissipation.

  5. Atomic force microscopy reveals hydroxyapatite-citrate interfacial structure at the atomic level.

    Science.gov (United States)

    Jiang, Wenge; Pan, Haihua; Cai, Yurong; Tao, Jinhui; Liu, Peng; Xu, Xurong; Tang, Ruikang

    2008-11-04

    An approach to organic-inorganic interfacial structure at the atomic level is a great challenge in the studies of biomineralization. We demonstrate that atomic force microscopy (AFM) is powerful tool to discover the biomineral interface in detail. By using a model system of (100) hydroxyapatite (HAP) face and citrate, it reveals experimentally that only a side carboxylate and a surface calcium ion are involved in the binding effect during the citrate adsorption, which is against the previous understandings by using Langmuir adsorption and computer simulation. Furthermore, the adsorbed citrate molecules can use their free carboxylate and hydroxyl groups to be self-assembled on the HAP surface. AFM examination also finds that the presence of citrate molecules on the HAP crystal faces can enhance the adhesion force of the HAP surface. We suggest that the established AFM method can be used for a precise and direct understanding of biointerfaces at the atomic level.

  6. Atomic scale structures of interfaces between kaolinite edges and water

    NARCIS (Netherlands)

    Liu, X.; Lu, X.; Wang, R.; Meijer, E.J.; Zhou, H.; He, H.

    2012-01-01

    This paper reports the atomic scale structures of kaolinite edge surfaces in contact with water. The commonly occurring edge surfaces are investigated (i.e. (0 1 0) and (1 1 0)) by using first principles molecular dynamics (FPMD) technique. For (1 1 0)-type edge surface, there are two different

  7. 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...

  8. Crystal structures and atomic model of NADPH oxidase

    NARCIS (Netherlands)

    Magnani, Francesca; Nenci, Simone; Fananas, Elisa Millana; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W.; Mattevi, Andrea

    2017-01-01

    NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic

  9. 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)

  10. Identifying local structural states in atomic imaging by computer vision.

    Science.gov (United States)

    Laanait, Nouamane; Ziatdinov, Maxim; He, Qian; Borisevich, Albina

    2017-01-01

    The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both local and nonlocal information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect-engineered multilayer graphene surface.

  11. Toward the Atomic Structure of PrPSc.

    Science.gov (United States)

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

    2017-09-01

    In this review, we detail our current knowledge of PrP Sc structure on the basis of structural and computational studies. We discuss the progress toward an atomic resolution description of PrP Sc and results from the broader field of amyloid studies that may further inform our knowledge of this structure. Moreover, we summarize work that investigates the role of PrP Sc structure in its toxicity, transmissibility, and species specificity. We look forward to an atomic model of PrP Sc , which is expected to bring diagnostics and/or therapeutics to the field of prion disease. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  12. Atomic Structure and Properties of Extended Defects in Silicon

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-10-15

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

  13. Atomic structure of a decagonal Al-Pd-Mn phase

    Science.gov (United States)

    Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer

    2017-12-01

    We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.

  14. 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)

  15. 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.

  16. Modeling Protein Structure at Near Atomic Resolutions With Gorgon

    Science.gov (United States)

    Baker, Matthew L.; Abeysinghe, Sasakthi S.; Schuh, Stephen; Coleman, Ross A.; Abrams, Austin; Marsh, Michael P.; Hryc, Corey F.; Ruths, Troy; Chiu, Wah; Ju, Tao

    2011-01-01

    Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. PMID:21296162

  17. The electronic structure of small nickel atom clusters

    Science.gov (United States)

    Basch, Harold; Newton, M. D.; Moskowitz, J. W.

    1980-11-01

    The ground state electronic structure of small nickel atom clusters (Nin, n=1-6) has been calculated using the ab initio effective core potential self-consistent field (SCF) method in a Gaussian expansion basis. The electronic configuration of the nickel atoms in the clusters is found to be very close to 3d94s1. The ground state electronic configurations for Nin generally have n unpaired 3d electrons in molecular orbitals (MO's) spanning the same irreducible representations as the 4s atomic orbitals while the n 4s electrons fill their MO's in accord with a simple three-dimensional Hückel model with overlap. Exceptions to this description are found in the cases of linear systems where the 3d holes prefer δ over σ symmetry and in octahedral Ni6 where a different preferred set of 3d holes is obtained. The SCF ground state wave functions correspond roughly to a model in which the 3d electrons can be viewed as weakly interacting localized 3d9 units. The clusters are bound together primarily by the 4s electrons with the 4p orbital contribution increasing in importance with cluster size and dimensionality. The binding energy per nickel atom generally increases as the size of the cluster increases, although at six atoms this quantity has not yet converged with cluster size. The density of states diagram for the occupied one electron energy levels in Ni6 is found to be very different from the corresponding types of diagrams obtained in the muffin tin (MT)-Xα method for small nickel atom clusters. This difference is examined in detail, with consideration given to the effects of relaxation energy and to the different orbital level filling criteria used in the two methods.

  18. 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.

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

    Directory of Open Access Journals (Sweden)

    Shrihari Sonavane

    2008-09-01

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

  20. Efficient evaluation of atom tunneling combined with electronic structure calculations

    Science.gov (United States)

    Ásgeirsson, Vilhjálmur; Arnaldsson, Andri; Jónsson, Hannes

    2018-03-01

    Methodology for finding optimal tunneling paths and evaluating tunneling rates for atomic rearrangements is described. First, an optimal JWKB tunneling path for a system with fixed energy is obtained using a line integral extension of the nudged elastic band method. Then, a calculation of the dynamics along the path is used to determine the temperature at which it corresponds to an optimal Feynman path for thermally activated tunneling (instanton) and a harmonic approximation is used to estimate the transition rate. The method is illustrated with calculations for a modified two-dimensional Müller-Brown surface but is efficient enough to be used in combination with electronic structure calculations of the energy and atomic forces in systems containing many atoms. An example is presented where tunneling is the dominant mechanism well above room temperature as an H3BNH3 molecule dissociates to form H2. Also, a solid-state example is presented where density functional theory calculations of H atom tunneling in a Ta crystal give close agreement with experimental measurements on hydrogen diffusion over a wide range in temperature.

  1. 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).

  2. Partial structure factors reveal atomic dynamics in metallic alloy melts

    Science.gov (United States)

    Nowak, B.; Holland-Moritz, D.; Yang, F.; Voigtmann, Th.; Kordel, T.; Hansen, T. C.; Meyer, A.

    2017-07-01

    We investigate the dynamical decoupling of the diffusion coefficients of the different components in a metallic alloy melt, using a combination of neutron diffraction, isotopic substitution, and electrostatic levitation in Zr-Ni melts. We show that excess Ni atoms can diffuse more freely in a background of saturated chemical interaction, causing their dynamics to become much faster and thus decoupled than anticipated from the interparticle interactions. Based on the mode-coupling theory of the glass transition, the averaged structure as given by the partial static structure factors is able to explain the observed dynamical behavior.

  3. On atom-bond connectivity molecule structure descriptors

    Directory of Open Access Journals (Sweden)

    Furtula Boris

    2016-01-01

    Full Text Available The atom-bond connectivity index (ABC is a degree-based molecular structure descriptor with well-documented chemical applications. In 2010 a distance-based new variant of this index (ABCGG has been proposed. Until now, the relation between ABC and ABCGG has not been analyzed. In this paper, we establish the basic characteristics of this relation. In particular, ABC and ABCGG are not correlated and both cases ABC > ABCGG and ABC < ABCGG may occur in the case of (structurally similar molecules. However, in the case of benzenoid hydrocarbons, ABC always exceeds ABCGG. [Projekat Ministarstva nauke Republike Srbije, br. 174033

  4. Atomic and electronic structures of novel silicon surface structures

    Energy Technology Data Exchange (ETDEWEB)

    Terry, J.H. Jr.

    1997-03-01

    The modification of silicon surfaces is presently of great interest to the semiconductor device community. Three distinct areas are the subject of inquiry: first, modification of the silicon electronic structure; second, passivation of the silicon surface; and third, functionalization of the silicon surface. It is believed that surface modification of these types will lead to useful electronic devices by pairing these modified surfaces with traditional silicon device technology. Therefore, silicon wafers with modified electronic structure (light-emitting porous silicon), passivated surfaces (H-Si(111), Cl-Si(111), Alkyl-Si(111)), and functionalized surfaces (Alkyl-Si(111)) have been studied in order to determine the fundamental properties of surface geometry and electronic structure using synchrotron radiation-based techniques.

  5. Atomic structure of graphene supported heterogeneous model catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Franz, Dirk

    2017-04-15

    Graphene on Ir(111) forms a moire structure with well defined nucleation centres. Therefore it can be utilized to create hexagonal metal cluster lattices with outstanding structural quality. At diffraction experiments these 2D surface lattices cause a coherent superposition of the moire cell structure factor, so that the measured signal intensity scales with the square of coherently scattering unit cells. This artificial signal enhancement enables the opportunity for X-ray diffraction to determine the atomic structure of small nano-objects, which are hardly accessible with any experimental technique. The uniform environment of every metal cluster makes the described metal cluster lattices on graphene/Ir(111) an attractive model system for the investigation of catalytic, magnetic and quantum size properties of ultra-small nano-objects. In this context the use of x-rays provides a maximum of flexibility concerning the possible sample environments (vacuum, selected gases, liquids, sample temperature) and allows in-situ/operando measurements. In the framework of the present thesis the structure of different metal clusters grown by physical vapor deposition in an UHV environment and after gas exposure have been investigated. On the one hand the obtained results will explore many aspects of the atomic structure of these small metal clusters and on the other hand the presented results will proof the capabilities of the described technique (SXRD on cluster lattices). For iridium, platinum, iridium/palladium and platinum/rhodium the growth on graphene/Ir(111) of epitaxial, crystalline clusters with an ordered hexagonal lattice arrangement has been confirmed using SXRD. The clusters nucleate at the hcp sites of the moire cell and bind via rehybridization of the carbon atoms (sp{sup 2} → sp{sup 3}) to the Ir(111) substrate. This causes small displacements of the substrate atoms, which is revealed by the diffraction experiments. All metal clusters exhibit a fcc structure

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

    Science.gov (United States)

    Usman, Muhammad

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

  7. Atomic-Level Structural Dynamics of Polyoxoniobates during DMMP Decomposition.

    Science.gov (United States)

    Wang, Qi; Chapleski, Robert C; Plonka, Anna M; Gordon, Wesley O; Guo, Weiwei; Nguyen-Phan, Thuy-Duong; Sharp, Conor H; Marinkovic, Nebojsa S; Senanayake, Sanjaya D; Morris, John R; Hill, Craig L; Troya, Diego; Frenkel, Anatoly I

    2017-04-10

    Ambient pressure in situ synchrotron-based spectroscopic techniques have been correlated to illuminate atomic-level details of bond breaking and formation during the hydrolysis of a chemical warfare nerve agent simulant over a polyoxometalate catalyst. Specifically, a Cs8[Nb6O19] polyoxoniobate catalyst has been shown to react readily with dimethyl methylphosphonate (DMMP). The atomic-level transformations of all reactant moieties, the [Nb6O19]8- polyanion, its Cs+ counterions, and the DMMP substrate, were tracked under ambient conditions by a combination of X-ray absorption fine structure spectroscopy, Raman spectroscopy, and X-ray diffraction. Results reveal that the reaction mechanism follows general base (in contrast to specific base) hydrolysis. Together with computational results, the work demonstrates that the ultimate fate of DMMP hydrolysis at the Cs8[Nb6O19] catalyst is strong binding of the (methyl) methylphosphonic acid ((M)MPA) product to the polyanions, which ultimately inhibits catalytic turnover.

  8. 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.

  9. Studying atomic structures by aberration-corrected transmission electron microscopy.

    Science.gov (United States)

    Urban, Knut W

    2008-07-25

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

  10. 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.

  11. Structure formation in atom lithography using geometric collimation

    NARCIS (Netherlands)

    Meijer, T.; Beardmore, J.P.; Fabrie, C.G.C.H.M.; van Lieshout, J.P.; Notermans, R.P.M.J.W.; Sang, R.T.; Vredenbregt, E.J.D.; Van Leeuwen, K.A.H.

    2011-01-01

    Atom lithography uses standing wave light fields as arrays of lenses to focus neutral atom beams into line patterns on a substrate. Laser cooled atom beams are commonly used, but an atom beam source with a small opening placed at a large distance from a substrate creates atom beams which are locally

  12. Partially Assembled Nucleosome Structures at Atomic Detail.

    Science.gov (United States)

    Rychkov, Georgy N; Ilatovskiy, Andrey V; Nazarov, Igor B; Shvetsov, Alexey V; Lebedev, Dmitry V; Konev, Alexander Y; Isaev-Ivanov, Vladimir V; Onufriev, Alexey V

    2017-02-07

    The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  13. 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.

  14. 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.

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

    Science.gov (United States)

    Murshudov, G N

    2016-01-01

    This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models. © 2016 Elsevier Inc. All rights reserved.

  16. Atomic and Electronic Structure of Defects in Semiconductors.

    Science.gov (United States)

    1983-08-01

    Ultramicroscopy, (1981) Vol 7, p. 59-64. 3. "Electron Energy Loss Spectroscopy as a probe of the Local Atomic Environment" O.L. Krivanek , M.M. Disko, J...Electron Energy-Loss Spectra, M.M. Disko, O.L. Krivanek and P. Rez, Phys. Rev. B15, #6, p. 4252 (1982). 8. "Electronic Structure of the Unreconstructed 30...and Preliminary Orientation Depencence Results" M. Disko, 0. Krivanek and J.C.H. Spence, Proc. EMSA, 1981. G.W. Bailey, Ed, Claitors Publishing Division

  17. Equilibrium structure and atomic vibrations of Nin clusters

    Science.gov (United States)

    Borisova, Svetlana D.; Rusina, Galina G.

    2017-12-01

    The equilibrium bond lengths and binding energy, second differences in energy and vibrational frequencies of free clusters Nin (2 ≤ n ≤ 20) were calculated with the use of the interaction potential obtained in the tight-binding approximation (TBA). The results show that the minimum vibration frequency plays a significant role in the evaluation of the dynamic stability of the clusters. A nonmonotonic dependence of the minimum vibration frequency of clusters on their size and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 are demonstrated. This result agrees with the theoretical and experimental data on stable structures of small metallic clusters.

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

    CERN Document Server

    Shevlin, S A

    2001-01-01

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

  19. Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa.

    Science.gov (United States)

    Salih, Osman; He, Shaoda; Planamente, Sara; Stach, Lasse; MacDonald, James T; Manoli, Eleni; Scheres, Sjors H W; Filloux, Alain; Freemont, Paul S

    2017-12-21

    Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  20. Structure of Nanocrystals by the atomic Pair Distribution Function technique

    Science.gov (United States)

    Petkov, Valeri

    2003-03-01

    Knowledge of the atomic-scale structure is an important prerequisite to understand and predict the properties of materials. In the case of crystals it is obtained from the positions and intensities of the Bragg peaks in the diffraction data. Materials constructed at the nanoscale, however, lack the long-range order and symmetry of perfect crystals. The result is that the diffraction patterns of nanocrystals are much more diffuse with few if any Bragg peaks. This poses a real challenge to the traditional techniques for structure determination. The challenge can be met by employing the so-called atomic Pair Distribution Function (PDF) technique. The basics of the PDF technique will be outlined and it advantages illustrated with results from recent studies of nanocrystalline WS_2, LiMoS_2, V_2O_5.nH_2O, GdAl2 nanomagnets, nanoporous silicates and Cs doped zeolites. Acknowledgements: Thanks are due to M. Kanatzidis, T. Pinnavaia, T. Vogt, S. Shastri, S.J.L. Billinge, D. Leslie-Pelecky and J. Dye for providing the samples and help with the experiments.

  1. Correlation between muonic levels and nuclear structure in muonic atoms

    Energy Technology Data Exchange (ETDEWEB)

    Dong, J.M., E-mail: dongjm07@lzu.edu.cn [Research Center for Nuclear Science and Technology, Lanzhou University and Institute of Modern Physics of CAS, Lanzhou 730000 (China); Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Graduate University of Chinese Academy of Sciences, Beijing 100049 (China); School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); China Institute of Atomic Energy, P.O. Box 275(18), Beijing 102413 (China); Zuo, W., E-mail: zuowei@impcas.ac.cn [Research Center for Nuclear Science and Technology, Lanzhou University and Institute of Modern Physics of CAS, Lanzhou 730000 (China); Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Zhang, H.F. [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Scheid, W. [Institute for Theoretical Physics, Justus-Liebig-University, D-35392 Giessen (Germany); Gu, J.Z., E-mail: gujianzhong2000@yahoo.com.cn [China Institute of Atomic Energy, P.O. Box 275(18), Beijing 102413 (China); Wang, Y.Z. [China Institute of Atomic Energy, P.O. Box 275(18), Beijing 102413 (China)

    2011-10-25

    A method that deals with the nucleons and the muon unitedly is employed to investigate the muonic lead, with which the correlation between the muon and nucleus can be studied distinctly. A 'kink' appears in the muonic isotope shift at a neutron magic number where the nuclear shell structure plays a key role. This behavior may have very important implications for the experimentally probing the shell structure of the nuclei far away from the {beta}-stable line. We investigate the variations of the nuclear structure due to the interaction with the muon in the muonic atom and find that the nuclear structure remains basically unaltered. Therefore, the muon is a clean and reliable probe for studying the nuclear structure. In addition, a correction that the muon-induced slight change in the proton density distribution in turn shifts the muonic levels is investigated. This correction to muonic level is as important as the Lamb shift and high order vacuum polarization correction, but is larger than anomalous magnetic moment and electron shielding correction.

  2. Build-up algorithm for atomic correspondence between chemical structures.

    Science.gov (United States)

    Kawabata, Takeshi

    2011-08-22

    Determining a one-to-one atom correspondence between two chemical compounds is important to measure molecular similarities and to find compounds with similar biological activities. This calculation can be formalized as the maximum common substructure (MCS) problem, which is well-studied and has been shown to be NP-complete. Although many rigorous and heuristic algorithms have been developed, none of these algorithms is sufficiently fast and accurate. We developed a new program, called "kcombu" using a build-up algorithm, which is a type of the greedy heuristic algorithms. The program can search connected and disconnected MCSs as well as topologically constrained disconnected MCS (TD-MCS), which is introduced in this study. To evaluate the performance of our program, we prepared two correct standards: the exact correspondences generated by the maximum clique algorithms and the 3D correspondences obtained from superimposed 3D structure of the molecules in a complex 3D structure with the same protein. For the five sets of molecules taken from the protein structure database, the agreement value between the build-up and the exact correspondences for the connected MCS is sufficiently high, but the computation time of the build-up algorithm is much smaller than that of the exact algorithm. The comparison between the build-up and the 3D correspondences shows that the TD-MCS has the best agreement value among the other types of MCS. Additionally, we observed a strong correlation between the molecular similarity and the agreement with the correct and 3D correspondences; more similar molecule pairs are more correctly matched. Molecular pairs with more than 40% Tanimoto similarities can be correctly matched for more than half of the atoms with the 3D correspondences.

  3. 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure

    Energy Technology Data Exchange (ETDEWEB)

    Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be

    2017-06-15

    Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod. - Highlights: • Depth sectioning in HAADF STEM is combined with atom-counting. • This can be used to retrieve the 3D atomic structure. • The theoretical precision with atoms can be located is investigated. • An algorithm is introduced to reconstruct the morphology of a nanoparticle. • The method is applied to reconstruct a gold nanorod.

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

    National Research Council Canada - National Science Library

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

    2004-01-01

    Direct atomic resolution images have been obtained that illustrate how a range of rare-earth atoms bond to the interface between the intergranular phase and the matrix grains in an advanced silicon nitride ceramic...

  6. Structure and Thermodynamics of Metal Clusters on Atomically Smooth Substrates.

    Science.gov (United States)

    Eckhoff, M; Schebarchov, D; Wales, D J

    2017-10-23

    We analyze the structure of model NiN and CuN clusters (N = 55, 147) supported on a variety of atomically smooth van der Waals surfaces. The global minima are mapped in the space of two parameters: (i) the laterally averaged surface stickiness, γ, which controls the macroscopic wetting angle, and (ii) the surface microstructure, which produces more subtle but important templating via epitaxial stresses. We find that adjusting the substrate lattice (even at constant γ) can favor different crystal plane orientations in the cluster, stabilize hexagonal close-packed order, or induce various defects, such as stacking faults, twin boundaries, and five-fold disclinations. Thermodynamic analysis reveals substrate-dependent solid-solid transitions in cluster morphology, with tunable transition temperature and sometimes exhibiting re-entrant behavior. These results shed new light on the extent to which a supporting surface can be used to influence the equilibrium behavior of nanoparticles.

  7. The atomic and electronic structure of amorphous silicon nitride

    CERN Document Server

    Alvarez, F

    2002-01-01

    Using a novel approach to the ab initio generation of random networks we constructed two nearly stoichiometric samples of amorphous silicon nitride with the same content x= 1.29. The two 64-atom periodically-continued cubic diamond-like cells contain 28 silicons and 36 nitrogens randomly substituted, and were amorphized with a 6 f s time step by heating them to just below their melting temperature with a Harris-functional based, molecular dynamics code in the LDA approximation. The averaged total radial distribution function (RDF) obtained is compared with some existing Tersoff-like potential simulations and with experiment; ours agree with experiment. All the partial radial features are calculated and the composition of the second peak also agrees with experiment. The electronic structure is calculated and the optical gaps obtained using both a HOMO-LUMO approach and the Tauc-like procedure developed recently that gives reasonable gaps. (Author)

  8. 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.

  9. 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

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

    Science.gov (United States)

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

    2009-11-01

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

  11. 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.

  12. Iron phosphate glasses: Bulk properties and atomic scale structure

    Energy Technology Data Exchange (ETDEWEB)

    Joseph, Kitheri; Stennett, Martin C.; Hyatt, Neil C.; Asuvathraman, R.; Dube, Charu L.; Gandy, Amy S.; Govindan Kutty, K. V.; Jolley, Kenny; Vasudeva Rao, P. R.; Smith, Roger

    2017-10-01

    Bulk properties such as glass transition temperature, density and thermal expansion of iron phosphate glass compositions, with replacement of Cs by Ba, are investigated as a surrogate for the transmutation of 137Cs to 137Ba, relevant to the immobilisation of Cs in glass. These studies are required to establish the appropriate incorporation rate of 137Cs in iron phosphate glass. Density and glass transition temperature increases with the addition of BaO indicating the shrinkage and reticulation of the iron phosphate glass network. The average thermal expansion coefficient reduces from 19.8 × 10-6 K-1 to 13.4 × 10-6 K-1, when 25 wt. % of Cs2O was replaced by 25 wt. % of BaO in caesium loaded iron phosphate glass. In addition to the above bulk properties, the role of Ba as a network modifier in the structure of iron phosphate glass is examined using various spectroscopic techniques. The FeII content and average coordination number of iron in the glass network was estimated using Mössbauer spectroscopy. The FeII content in the un-doped iron phosphate glass and barium doped iron phosphate glasses was 20, 21 and 22 ± 1% respectively and the average Fe coordination varied from 5.3 ± 0.2 to 5.7 ± 0.2 with increasing Ba content. The atomic scale structure was further probed by Fe K-edge X-ray absorption spectroscopy. The average coordination number provided by extended X-ray absorption fine structure spectroscopy and X-ray absorption near edge structure was in good agreement with that given by the Mössbauer data.

  13. 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

  14. Fast-ion-beam laser probing of ion-source energy distributions and atomic structure

    Energy Technology Data Exchange (ETDEWEB)

    Holt, Richard A., E-mail: rholt@uwo.ca; Rosner, S. David [University of Western Ontario, Physics and Astronomy Department (Canada)

    2013-04-15

    Collinear fast-ion-beam laser spectroscopy is a very high resolution probe for measuring ion-beam energy distributions and atomic structure parameters of interest in nuclear physics, atomic physics, and astrophysics. We have used offline 10-keV beams of atomic ions and a CW laser system to study the behavior of a Penning ion source and to measure hyperfine structure, isotope shifts, atomic lifetimes, spontaneous-emission branching fractions, oscillator strengths, and absolute wavelengths of a variety of atomic species from the lanthanide and transition-metal groups.

  15. Atomic Structure and Dynamics of Single Platinum Atom Interactions with Monolayer MoS2.

    Science.gov (United States)

    Li, Huashan; Wang, Shanshan; Sawada, Hidetake; Han, Grace G D; Samuels, Thomas; Allen, Christopher S; Kirkland, Angus I; Grossman, Jeffrey C; Warner, Jamie H

    2017-03-28

    We have studied atomic level interactions between single Pt atoms and the surface of monolayer MoS2 using aberration-corrected annular dark field scanning transmission electron microscopy at an accelerating voltage of 60 kV. Strong contrast from single Pt atoms on the atomically resolved monolayer MoS2 lattice enables their exact position to be determined with respect to the MoS2 lattice, revealing stable binding sites. In regions of MoS2 free from surface contamination, the Pt atoms are localized in S vacancy sites and exhibit dynamic hopping to nearby vacancy sites driven by the energy supplied by the electron beam. However, in areas of MoS2 contaminated with carbon surface layers, the Pt atoms appear at various positions with respect to the underlying MoS2 lattice, including on top of Mo and in off-axis positions. These variations are due to the Pt bonding with the surrounding amorphous carbon layer, which disrupts the intrinsic Pt-MoS2 interactions, leading to more varied positions. Density functional theory (DFT) calculations reveal that Pt atoms on the surface of MoS2 have a small barrier for migration and are stabilized when bound to either a single or double sulfur vacancies. DFT calculations have been used to understand how the catalytic activity of the MoS2 basal plane for hydrogen evolution reaction is influenced by Pt dopants by variation of the hydrogen adsorption free energy. This strong dependence of catalytic effect on interfacial configurations is shown to be common for a series of dopants, which may provide a means to create and optimize reaction centers.

  16. Ab initio calculations and modelling of atomic cluster structure

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  17. 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

    1975-01-01

    The radial distribution function calculated from x-ray diffraction of mineralized cytoplasmic structures isolated from the hepatopancreas of the blue crab (Callinectes sapidus) is very similar to that previously found for synthetic amorphous calcium phosphate. Both types of mineral apparently have only short-range atomic order, represented as a neutral ion cluster of about 10 A in longest dimension, whose probable composition is expressed by the formula Ca9(PO4)6. The minor differences observed are attributed to the presence in the biological mineral of significant amounts of Mg-2+ and ATP. Synthetic amorphous calcium phosphate in contact with a solution containing an amount of ATP equivalent to that of the biological mineral failed to undergo conversion to the thermodynamically more stable hydroxyapatite. The amorphous calcium phosphate of the cytoplasmic mineral granules is similarly stable, and does not undergo conversion to hydroxyapatite, presumably owing to the presence of ATP and Mg-2+, known in inhibitors of the conversion process. The physiological implications of mineral deposits consisting of stabilized calcium phosphate ion clusters are discussed. PMID:1056015

  18. Calculation of atomic structures and radiative properties of fusion plasmas

    Science.gov (United States)

    Jarrah, Walid; Pain, Jean-Christophe; Benredjem, Djamel

    2017-03-01

    The opacity is an important issue in the knowledge of the radiative properties of Inertial Confinement Fusion (ICF) and astrophysical plasmas. In this work we present the opacity of the mixture C+Si, composing the ablator of some ICF capsules. We have used Cowan's code to calculate the atomic structure of carbon and silicon. We also have developed a collisional-radiative model in order to obtain the opacity of the mixture. Line broadening, line shift and ionization potential depression are taken into account in the opacity profile. Comparisons to other calculations are carried out. NLTE and LTE opacity calculations show discrepancies mainly in the range 1900-2000 eV for the bound-bound contribution to the total opacity and in the range 50-350 eV for the bound-free contribution. We have also accounted for photoexcitation and photoionization processes. The corresponding rates are obtained by modeling the Hohlraum radiation by a Planckian distribution at a radiative temperature of 300 eV.

  19. Lens capsule structure assessed with atomic force microscopy

    Science.gov (United States)

    Sueiras, Vivian M.; Moy, Vincent T.

    2015-01-01

    Purpose To image the ultrastructure of the anterior lens capsule at the nanoscale level using atomic force microscopy (AFM). Methods Experiments were performed on anterior lens capsules maintained in their in situ location surrounding the lens from six human cadavers (donor age range: 44–88 years), four cynomolgus monkeys (Macaca fascicularis age range: 4.83–8.92 years), and seven pigs (<6 months). Hydration of all samples was maintained using Dulbecco’s Modified Eagle Medium (DMEM). Whole lenses were removed from the eye and placed anterior side up in agarose gel before gel hardening where only the posterior half of the lens was contained within the gel. After the gel hardened, the Petri dish was filled with DMEM until the point where the intact lens was fully submerged. AFM was used to image the anterior lens surface in contact mode. An integrated analysis program was used to calculate the interfibrillar spacing, fiber diameter, and surface roughness of the samples. Results The AFM images depict a highly ordered fibrous structure at the surface of the lens capsule in all three species. The interfibrillar spacing for the porcine, cynomolgus monkey, and human lens capsules was 0.68±0.25, 1.80±0.39, and 1.08±0.25 μm, respectively. In the primate, interfibrillar spacing significantly decreased linearly as a function of age. The fiber diameters ranged from 50 to 950 nm. Comparison of the root mean square (RMS) and average deviation demonstrate that the surface of the porcine lens capsule is the smoothest, and that the human and cynomolgus monkey capsules are significantly rougher. Conclusions AFM was successful in providing high-resolution images of the nanostructure of the lens capsule samples. Species-dependent differences were observed in the overall structure and surface roughness. PMID:25814829

  20. 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.

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

    NARCIS (Netherlands)

    Sîretanu, Igor; van den Ende, Henricus T.M.; Mugele, Friedrich Gunther

    2016-01-01

    Atomic scale details of surface structure play a crucial role for solid–liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to

  2. Revealing electronic structure in atomically-engineered manganite thin films

    Science.gov (United States)

    Monkman, Eric Justin

    Semiconductor technology is based on tuning the properties of devices by manipulating thin films and interfaces. Recently, this approach has been extended to complex oxides, where quantum many-body interactions give rise to emergent ground states not present in the parent materials. Rationally controlling and engineering correlated electronic phases has the potential to revolutionize modern electronics, but is hindered by the inability of current theory to account for the effects of many-body interactions on the underlying electronic structure. Manganites provide a particularly model system for studying many-body effects due to their complex electronic and magnetic phase diagrams, which give rise to many potentially useful properties. Despite extensive work on manganite films demonstrating numerous electronic phase transitions, little is directly known about how the electronic structure responds to the 'control parameters' accessible in thin films. This dissertation presents direct measurements of the electronic structure in La1-- xSrxMnO3 based thin films and interfaces through several phase transitions using a unique integrated oxide molecular-beam epitaxy and angle-resolved photoemission spectroscopy system. We observe the full Fermi surface and near-EF electronic structure of the ferromagnetic and A-type antiferromagnetic metallic phases, reconciling first-principles calculations with experiment for the first time. Furthermore, our results provide key insights into the polaronic nature of the metallic charge carriers. We then explore the mechanism underlying the insulating ground state for La2/3Sr1/3MnO3 under strong tensile strain. Our measurements rule out the scenarios of bandwidth or localization-driven metal-insulator transitions, and reveal an instability of the strongly interacting metal towards an ordered insulating phase that can be accessed through epitaxial strain. By next studying atomically precise interfaces in (LaMnO3)2n/(SrMnO 3)n superlattices

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

    Energy Technology Data Exchange (ETDEWEB)

    Paesler, M.; Sayers, D.

    1988-12-01

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

  4. 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.

  5. Structural examination of lithium niobate ferroelectric crystals by combining scanning electron microscopy and atomic force microscopy

    Science.gov (United States)

    Efremova, P. V.; Ped'ko, B. B.; Kuznecova, Yu. V.

    2016-02-01

    The structure of lithium niobate single crystals is studied by a complex technique that combines scanning electron microscopy and atomic force microscopy. By implementing the piezoresponse force method on an atomic force microscope, the domain structure of lithium niobate crystals, which was not revealed without electron beam irradiation, is visualized

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

    Energy Technology Data Exchange (ETDEWEB)

    Clade, P

    2005-10-15

    From a measurement of the recoil velocity of an atom absorbing a photon, it is possible to deduce a determination of the ratio h/m between the Planck constant and the mass of the atoms and then to deduce a value of the fine structure constant alpha. To do this measurement, we use the technique of Bloch oscillations, which allows us to transfer a large number of recoils to atoms. A velocity sensor, based on velocity selective Raman transition, enables us to measure the momentum transferred to the atoms. A measurement with a statistical uncertainty of 4.4 10{sup -9}, in conjunction with a careful study of systematic effects (5 10{sup -9}), has led us to a determination of alpha with an uncertainty of 6.7 10{sup -9}: {alpha}{sup -1}(Rb) = 137.03599878 (91). This uncertainty is similar to the uncertainty of the best determinations of alpha based on atom interferometry. (author)

  7. Intracluster atomic and electronic structural heterogeneities in supported nanoscale metal catalysts

    NARCIS (Netherlands)

    Elsen, A.; Jung, U.; Vila, F.; Li, Y.; Safonova, O.V.; Thomas, R.; Tromp, M.; Rehr, J.J.; Nuzzo, R.G.; Frenkel, A.I.

    2015-01-01

    This work reveals and quantifies the inherent intracluster heterogeneity in the atomic structure and charge distribution present in supported metal catalysts. The results demonstrate that these distributions are pronounced and strongly coupled to both structural and dynamic perturbations. They also

  8. Atomic Structures of Molecules Based on Additivity of Atomic and/or Ionic Radii

    OpenAIRE

    Raji Heyrovska; Sara Narayan

    2009-01-01

    The authors have shown in recent years that interatomic and interionic distances are sums of the radii of the adjacent atoms and/or ions. Many examples will be provided and it will be shown how the experimental bond lengths agree with the radii sums. The examples include inorganic compounds like alkali halides, metal hydrides, graphene, etc., organic like aliphatic and aromatic compounds and biochemical like nucleic acids, amino acids, caffeine-related compounds and vitamins.

  9. 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.

  10. Solving atomic structures using statistical mechanical searches on x-ray scattering derived potential energy surfaces

    Science.gov (United States)

    Wright, Christopher James

    Engineering the next generation of materials, especially nanomaterials, requires a detailed understanding of the material's underlying atomic structure. These structures give us better insight into structure-property relationships, allowing for property driven material design on the atomic level. Even more importantly, understanding structures in-situ will translate stimuli and responses on the macroscopic scale to changes on the nanoscale. Despite the importance of precise atomic structures for materials design, solving atomic structures is difficult both experimentally and computationally. Atomic pair distribution functions (PDFs) provide information on atomic structure, but the difficulty of extracting the PDF from x-ray total scattering measurements limits their use. Translating the PDF into an atomic structure requires the search of a very high dimensional space, the set of all potential atomic configurations. The large computational cost of running these simulations also limits the use of PDF as an atomistic probe. This work aims to address these issues by developing 1) novel statistical mechanical approaches to solving material structures, 2) fast simulation of x-ray total scattering and atomic pair distribution functions (PDFs), and 3) data processing procedures for experimental x-ray total scattering measurements. First, experimentally derived potential energy surfaces (PES) and the statistical mechanical ensembles used to search them are developed. Then the mathematical and computational framework for the PDF and its gradients will be discussed. The combined PDF-PES-ensemble system will be benchmarked against a series of nanoparticle structures to ascertain the efficiency and effectiveness of the system. Experimental data processing procedures, which maximize the usable data, will be presented. Finally, preliminary results from experimental x-ray total scattering measurements will be discussed. This work presents one of the most complete end

  11. 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

  12. The Atom in a Molecule: Implications for Molecular Structure and Properties

    Science.gov (United States)

    2016-05-23

    Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

  13. Atomic and Electronic Structure of Polar Oxide Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Gajdardziska-Josifovska, Marija [University of Wisconsin Milwaukee

    2014-01-17

    In this project we developed fundamental understanding of atomic and electronic mechanisms for stabilization of polar oxide interfaces. An integrated experimental and theoretical methodology was used to develop knowledge on this important new class of ionic materials with limited dimensionality, with implications for multiple branches of the basic and applied energy sciences.

  14. QUASI-LANDAU STRUCTURE OF DIAMAGNETIC HELIUM RYDBERG ATOMS

    NARCIS (Netherlands)

    Vanderveldt, T.; Vassen, W.; Hogervorst, W.

    1993-01-01

    Diamagnetism in helium Rydberg atoms is studied near the ionisation threshold using constant scaled-energy laser spectroscopy. Quasi-Landau resonances in the Fouriertransform of the energy spectrum are explained using the classical periodic-orbit theory. Longlaser scans combined with a

  15. Atomically Monodisperse Gold Nanoclusters Catalysts with Precise Core-Shell Structure

    Directory of Open Access Journals (Sweden)

    Yuhan Sun

    2011-09-01

    Full Text Available The emphasis of this review is atomically monodisperse Aun nanoclusters catalysts (n = number of metal atom in cluster that are ideally composed of an exact number of metal atoms. Aun which range in size from a dozen to a few hundred atoms are particularly promising for nanocatalysis due to their unique core-shell structure and non-metallic electronic properties. Aun nanoclusters catalysts have been demonstrated to exhibit excellent catalytic activity in hydrogenation and oxidation processes. Such unique properties of Aun significantly promote molecule activation by enhancing adsorption energy of reactant molecules on catalyst surface. The structural determination of Aun nanoclusters allows for a precise correlation of particle structure with catalytic properties and also permits the identification of catalytically active sites on the gold particle at an atomic level. By learning these fundamental principles, one would ultimately be able to design new types of highly active and highly selective gold nanocluster catalysts for a variety of catalytic processes.

  16. Structures at the Atomic Level of Cobalt, Zinc and Lead Niobates (with an Appendix: Atomic structure of cobalt niobate crystal)

    OpenAIRE

    Raji Heyrovska

    2011-01-01

    The author has found in recent years that bond lengths are exact sums of the radii of adjacent atoms and or ions, where the ions have Golden ratio based radii. This work was prompted by the exciting observation last year of the Golden ratio in the magnetic properties of cobalt niobate. It is shown here that in cobalt and zinc niobates, cobalt, zinc and oxygen ions have Golden ratio based ionic radii, whereas in lead niobate, all atoms have covalent radii. Also, the angles at the single bond o...

  17. 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…

  18. Construction of the energy matrix for complex atoms. Part VIII: Hyperfine structure HPC calculations for terbium atom

    Science.gov (United States)

    Elantkowska, Magdalena; Ruczkowski, Jarosław; Sikorski, Andrzej; Dembczyński, Jerzy

    2017-11-01

    A parametric analysis of the hyperfine structure (hfs) for the even parity configurations of atomic terbium (Tb I) is presented in this work. We introduce the complete set of 4fN-core states in our high-performance computing (HPC) calculations. For calculations of the huge hyperfine structure matrix, requiring approximately 5000 hours when run on a single CPU, we propose the methods utilizing a personal computer cluster or, alternatively a cluster of Microsoft Azure virtual machines (VM). These methods give a factor 12 performance boost, enabling the calculations to complete in an acceptable time.

  19. Controlling atomic structures and photoabsorption processes by an infrared laser

    OpenAIRE

    Tong, X. M.; Toshima, N.

    2010-01-01

    We propose a theoretical method to calculate the infrared (IR) laser-assisted photoabsorption cross sections over a broad energy range by a single calculation. In this method we define an initial wave function as the product of the dipole operator and the atomic ground state, propagate the initial wave function in the IR laser field with different initial phases, then calculate the generalized autocorrelation function, which is defined as the averaged value of the autocorrelation function ove...

  20. Structure and transport properties of atomic chains and molecules

    DEFF Research Database (Denmark)

    Strange, Mikkel

    2008-01-01

    with the experimental findings [5]. The observed conductance properties of Metal/CO are shown to be determined by the local d-band at the Metal apex atoms. For carbon nanotubes it is shown that the conductance may be controlled by site selective adsorption of molecules. A model to explain this behavior is verified...... of atomically thin, suspended chains containing silver and oxygen atoms in an alternating sequence has been studied. The conductances of the chains exhibit weak even-odd oscillations around an anomalously low value of 0.1G0 (G0 = 2e2/h) in agreement with experiments [1] in the long chain limit. These unusual...... conductance properties are explained in terms of a resonating-chain model, which takes the reflection probability and phase-shift of a single bulk-chain interface as the only input. The stability of silver-oxygen chains was studied with a thermodynamic model. This model has been developed in this work...

  1. Controlling Mobility in Perovskite Oxides by Ferroelectric Modulation of Atomic-Scale Interface Structure.

    Science.gov (United States)

    Malashevich, Andrei; Marshall, Matthew S J; Visani, Cristina; Disa, Ankit S; Xu, Haichao; Walker, Frederick J; Ahn, Charles H; Ismail-Beigi, Sohrab

    2017-12-26

    Coherent and epitaxial interfaces permit the realization of electric field driven devices controlled by atomic-scale structural and electronic effects at interfaces. Compared to conventional field effect devices where channel conductivity is modulated by carrier density modification, the propagation of atomic-scale distortions across an interface can control the atomic scale bonding, interatomic electron tunneling rates and thus the mobility of the channel material. We use first-principles theory to design an atomically abrupt epitaxial perovskite heterostructure involving an oxide ferroelectric (PbZr0.2Ti0.8O3) and conducting oxide channel (LaNiO3) where coupling of polar atomic motions to structural distortions can induce large, reversible changes in the channel mobility. We fabricate and characterize the heterostructure and measure record values, larger than 1000%, for the conductivity modulation. Our results describe how purely interfacial effects can be engineered to deliver unique electronic device properties and large responses to external fields.

  2. Chromatin Structure in Bands and Interbands of Polytene Chromosomes Imaged by Atomic Force Microscopy

    NARCIS (Netherlands)

    de Grauw, C.J.; de Grauw, C.J.; Avogadro, A.; van den Heuvel, D.J.; van den Heuvel, D.J.; van der Werf, Kees; Otto, Cornelis; Kraan, Yvonne M.; van Hulst, N.F.; Greve, Jan

    1998-01-01

    Polytene chromosomes from Drosophila melanogaster, observed from squash preparations, and chromosomes from Chironomus thummi thummi, investigated under physiological conditions, are imaged using an Atomic Force Microscope. Various chromatin fiber structures can be observed with high detail in fixed

  3. Structural influence on atomic hopping and electronic states of Pd-based bulk metallic glasses

    OpenAIRE

    Tang, X.-P.; Löffler, Jörg F.; Schwarz, R. B.; Johnson, William L.; Wu, Yue

    2005-01-01

    Atomic motion and electronic structures of Pd–Ni–Cu–P bulk metallic glasses were investigated using 31P nuclear magnetic resonance. The hopping rate of P atoms was determined by the stimulated echo technique. Significant hopping was observed in all alloys well below the glass transition temperature. Increasing the Cu content to above 25 at. % increases P hopping significantly, consistent with the previous finding that the openness of the structure increases with Cu content. In contrast, P h...

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

    OpenAIRE

    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.

  5. Atomic structure of self-organizing iridium induced nanowires on Ge(001)

    Energy Technology Data Exchange (ETDEWEB)

    Kabanov, N.S., E-mail: n.kabanov@utwente.nl [Faculty of Physics, Moscow State University, 119991 (Russian Federation); Physics of Interfaces and Nanomaterials, MESA+ Institute for Nanotechnology, University of Twente, P. O. Box 217, Enschede 7500 AE (Netherlands); Heimbuch, R.; Zandvliet, H.J.W. [Physics of Interfaces and Nanomaterials, MESA+ Institute for Nanotechnology, University of Twente, P. O. Box 217, Enschede 7500 AE (Netherlands); Saletsky, A.M.; Klavsyuk, A.L. [Faculty of Physics, Moscow State University, 119991 (Russian Federation)

    2017-05-15

    Highlights: • Ir/Ge(001) structure has been studied with DFT calculations and scanning tunneling microscopy. • Ir/Ge(001) nanowires are composed of Ge atoms and Ir atoms are located in subsurface positions. • The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. - Abstract: The atomic structure of self-organizing iridium (Ir) induced nanowires on Ge(001) is studied by density functional theory (DFT) calculations and variable-temperature scanning tunneling microscopy. The Ir induced nanowires are aligned in a direction perpendicular to the Ge(001) substrate dimer rows, have a width of two atoms and are completely kink-less. Density functional theory calculations show that the Ir atoms prefer to dive into the Ge(001) substrate and push up the neighboring Ge substrate atoms. The nanowires are composed of Ge atoms and not Ir atoms as previously assumed. The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. Time-resolved scanning tunneling microscopy measurements reveal that this dynamics is caused by buckled Ge substrate dimers that flip back and forth between their two buckled configurations.

  6. 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.

  7. Atomic-structural synergy for catalytic CO oxidation over palladium-nickel nanoalloys.

    Science.gov (United States)

    Shan, Shiyao; Petkov, Valeri; Yang, Lefu; Luo, Jin; Joseph, Pharrah; Mayzel, Dina; Prasai, Binay; Wang, Lingyan; Engelhard, Mark; Zhong, Chuan-Jian

    2014-05-14

    Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly active and stable catalysts. However, the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium-nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable maximal catalytic activity at Pd:Ni ratio of ~50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies.

  8. Precise Atomic Structures of Three Novel Nanomaterials in Nanotechnology, Biomedicine and Cosmology: Graphene, Boron Nitride and Coronene

    OpenAIRE

    Raji Heyrovska; Lakshmi Atchison; Sara Narayan

    2010-01-01

    Nanomaterials are currently of great importance in science, technology and commercial applications. Since these materials are atomic layer thick and are a few square nanometers of area, a knowledge of their precise atomic structures will help in the exact understanding of the properties at the nanoscale and in the fabrication and design of the nanomaterials for their many uses. Their known inter-atomic distances have been used here to obtain the exact atomic radii of the component atoms and t...

  9. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Xiaojuan [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Dongguan Institute of Neutron Science, Dongguan 523808 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zong, Peng-an [State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Chen, Xihong [Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Tao, Juzhou, E-mail: taoj@ihep.ac.cn [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Dongguan Institute of Neutron Science, Dongguan 523808 (China); Lin, He, E-mail: linhe@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201204 (China)

    2017-02-15

    Both of atomic pair distribution function (PDF) and extended x-ray absorption fine structure (EXAFS) experiments have been carried out on unfilled and Yb-filled skutterudites Yb{sub x}Co{sub 4}Sb{sub 12} (x=0, 0.15, 0.2 and 0.25) samples. The structure refinements on PDF data confirm the large amplitude vibration of Yb atom and the dependence of Yb vibration amplitude on the filling content. Temperature dependent EXAFS experiment on filled skutterudites have been carried out at Yb L{sub Ⅲ}-edge in order to explore the local vibration behavior of filled atom. EXAFS experiments show that the Einstein temperature of the filled atom is very low (70.9 K) which agrees with the rattling behavior.

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

    OpenAIRE

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

    2014-01-01

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

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

    OpenAIRE

    Gabriel Gonzalez; Brett Hannigan; DeGrado, William F.

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Long, A.; Rydberg, Patrik

    2013-01-01

    To enhance the discrimination rate for methods applying structural alerts and biotransformation rules in the prediction of toxicity and drug metabolism we have developed a set of novel fragment based atomic descriptors. These atomic descriptors encode the properties of the fragments separating...... an atom from the closest end of a branch or the molecule. The end of a branch and the end of a molecule, as well as the selection of the fragments, are made by an algorithm that uses only the distance matrix of the molecule. The novel descriptors are applied to a small set of biotransformation rules...

  14. Atomic tritium as a surface nanoprobe in a structural investigation of molecular assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Badun, G.A.; Lukashina, E.V.; Batuk, O.N.; Ksenofontov, A.L.; Fedoseev, V.M

    2003-12-15

    Possibilities of atomic tritium application as surface nanoprobe for structural investigations of adsorption layers on the liquid-air interface have been demonstrated. Frozen aqueous solutions of a series of amino acids and their mixtures and one well-known surface-active substance (cetyltrimethylammonium bromide, CTAB) were exposed to bombardment by tritium atoms generated on hot tungsten wire in a special vacuum device. This procedure resulted in substitution of hydrogen atoms by radioactive tritium in the thin surface layer of investigated samples. Curves of radioactivity changes depending on bombardment time and solution concentration for applied compounds were obtained and analyzed.

  15. 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.

  16. 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.

  17. Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Debela, T T; Wang, X D; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

    2014-02-05

    Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt-Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

  18. BNC nanoshells: a novel structure for atomic storage

    Science.gov (United States)

    Silva, F. W. N.; Cruz-Silva, E.; Terrones, M.; Terrones, H.; Barros, E. B.

    2017-11-01

    Quantum molecular dynamics (QMD) and density functional theory are employed in this work in order to study the structural and electronic properties of carbon, boron nitride or hybrid BNC nanoshells. The studied nanoshells can be formed by stacking two zigzag graphene nanoribbons, two zigzag boron nitride nanoribbons or one zigzag graphene nanoribbon on a boron nitride nanoribbon. In all cases only one of the edges of the ribbon is passivated, while the other one is left unpassivated. Our QMD results show that these nanoribbons collapse just a few femtoseconds after the beginning of the simulation, forming a coalesced structure in the shape of a shell. Our band structure calculations revealed that this structures may be metallic or semiconductor, depending on its stoichiometry. Furthermore, a spin splitting for energies near the Fermi level is predicted for both the pure carbon and the hybrid BNC-nanoshell systems. We further show that when a transverse electric field is applied to these systems, the nanoshell structure tends to open up. This effect can lead to the application of these nanoshells for molecular storage. As a proof of concept, We investigate this storage effect for the H2 molecule.

  19. 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…

  20. 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...

  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...... for calculating Gibbs free energy of the edges in terms of the DFT energies is also presented. This model allows us to determine the stable edge structure in thermodynamic equilibrium under different conditions. We find that both the insulating and metallic edges may be stable depending on the temperature...

  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. 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...

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

    CERN Document Server

    Bengio, S

    2003-01-01

    This thesis work has been concerned with adsorption properties of silicon surfaces.The atomic and electronic structure of molecules and atoms adsorbed on Si has been investigated by means of photoemission experiments combined with synchrotron radiation.The quantitative atomic structure determination was held applying the photoelectron diffraction technique.This technique is sensible to the local structure of a reference atomic specie and has elemental and chemical-state specificity.This approach has been applied to three quite different systems with different degrees of complexity, Sb/Si(111) sq root 3x sq root 3R30 sup 0 , H sub 2 O/Si(100)2x1 and NH sub 3 /Si(111)7x7.Our results show that Sb which forms a ( sq root 3 sq root 3)R30 sup 0 phase produces a bulklike-terminated Si(111)1x1 substrate free of stacking faults.Regarding the atomic structure of its interface, this study strongly favours the T4-site milkstool model over the H3 one.An important aspect regarding the H sub 2 O/Si(100)(2x1) system was esta...

  5. Large scale structural optimization of trimetallic Cu-Au-Pt clusters up to 147 atoms

    Science.gov (United States)

    Wu, Genhua; Sun, Yan; Wu, Xia; Chen, Run; Wang, Yan

    2017-10-01

    The stable structures of Cu-Au-Pt clusters up to 147 atoms are optimized by using an improved adaptive immune optimization algorithm (AIOA-IC method), in which several motifs, such as decahedron, icosahedron, face centered cubic, sixfold pancake, and Leary tetrahedron, are randomly selected as the inner cores of the starting structures. The structures of Cu8AunPt30-n (n = 1-29), Cu8AunPt47-n (n = 1-46), and partial 75-, 79-, 100-, and 147-atom clusters are analyzed. Cu12Au93Pt42 cluster has onion-like Mackay icosahedral motif. The segregation phenomena of Cu, Au and Pt in clusters are explained by the atomic radius, surface energy, and cohesive energy.

  6. 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

  7. 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...

  8. Atomic shell structures observed in photoionization spectra of nickel and cobalt clusters

    Energy Technology Data Exchange (ETDEWEB)

    Vialle, J.L. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire; Pellarin, M. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire; Baguenard, B. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire; Lerme, J. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire; Broyer, M. [Lyon-1 Univ., 69 - Villeurbanne (France). Lab. de Spectrometrie Ionique et Moleculaire

    1995-12-31

    Nickel and cobalt clusters have been studied by near threshold laser-photoionization and time-of-flight mass spectrometry. In the size domain from 50 up to 800 atoms, the mass distributions of the photoionized products look very similar for nickel and cobalt clusters. In both cases a regular structure is observed which is periodic on a N{sup 1/3} scale. It is found to be consistent with the filling of successive icosahedral shells of atoms. The recurring details of this structure agree with the so-called umbrellas model. (orig.)

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

    OpenAIRE

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

    1992-01-01

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

  10. Energetic Materials and Atomic Force Microscopy: Structure and Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Weeks, B.L.; Weese, R.K.; Zaug, J.M.

    2002-07-31

    Understanding the structure and composition of energetic materials at the sub-micron level is imperative for the fundamental studies of hot-spot formation and structural composition of energetic materials. Using in situ high-temperature AFM we have observed the solid-solid phase transition of Octahydro-1,3,5,7,-tetrazocine, HMX, in real time. Massive surface reconstruction occurs during the 1st-order transition. The temperature induced increase in void space and surface roughness observed in the delta phase polymorph of HMX serve to increase the growth rate and volume of shock initiated hot spots and possibly reaction sensitivity. HMX exists in four solid phase polymorphs, labeled {alpha}, {beta}, {chi}, and {delta}. The phase conversion of the {beta} phase to the {delta} phase involves a major disruption of the crystal lattice. The energy required to bring about this change is a measurable quantity. Multiple thermal analysis techniques carried out simultaneously are preferable because the results are directly comparable. Thermal methods are dynamic techniques, where heating or cooling is applied to a sample, unless isothermal conditions are employed. Thermogravimetic Analysis, TGA, can be used to quantify decomposition components in a substance while Differential Thermal Analysis, DTA, can be used to measure the heat flow or the specific heat capacity, with respect to time and temperature. The advantage of TGA/DTA analysis is that the measurement of weight loss and heat flow are taken simultaneously and the observed events are directly related with respect to time and temperature. TGA/DTA experiments were performed to help us take a different look at the chemical nature of HMX and aid us in understanding the void formation process.

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

    Science.gov (United States)

    Schnohr, C. S.

    2015-09-01

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

  12. A thermally driven differential mutation approach for the structural optimization of large atomic systems

    Science.gov (United States)

    Biswas, Katja

    2017-09-01

    A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating a thermal selection criterion, which makes it possible to reliably obtain low lying minima with just a small population size and is suitable for multimodal structural optimization. The method is tested on the structural optimization of amorphous graphene from unbiased atomic starting configurations. With just a population size of six systems, energetically very low structures are obtained. While each of the structures represents a distinctly different arrangement of the atoms, their properties, such as energy, distribution of rings, radial distribution function, coordination number, and distribution of bond angles, are very similar.

  13. Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions.

    Science.gov (United States)

    Volkmann, Niels

    2012-02-01

    A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Using a matter wave model to study the structure of the electron inside an atom

    Science.gov (United States)

    Chang, Donald

    In Bohr's atomic model, the atom was conceptually modeled as a miniature solar system. With the development of the Schrödinger equation, the wave function of the electron inside an atom becomes much better known. But the electron is still regarded as a pointed object; according to the Copenhagen Interpretation, the wave function is thought to describe only the probability of finding the electron. Such an interpretation, however, has raised some conceptual questions. For example, how can a point-like electron form a chemical bond between neighboring atoms? In an attempt to overcome this difficulty, we use a matter wave theory to model the structure of an electron inside the atom. This model is inspired by noticing the similarity between a free electron and a photon; both particles behave like a corpuscular object as well as a physical wave. Thus, we hypothesize that, like the photon, an electron is an excitation wave of a real physical field. Based on this hypothesis, we have derived a basic wave equation for the free electron. We show that, in the presence of an electrical potential, this basic wave equation can lead to the Schrödinger equation. This work implies that the solution of the Schrödinger equation actually represents the physical waves of the electron. Thus, the electron inside the atom should behave more like a topologically distributive wave than a pointed object. In this presentation, we will discuss the advantages and limitations of this model.

  15. Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.

    Science.gov (United States)

    Torres, A E; Fomine, S

    2015-04-28

    The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.

  16. Direct evidence of atomic-scale structural fluctuations in catalyst nanoparticles.

    Science.gov (United States)

    Lin, Pin Ann; Gomez-Ballesteros, Jose L; Burgos, Juan C; Balbuena, Perla B; Natarajan, Bharath; Sharma, Renu

    2017-05-01

    Rational catalyst design requires an atomic scale mechanistic understanding of the chemical pathways involved in the catalytic process. A heterogeneous catalyst typically works by adsorbing reactants onto its surface, where the energies for specific bonds to dissociate and/or combine with other species (to form desired intermediate or final products) are lower. Here, using the catalytic growth of single-walled carbon nanotubes (SWCNTs) as a prototype reaction, we show that the chemical pathway may in-fact involve the entire catalyst particle, and can proceed via the fluctuations in the formation and decomposition of metastable phases in the particle interior. We record in situ and at atomic resolution, the dynamic phase transformations occurring in a Cobalt catalyst nanoparticle during SWCNT growth, using a state-of-the-art environmental transmission electron microscope (ETEM). The fluctuations in catalyst carbon content are quantified by the automated, atomic-scale structural analysis of the time-resolved ETEM images and correlated with the SWCNT growth rate. We find the fluctuations in the carbon concentration in the catalyst nanoparticle and the fluctuations in nanotube growth rates to be of complementary character. These findings are successfully explained by reactive molecular dynamics (RMD) simulations that track the spatial and temporal evolution of the distribution of carbon atoms within and on the surface of the catalyst particle. We anticipate that our approach combining real-time, atomic-resolution image analysis and molecular dynamics simulations will facilitate catalyst design, improving reaction efficiencies and selectivity towards the growth of desired structure.

  17. 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...

  18. 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.

  19. Atomic structure of self-organizing iridium induced nanowires on Ge(001)

    NARCIS (Netherlands)

    Kabanov, Nikolai; Heimbuch, Rene; Zandvliet, Henricus J.W.; Saletsky, A.M.; Klavsyuk, A.L.

    2017-01-01

    The atomic structure of self-organizing iridium (Ir) induced nanowires on Ge(001) is studied by density functional theory (DFT) calculations and variable-temperature scanning tunneling microscopy. The Ir induced nanowires are aligned in a direction perpendicular to the Ge(001) substrate dimer rows,

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

    Directory of Open Access Journals (Sweden)

    Tsunetomo Yamada

    2016-07-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  2. 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

  3. Studying the Consistency between and within the Student Mental Models for Atomic Structure

    Science.gov (United States)

    Zarkadis, Nikolaos; Papageorgiou, George; Stamovlasis, Dimitrios

    2017-01-01

    Science education research has revealed a number of student mental models for atomic structure, among which, the one based on Bohr's model seems to be the most dominant. The aim of the current study is to investigate the coherence of these models when students apply them for the explanation of a variety of situations. For this purpose, a set of…

  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. 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.

  6. Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

    2014-04-01

    The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  7. An effective introduction to structural crystallography using 1D Gaussian atoms

    Science.gov (United States)

    Smith, Emily; Evans, Gwyndaf; Foadi, James

    2017-11-01

    The most important quantitative aspects of computational structural crystallography can be introduced in a satisfactory way using 1D truncated and periodic Gaussian functions to represent the atoms in a crystal lattice. This paper describes in detail and demonstrates 1D structural crystallography starting with the definition of such truncated Gaussians. The availability of the computer programme CRONE makes possible the repetition of the examples provided in the paper as well as the creation of new ones.

  8. Chemical structure of descriptors with an active hydrogen atom in certain bioregulators.

    Science.gov (United States)

    Kurchii, B A

    1996-01-01

    The chemical structure of descriptors (D) for some plant growth regulators (PGR), herbicides, pesticides and drugs is described. The presence of an active hydrogen atom in molecules is an essential factor determining biological activity of chemicals. The results obtained from the study of dependence existing between the structure of a certain substance and its biological activity may be used in designing of novel compounds which possess in biological activity.

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

    OpenAIRE

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

    2008-01-01

    The structural evolution and dynamics of silver nanodrops Ag${}_{2896}$ (4.4 nm in diameter) during rapid cooling conditions has been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modeled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique is applied to reveal the structural transition in the process of solidifica...

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

    Science.gov (United States)

    Xie, Jianming [San Diego, CA; Wang, Lei [San Diego, CA; Wu, Ning [Boston, MA; Schultz, Peter G [La Jolla, CA

    2008-07-15

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

  11. 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...

  12. A history of gap junction structure: hexagonal arrays to atomic resolution.

    Science.gov (United States)

    Grosely, Rosslyn; Sorgen, Paul L

    2013-02-01

    Gap junctions are specialized membrane structures that provide an intercellular pathway for the propagation and/or amplification of signaling cascades responsible for impulse propagation, cell growth, and development. Prior to the identification of the proteins that comprise gap junctions, elucidation of channel structure began with initial observations of a hexagonal nexus connecting apposed cellular membranes. Concomitant with technological advancements spanning over 50 years, atomic resolution structures are now available detailing channel architecture and the cytoplasmic domains that have helped to define mechanisms governing the regulation of gap junctions. Highlighted in this review are the seminal structural studies that have led to our current understanding of gap junction biology.

  13. Novel low-dose imaging technique for characterizing atomic structures through scanning transmission electron microscope

    Science.gov (United States)

    Su, Chia-Ping; Syu, Wei-Jhe; Hsiao, Chien-Nan; Lai, Ping-Shan; Chen, Chien-Chun

    2017-08-01

    To investigate dislocations or heterostructures across interfaces is now of great interest to condensed matter and materials scientists. With the advances in aberration-corrected electron optics, the scanning transmission electron microscope has demonstrated its excellent capability of characterizing atomic structures within nanomaterials, and well-resolved atomic-resolution images can be obtained through long-exposure data acquisition. However, the sample drifting, carbon contamination, and radiation damage hinder further analysis, such as deriving three-dimensional (3D) structures from a series of images. In this study, a method for obtaining atomic-resolution images with significantly reduced exposure time was developed, using which an original high-resolution image with approximately one tenth the electron dose can be obtained by combining a fast-scan high-magnification image and a slow-scan low-magnification image. The feasibility of obtaining 3D atomic structures using the proposed approach was demonstrated through multislice simulation. Finally, the feasibility and accuracy of image restoration were experimentally verified. This general method cannot only apply to electron microscopy but also benefit to image radiation-sensitive materials using various light sources.

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

    Science.gov (United States)

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

    2016-05-05

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

  15. Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy.

    Science.gov (United States)

    Ho, Phuong T; Reddy, Vijay S

    2017-10-27

    The recent technological advances in electron microscopes, detectors, as well as image processing and reconstruction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structures on the methods of structure determination, resolution of the structures, and size of the virus particles revealed a rapid increase in the virus structures determined by cryo-EM at near atomic resolution since 2010. In addition, the data highlight the median resolution (∼3.0 Å) and size (∼310.0 Å in diameter) of the virus particles determined by X-ray crystallography while no such limits exist for cryo-EM structures, which have a median diameter of 508 Å. Notably, cryo-EM virus structures in the last four years have a median resolution of 3.9 Å. Taken together with minimal sample requirements, not needing diffraction quality crystals, and being able to achieve similar resolutions of the crystal structures makes cryo-EM the method of choice for current and future virus capsid structure determinations. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. 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.

  17. 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.

  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. Dislocations in AlGaN: Core Structure, Atom Segregation, and Optical Properties.

    Science.gov (United States)

    Massabuau, Fabien C-P; Rhode, Sneha L; Horton, Matthew K; O'Hanlon, Thomas J; Kovács, András; Zielinski, Marcin S; Kappers, Menno J; Dunin-Borkowski, Rafal E; Humphreys, Colin J; Oliver, Rachel A

    2017-08-09

    We conducted a comprehensive investigation of dislocations in Al0.46Ga0.54N. Using aberration-corrected scanning transmission electron microscopy and energy dispersive X-ray spectroscopy, the atomic structure and atom distribution at the dislocation core have been examined. We report that the core configuration of dislocations in AlGaN is consistent with that of other materials in the III-Nitride system. However, we observed that the dissociation of mixed-type dislocations is impeded by alloying GaN with AlN, which is confirmed by our experimental observation of Ga and Al atom segregation in the tensile and compressive parts of the dislocations, respectively. Investigation of the optical properties of the dislocations shows that the atom segregation at dislocations has no significant effect on the intensity recorded by cathodoluminescence in the vicinity of the dislocations. These results are in contrast with the case of dislocations in In0.09Ga0.91N where segregation of In and Ga atoms also occurs but results in carrier localization limiting non-radiative recombination at the dislocation. This study therefore sheds light on why InGaN-based devices are generally more resilient to dislocations than their AlGaN-based counterparts.

  20. Local atomic structure and discommensurations in the charge density wave of CeTe3.

    Science.gov (United States)

    Kim, H J; Malliakas, C D; Tomić, A T; Tessmer, S H; Kanatzidis, M G; Billinge, S J L

    2006-06-09

    The local structure of in the incommensurate charge density wave (IC-CDW) state has been obtained using atomic pair distribution function analysis of x-ray diffraction data. Local atomic distortions in the Te nets due to the CDW are larger than observed crystallographically, resulting in distinct short and long Te-Te bonds. Observation of different distortion amplitudes in the local and average structures is explained by the discommensurated nature of the CDW, since the pair distribution function is sensitive to the local displacements within the commensurate regions, whereas the crystallographic result averages over many discommensurated domains. The result is supported by STM data. This is the first quantitative local structural study within the commensurate domains in an IC-CDW system.

  1. Integrative, dynamic structural biology at atomic resolution--it's about time.

    Science.gov (United States)

    van den Bedem, Henry; Fraser, James S

    2015-04-01

    Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and other techniques are helping us realize the dream of seeing--in atomic detail--how different parts of biomolecules shift between functional substates using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution.

  2. Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

    Science.gov (United States)

    van den Bedem, Henry; Fraser, James S.

    2015-01-01

    Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

  3. Atomic structures and gram scale synthesis of three tetrahedral quantum dots.

    Science.gov (United States)

    Beecher, Alexander N; Yang, Xiaohao; Palmer, Joshua H; LaGrassa, Alexandra L; Juhas, Pavol; Billinge, Simon J L; Owen, Jonathan S

    2014-07-30

    Luminescent semiconducting quantum dots (QDs) are central to emerging technologies that range from tissue imaging to solid-state lighting. However, existing samples are heterogeneous, which has prevented atomic-resolution determination of their structures and obscured the relationship between their atomic and electronic structures. Here we report the synthesis, isolation, and structural characterization of three cadmium selenide QDs with uniform compositions (Cd35Se20(X)30(L)30, Cd56Se35(X)42(L)42, Cd84Se56(X)56(L)56; X = O2CPh, L = H2N-C4H9). Their UV-absorption spectra show a lowest energy electronic transition that decreases in energy (3.54 eV, 3.26 eV, 3.04 eV) and sharpens as the size of the QD increases (fwhm = 207 meV, 145 meV, 115 meV). The photoluminescence spectra of all three QDs are broad with large Stokes shifts characteristic of trap-luminescence. Using a combination of single-crystal X-ray diffraction and atomic pair distribution function analysis, we determine the structures of their inorganic cores, revealing a series of pyramidal nanostuctures with cadmium terminated {111} facets. Theoretical and experimental studies on these materials will open the door to a deeper fundamental understanding of structure-property relationships in quantum-confined semiconductors.

  4. Morphology and atomic structure of InGaN(0001) surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Biermann, Amelie; Friedrich, Christian; Kneissl, Michael; Vogt, Patrick [TU Berlin (Germany). Institute of Solid State Physics EW6-1; Hoffmann, Veit [Ferdinand-Braun-Institut f. Hoechstfrequenztechnik, Berlin (Germany); Esser, Norbert [ISAS-Berlin (Germany); TU Berlin (Germany). Institute of Solid State Physics EW6-1

    2010-07-01

    Group III-nitrides offer a broad application spectrum in optoelectronic devices. Although the fabrication of high-quality devices requires the control of nanometer thick layers, there is only limited knowledge about the atomic structure of the surface. Here we present a study on the morphology and atomic structure of (0001) In{sub x}Ga{sub 1-x}N surfaces grown by MOVPE. Samples are prepared under UHV conditions by thermal annealing between 600 C and 800 C to achieve clean, decontaminated surfaces. Additionally thermally cracked ammonia and nitrogen plasma are used as nitrogen sources in order to vary surface stoichiometries and to prevent nitrogen depletion of the crystal. The chemical composition of the surface during preparation is determined by Auger Electron Spectroscopy. Clean (0001) In{sub x}Ga{sub 1-x}N surfaces were prepared at 760 C revealing no surface carbon and low residual oxygen compounds. Depending on the surface preparation, surface structures showing different surface symmetries such as (1 x 1), (1+1/6) or (2 x 2) were obtained as determined by LEED. The chemical composition remains similar for all structures. In order to get further information STM measurements of the atomic structure are presented.

  5. Strain engineering of atomic and electronic structures of few-monolayer-thick GaN

    Science.gov (United States)

    Kolobov, A. V.; Fons, P.; Saito, Y.; Tominaga, J.; Hyot, B.; André, B.

    2017-07-01

    Two-dimensional (2D) semiconductors possess the potential to ultimately minimize the size of devices and concomitantly drastically reduce the corresponding energy consumption. In addition, materials in their atomic-scale limit often possess properties different from their bulk counterparts paving the way to conceptually novel devices. While graphene and 2D transition-metal dichalcogenides remain the most studied materials, significant interest also exists in the fabrication of atomically thin structures from traditionally 3D semiconductors such as GaN. While in the monolayer limit GaN possesses a graphenelike structure and an indirect band gap, it was recently demonstrated that few-layer GaN acquires a Haeckelite structure in the direction of growth with an effectively direct gap. In this work, we demonstrate the possibility of strain engineering of the atomic and electronic structure of few-monolayer-thick GaN structures, which opens new avenues for their practical application in flexible nanoelectronics and nano-optoelectronics. Our simulations further suggest that due to the weak van der Waals-like interaction between a substrate and an overlayer, the use of a MoS2 substrate may be a promising route to fabricate few-monolayer Haeckelite GaN experimentally.

  6. 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/. © 2015 Wiley Periodicals, Inc.

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

  9. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization.

    Science.gov (United States)

    Xu, Dong; Zhang, Yang

    2011-11-16

    Most protein structural prediction algorithms assemble structures as reduced models that represent amino acids by a reduced number of atoms to speed up the conformational search. Building accurate full-atom models from these reduced models is a necessary step toward a detailed function analysis. However, it is difficult to ensure that the atomic models retain the desired global topology while maintaining a sound local atomic geometry because the reduced models often have unphysical local distortions. To address this issue, we developed a new program, called ModRefiner, to construct and refine protein structures from Cα traces based on a two-step, atomic-level energy minimization. The main-chain structures are first constructed from initial Cα traces and the side-chain rotamers are then refined together with the backbone atoms with the use of a composite physics- and knowledge-based force field. We tested the method by performing an atomic structure refinement of 261 proteins with the initial models constructed from both ab initio and template-based structure assemblies. Compared with other state-of-art programs, ModRefiner shows improvements in both global and local structures, which have more accurate side-chain positions, better hydrogen-bonding networks, and fewer atomic overlaps. ModRefiner is freely available at http://zhanglab.ccmb.med.umich.edu/ModRefiner. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Verma, Abhinav; Wenzel, Wolfgang

    2007-01-01

    Background The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01) that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure prediction purposes. We therefore investigate here a low-cost free-energy relaxation protocol for protein structure prediction that combines heuristic methods for model generation with all-atom free-energy relaxation in PFF01. Results We use PFF01 to rank and cluster the conformations for 32 proteins generated by ROSETTA. For 22/10 high-quality/low quality decoy sets we select near-native conformations with an average Cα root mean square deviation of 3.03 Å/6.04 Å. The protocol incorporates an inherent reliability indicator that succeeds for 78% of the decoy sets. In over 90% of these cases near-native conformations are selected from the decoy set. This success rate is rationalized by the quality of the decoys and the selectivity of the PFF01 forcefield, which ranks near-native conformations an average 3.06 standard deviations below that of the relaxed decoys (Z-score). Conclusion All-atom free-energy relaxation with PFF01 emerges as a powerful low-cost approach toward generic de-novo protein structure prediction. The approach can be applied to large all-atom decoy sets of any origin and requires no preexisting structural information to identify the native conformation. The study provides evidence that a large class of proteins may be foldable by PFF01. PMID:17371594

  11. Atomic Structures of Minor Proteins VI and VII in the Human Adenovirus.

    Science.gov (United States)

    Dai, Xinghong; Wu, Lily; Sun, Ren; Zhou, Z Hong

    2017-10-04

    Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts towards more effective applications. Since 2010, atomic models of human Ad5 have been independently derived from photographic film cryoEM and X-ray crystallography, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII and IX. To clarify these discrepancies, here we have employed the technology of direct electron-counting to obtain a cryoEM structure of human Ad5 at 3.2 Å resolution. Our improved structure unambiguously confirmed our previous cryoEM models of proteins IIIa, VIII and IX and explained the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavities of hexons - the cleaved N-terminus of precursor protein VI (pVIn), the cleaved N-terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2--by extension that of genome-condensing pVII--to hexons is consistent with the previously proposed dsDNA genome-capsid co-assembly for adenoviruses, which resembles that of ssRNA viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid, as exemplified by tailed bacteriophages and herpesviruses. IMPORTANCE Adenovirus is a double-edged sword to humans - as a widespread pathogen and a bioengineering tool for anti-cancer and gene therapy. Atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models from conventional/film cryoEM and X-ray crystallography for important cement proteins IIIa, VIII, and IX have caused confusion. Using the cutting-edge cryoEM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our

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

    Science.gov (United States)

    Jonikas, Magdalena A; Radmer, Randall J; Altman, Russ B

    2009-12-15

    The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87-3.31 A RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 A RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure. Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org/home/c2a. russ.altman@stanford.edu

  13. Small angle neutron and X-ray studies of carbon structures with metal atoms

    Science.gov (United States)

    Lebedev, V. T.; Szhogina, A. A.; Bairamukov, V. Yu

    2017-05-01

    Encapsulation of metal atoms inside carbon single-wall cages or within multi-layer cells has been realized using molecular precursors and high temperature processes transforming them into desirable structures. Endohedral fullerenols Fe@C60(OH)X with 3d-metal (iron) have been studied by SANS in aqueous solutions where they form stable globular clusters with radii R C ∼ 10-12 nm and aggregation numbers N C ∼ 104. This self-assembly is a crucial feature of paramagnetic fullerenols as perspective contrast agents for Magneto-Resonance Imaging in medicine. Cellular carbon-metal structures have been created by the pyrolysis of diphthalocyanines of lanthanides and actinides. It was established that these ultra porous matrices consist of globular cells of molecular precursor size (∼ 1 nm) which are aggregated into superstructures. This provides retain of metal atoms inside matrices which may serve for safety storage of spent fuel of nuclear power plants.

  14. 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

    2012-01-01

    Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy (cryoEM) or X-ray crystallography. In these density maps the general arrangement of secondary structure elements is revealed while their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the secondary structure elements de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins the protocol consistently and reproducibly achieves models with RMSD values smaller than 3 Å. PMID:22405005

  15. High-speed atomic force microscopy: Structure and dynamics of single proteins.

    Science.gov (United States)

    Casuso, Ignacio; Rico, Felix; Scheuring, Simon

    2011-10-01

    For surface analysis of biological molecules, atomic force microscopy (AFM) is an appealing technique combining data acquisition under physiological conditions, for example buffer solution, room temperature and ambient pressure, and high resolution. However, a key feature of life, dynamics, could not be assessed until recently because of the slowness of conventional AFM setups. Thus, for observing bio-molecular processes, the gain of image acquisition speed signifies a key progress. Here, we review the development and recent achievements using high-speed atomic force microscopy (HS-AFM). The HS-AFM is now the only technique to assess structure and dynamics of single molecules, revealing molecular motor action and diffusion dynamics. From this imaging data, watching molecules at work, novel and direct insights could be gained concerning the structure, dynamics and function relationship at the single bio-molecule level. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. NMR Investigation of Atomic Structure and Dynamics of Bulk Metallic Glasses

    Science.gov (United States)

    2013-09-17

    that, via Al-27 nuclear magnetic resonance (NMR) measurements, that atomic level structures characterized by electric-field-gradient tensors and the...only by the second-order quadrupole effect, and wide satellite transitions 1m m  ( 1/ 2m   ) broadened by the first-order quadrupole ...was used to determine the corresponding linewidths of the central and satellite transitions as noted by the dashed curves in Fig 3.1. In addition, the

  17. Atomic Force Microscopy in Microbiology: New Structural and Functional Insights into the Microbial Cell Surface

    Science.gov (United States)

    2014-01-01

    ABSTRACT Microbial cells sense and respond to their environment using their surface constituents. Therefore, understanding the assembly and biophysical properties of cell surface molecules is an important research topic. With its ability to observe living microbial cells at nanometer resolution and to manipulate single-cell surface molecules, atomic force microscopy (AFM) has emerged as a powerful tool in microbiology. Here, we survey major breakthroughs made in cell surface microbiology using AFM techniques, emphasizing the most recent structural and functional insights. PMID:25053785

  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. On the emergence of molecular structure from atomic shape in the 1/r2 harmonium model.

    Science.gov (United States)

    Müller-Herold, Ulrich

    2006-01-07

    The formal similarity of the three-body Hamiltonians for helium and the hydrogen molecule ion is used to demonstrate the unfolding of a rotating dumbbell-like proton distribution from a (1s)2-type electron distribution by smooth variation of the particles' masses in the 1/r2 harmonium model. The 1/r2 harmonium is an exactly solvable modification of the harmonium model (also known as Hooke's law atom) where the attraction between different particles is harmonic and the repulsion between the two equal particles is given by a 1/r2 potential. The dumbbell-like molecular structure appears as an expression of increasing spatial correlation due to increasing mass. It gradually appears in the one-density distribution of the two equal particles if their mass exceeds a critical value depending on the mass of the third particle. For large mass of the equal particles, their one-density distribution approaches an asymptotic form derived from the Born-Oppenheimer treatment of H2+ in the 1/r2 harmonium model. Below the critical value, the one density is a spherical, Gaussian-type atomic density distribution with a maximum at the center of mass. The topological transition at the critical value separates molecular structure and atomic shape as two qualitatively different manifestations of spatial structure.

  20. A quantitative comparison of dura mater tissue structures measured with atomic force microscopy.

    Science.gov (United States)

    Sikora, Andrzej; Kedzia, Alicja

    2012-01-01

    The growth of a human embryo is a very sophisticated process. Understanding the way it proceeds is a key factor in pathology preventing and treating diseases. Therefore one needs to use advanced to tools and methods to investigate various aspects of the anatomy and physiology of humans during the first months of growth. This work is focused on the structure of dura mater tissue, one of the membranes protecting the brain, which can be responsible for a number of health issues if it develops abnormally. The aim of the work was to observe dura mater tissue structure with atomic force microscopy and to provide a quantitative method of discrimination of both the periosteal and meningeal layers in a 6-month-old human embryo. The measurements were performed with atomic force microscopy, in air, using tapping mode. The sample was stored in formaldehyde and dried prior to the measurements. The results obtained permitted observation of the structure of the tissue, in particular the presence of collagen fibers. By applying various image analysis tools, quantitative descriptions of both layers were created in order to distinguish them. The experiment proved that atomic force microscopy can be a useful tool in the investigation of the development process of the dura mater tissue in terms of the appearance of differences related to various functions of the periosteal and meningeal layers.

  1. SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

    Science.gov (United States)

    Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

    2017-10-01

    As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhuiykov, Serge, E-mail: serge.zhuiykov@ugent.be [Ghent University Global Campus, Department of Applied Analytical & Physical Chemistry, Faculty of Bioscience Engineering, 119 Songdomunhwa-ro, Yeonsu-Gu, Incheon 406-840 (Korea, Republic of); Kawaguchi, Toshikazu [Global Station for Food, Land and Water Resources, Global Institution for Collaborative Research and Education, Hokkaido University, N10W5 Kita-ku, Sapporo, Hokkaido 060-0810 (Japan); Graduate School of Environmental Science, Hokkaido University, N10W5 Kita-ku, Sapporo, Hokkaido 060-0810 (Japan); Hai, Zhenyin; Karbalaei Akbari, Mohammad; Heynderickx, Philippe M. [Ghent University Global Campus, Department of Applied Analytical & Physical Chemistry, Faculty of Bioscience Engineering, 119 Songdomunhwa-ro, Yeonsu-Gu, Incheon 406-840 (Korea, Republic of)

    2017-01-15

    Highlights: • Advantages of atomic layer deposition technology (ALD) for two-dimensional nano-crystals. • Conformation of ALD technique and chemistry of precursors. • ALD of semiconductor oxide thin films. • Ultra-thin (∼1.47 nm thick) ALD-developed tungsten oxide nano-crystals on large area. - Abstract: Atomic Layer Deposition (ALD) is an enabling technology which provides coating and material features with significant advantages compared to other existing techniques for depositing precise nanometer-thin two-dimensional (2D) nanostructures. It is a cyclic process which relies on sequential self-terminating reactions between gas phase precursor molecules and a solid surface. ALD is especially advantageous when the film quality or thickness is critical, offering ultra-high aspect ratios. ALD provides digital thickness control to the atomic level by depositing film one atomic layer at a time, as well as pinhole-free films even over a very large and complex areas. Digital control extends to sandwiches, hetero-structures, nano-laminates, metal oxides, graded index layers and doping, and it is perfect for conformal coating and challenging 2D electrodes for various functional devices. The technique’s capabilities are presented on the example of ALD-developed ultra-thin 2D tungsten oxide (WO{sub 3}) over the large area of standard 4” Si substrates. The discussed advantages of ALD enable and endorse the employment of this technique for the development of hetero-nanostructure 2D semiconductors with unique properties.

  3. Structure stability and magnetism in graphene impurity complexes with embedded V and Nb atoms

    Energy Technology Data Exchange (ETDEWEB)

    Thakur, Jyoti [Department of Physics, University College, Kurukshetra University, Kurukshetra 136119, Haryana (India); Kashyap, Manish K., E-mail: manishdft@gmail.com [Department of Physics, Kurukshetra University, Kurukshetra 136119, Haryana (India); Ames Laboratory, U.S. Department of Energy, Iowa State University, Ames, IA 50011-3020 (United States); Taya, Ankur; Rani, Priti [Department of Physics, Kurukshetra University, Kurukshetra 136119, Haryana (India); Saini, Hardev S. [Department of Physics, Guru Jambheshwar University of Science & Technology, Hisar 125001, Haryana (India); Reshak, A.H. [New Technologies – Research Centre, University of West Bohemia, Univerzitni 8, 306 14 Pilsen (Czech Republic); School of Material Engineering, University Malaysia Perlis, 01007 Kangar, Perlis (Malaysia)

    2017-07-01

    Highlights: • V/Nb embedding in graphene containing monovacancies/divacancies is presented. • Spin polarization near/equal to 100% ensures use of studied nanosystems in spin filter devices. • Bandstructures are analyzed to identify shifting of Dirac cone of graphene. - Abstract: The appearance of vacancy defects could produce appropriate magnetic moment in graphene and the sensitivity to absorb atoms/molecules also increases with this. In this direction, a DFT study of embedding V and Nb atom in graphene containing monovacancies (MV) and divacancies (DV) is reported. Complete/almost complete spin polarization is detected for V/Nb embedding. The origin of magnetism has been identified via interaction of 3d-states of embedded atom with C-p states present in the vicinity of embedded site. The band structures have been analyzed to counter the observed semiconducting nature of graphene in minority spin on embedding V/Nb atom. The isosurface analysis also confirms the induced magnetism of present nanosystems. The present results reveal that these nanosystems have the potential for futuristic applications like spintronics and energy resources.

  4. Fine-structure transitions of interstellar atomic sulfur and silicon induced by collisions with helium.

    Science.gov (United States)

    Lique, F; Kłos, J; Le Picard, S D

    2017-10-02

    Atomic sulfur and silicon are important constituents of the interstellar matter and are both used as tracers of the physical conditions in interstellar shocks and outflows. We present an investigation of the spin-orbit (de-)excitation of S((3)P) and Si((3)P) atoms induced by collisions with helium with the aim to improve the determination of atomic sulfur and silicon abundances in the interstellar medium from S and Si emission spectra. Quantum-mechanical calculations have been performed in order to determine rate coefficients for the fine-structure transitions in the 5-1000 K temperature range. The scattering calculations are based on new highly correlated ab initio potentials. The theoretical results show that the (de-)excitation of Si is much faster than that of S. The rate coefficients deduced from this study are in good agreement with previous experimental and theoretical findings despite some deviations at low temperatures. From the computation of critical densities defined as the ratios between Einstein coefficients and the sum of the relevant collisional de-excitation rate coefficients, we show that local thermodynamic equilibrium conditions are not fulfilled for analyzing S and Si emission spectra observed in the interstellar medium. Hence, the present rate coefficients will be extremely useful for the accurate determination of interstellar atomic sulfur and silicon abundances.

  5. Atomically-thick two-dimensional crystals: electronic structure regulation and energy device construction.

    Science.gov (United States)

    Sun, Yongfu; Gao, Shan; Xie, Yi

    2014-01-21

    Atomically-thick two-dimensional crystals can provide promising opportunities to satisfy people's requirement of next-generation flexible and transparent nanodevices. However, the characterization of these low-dimensional structures and the understanding of their clear structure-property relationship encounter many great difficulties, owing to the lack of long-range order in the third dimensionality. In this review, we survey the recent progress in fine structure characterization by X-ray absorption fine structure spectroscopy and also overview electronic structure modulation by density-functional calculations in the ultrathin two-dimensional crystals. In addition, we highlight their structure-property relationship, transparent and flexible device construction as well as wide applications in photoelectrochemical water splitting, photodetectors, thermoelectric conversion, touchless moisture sensing, supercapacitors and lithium ion batteries. Finally, we outline the major challenges and opportunities that face the atomically-thick two-dimensional crystals. It is anticipated that the present review will deepen people's understanding of this field and hence contribute to guide the future design of high-efficiency energy-related devices.

  6. Atomic configuration and electronic structure of extended defects from the point of view of positron annihilation: a grain boundary example

    Energy Technology Data Exchange (ETDEWEB)

    Sob, M.; Turek, I. [Akademie Ved Ceske Republiky, Brno (Czech Republic). Ustav Fyzikalni Metalurgie; Vitek, V. [Pennsylvania Univ., Philadelphia, PA (United States). Dept. of Materials Science and Engineering

    1997-10-01

    A quantum-mechanical approach for determining the electronic structure and atomic configuration of extended defects in metals is described and importance of theoretical methods for interpretation of positron annihilation spectroscopy data is stressed. As an example, atomic configuration of the {Sigma} = 5(210)/[001] tilt grain boundary in tungsten is determined and local densities of states at atoms in defect region are discussed. (author). 19 refs, 3 figs.

  7. Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin

    Science.gov (United States)

    Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong

    2004-04-01

    We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

  8. Structure of nanocrystalline Ti3C2 MXene using atomic pair distribution function.

    Science.gov (United States)

    Shi, Chenyang; Beidaghi, Majid; Naguib, Michael; Mashtalir, Olha; Gogotsi, Yury; Billinge, Simon J L

    2014-03-28

    The structures of nanocrystalline pristine, potassium hydroxide and sodium acetate intercalated new two-dimensional materials Ti3C2 MXenes were studied using the x-ray atomic pair distribution function technique. Pristine MXene has a hexagonal structure with a=b=3.0505(5)  Å, c=19.86(2)  Å (S.G. P63/mmc No. 194). Both hydroxyl and fluoride terminating species are present. The intercalation of K+ or Na+ ions expands the Ti3C2 layers perpendicular to the planes but shrinks the in-plane a and b lattice parameters.

  9. MFI structure catalyst and utilization for aromatization hydrocarbons comprising 5 to 12 carbon atoms

    Energy Technology Data Exchange (ETDEWEB)

    Alario, F.; Deves, J.M.

    1993-05-21

    The invention describes a composite catalyst which contains: a MFI structure zeolite containing, at least, an element chosen among alkaline or alkaline-earth metals, with a structure made of Silicon, Aluminium and / or Gallium; a matrix; platinum metals and additive metal chosen among Stain, Germanium, Indium, Copper, Iron, Molybdenum, Gallium, Thallium, Gold, Silver, Ruthenium, Chrome, Tungsten and Lead at least; an halogen chosen among Fluorine, Chlorine, Bromine and Iodine at least; Gallium and Zinc possibly; alkaline or alkaline-earth metal in the matrix preferentially. The invention describes also the use of this catalyst for aromatization reactions of hydrocarbons containing 5 to 12 carbon atoms per molecule.

  10. Probing the atomic structure of amorphous Ta2O5 coatings

    Science.gov (United States)

    Bassiri, R.; Borisenko, K. B.; Cockayne, D. J. H.; Hough, J.; MacLaren, I.; Rowan, S.

    2011-01-01

    Low optical and mechanical loss Ta2O5 amorphous coatings have a growing number of applications in precision optical measurements systems. Transmission electron microscopy is a promising way to probe the atomic structure of these coatings in an effort to better understand the causes of the observed mechanical and optical losses. Analysis of the experimental reduced density functions using a combination of reverse Monte Carlo refinements and density functional theory molecular dynamics simulations reveals that the structure of amorphous Ta2O5 consists of clusters with increased contribution from a Ta2O2 ring fragment.

  11. 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).

  12. 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).

  13. Influence of endohedral confinement of atoms on structural and dynamical properties of the C60 fullerene

    Science.gov (United States)

    Etindele, A. J.; Maezono, R.; Melingui Melono, R. L.; Motapon, O.

    2017-10-01

    The influence of encapsulated atoms in the structural and dynamical properties of C60 in A@C60 complexes is studied in the framework of the Density Functional Theory using Density of states and the theoretical Electron Energy Loss Spectroscopy. It is shown that C60 preserves its spherical geometry no matter the equilibrium position of the encapsulated atom. The Infrared and Raman spectra of the H@C60, He@C60 and Ne@C60 complexes are found not to differ significantly from that of C60 whereas those for Li@C60 and Na@C60 exhibit more peaks. The analysis shows that the changes on the cage properties come from inside it.

  14. 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...

  15. Electronic structure of atomic-plane doped superlattice in GaAs

    Science.gov (United States)

    Zehe, A.; de la Cruz Estenoz, D.

    A special atomic-plane doped superlattice is proposed and studied, where both donors and acceptors are incorporated during MBE growth simultaneously into sheets spaced equidistantly by intrinsic regions of the growing semiconductor material. The donor-acceptor Pair (DAP)-distribution function displays characteristics features of the proposed pair-doped delta-superlattice (PD-δiδi-SL) which allow for their experimental verification by luminescence measurements. With excess doping of one type a narrow V-shaped potential is formed about the atomic planes generating a multiquantum-well structure. In the present paper the size quantization in V-shaped potential wells is studied, and exact analytic expressions for wavefunctions and energy levels are given as function of determining measures of potential well and superlattices. The sawtooth doping superlattice is a special case in our calculus.

  16. The evolution of structural and chemical heterogeneity during rapid solidification at gas atomization

    Science.gov (United States)

    Golod, V. M.; Sufiiarov, V. Sh

    2017-04-01

    Gas atomization is a high-performance process for manufacturing superfine metal powders. Formation of the powder particles takes place primarily through the fragmentation of alloy melt flow with high-pressure inert gas, which leads to the formation of non-uniform sized micron-scale particles and subsequent their rapid solidification due to heat exchange with gas environment. The article presents results of computer modeling of crystallization process, simulation and experimental studies of the cellular-dendrite structure formation and microsegregation in different size particles. It presents results of adaptation of the approach for local nonequilibrium solidification to conditions of crystallization at gas atomization, detected border values of the particle size at which it is possible a manifestation of diffusionless crystallization.

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

    Science.gov (United States)

    Das, Rhiju

    2013-01-01

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

  18. 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

  19. 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....

  20. Temperature Dependent Local Atomic Structure of LuFe2O4

    Science.gov (United States)

    Liu, S.; Zhang, H.; Ghose, S.; Cheong, S.-W.; Emge, T.; Chen, Y.-S.; Tyson, T.

    The LuFe2O4 system has be studied intensively as a novel material with charge ordered driven ferroelectricity. However, the existence and origin of electric polarization and it coupling to the magnetic structure are open questions still to be addressed. Distinctly differing experiments yield different results. In this work, structural measurements on multiple length scales have been conducted over a broad range of temperatures. We have studied the correlation between the structural distortion and the electronic/magnetic properties in single-crystalline LuFe2O4 by using X-ray diffraction (XRD), temperature and orientation dependent Raman spectroscopy, temperature dependent X-ray pair distribution function (PDF) measurements and DFT modeling. The nature of the observed local atomic and electronic structural changes will be discussed and compared with previous work. This work is supported by DOE Grant DE-FG02-07ER46402.

  1. 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...

  2. Structural, atomic Hirschfeld surface, magnetic and magnetocaloric properties of SmNi{sub 5} compound

    Energy Technology Data Exchange (ETDEWEB)

    Nouri, K., E-mail: nouri@icmpe.cnrs.fr [C.M.T.R, I.C.M.P.E, CNRS, Université Paris Est Créteil, UMR 7182, 2-8 rue Henri Dunant, F-94320 Thiais (France); Laboratoire des Sciences des Matériaux et de l' Environnement, Faculté des Sciences de Sfax- Université de Sfax, BP 1171, Sfax, 3018 (Tunisia); Jemmali, M. [Laboratoire des Sciences des Matériaux et de l' Environnement, Faculté des Sciences de Sfax- Université de Sfax, BP 1171, Sfax, 3018 (Tunisia); Chemistry Departement, College of Science and Arts at Ar-Rass, Qassim University, P.O. Box53 (Saudi Arabia); Walha, S. [Laboratoire des Sciences des Matériaux et de l' Environnement, Faculté des Sciences de Sfax- Université de Sfax, BP 1171, Sfax, 3018 (Tunisia); Zehani, K. [C.M.T.R, I.C.M.P.E, CNRS, Université Paris Est Créteil, UMR 7182, 2-8 rue Henri Dunant, F-94320 Thiais (France); Ben Salah, A. [Laboratoire des Sciences des Matériaux et de l' Environnement, Faculté des Sciences de Sfax- Université de Sfax, BP 1171, Sfax, 3018 (Tunisia); Bessais, L. [C.M.T.R, I.C.M.P.E, CNRS, Université Paris Est Créteil, UMR 7182, 2-8 rue Henri Dunant, F-94320 Thiais (France)

    2016-07-05

    The SmNi{sub 5} intermetallic compound has been investigated by arc-melting. Powder X-ray diffraction analysis and Rietveld refinement revealed that the sample crystallized in the hexagonal CaCu{sub 5}-type structure P6/mmm space group with the following lattice parameters: a = 4.9203 (1) Å, c = 3.9662 (1) Å. These lattice parameters for the compound are in good agreement with previous theoretical result and experimental data. The EDX analysis has been performed to confirm the composition of this compound. The chemical bonding in SmNi{sub 5} was analyzed using atomic Hirshfeld surfaces, and this analysis supports the presence of the structural elements and the coordination of Sm (1a), Ni (2c) and Ni (3 g). This study indicates the different types of interatomic interactions between the Sm and Ni atoms and the weak interactions between Sm–Sm atoms were also observed along the c axis. The magnetic properties and magnetocaloric effect (MCE) have been established by the magnetization and isothermal magnetization of different temperature measurements. The magnetization curve as a function of temperature shows a magnetic transition from ferromagnetic to paramagnetic state at the Curie temperature T{sub C} = 29 K. We have studied the MCE phenomena in the vicinity of magnetic phase transitions in terms of magnetic entropy change. The temperature dependence of the magnetization, the magnetic entropy changeΔS{sub M}, as well as the relative cooling power around the second-order magnetic transition and the Arrott plots for the alloys are reported. - Highlights: • The SmNi{sub 5} intermetallic compound has been investigated by arc-melting. • The chemical bonding in SmNi{sub 5} was analyzed using atomic Hirshfeld surfaces. • The second order magnetocaloric material SmNi{sub 5} is investigated.

  3. Use of Complementary Cation And Anion Heavy Atom-Atom Salt Derivatives to Solve the Structure of Cytochrome P450 46a1

    Energy Technology Data Exchange (ETDEWEB)

    White, M.A.; Mast, N.; Bjorkhem, I.; Johnson, E.F.; Stout, C.D.; Pikuleva, I.A.

    2009-05-26

    Human cytochrome P450 46A1 (CYP46A1) is one of the key enzymes in cholesterol homeostasis in the brain. The crystallization and heavy-atom structure solution of an active truncated CYP46A1 in complex with the high-affinity substrate analogue cholesterol-3-sulfate (CH-3S) is reported. The 2.6 {angstrom} structure of CYP46A1-CH-3S was solved using both anion and cation heavy-atom salts. In addition to the native anomalous signal from the haem iron, an NaI anion halide salt derivative and a complementary CsCl alkali-metal cation salt derivative were used. The general implications of the use of halide and alkali-metal quick soaks are discussed. The importance of using isoionic strength buffers, the titration of heavy-atom salts into different ionic species and the role of concentration are considered. It was observed that cation/anion-binding sites will occasionally overlap, which could negatively impact upon mixed RbBr soaks used for multiple anomalous scatterer MAD (MMAD). The use of complementary cation and anion heavy-atom salt derivatives is a convenient and powerful tool for MIR(AS) structure solution.

  4. Atomic structure of nanometer-sized amorphous TiO2

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, H.; Chen, B.; Banfield, J.F.; Waychunas, G.A.

    2008-10-15

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

  5. 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)

  6. Atomic Structure of Salutaridine Reductase from the Opium Poppy (Papaver somniferum)

    Energy Technology Data Exchange (ETDEWEB)

    Higashi, Yasuhiro; Kutchan, Toni M.; Smith, Thomas J. (Danforth)

    2011-11-18

    The opium poppy (Papaver somniferum L.) is one of the oldest known medicinal plants. In the biosynthetic pathway for morphine and codeine, salutaridine is reduced to salutaridinol by salutaridine reductase (SalR; EC 1.1.1.248) using NADPH as coenzyme. Here, we report the atomic structure of SalR to a resolution of {approx}1.9 {angstrom} in the presence of NADPH. The core structure is highly homologous to other members of the short chain dehydrogenase/reductase family. The major difference is that the nicotinamide moiety and the substrate-binding pocket are covered by a loop (residues 265-279), on top of which lies a large 'flap'-like domain (residues 105-140). This configuration appears to be a combination of the two common structural themes found in other members of the short chain dehydrogenase/reductase family. Previous modeling studies suggested that substrate inhibition is due to mutually exclusive productive and nonproductive modes of substrate binding in the active site. This model was tested via site-directed mutagenesis, and a number of these mutations abrogated substrate inhibition. However, the atomic structure of SalR shows that these mutated residues are instead distributed over a wide area of the enzyme, and many are not in the active site. To explain how residues distal to the active site might affect catalysis, a model is presented whereby SalR may undergo significant conformational changes during catalytic turnover.

  7. 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.

  8. Atomic structures of symmetric tilt grain boundaries in hexagonal close packed (hcp) crystals

    Science.gov (United States)

    Wang, J.; Beyerlein, I. J.

    2012-03-01

    Using molecular dynamics (MD) simulations, the dislocation structures of [1 \\bar {2} 1 0] symmetric tilt grain boundaries (STGBs) in hexagonal close packed (hcp) crystal structures are studied. STGBs over the entire range of possible rotation angles θ from 0° to 90° are found to have an ordered atomic structure. Formation energy calculations reveal four local minimum-energy boundaries that correspond to coherent grain boundaries (GBs). Deviations in tilt from the basal plane (θ = 0°, P_B(1) ) , prismatic plane (θ = 90°, P_B(6) ) , or one of these four minimum-energy boundaries, P_B(2) ,P_B(3) ,P_B(4) ,P_B(5) , result in the formation of a tilt wall (edge-type grain boundary dislocations, GBDs) superimposed on the nearest GB structure P_B(i) in θ-space. As θ deviates far from the rotation angle of one P_B(i) and draws closer to that of an adjacent P_B(j) , an abrupt transition in STGB base boundary structure and GBD Burgers vector occurs. For all θ, the sign and spacing of GBDs depend on θ, and their Burgers vector is either one or two times the interplanar spacing of PB. We present a simple model that generalizes the results to other c/a ratios. Subsequent MD simulations show that (1) the model forecasts the STGB structure to first-order and (2) STGBs with two distinct atomic structures can have remarkably different responses when interacting with basal lattice dislocations originating from the adjoining crystals.

  9. Atomic physics

    CERN Document Server

    Born, Max

    1969-01-01

    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.

  10. Atomic Physics

    CERN Document Server

    Foot, Christopher J

    2007-01-01

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

  11. 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.

  12. 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.

  13. Effect of Doped Transition Metal Atoms on Structure and Nonlinear Optical Properties of Decaborane

    Science.gov (United States)

    Beigi, Motahareh Noormohammad; Shamlouei, Hamid Reza; Omidi, Masoome; Jalalvandi, Esmat

    2017-11-01

    In this study, electrical and nonlinear optical properties of decaborane (B10H14) were investigated using the density functional theory method when transition metal atoms (scandium, titanium and vanadium) were doped on the structure. Hydrogen and boron atoms in B10H14 were substituted by the transition metals. This doping process resulted in a drastic reduction in the energy gap of decaborane. First, the hyperpolarizability ( β 0) of B10H14 dramatically increased in the presence of titanium (Ti) in the place of hydrogen atoms. The highest value of β 0 (≈ 98,387.90 a.u.) was obtained for B10TiH13 (in the S3 position) and calculated to be 1700 times larger than the β 0 value for B10H14 (≈57.82 a.u.). Therefore, the Ti-doped systems showed a significantly larger non-linear optical (NLO) response than the other studied transition metals, suggesting that its system might be useful as a promising NLO material.

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

    CERN Document Server

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

    2003-01-01

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

  15. Structural evolution and atomic dynamics in Ni-Nb metallic glasses: A molecular dynamics study

    Science.gov (United States)

    Xu, T. D.; Wang, X. D.; Zhang, H.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

    2017-10-01

    The composition and temperature dependence of static and dynamic structures in NixNb1-x (x = 50-70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu-Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni-Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni-Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.

  16. Identifying dynamic membrane structures with atomic-force microscopy and confocal imaging.

    Science.gov (United States)

    Timmel, Tobias; Schuelke, Markus; Spuler, Simone

    2014-04-01

    Combining the biological specificity of fluorescence microscopy with topographical features revealed by atomic force microscopy (AFM) provides new insights into cell biology. However, the lack of systematic alignment capabilities especially in scanning-tip AFM has limited the combined application approach as AFM drift leads to increasing image mismatch over time. We present an alignment correction method using the cantilever tip as a reference landmark. Since the precise tip position is known in both the fluorescence and AFM images, exact re-alignment becomes possible. We used beads to demonstrate the validity of the method in a complex artificial sample. We then extended this method to biological samples to depict membrane structures in fixed and living human fibroblasts. We were able to map nanoscale membrane structures, such as clathrin-coated pits, to their respective fluorescent spots. Reliable alignment between fluorescence signals and topographic structures opens possibilities to assess key biological processes at the cell surface such as endocytosis and exocytosis.

  17. Atomic structure and electronic properties of MgO grain boundaries in tunnelling magnetoresistive devices

    Science.gov (United States)

    Bean, Jonathan J.; Saito, Mitsuhiro; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi; McKenna, Keith P.

    2017-04-01

    Polycrystalline metal oxides find diverse applications in areas such as nanoelectronics, photovoltaics and catalysis. Although grain boundary defects are ubiquitous their structure and electronic properties are very poorly understood since it is extremely challenging to probe the structure of buried interfaces directly. In this paper we combine novel plan-view high-resolution transmission electron microscopy and first principles calculations to provide atomic level understanding of the structure and properties of grain boundaries in the barrier layer of a magnetic tunnel junction. We show that the highly [001] textured MgO films contain numerous tilt grain boundaries. First principles calculations reveal how these grain boundaries are associated with locally reduced band gaps (by up to 3 eV). Using a simple model we show how shunting a proportion of the tunnelling current through grain boundaries imposes limits on the maximum magnetoresistance that can be achieved in devices.

  18. Atomic simulations of twist grain boundary structures and deformation behaviors in aluminum

    Directory of Open Access Journals (Sweden)

    Qing Yin

    2017-01-01

    Full Text Available The structures and behaviors of grain boundaries (GBs have profound effects on the mechanical properties of polycrystalline materials. In this paper, twist GBs in aluminum were investigated with molecular dynamic simulations to reveal their atomic structures, energy and interactions with dislocations. One hundred twenty-six twist GBs were studied, and the energy of all these twist GBs were calculated. The result indicates that and twist GBs have lower energy than twist GBs because of their higher interplanar spacing. In addition, 12 types of twist GBs in aluminum were chosen to explore the deformation behaviors. Low angle twist GBs with high density of network structures can resist greater tension because mutually hindering behaviors between partial dislocations increase the twist GB strength.

  19. 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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Atomic and electronic structure of mixed and partial dislocations in GaN.

    Science.gov (United States)

    Arslan, Ilke; Bleloch, Andrew; Stach, Eric A; Browning, Nigel D

    2005-01-21

    Here we present a detailed study of mixed dislocations in GaN, in which the complexities of the atomic arrangement in the cores have been imaged directly for the first time using an aberration corrected scanning transmission electron microscope. In addition to being present as a full-core structure, the mixed dislocation is observed to dissociate into partial dislocations separated by a stacking fault only a few unit cells in length. The generation of this stacking fault appears to be impurity driven and its presence is consistent with theoretical predictions for dislocation dissociation in materials with hexagonal crystal symmetry.

  1. 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....

  2. On-the-Fly Machine Learning of Atomic Potential in Density Functional Theory Structure Optimization

    Science.gov (United States)

    Jacobsen, T. L.; Jørgensen, M. S.; Hammer, B.

    2018-01-01

    Machine learning (ML) is used to derive local stability information for density functional theory calculations of systems in relation to the recently discovered SnO2 (110 )-(4 ×1 ) reconstruction. The ML model is trained on (structure, total energy) relations collected during global minimum energy search runs with an evolutionary algorithm (EA). While being built, the ML model is used to guide the EA, thereby speeding up the overall rate by which the EA succeeds. Inspection of the local atomic potentials emerging from the model further shows chemically intuitive patterns.

  3. Multi-technology Investigation of the Atomic Structure of Calcium Silicate Hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Guoqing; Kilcoyne, David A.; Benmore, Chris J.; Monteiro, Paul J.M.

    2015-01-01

    In this study, synthetic C-S-H samples were investigated to reveal the feature at atomic scale. Rietveld refinement was applied to high resolution X-ray scattering data, yielding the lattice constants of the pseudocrystal structure, as well as the crystallinity along three axes. Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra was collected at calcium L3,2-edge. Evolution of calcium coordination symmetry were studied by investigating spectra characteristics. Pair Distribution Function (PDF) study yields the statistics of atom pair distribution. Coordination number of Ca and Si were obtained by integrating Radial distribution function. Atomic model based on dimeric structure were discussed and compared with experimental data. Synthetic C-S-H samples with increasing Ca/Si ratio exhibit pseudo-crystal structure, resembling Dreierketten configuration similar to natural tobermorite structure. Along c-axis, the repeated structure could not survives two layers in case of low Ca/Si ratio (0.70, 1.05). But in high Ca/Si ratio (1.42) case, the crystallinity along c-axis is much bigger. The coordination number of Ca decreases with increasing Ca/Si ratio. Octahedrally coordinated Ca are observed in sample with Ca/Si ratio of 1.42. Various dimeric models are compared with experimental data. In case of Ca/Si ratio of 1.42, SiO4 tetrahedron chain needs to be shortened in linkage, most probably by substituting bridging SiO4 tetrahedron with CaO6 octahedron. These octahedrons in interlayer space act like pins to join two adjacent layer structures together. The crystallinity is thus increased along c-axis, and average coordination number is therefore reduced. In case of Ca/Si 1.05, crystallinity is low along c-axis since, indicating that not too many Ca ions exist in interlayer space to hold two layers together. Instead, negative charge of end oxygen could be balanced by proton. Ca/Si 0.70 has long tetrahedron chain linkage within layer while the linkage between adjacent

  4. Exploring the atomic structure of 1.8nm monolayer-protected gold clusters with aberration-corrected STEM.

    Science.gov (United States)

    Liu, Jian; Jian, Nan; Ornelas, Isabel; Pattison, Alexander J; Lahtinen, Tanja; Salorinne, Kirsi; Häkkinen, Hannu; Palmer, Richard E

    2017-05-01

    Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au 144 (SCH 2 CH 2 Ph) 60 provided by two different research groups. The MP Au clusters were "weighed" by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123-151 atoms, only 3% of clusters matched the theoretically predicted Au 144 (SR) 60 structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters. Copyright © 2017. Published by Elsevier B.V.

  5. 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.

    2014-01-01

    Maximizing the scientific impact of NMR-based structure determination requires robust and statistically sound methods for assessing the precision of NMR-derived structures. In particular, a method to define a core atom set for calculating superimpositions and validating structure predictions is critical to the use of NMR-derived structures as targets in the CASP competition. FindCore (D.A. Snyder and G.T. Montelione PROTEINS 2005;59:673–686) is a superimposition independent method for identifying a core atom set, and partitioning that set into domains. However, as FindCore optimizes superimposition by sensitively excluding not-well-defined atoms, the FindCore core may not comprise all atoms suitable for use in certain applications of NMR structures, including the CASP assessment process. Adapting the FindCore approach to assess predicted models against experimental NMR structures in CASP10 required modification of the FindCore method. This paper describes conventions and a standard protocol to calculate an “Expanded FindCore” atom set suitable for validation and application in biological and biophysical contexts. A key application of the Expanded FindCore method is to identify a core set of atoms in the experimental NMR structure for which it makes sense to validate predicted protein structure models. We demonstrate the application of this Expanded FindCore method in characterizing well-defined regions of 18 NMR-derived CASP10 target structures. The Expanded FindCore protocol defines “expanded core atom sets” that match an expert’s intuition of which parts of the structure are sufficiently well-defined to use in assessing CASP model predictions. We also illustrate the impact of this analysis on the CASP GDT assessment scores. PMID:24327305

  6. 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.

  7. 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. Copyright © 2013 Wiley Periodicals, Inc.

  8. Exploring the atomic structure of 1.8 nm monolayer-protected gold clusters with aberration-corrected STEM

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jian; Jian, Nan; Ornelas, Isabel; Pattison, Alexander J. [Nanoscale Physics Research Laboratory, School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom); Lahtinen, Tanja; Salorinne, Kirsi [Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä (Finland); Häkkinen, Hannu [Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä (Finland); Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä (Finland); Palmer, Richard E., E-mail: richardepalmerwork@yahoo.com [Nanoscale Physics Research Laboratory, School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom)

    2017-05-15

    Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au{sub 144}(SCH{sub 2}CH{sub 2}Ph){sub 60} provided by two different research groups. The MP Au clusters were “weighed” by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123–151 atoms, only 3% of clusters matched the theoretically predicted Au{sub 144}(SR){sub 60} structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters. - Highlights: • Chemically synthesised gold clusters were “weighed” by atom counting to get true size. • Image simulations show a few percent of clusters have the predicted atomic structure. • But a specific ring-dot feature indicates local icosahedral order in many clusters.

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

    Science.gov (United States)

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

    2015-08-01

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

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

    Science.gov (United States)

    Parpia, F. A.; Froese Fischer, C.; Grant, I. P.

    2006-12-01

    of CSFs sharing the same quantum numbers is determined using the configuration-interaction (CI) procedure that results upon varying the expansion coefficients to determine the extremum of a variational functional. Radial functions may be determined by numerically solving the multiconfiguration Dirac-Fock (MCDF) equations that result upon varying the orbital radial functions or some subset thereof so as to obtain an extremum of the variational functional. Radial wavefunctions may also be determined using a screened hydrogenic or Thomas-Fermi model, although these schemes generally provide initial estimates for MCDF self-consistent-field (SCF) calculations. Transition properties for pairs of ASFs are computed from matrix elements of multipole operators of the electromagnetic field. All matrix elements of CSFs are evaluated using the Racah algebra. Reasons for the new version: During recent studies using the general relativistic atomic structure package (GRASP92), several errors were found, some of which might have been present already in the earlier GRASP92 version (program ABJN_v1_0, Comput. Phys. Comm. 55 (1989) 425). These errors were reported and discussed by Froese Fischer, Gaigalas, and Ralchenko in a separate publication [C. Froese Fischer, G. Gaigalas, Y. Ralchenko, Comput. Phys. Comm. 175 (2006) 738-744. [7

  11. Visualization and automatic detection of defect distribution in GaN atomic structure from sampling Moiré phase

    Science.gov (United States)

    Wang, Q. H.; Ri, S.; Tsuda, H.; Kodera, M.; Suguro, K.; Miyashita, N.

    2017-11-01

    Quantitative detection of defects in atomic structures is of great significance to evaluating product quality and exploring quality improvement process. In this study, a Fourier transform filtered sampling Moiré technique was proposed to visualize and detect defects in atomic arrays in a large field of view. Defect distributions, defect numbers and defect densities could be visually and quantitatively determined from a single atomic structure image at low cost. The effectiveness of the proposed technique was verified from numerical simulations. As an application, the dislocation distributions in a GaN/AlGaN atomic structure in two directions were magnified and displayed in Moiré phase maps, and defect locations and densities were detected automatically. The proposed technique is able to provide valuable references to material scientists and engineers by checking the effect of various treatments for defect reduction.

  12. Effects of doping of calcium atom(s) on structural, electronic and optical properties of binary strontium chalcogenides - A theoretical investigation using DFT based FP-LAPW methodology

    Science.gov (United States)

    Bhattacharjee, Rahul; Chattopadhyaya, Surya

    2017-09-01

    The effects of doping of Ca atom(s) on structural, electronic and optical properties of binary strontium chalcogenide semiconductor compounds have been investigated theoretically using DFT based FP-LAPW approach by modeling the rock-salt (B1) ternary alloys CaxSr1-xS, CaxSr1-xSe and CaxSr1-xTe at some specific concentrations 0 ≤ x ≤ 1 and studying their aforesaid properties. The exchange-correlation potentials for their structural properties have been computed using the Wu-Cohen generalized-gradient approximation (WC-GGA) scheme, while those for the electronic and optical properties have been computed using recently developed Tran-Blaha modified Becke-Johnson (TB-mBJ) scheme. In addition, we have computed the electronic and optical properties with the traditional BLYP and PBE-GGA schemes for comparison. The atomic and orbital origin of different electronic states in the band structure of each of the compounds have been identified from the respective density of states (DOS). Using the approach of Zunger and co-workers, the microscopic origin of band gap bowing has been discussed in term of volume deformation, charge exchange and structural relaxation. Bonding characteristics among the constituent atoms of each of the specimens have been discussed from their charge density contour plots. Optical properties of the binary compounds and ternary alloys have been investigated theoretically in terms of their respective dielectric function, refractive index, normal incidence reflectivity and optical conductivity. Several calculated results have been compared with available experimental and other theoretical data.

  13. 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.

  14. 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

    2009-02-04

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

  15. The Complete Heavy-Atom Structure of a Cp-Ftmw Chiral Tag Precursor, Verbenone

    Science.gov (United States)

    Marshall, Frank E.; West, Channing; Sedo, Galen; Pate, Brooks; Grubbs, G. S., II

    2017-06-01

    The microwave spectrum of the chiral molecule verbenone has been recorded from 2-18 GHz using two CP-FTMW spectrometers. 2-8 GHz data has been acquired on a 2-8 GHz CP-FTMW located at the University of Virginia and 8-18 data has been acquired on a 6-18 GHz spectrometer located at Missouri S&T. From the experiments the authors were able to assign and fit isotopologues corresponding to each heavy atom position (either ^{13}C or ^{18}O), providing for the heavy-atom structure. Previous studies by Evans and coworkers have been added to these measurements in a global fit of the parent species. The measurement and assignment of these transitions provide preliminary information needed for enatiomeric excess experiments using CP-FTMW van der Waals-type chiral tagging processes already being performed at UVa. Details of the experiment, fits, and structure will be discussed. C. J. Evans, S. M. Allpress, P. D. Godfrey, D. McNaughton, 67th International Symposium on Molecular Spectroscopy, 2012, RH13 S. M. Allpress, Spectroscopic and Computational Chemistry Studies on Terpene Related Compounds, University of Leicester, 2015, Chapter 6: Microwave Spectroscopy of Verbenone

  16. 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...

  17. Atomic resolution of structural changes in elastic crystals of copper(II) acetylacetonate

    Science.gov (United States)

    Worthy, Anna; Grosjean, Arnaud; Pfrunder, Michael C.; Xu, Yanan; Yan, Cheng; Edwards, Grant; Clegg, Jack K.; McMurtrie, John C.

    2018-01-01

    Single crystals are typically brittle, inelastic materials. Such mechanical responses limit their use in practical applications, particularly in flexible electronics and optical devices. Here we describe single crystals of a well-known coordination compound—copper(II) acetylacetonate—that are flexible enough to be reversibly tied into a knot. Mechanical measurements indicate that the crystals exhibit an elasticity similar to that of soft materials such as nylon, and thus display properties normally associated with both hard and soft matter. Using microfocused synchrotron radiation, we mapped the changes in crystal structure that occur on bending, and determined the mechanism that allows this flexibility with atomic precision. We show that, under strain, the molecules in the crystal reversibly rotate, and thus reorganize to allow the mechanical compression and expansion required for elasticity and still maintain the integrity of the crystal structure.

  18. 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.

  19. 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.

  20. Electronic structures, magnetic properties and band alignments of 3d transition metal atoms doped monolayer MoS2

    Science.gov (United States)

    Wu, Maokun; Yao, Xiaolong; Hao, Yuan; Dong, Hong; Cheng, Yahui; Liu, Hui; Lu, Feng; Wang, Weichao; Cho, Kyeongjae; Wang, Wei-Hua

    2018-01-01

    Utilizing first-principles calculations, the electronic structures, magnetic properties and band alignments of monolayer MoS2 doped by 3d transition metal atoms have been investigated. It is found that in V, Cr, Mn, Fe-doped monolayers, the nearest neighboring S atoms (SNN) are antiferromagnetically polarized with the doped atoms. While in Co, Ni, Cu, Zn-doped systems, the SNN are ferromagnetically coupled with the doped atoms. Moreover, the nearest neighboring Mo atoms also demonstrate spin polarization. Compared with pristine monolayer MoS2, little change is found for the band edges' positions in the doped systems. The Fermi level is located in the spin-polarized impurity bands, implying a half-metallic state. These results provide fundamental insights for doped monolayer MoS2 applying in spintronic, optoelectronic and electronic devices.

  1. 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.

  2. Resolving structure and mechanical properties at the nanoscale of viruses with frequency modulation atomic force microscopy.

    Directory of Open Access Journals (Sweden)

    David Martinez-Martin

    Full Text Available Structural Biology (SB techniques are particularly successful in solving virus structures. Taking advantage of the symmetries, a heavy averaging on the data of a large number of specimens, results in an accurate determination of the structure of the sample. However, these techniques do not provide true single molecule information of viruses in physiological conditions. To answer many fundamental questions about the quickly expanding physical virology it is important to develop techniques with the capability to reach nanometer scale resolution on both structure and physical properties of individual molecules in physiological conditions. Atomic force microscopy (AFM fulfills these requirements providing images of individual virus particles under physiological conditions, along with the characterization of a variety of properties including local adhesion and elasticity. Using conventional AFM modes is easy to obtain molecular resolved images on flat samples, such as the purple membrane, or large viruses as the Giant Mimivirus. On the contrary, small virus particles (25-50 nm cannot be easily imaged. In this work we present Frequency Modulation atomic force microscopy (FM-AFM working in physiological conditions as an accurate and powerful technique to study virus particles. Our interpretation of the so called "dissipation channel" in terms of mechanical properties allows us to provide maps where the local stiffness of the virus particles are resolved with nanometer resolution. FM-AFM can be considered as a non invasive technique since, as we demonstrate in our experiments, we are able to sense forces down to 20 pN. The methodology reported here is of general interest since it can be applied to a large number of biological samples. In particular, the importance of mechanical interactions is a hot topic in different aspects of biotechnology ranging from protein folding to stem cells differentiation where conventional AFM modes are already being used.

  3. Resolving structure and mechanical properties at the nanoscale of viruses with frequency modulation atomic force microscopy.

    Science.gov (United States)

    Martinez-Martin, David; Carrasco, Carolina; Hernando-Perez, Mercedes; de Pablo, Pedro J; Gomez-Herrero, Julio; Perez, Rebeca; Mateu, Mauricio G; Carrascosa, Jose L; Kiracofe, Daniel; Melcher, John; Raman, Arvind

    2012-01-01

    Structural Biology (SB) techniques are particularly successful in solving virus structures. Taking advantage of the symmetries, a heavy averaging on the data of a large number of specimens, results in an accurate determination of the structure of the sample. However, these techniques do not provide true single molecule information of viruses in physiological conditions. To answer many fundamental questions about the quickly expanding physical virology it is important to develop techniques with the capability to reach nanometer scale resolution on both structure and physical properties of individual molecules in physiological conditions. Atomic force microscopy (AFM) fulfills these requirements providing images of individual virus particles under physiological conditions, along with the characterization of a variety of properties including local adhesion and elasticity. Using conventional AFM modes is easy to obtain molecular resolved images on flat samples, such as the purple membrane, or large viruses as the Giant Mimivirus. On the contrary, small virus particles (25-50 nm) cannot be easily imaged. In this work we present Frequency Modulation atomic force microscopy (FM-AFM) working in physiological conditions as an accurate and powerful technique to study virus particles. Our interpretation of the so called "dissipation channel" in terms of mechanical properties allows us to provide maps where the local stiffness of the virus particles are resolved with nanometer resolution. FM-AFM can be considered as a non invasive technique since, as we demonstrate in our experiments, we are able to sense forces down to 20 pN. The methodology reported here is of general interest since it can be applied to a large number of biological samples. In particular, the importance of mechanical interactions is a hot topic in different aspects of biotechnology ranging from protein folding to stem cells differentiation where conventional AFM modes are already being used.

  4. Atomic structure of nanoscale quasicrystal-forming Zr-noble metal binary metallic glasses

    Energy Technology Data Exchange (ETDEWEB)

    Saida, J., E-mail: jsaida@cir.tohoku.ac.jp [Center for Interdisciplinary Research, Tohoku University, Aramaki Aoba, Aoba-ku, Sendai 980-8578 (Japan); Itoh, K. [Graduate School of Education, Okayama University, Tsushimanaka, Kita-ku, Okayama 700-8530 (Japan); Sanada, T. [Research Department, Nissan ARC Ltd., Natsushima, Yokosuka 237-0061 (Japan); Sato, S. [Institute for Materials Research, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577 (Japan); Imafuku, M. [Faculty of Engineering, Tokyo City University, Setagaya-ku, Tokyo 158-8557 (Japan); Ohnuma, M. [National Institute of Materials Science (NIMS), Sengen, Tsukuba, Ibaraki 305-0047 (Japan); Inoue, A. [WPI-AIMR, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577 (Japan)

    2011-06-15

    Research highlights: > Zr{sub 70}Pd{sub 30} and Zr{sub 80}Pt{sub 20} are the quasicrystal (QC)-forming glassy alloys. > The QC phase precipitates by a cooperative motion of atoms or clusters. > Relatively perfect icosahedrons frequently exist around Zr in Zr{sub 70}Pd{sub 30}, however, distorted icosahedral-like clusters are formed around Zr and Pt in Zr{sub 80}Pt{sub 20}. > The QC phase formation originates from a different mechanism in the two alloys. - Abstract: We report the results of the local structural evaluation and mechanism of QC formation in the Zr{sub 70}Pd{sub 30} and Zr{sub 80}Pt{sub 20} glassy alloys. Voronoi analysis indicates the difference of local environment between two alloys. The perfect icosahedron frequently exists around Zr atom and major polyhedra have prism-like structure around Pd in Zr{sub 70}Pd{sub 30}. In contrast, icosahedral-like distorted polyhedra formation is favorable around Pt as well as Zr in Zr{sub 80}Pt{sub 20}. It is therefore, concluded that the quasicrystallization originates from the medium-range order based on the Zr-centered perfect icosahedron and the Pd-centered prism-like ones remain during the QC phase formation in Zr{sub 70}Pd{sub 30}. Icosahedral-like local structure around Zr and Pt might contribute together to the nucleation of QC phase in Zr{sub 80}Pt{sub 20}. This feature with a different mechanism of QC formation in the two alloys may correlate to the difference of solute concentration and the structure of stable crystalline phase after the decomposition of QC phase.

  5. Structural elucidation of galactomannan from seeds of Crotalaria mucronata Desv. by atomic force microscopy.

    Science.gov (United States)

    Yang, Yong-Li; Guo, Shou-Jun; Zhang, Zheng-Xia; Zhang, Yong; Liu, Ang; Xie, Li-Ling; Zheng, Yu-Zhong

    2018-03-01

    A non-ionic water-soluble galactomannan, isolated from the seed endosperm of Crotalaria mucronata Desv., may be an ideal thickener to increase food viscosity. The present study hypothesized that the viscous property of Crotalaria galactomannan may be associated with its spatial structure. Therefore, the structure of Crotalaria galactomannan was elucidated using an atomic force microscope. The results of the present study demonstrated that the polysaccharide consisted of a D‑mannose backbone with D‑galactose branches, and the D‑mannose/D‑galactose ratio was 2.375:1. In the three‑dimensional structure of Crotalaria galactomannan, the helix was a common secondary structure, containing numerous ring structures of different sizes. In addition, multiple helixes may link together via hydrogen bonding and van der Waals forces, forming aggregations with small rings or spiral windings. The results of the present study indicated that the multiple‑branching construction of Crotalaria galactomannan may underlie its viscosity‑enhancing properties in the water phase.

  6. Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

    Science.gov (United States)

    Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.

    2011-01-01

    Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples. PMID:21997909

  7. Mechanical properties and electronic structure of edge-doped graphene nanoribbons with F, O, and Cl atoms.

    Science.gov (United States)

    Piriz, Sebastián; Fernández-Werner, Luciana; Pardo, Helena; Jasen, Paula; Faccio, Ricardo; Mombrú, Álvaro W

    2017-08-16

    In this study, we present the structural, electronic, and mechanical properties of edge-doped zigzag graphene nanoribbons (ZGNRs) doped with fluorine, oxygen, and chlorine atoms. To the best of our knowledge, to date, no experimental results concerning the mechanical properties of graphene-derived nanoribbons have been reported in the literature. Simulations indicate that Cl- and F-doped ZGNRs present an equivalent 2-dimensional Young's modulus E 2D , which seems to be higher than those of graphene and H-doped ZGNRs. This is a consequence of the electronic structure of the system, particularly originating from strong interactions between the dopant atoms localized at the edges. The interaction between dopant atoms located at the edges is higher for Cl and lower for F and O atoms. This is the origin of the observed trend, in which E > E > E for all the analyzed ZGNRs.

  8. Local atomic structure in iron copper binary alloys: An extended X-ray absorption fine structure study

    Energy Technology Data Exchange (ETDEWEB)

    Kuri, G. [LWV, NES, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland)]. E-mail: goutam.kuri@psi.ch; Degueldre, C. [LWV, NES, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Bertsch, J. [LWV, NES, Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Rothe, J. [INE, Forschungszentrum Karlsruhe, 76344 Karlsruhe (Germany)

    2007-05-31

    Understanding the clustering process and the evolution of the precipitate structure of copper in Fe-Cu system is an important step in the description of material hardening and the embrittlement process normally observed under irradiation conditions. In this work, an extended X-ray absorption fine structure (EXAFS) spectroscopy characterization of Fe-0.3 wt%Cu and Fe-1.0 wt%Cu binary model alloys has been performed in order to investigate the local structure around Cu and Fe atoms in the matrix. The effect of thermal ageing was studied on one Fe-Cu specimen containing 1.0 wt% Cu annealed at 775 K for a duration of 1 h. The near-neighbour environment of Cu and Fe was examined by determining the best-fit structural parameters after curve fitting to the first-few-shells EXAFS functions. The results provide an indication of the formation of sub-nanometer-size Cu clusters in Fe matrix for the specimens examined. The average structural parameters estimated from the EXAFS data are presented and discussed.

  9. 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.

  10. 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

  11. Early Atomism

    Indian Academy of Sciences (India)

    http://www.ias.ac.in/article/fulltext/reso/015/10/0905-0925. Keywords. Atomic theory; Avogadro's hypothesis; atomic weights; periodic table; valence; molecular weights; molecular formula; isomerism. Author Affiliations. S Ramasesha1. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, ...

  12. Using invariom modelling to distinguish correct and incorrect central atoms in `duplicate structures' with neighbouring 3d elements.

    Science.gov (United States)

    Wandtke, Claudia M; Weil, Matthias; Simpson, Jim; Dittrich, Birger

    2017-10-01

    Modelling coordination compounds has been shown to be feasible using the invariom method; for the best fit to a given set of diffraction data, additional steps other than using lookup tables of scattering factors need to be carried out. Here such procedures are applied to a number of `duplicate structures', where structures of two or more supposedly different coordination complexes with identical ligand environments, but with different 3d metal ions, were published. However, only one metal atom can be plausibly correct in these structures, and other spectroscopic data are unavailable. Using aspherical scattering factors, a structure can be identified as correct from the deposited Bragg intensities alone and modelling only the ligand environment often suffices to make this distinction. This is not possible in classical refinements using the independent atom model. Quantum-chemical computations of the better model obtained after aspherical-atom refinement further confirm the assignment of the element in the respective figures of merit.

  13. Local structural studies of Ba(1-x)K(x)Fe2As2 using atomic pair distribution function analysis.

    Science.gov (United States)

    Joseph, B; Zinth, V; Brunelli, M; Maroni, B; Johrendt, D; Malavasi, L

    2011-03-23

    Systematic local structural studies of the Ba(1-x)K(x)Fe(2)As(2) system are undertaken at room temperature using atomic pair distribution function analysis. The local structure of the Ba(1-x)K(x)Fe(2)As(2) is found to be well described by the long-range structure extracted from diffraction experiments, but with anisotropic atomic vibrations of the constituent atoms (U11 = U22 not equal U33). The crystal unit cell parameters, the FeAs(4) tetrahedral angle and the pnictogen height above the Fe-plane are seen to show systematic evolution with K doping, underlining the importance of the structural changes, in addition to the charge doping, in determining the properties of Ba(1-x)K(x)Fe(2)As(2).

  14. Local atomic structure in equilibrium and supercooled liquid Zr[subscript 75.5]Pd[subscript 24.5

    Energy Technology Data Exchange (ETDEWEB)

    Mauro, N.A.; Fu, W.; Bendert, J.C.; Cheng, Y.Q.; Ma, E.; Kelton, K.F. (WU); (ORNL); (JHU)

    2012-09-06

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

  15. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

    Science.gov (United States)

    Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

    2015-04-28

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand-strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.

  16. Primed for Discovery: Atomic-Resolution Cryo-EM Structure of a Reovirus Entry Intermediate

    Directory of Open Access Journals (Sweden)

    Shane D. Trask

    2010-06-01

    Full Text Available A recently solved structure of the aquareovirus virion (Zhang, X; Jin, L.; Fang, Q; Hui, W.H.; Zhou Z.H. 3.3 Å Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry. Cell 2010, 141, 472-482 [1] provides new insights into the order of entry events, as well as confirming and refining several aspects of the entry mechanism, for aquareovirus and the related orthoreovirus. In particular, the structure provides evidence of a defined order for the progressive proteolytic cleavages of myristoylated penetration protein VP5 that prime the virion for membrane penetration. These observations reinforce the concept that, much like enveloped viruses, nonenveloped virions often undergo priming events that lead to a meta-stable state, preparing the virus for membrane penetration under the appropriate circumstances. In addition, this and other recent studies highlight the increasing power of electron cryomicroscopy to analyze large, geometrically regular structures, such as icosahedral viruses, at atomic resolution.

  17. Atomic-scale structural signature of dynamic heterogeneities in metallic liquids

    Science.gov (United States)

    Pasturel, Alain; Jakse, Noel

    2017-08-01

    With sufficiently high cooling rates, liquids will cross their equilibrium melting temperatures and can be maintained in a metastable undercooled state before solidifying. Studies of undercooled liquids reveal several intriguing dynamic phenomena and because explicit connections between liquid structure and liquids dynamics are difficult to identify, it remains a major challenge to capture the underlying structural link to these phenomena. Ab initio molecular dynamics (AIMD) simulations are yet especially powerful in providing atomic-scale details otherwise not accessible in experiments. Through the AIMD-based study of Cr additions in Al-based liquids, we evidence for the first time a close relationship between the decoupling of component diffusion and the emergence of dynamic heterogeneities in the undercooling regime. In addition, we demonstrate that the origin of both phenomena is related to a structural heterogeneity caused by a strong interplay between chemical short-range order (CSRO) and local fivefold topology (ISRO) at the short-range scale in the liquid phase that develops into an icosahedral-based medium-range order (IMRO) upon undercooling. Finally, our findings reveal that this structural signature is also captured in the temperature dependence of partial pair-distribution functions which opens up the route to more elaborated experimental studies.

  18. 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.

  19. 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.

  20. Structural, Nanomechanical and Nanotribological Characterization of Human Hair Using Atomic Force Microscopy and Nanoindentation

    Science.gov (United States)

    Bhushan, Bharat; Latorre, Carmen; Wei, Guohua

    Human hair is a nanocomposite biological fiber. Healthy, soft hair with good feel, shine, color and overall aesthetics is generally highly desirable. It is important to study hair care products such as shampoos and conditioners as well as damaging processes such as chemical dyeing and permanent wave treatments because they affect the maintenance and grooming process and therefore alter many hair properties. Nanoscale characterization of the cellular structure, the mechanical properties, as well as the morphological, frictional and adhesive properties (tribological properties) of hair is essential if we wish to evaluate and develop better cosmetic products, and crucial to advancing the understanding of biological and cosmetic science. The atomic/friction force microscope (AFM/FFM) and nanoindenter have recently become important tools for studying the micro/nanoscale properties of human hair. In this chapter, we present a comprehensive review of structural, mechanical, and tribological properties of various hair and skin as a function of ethnicity, damage, conditioning treatment, and various environments. Various cellular structures of human hair and fine sublamellar structures of the cuticle are identified and studied. Nanomechanical properties such as hardness, elastic modulus, creep and scratch resistance are discussed. Nanotribological properties such as roughness, friction, and adhesion are presented, as well as investigations of conditioner distribution, thickness and binding interactions.

  1. 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.

  2. 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

  3. 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.

  4. MolProbity: More and better reference data for improved all-atom structure validation.

    Science.gov (United States)

    Williams, Christopher J; Headd, Jeffrey J; Moriarty, Nigel W; Prisant, Michael G; Videau, Lizbeth L; Deis, Lindsay N; Verma, Vishal; Keedy, Daniel A; Hintze, Bradley J; Chen, Vincent B; Jain, Swati; Lewis, Steven M; Arendall, W Bryan; Snoeyink, Jack; Adams, Paul D; Lovell, Simon C; Richardson, Jane S; Richardson, David C

    2017-10-25

    This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore. This article is protected by copyright. All rights reserved. © 2017 The Protein Society.

  5. Structure and transport at grain boundaries in polycrystalline olivine: An atomic-scale perspective

    Science.gov (United States)

    Mantisi, Boris; Sator, Nicolas; Guillot, Bertrand

    2017-12-01

    Structure and transport properties at grain boundaries in polycrystalline olivine have been investigated at the atomic scale by molecular dynamics simulation (MD) using an empirical ionocovalent interaction potential. On the time scale of the simulation (a few tens of nanoseconds for a system size of ∼650,000 atoms) grain boundaries and grain interior were identified by mapping the atomic displacements along the simulation run. In the investigated temperature range (1300-1700 K) the mean thickness of the grain boundary phase is evaluated between 0.5 and 2 nm, a value which depends on temperature and grain size. The structure of the grain boundary phase is found to be disordered (amorphous-like) and is different from the one exhibited by the supercooled liquid. The self-diffusion coefficients of major elements in the intergranular region range from ∼10-13 to 10-10 m2/s between 1300 and 1700 K (with DSigb < DOgb < DFegb < DMggb) and are only one order of magnitude smaller than those evaluated in the supercooled melt. In using a newly derived expression for the bulk self-diffusion coefficient it is concluded that the latter one is driven by the grain boundary contribution as long as the grain size is smaller than a centimeter. In assuming that the electrical conduction at grain boundaries is purely ionic, the macroscopic grain boundary conductivity is found to be two orders of magnitude lower than in molten olivine, and one order of magnitude higher than the lattice conductivity. A consequence is that the conductivity of the olivine polycrystal is dominated by the grain interior contribution as soon as the grain size is larger than a micrometer or so. The grain boundary viscosity has been evaluated from the Green-Kubo relation expressing the viscosity as function of the stress tensor time correlation function. In spite of a slow convergence of the calculation by MD, the grain boundary viscosity was estimated about ∼105 Pa s at 1500 K, a value in agreement with

  6. Atomic Force Microscopy of virus capsids uncover the interplay between mechanics, structure and function

    Science.gov (United States)

    de Pablo, Pedro J.

    The basic architecture of a virus consists of the capsid, a shell made up of repeating protein subunits, which packs, shuttles and delivers their genome at the right place and moment. Viral particles are endorsed with specific physicochemical properties which confer to their structures certain meta-stability whose modulation permits fulfilling each task of the viral cycle. These natural designed capabilities have impelled using viral capsids as protein containers of artificial cargoes (drugs, polymers, enzymes, minerals) with applications in biomedical and materials sciences. Both natural and artificial protein cages have to protect their cargo against a variety of physicochemical aggressive environments, including molecular impacts of highly crowded media, thermal and chemical stresses, and osmotic shocks. Viral cages stability under these ambiences depend not only on the ultimate structure of the external capsid, which rely on the interactions between protein subunits, but also on the nature of the cargo. During the last decade our lab has focused on the study of protein cages with Atomic Force Microscopy (AFM) (figure 1). We are interested in stablishing links of their mechanical properties with their structure and function. In particular, mechanics provide information about the cargo storage strategies of both natural and virus-derived protein cages. Mechanical fatigue has revealed as a nanosurgery tool to unveil the strength of the capisd subunit bonds. We also interrogated the electrostatics of individual protein shells. Our AFM-fluorescence combination provided information about DNA diffusing out cracked-open protein cages in real time.

  7. 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.

  8. The Effect of Atom Vacancy Defect on the Vibrational Behavior of Single-Walled Carbon Nanotubes: A Structural Mechanics Approach

    Directory of Open Access Journals (Sweden)

    S. K. Georgantzinos

    2014-04-01

    Full Text Available An atomistic structural mechanics method, which is based on the exclusive use of spring elements, is developed in order to study the effect of imperfections due to atom vacancy on the vibrational characteristics of single-walled carbon nanotubes (SWCNTs. The developed elements simulate the relative translations and rotations between atoms as well as the mass of the atoms. In this way, molecular mechanics theory can be applied directly because the atomic bonds are modeled by using exclusively physical variables such as bond stretching. The method is validated for its predictability comparing with vibration results found in the open literature for pristine nanotubes. Then, it is used for the vibration analysis of defective nanotubes. Imperfections such as one-atom vacancy, two-atom vacancy, and one carbon hexagonal cell vacancy are investigated. Their effect on vibrational behavior is explored for different defect positions, nanotube diameters, and support conditions. According to the obtained results, the fundamental frequency is decreased as the size of imperfection increases, and the percentage reduction in fundamental frequency due to the atomic vacancy defect is more affected for a single-clamped SWCNT than for a double-clamped one.

  9. 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.

  10. 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…

  11. Operando X-ray spectroscopic observations of modulations of local atomic and electronic structures of color switching smart film.

    Science.gov (United States)

    Lu, Ying-Rui; Wu, Tzung-Zing; Chang, Han-Wei; Chen, Jeng-Lung; Chen, Chi-Liang; Wei, Da-Hau; Chen, Jin-Ming; Chou, Wu-Ching; Dong, Chung-Li

    2017-06-07

    Smart windows, which change color in response to external stimuli, are extensively studied owing to their potential technological applications in sensors and their ability to reduce the energy consumed by buildings. Most related studies focus on the optical properties of smart color switching films that can control the transmission of light and that of heat independently. This study examines the vanadium pentoxide thin film as a model system of a color switchable window. A gasochromic thin film of V2O5 is fabricated using sol-gel spin coating. In operando soft X-ray absorption spectroscopy (XAS) at the V L-edge is used to determine the evolutions of the electronic and atomic structures of V2O5 thin film under gasochromic color switching. Analysis of the V K-edge with respect to crystalline structural symmetry and valence requires many reference samples, whereas the V L-edge, which involves V 3d orbitals of various symmetries, can provide information about the atomic/electronic structures without many reference samples. A new gas reaction in situ cell was developed to collect the total-electron-yield XAS. The total-electron-yield signal can provide more accurate information about atomic and electronic structures than can the fluorescence-yield signal, which typically exerts a saturation effect. Analytical results reveal that the gasochromic reaction changes the charge state and causes a local atomic structural deformation of the film. The suggestion has been made that in the reaction, the central vanadium atom within the octahedron moves closer to the basal plane such that the apical V-O bond becomes more symmetrical than the film before gasochromic coloration. Unlike the cell that is used for hard XAS, and for which only cation sites can be studied, this in situ gas cell enables the real-time studies of atomic/electronic structures at gas-solid interfaces from viewpoints of both cation and anion sites.

  12. 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...

  13. Atomic structure of defects in anion-deficient perovskite-based ferrites with a crystallographic shear structure.

    Science.gov (United States)

    Batuk, Maria; Turner, Stuart; Abakumov, Artem M; Batuk, Dmitry; Hadermann, Joke; Van Tendeloo, Gustaaf

    2014-02-17

    Crystallographic shear (CS) planes provide a new structure-generation mechanism in the anion-deficient perovskites containing lone-pair cations. Pb2Sr2Bi2Fe6O16, a new n = 6 representative of the A(n)B(n)O(3n-2) homologous series of the perovskite-based ferrites with the CS structure, has been synthesized using the solid-state technique. The structure is built of perovskite blocks with a thickness of four FeO6 octahedra spaced by double columns of FeO5 edge-sharing distorted tetragonal pyramids, forming 1/2[110](101)p CS planes (space group Pnma, a = 5.6690(2) Å, b = 3.9108(1) Å, c = 32.643(1) Å). Pb2Sr2Bi2Fe6O16 features a wealth of microstructural phenomena caused by the flexibility of the CS planes due to the variable ratio and length of the constituting fragments with {101}p and {001}p orientation. This leads to the formation of "waves", "hairpins", "Γ-shaped" defects, and inclusions of the hitherto unknown layered anion-deficient perovskites Bi2(Sr,Pb)Fe3O8.5 and Bi3(Sr,Pb)Fe4O11.5. Using a combination of diffraction, imaging, and spectroscopic transmission electron microscopy techniques this complex microstructure was fully characterized, including direct determination of positions, chemical composition, and coordination number of individual atomic species. The complex defect structure makes these perovskites particularly similar to the CS structures in ReO3-type oxides. The flexibility of the CS planes appears to be a specific feature of the Sr-based system, related to the geometric match between the SrO perovskite layers and the {100}p segments of the CS planes.

  14. Contribution to viscosity from the structural relaxation via the atomic scale Green-Kubo stress correlation function.

    Science.gov (United States)

    Levashov, V A

    2017-11-14

    We studied the connection between the structural relaxation and viscosity for a binary model of repulsive particles in the supercooled liquid regime. The used approach is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the correlation functions between the atomic level stresses. Previously we used the approach to study an iron-like single component system of particles. The role of vibrational motion has been addressed through the demonstration of the relationship between viscosity and the shear waves propagating over large distances. In our previous considerations, however, we did not discuss the role of the structural relaxation. Here we suggest that the contribution to viscosity from the structural relaxation can be taken into account through the consideration of the contribution from the atomic stress auto-correlation term only. This conclusion, however, does not mean that only the auto-correlation term represents the contribution to viscosity from the structural relaxation. Previously the role of the structural relaxation for viscosity has been addressed through the considerations of the transitions between inherent structures and within the mode-coupling theory by other authors. In the present work, we study the structural relaxation through the considerations of the parent liquid and the atomic level stress correlations in it. The comparison with the results obtained on the inherent structures also is made. Our current results suggest, as our previous observations, that in the supercooled liquid regime, the vibrational contribution to viscosity extends over the times that are much larger than the Einstein's vibrational period and much larger than the times that it takes for the shear waves to propagate over the model systems. Besides addressing the atomic level shear stress correlations, we also studied correlations between the atomic level pressure elements.

  15. Contribution to viscosity from the structural relaxation via the atomic scale Green-Kubo stress correlation function

    Science.gov (United States)

    Levashov, V. A.

    2017-11-01

    We studied the connection between the structural relaxation and viscosity for a binary model of repulsive particles in the supercooled liquid regime. The used approach is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the correlation functions between the atomic level stresses. Previously we used the approach to study an iron-like single component system of particles. The role of vibrational motion has been addressed through the demonstration of the relationship between viscosity and the shear waves propagating over large distances. In our previous considerations, however, we did not discuss the role of the structural relaxation. Here we suggest that the contribution to viscosity from the structural relaxation can be taken into account through the consideration of the contribution from the atomic stress auto-correlation term only. This conclusion, however, does not mean that only the auto-correlation term represents the contribution to viscosity from the structural relaxation. Previously the role of the structural relaxation for viscosity has been addressed through the considerations of the transitions between inherent structures and within the mode-coupling theory by other authors. In the present work, we study the structural relaxation through the considerations of the parent liquid and the atomic level stress correlations in it. The comparison with the results obtained on the inherent structures also is made. Our current results suggest, as our previous observations, that in the supercooled liquid regime, the vibrational contribution to viscosity extends over the times that are much larger than the Einstein's vibrational period and much larger than the times that it takes for the shear waves to propagate over the model systems. Besides addressing the atomic level shear stress correlations, we also studied correlations between the atomic level pressure elements.

  16. 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

  17. Claisen rearrangement of allyl phenyl ether: heavy-atom kinetic isotope effects and bond orders in the transition structure

    Energy Technology Data Exchange (ETDEWEB)

    Kupczyk-Subotkowska, L.; Saunders, W.H. Jr.; Shine, H.J.

    1988-10-12

    Kinetic isotope effects (KIE) were measured for the rearrangement at 220/degree/C of allyl ether (1) which was labeled successively at its oxygen atom ((/sup 18/O)-1), /alpha/-carbon atom ((/alpha/-/sup 14/C)-1), /gamma/-carbon atom ((/gamma/-/sup 14/C)-1), and ortho-carbon atom ((2-/sup 14/C)-1). The KIE were 1.0297 (/sup 18/O), 1.0306 (/alpha/-/sup 14/C), 1.0362 (/gamma/-/sup 14/C), and 1.0375 (2-/sup 14/C). KIE were determined from isotopic abundances in the product, o-allylphenol (2), which were measured by multiscan mass spectrometry (/sup 18/O) and scintillation counting (/sup 14/C). A model of the transition structure was then developed, whose bond orders gave calculated KIE in reasonably good agreement not only with the experimentally determined heavy-atom KIE but also with the deuterium KIE reported earlier by McMichael and Korver. A loose transition structure was thus found for the rearrangement of 1 into 2. In this transition structure the C/sub /alpha//-O bond is 50-60% broken while the C/sub /gamma//-C/sub ortho/ bond is only 10-20% complete. The results thus define this concerted, nonsynchronous rearrangement more explicitly than hitherto possible. 40 references, 8 tables.

  18. International Atomic Energy Agency (IAEA) Coordinated Research Projects on Structural Integrity of Reactor Pressure Vessels

    Energy Technology Data Exchange (ETDEWEB)

    Server, W. L. [ATI Consulting, Pinehurst, NC; Nanstad, Randy K [ORNL

    2009-01-01

    The International Atomic Energy Agency (IAEA) has conducted a series of Coordinated Research Projects (CRPs) that have focused on irradiated reactor pressure vessel (RPV) steel fracture toughness properties and approaches for assuring structural integrity of RPVs throughout operating life. A series of nine CRPs have been sponsored by the IAEA, starting in the early 1970s, focused on neutron radiation effects on RPV steels. The purpose of the CRPs was to develop comparisons and correlations to test the uniformity of irradiated results through coordinated international research studies and data sharing. Consideration of dose rate effects, effects of alloying (nickel, manganese, silicon, etc.) and residual elements (eg., copper and phosphorus), and drop in upper shelf toughness are also important for assessing neutron embrittlement effects. The ultimate use of embrittlement understanding is assuring structural integrity of the RPV under current and future operation and accident conditions. Material fracture toughness is the key ingredient needed for this assessment, and many of the CRPs have focused on measurement and application of irradiated fracture toughness. This paper presents an overview of the progress made since the inception of the CRPs in the early 1970s. The chronology and importance of each CRP have been reviewed and put into context for continued and long-term safe operation of RPVs.

  19. A distinct atomic structure-catalytic activity relationship in 3-10 nm supported Au particles.

    Science.gov (United States)

    Petkov, Valeri; Ren, Yang; Shan, Shiyao; Luo, Jin; Zhong, Chuan-Jian

    2014-01-07

    Bulk Au is very inert but Au nanoparticles less than 5 nm in size have been found to be catalytically active for several reactions, in particular for low-temperature oxidation of CO. Using high-energy X-ray diffraction coupled with atomic pair distribution function analysis and computer simulations we determine the structure of 3 nm and 10 nm Au particles supported on titania and silica as typical representatives of reducible and irreducible supports, respectively. We find that the synthesis protocol adopted in our work affects strongly and differently the structure of the Au nanoparticles on the different supports. This leads to clearly distinct dependences of the catalytic activity of the nanoparticles on their size. In the case of the silica support the catalytic activity of Au nanoparticles increases and in the case of the titania support it decreases with decreasing nanoparticle size. The experimental results are considered in terms of current theoretical predictions and found to be in good accord with them.

  20. Physics-based all-atom modeling of RNA energetics and structure.

    Science.gov (United States)

    Smith, Louis G; Zhao, Jianbo; Mathews, David H; Turner, Douglas H

    2017-09-01

    The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422. © 2017 Wiley Periodicals, Inc.

  1. 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.

  2. 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.

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

    Science.gov (United States)

    Proffen, T.; Billinge, S. J. L.

    We have used atomic pair distribution function (PDF) analysis based on neutron powder diffraction data to investigate the local structure of the colossal magnetoresistant manganite La0.75Ca0.25MnO3 as a function of temperature. In the doping range 0.17materials show a metal-to-insulator transition, transforming from a ferromagnetic metal (FM) at low temperature to a paramagnetic insulator (PI). We can probe the charge distribution of the sample using the PDF by searching for evidence of Jahn-Teller (JT) distorted octahedra, implying the presence of Mn3+ ions. A two-phase model based on the local structures of the FM and PI phases was used to refine the experimental PDFs quantitatively. We observe the co-existence of both phases over a wide temperature range: approximately 10% of the localized JT phase (PI) is present even at the lowest temperature (T=20K), whereas at room temperature nearly half of the sample remains in the delocalized (FM) phase.

  4. Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.

    Science.gov (United States)

    Hipp, Katharina; Grimm, Clemens; Jeske, Holger; Böttcher, Bettina

    2017-08-01

    African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. 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.

  6. Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases.

    Science.gov (United States)

    Kiliszek, Agnieszka; Kierzek, Ryszard; Krzyzosiak, Wlodzimierz J; Rypniewski, Wojciech

    2010-12-01

    CAG repeats occur predominantly in the coding regions of human genes, which suggests their functional importance. In some genes, these sequences can undergo pathogenic expansions leading to neurodegenerative polyglutamine (poly-Q) diseases. The mutant transcripts containing expanded CAG repeats possibly contribute to pathogenesis in addition to the well-known pathogenic effects of mutant proteins. We have analysed two crystal forms of RNA duplexes containing CAG repeats: (GGCAGCAGCC)(2). One of the structures has been determined at atomic resolution (0.95 Å) and the other at 1.9 Å. The duplexes include non-canonical A-A pairs that fit remarkably well within a regular A-helix. All the adenosines are in the anti-conformation and the only interaction within each A-A pair is a single C2-H2···N1 hydrogen bond. Both adenosines in each A-A pair are shifted towards the major groove, although to different extents; the A which is the H-bond donor stands out more (the 'thumbs-up' conformation). The main effect on the helix conformation is a local unwinding. The CAG repeats and the previously examined CUG structures share a similar pattern of electrostatic charge distribution in the minor groove, which could explain their affinity for the pathogenesis-related MBNL1 protein.

  7. Packing schemes of cavities in selected clathrasils and zeolites and the analogous packings of atoms in crystal structures

    DEFF Research Database (Denmark)

    Hem, Caroline Piper; Makovicky, Emil; Balic Zunic, Tonci

    2010-01-01

    Sizes of cavities and their packing schemes in selected zeolites and clathrasils were studied by means of least squares fitting of circumscribed spheres to them. Resulting packing of spheres of different diameters was analyzed by the coordinates of their centers, their volumes and sphericity......, and interpreted by comparison with analogous packings of atoms in inorganic compounds and alloys. The topology is described qualitatively as “negative” structures formed by the cavities. Melanophlogite and dodecasils 3C and 1H are all clathrasils with isolated cavities. They all have pentagonal dodecahedral [512......] cages, associated with other cavity types. The packing of cavities in melanophlogite is analogous to the packing of atoms in the structure of Cr3Si, where the Cr atoms form icosahedra around the Si sites. Dodecasil 3C has a cubic arrangement of [512] cavities, which is described as ABC stacking...

  8. The effect of surface structure on Ag atom adsorption over CuO(111) surfaces: A first principles study

    Science.gov (United States)

    Hu, Riming; Zhou, Xiaolong; Yu, Jie

    2017-12-01

    The interactions of Ag atom with different types of CuO(111) surface, including the perfect, oxygen-vacancy and precovered oxygen surfaces, have been systematically investigated using density functional theory (DFT) calculations to examine the effect of surface structures on Ag atom adsorption. The calculated results indicate that the Cu1-Cu1 bridge site and the oxygen-vacancy site are the active centres for atomic Ag adsorption on the perfect surface and the oxygen-vacancy surface respectively, while atomic Ag preferentially adsorbs at the Op site on the precovered oxygen surface. The activity of the CuO(111) surface for atomic Ag adsorption can be improved both on the perfect and oxygen-vacancy surfaces, while the activity of the CuO(111) surface for atomic Ag adsorption will be suppressed on precovered oxygen surfaces. Furthermore, the adsorption of NO on different CuO(111) surfaces with Ag adsorption was investigated, and the calculation results show that the adsorption of NO on an Ag-loaded CuO(111) surface is greater than that on the pure CuO(111) surface.

  9. 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.

  10. 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.

  11. Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys

    Science.gov (United States)

    Zhang, Hao; Zhong, Cheng; Douglas, Jack F.; Wang, Xiaodong; Cao, Qingping; Zhang, Dongxian; Jiang, Jian-Zhong

    2015-04-01

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by "dynamic heterogeneity" in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations.

  12. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.

    Science.gov (United States)

    Hu, Jie; Chen, Tao; Wang, Moye; Chan, Hue Sun; Zhang, Zhuqing

    2017-05-31

    Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations. The conformations in the unfolded state in common Gō models are more extended, and are thus more in line with experiment, than those from all-atom MD simulations. Nevertheless, the structural features of transition states obtained by the two types of models are largely similar. In contrast, the folding transition paths are significantly more sensitive to modeling details. In particular, when common Gō-like models are augmented with nonnative interactions, the predicted dimensions of the unfolded conformations become similar to those computed using all-atom MD. With this connection, the large deviations of all-atom MD from simple diffusion theory are likely caused in part by the presence of significant nonnative effects in folding processes modelled by current atomic force fields. The ramifications of our findings to the application of coarse-grained modeling to more complex biomolecular systems are discussed.

  13. 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…

  14. 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 using...

  15. Students' Representations of the Atomic Structure--The Effect of Some Individual Differences in Particular Task Contexts

    Science.gov (United States)

    Papageorgiou, George; Markos, Angelos; Zarkadis, Nikolaos

    2016-01-01

    The current study aims to investigate students' representations of the atomic structure in a number of student cohorts with specific characteristics concerning age, grade, class curriculum and some individual differences, such as formal reasoning and field dependence/independence. Two specific task contexts, which were designed in accordance with…

  16. The atomic surface structure of SrTiO3 (001) studied with synchrotron X-rays

    NARCIS (Netherlands)

    Vonk, V.; Konings, S.; van Hummel, G.J.; Harkema, Sybolt; Graafsma, H

    2005-01-01

    The atomic surface structure of single terminated SrTiO3(0 0 1) (1 × 1) is investigated employing surface X-ray diffraction. In order to obtain these surfaces a special treatment is needed consisting of chemical etching and annealing. Since this is done in an aqueous and subsequently oxygen

  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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. 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 c....... 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.......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...

  19. 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...

  20. 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.

  1. 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.

  2. Investigation of structural transition of dsDNA on various substrates studied by atomic force microscopy.

    Science.gov (United States)

    Nguyen, T H; Kim, Y U; Kim, K J; Choi, S S

    2009-03-01

    Structural transition of single dsDNA molecule which is immobilized on 3-aminopropyltriethoxysilane (APTES) treated substrate (APTES/substrate) or alkylthiol treated substrate (alkylthiol/substrate) has been investigated by atomic force microscopy (AFM). The obtained force versus distance (F-D) curves are used to dissect the transition from B-form to S-form, the melting from double stranded (ds) to single stranded (ss) DNA, and its Young's modulus as well as persistence length. The melt from dsDNA to ssDNA is evidenced by fitting with freely jointed chain (FJC) model. FJC fit and Young's modulus or persistence length values when the molecules are fixed on alkylthiol/substrate are more agreeable with other studies than those on APTES. We have clarified the different results of those experiments by analyzing the binding force between DNA molecules and APTES or alkylthiol linkers on the substrate. The DNA binding to APTES linker is much stronger than that on alkylthiol/substrate.

  3. Decay study of neutron-deficient La isotopes for atomic masses and nuclear structure

    Energy Technology Data Exchange (ETDEWEB)

    Osa, Akihiko; Koizumi, Mitsuo; Sekine, Toshiaki [Department of Materials Science, Japan Atomic Energy Research Institute, Takasaki, Gunma (JP)] [and others

    2000-06-01

    We report the decay spectroscopic studies with the TIARA-ISOL connected to an AVF cyclotron at the Takasaki site of JAERI between 1994 and 1998 under the Universities-JAERI Collaborative Research Project. Decay spectroscopic studies have been carried out for neutron-deficient La-Ce-Pr isotopes in the mass 120-130 region, which were prepared by on-line mass-separation following the fusion-evaporation reactions {sup 92,nat}Mo({sup 36}Ar, 3pxn). The {sup 125}Pr isotope was newly identified with a half-life of 3.3(7) s and its decay scheme was presented. The assignment of the 135.8 keV {gamma}-ray to the decay of {sup 125}Pr was supported by its coincidence with Ce X-rays and {beta}{sup +} rays. Low-spin states in {sup 124,} {sup 126,} {sup 128,} {sup 130}Ba fed by the {beta}{sup +}/EC decay of their La parents were investigated by means of the {gamma}-{gamma} angular correlation measurement. Q{sub EC}-values/atomic masses of neutron-deficient {sup 124-130}La were determined by {beta}{sup +}-ray maximum energy measurement. Half-lives of the first 2{sup +} state in {sup 122,} {sup 124,} {sup 126}Ba were measured using a {beta}-{gamma} delayed coincidence method. The experimental results obtained for the nuclear structure of the Ba isotopes are discussed in comparison with theory. (author)

  4. Monte Carlo Simulation Study of Atomic Structure of alnico Permanent Magnets

    Science.gov (United States)

    Nguyen, Manh Cuong; Wang, Cai-Zhuang; Ho, Kai-Ming

    Lattice Monte Carlo simulation based on quinternary cluster expansion energy model is used to investigate nano-scale structure of alnico alloy, which is considered as a candidate material for rare-earth free high performance permanent magnets, especially for high or elevated temperature applications such as electric motor for vehicles. We observe phase decomposition of the master alnico alloy into FeCo-rich magnetic (α1) and NiAl-rich matrix (α2) phases. Concentrations of Fe and Co in α1 phase and Ni and Al in α2 phase are higher for lower annealing temperature. Ti is residing mostly in the α2 phase. The phase boundary between α1 and α2 phases are quite sharp with only few atomic layers. The α1 phase is in B2 ordering with Fe and Al occupying the α-site and Ni and Co occupying the β-site. The α2 phase is in L21 ordering with Al occupying the 4a-site. The phase composition profile again annealing temperature suggests that lower annealing temperature would improve the magnetism of α2 and diminish the magnetism of α2 phase, hence improve shape anisotropy of α1 phase rods and that of alnico.

  5. Determining the resolution of scanning microwave impedance microscopy using atomic-precision buried donor structures

    Science.gov (United States)

    Scrymgeour, D. A.; Baca, A.; Fishgrab, K.; Simonson, R. J.; Marshall, M.; Bussmann, E.; Nakakura, C. Y.; Anderson, M.; Misra, S.

    2017-11-01

    To quantify the resolution limits of scanning microwave impedance microscopy (sMIM), we created scanning tunneling microscope (STM)-patterned donor nanostructures in silicon composed of 10 nm lines of highly conductive silicon buried under a protective top cap of silicon, and imaged them with sMIM. This dopant pattern is an ideal test of the resolution and sensitivity of the sMIM technique, as it is made with nm-resolution and offers minimal complications from topography convolution. It has been determined that typical sMIM tips can resolve lines down to ∼80 nm spacing, while resolution is independent of tip geometry as extreme tip wear does not change the resolving power, contrary to traditional scanning capacitance microscopy (SCM). Going forward, sMIM is an ideal technique for qualifying buried patterned devices, potentially allowing for quantitative post-fabrication characterization of donor structures, which may be an important tool for the study of atomic-scale transistors and state of the art quantum computation schemes.

  6. 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.

  7. 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.

  8. Thin film growth into the ion track structures in polyimide by atomic layer deposition

    Science.gov (United States)

    Mättö, L.; Malm, J.; Arstila, K.; Sajavaara, T.

    2017-09-01

    High-aspect ratio porous structures with controllable pore diameters and without a stiff substrate can be fabricated using the ion track technique. Atomic layer deposition is an ideal technique for depositing thin films and functional surfaces on complicated 3D structures due to the high conformality of the films. In this work, we studied Al2O3 and TiO2 films grown by ALD on pristine polyimide (Kapton HN) membranes as well as polyimide membranes etched in sodium hypochlorite (NaOCl) and boric acid (BO3) solution by means of RBS, PIXE, SEM-EDX and helium ion microcopy (HIM). The focus was on the first ALD growth cycles. The areal density of Al2O3 film in the 400 cycle sample was determined to be 51 ± 3 × 1016 at./cm2, corresponding to the thickness of 55 ± 3 nm. Furthermore, the growth per cycle was 1.4 Å/cycle. The growth is highly linear from the first cycles. In the case of TiO2, the growth per cycle is clearly slower during the first 200 cycles but then it increases significantly. The growth rate based on RBS measurements is 0.24 Å/cycle from 3 to 200 cycles and then 0.6 Å/cycle between 200 and 400 cycles. The final areal density of TiO2 film after 400 cycles is 148 ± 3 × 1015 at./cm2 which corresponds to the thickness of 17.4 ± 0.4 nm. The modification of the polyimide surface by etching prior to the deposition did not have an effect on the Al2O3 and TiO2 growth.

  9. Order within disorder: The atomic structure of ion-beam sputtered amorphous tantala (a-Ta_2O_5)

    OpenAIRE

    Bassiri, Riccardo; Liou, Franklin; Abernathy, Matthew R.; Lin, Angie C.; Kim, Namjun; Mehta, Apurva; Shyam, Badri; Byer, Robert L.; Gustafson, Eric K.; Hart, Martin; MacLaren, Ian; Martin, Iain W.; Roger K. Route; Rowan, Sheila; Stebbins, Jonathan F.

    2015-01-01

    Amorphous tantala (a-Ta2O5) is a technologically important material often used in high-performance coatings. Understanding this material at the atomic level provides a way to further improve performance. This work details extended X-ray absorption fine structure measurements of a-Ta2O5 coatings, where high-quality experimental data and theoretical fits have allowed a detailed interpretation of the nearest-neighbor distributions. It was found that the tantalum atom is surrounded by four shells...

  10. 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...

  11. Order within disorder: The atomic structure of ion-beam sputtered amorphous tantala (a-Ta2O5)

    Science.gov (United States)

    Bassiri, Riccardo; Liou, Franklin; Abernathy, Matthew R.; Lin, Angie C.; Kim, Namjun; Mehta, Apurva; Shyam, Badri; Byer, Robert L.; Gustafson, Eric K.; Hart, Martin; MacLaren, Ian; Martin, Iain W.; Route, Roger K.; Rowan, Sheila; Stebbins, Jonathan F.; Fejer, Martin M.

    2015-03-01

    Amorphous tantala (a-Ta2O5) is a technologically important material often used in high-performance coatings. Understanding this material at the atomic level provides a way to further improve performance. This work details extended X-ray absorption fine structure measurements of a-Ta2O5 coatings, where high-quality experimental data and theoretical fits have allowed a detailed interpretation of the nearest-neighbor distributions. It was found that the tantalum atom is surrounded by four shells of atoms in sequence; oxygen, tantalum, oxygen, and tantalum. A discussion is also included on how these models can be interpreted within the context of published crystalline Ta2O5 and other a-T2O5 studies.

  12. Order within disorder: The atomic structure of ion-beam sputtered amorphous tantala (a-Ta2O5

    Directory of Open Access Journals (Sweden)

    Riccardo Bassiri

    2015-03-01

    Full Text Available Amorphous tantala (a-Ta2O5 is a technologically important material often used in high-performance coatings. Understanding this material at the atomic level provides a way to further improve performance. This work details extended X-ray absorption fine structure measurements of a-Ta2O5 coatings, where high-quality experimental data and theoretical fits have allowed a detailed interpretation of the nearest-neighbor distributions. It was found that the tantalum atom is surrounded by four shells of atoms in sequence; oxygen, tantalum, oxygen, and tantalum. A discussion is also included on how these models can be interpreted within the context of published crystalline Ta2O5 and other a-T2O5 studies.

  13. Curved-line search algorithm for ab initio atomic structure relaxation

    Science.gov (United States)

    Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

    2017-09-01

    Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

  14. 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.

  15. Structure of V(2)O(5)*nH(2)O xerogel solved by the atomic pair distribution function technique.

    Science.gov (United States)

    Petkov, Valeri; Trikalitis, Pantelis N; Bozin, Emil S; Billinge, Simon J L; Vogt, Thomas; Kanatzidis, Mercouri G

    2002-08-28

    A long-standing issue regarding the local and long-range structure of V(2)O(5)*nH(2)O xerogel has been successfully addressed. The full three-dimensional structure of the lamellar turbostratic V(2)O(5)*nH(2)O xerogel was determined by the atomic pair distribution function technique. We show that on the atomic scale the slabs of the xerogel can be described well as almost perfect pairs (i.e., bilayers) of single V(2)O(5) layers made of square pyramidal VO(5) units. These slabs are separated by water molecules and stack along the z-axis of a monoclinic unit cell (space group C2/m) with parameters a = 11.722(3) A, b = 3.570(3) A, c = 11.520(3) A, and beta = 88.65 degrees. The stacking sequence shows signatures of turbostratic disorder and a structural coherence limited to 50 A.

  16. Atomic resolution structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Sekar, K., E-mail: sekar@physics.iisc.ernet.in, E-mail: sekar@serc.iisc.ernet.in [Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012 (India); Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012 (India); Yogavel, M.; Gayathri, D.; Velmurugan, D. [Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025 (India); Krishna, R. [Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012 (India); Poi, M.-J. [Departments of Chemistry and Biochemistry and the Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210 (United States); Dauter, Z.; Dauter, M. [Synchrotron Radiation Research Section, National Cancer Institute, Brookhaven National Laboratory Building, Upton, NY 11973 (United States); Tsai, M.-D. [Departments of Chemistry and Biochemistry and the Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210 (United States); Academia Sinica,Taiwan (China); Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012 (India)

    2006-01-01

    The atomic resolution crystal structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A{sub 2} is reported. The structure of the double mutant K53,56M has previously been refined at 1.9 Å resolution using room-temperature data. The present paper reports the crystal structure of the same mutant K53,56M refined against 1.1 Å data collected using synchrotron radiation. A total of 116 main-chain atoms from 29 residues and 44 side chains are modelled in alternate conformations. Most of the interfacial binding residues are found to be disordered and alternate conformations could be recognized. The second calcium ion-binding site residue Glu92 adopts two alternate conformations. The minor and major conformations of Glu92 correspond to the second calcium ion bound and unbound states.

  17. 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.

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

    Science.gov (United States)

    Kahn, L. R.

    1982-01-01

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

  19. 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

  20. Atomic and electronic structure of amorphous Al-Zr alloy films

    Energy Technology Data Exchange (ETDEWEB)

    Vegelius, J; Korelis, P T; Hjoervarsson, B; Butorin, S M [Department of Physics and Materials Science, Uppsala University, Box 530, S-751 21 Uppsala (Sweden); Soroka, I L, E-mail: johan.vegelius@physics.uu.se [Nuclear Chemistry, KTH Chemical Science and Engineering, Royal Institute of Technology, SE-100 44 Stockholm (Sweden)

    2011-07-06

    Amorphous Al{sub 73}Zr{sub 27} alloy film, grown and then subjected to heat treatments at 400 and 700 {sup 0}C, was studied using a combination of x-ray diffraction and soft x-ray spectroscopic techniques. The Al L{sub 2,3} and Al K x-ray absorption spectroscopy (XAS) and Al L{sub 2,3} x-ray emission spectroscopy (XES) used allowed probing the unoccupied and occupied Al 3s, d states and unoccupied Al 3p states in the sample studied. An irreversible transition from amorphous alloy to a mixture of polycrystalline alloy and amorphous alloy, and then to an amorphous oxide phase was observed. After the annealing at 400 {sup 0}C the Al L{sub 2,3} spectra obtained by XAS could be explained as sums of spectra from amorphous Al{sub 73}Zr{sub 27} alloy and (poly)crystalline Al. This indicates that the sample consists of a mixture of Al-rich crystalline and Zr-enhanced amorphous alloys, as compared to the stoichiometry of the as-deposited Al{sub 73}Zr{sub 27} sample, and that the electronic wavefunctions in the crystalline and amorphous regions can be considered to be confined within the respective regions. The relative amounts of Al atoms were found to be around 1:3 in the crystalline and amorphous phases, respectively, as deduced from the analysis of changes in the electronic structure using Al L{sub 2,3} XAS data. The interpretation was confirmed by the Al K XAS and Al L{sub 2,3} XES. Upon further annealing at 700 {sup 0}C the polycrystalline phase transformed into amorphous oxide, while the amorphous alloy phase underwent gradual oxidation. The important finding was that the greater part of the sample remained in the amorphous state throughout the temperature regimes described.

  1. Atomic-scale Chemical Imaging and Quantification of Metallic Alloy Structures by Energy-Dispersive X-ray Spectroscopy

    Science.gov (United States)

    Lu, Ping; Zhou, Lin; Kramer, M. J.; Smith, David J.

    2014-01-01

    Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L21 phase with Ni0.48Co0.52 at A-sites, Al at BΙ-sites and Fe0.20Ti0.80 at BΙΙ-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems. PMID:24492747

  2. Ab initio calculations for structural, electronic and magnetic behaviors of nitrogenized monolayer graphene decorated with 5d transition metal atoms

    Science.gov (United States)

    Rafique, Muhammad; Shuai, Yong; Xu, Meng; Zhang, Guohua; Guo, Yanming

    2017-09-01

    Graphene-based magnetic materials have revealed great potential for developing high-performance electronic units at sub-nanometer such as spintronic data storage devices. However, a significant ferromagnetism behavior and ample band gap in the electronic structure of graphene is required before it can be used for actual engineering applications. Based on first-principles calculations, here we demonstrate the structural, electronic and magnetic behaviors of 5d transition metal (TM) atom-substituted nitrogenized monolayer graphene. We find that, during TMN(3)4 cluster-substitution, tight bonding occurs between impurity atoms and graphene with significant binding energies. Charge transfer occurs from graphene layer to the TMN(3)4 clusters. Interestingly, PtN3, TaN4 and ReN4 cluster-doped graphene structures exhibit dilute magnetic semiconductor behavior with 1.00 μB, 1.04 μB and 1.05 μB magnetic moments, respectively. While, OsN4 and PtN4 cluster-doped structures display nonmagnetic direct band gap semiconductor behavior. Remaining, TMN(3)4 cluster-doped graphene complexes exhibit half metal properties. Detailed analysis of density of states (DOS) plots indicate that d orbitals of TM atoms should be responsible for arising magnetic moments in graphene. Given results pave a new route for potential applications of dilute magnetic semiconductors and half-metals in spintronic devices by employing TMN(3)4 cluster-doped graphene complexes.

  3. Structural Dynamics and Activity of Nanocatalysts Inside Fuel Cells by in-operando Atomic Pair Distribution Studies

    Science.gov (United States)

    Prasai, Binay

    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). Using in-operando high-energy X-ray diffraction 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). Data were analyzed in terms of atomic pair distribution functions 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.

  4. Hydrogen storage and stability properties of Pd-Pt solid-solution nanoparticles revealed via atomic and electronic structure.

    Science.gov (United States)

    Kumara, Loku Singgappulige Rosantha; Sakata, Osami; Kobayashi, Hirokazu; Song, Chulho; Kohara, Shinji; Ina, Toshiaki; Yoshimoto, Toshiki; Yoshioka, Satoru; Matsumura, Syo; Kitagawa, Hiroshi

    2017-11-06

    Bimetallic Pd1-x Pt x solid-solution nanoparticles (NPs) display charging/discharging of hydrogen gas, which has relevance for fuel cell technologies; however, the constituent elements are immiscible in the bulk phase. We examined these material systems using high-energy synchrotron X-ray diffraction, X-ray absorption fine structure and hard X-ray photoelectron spectroscopy techniques. Recent studies have demonstrated the hydrogen storage properties and catalytic activities of Pd-Pt alloys; however, comprehensive details of their structural and electronic functionality at the atomic scale have yet to be reported. Three-dimensional atomic-scale structure results obtained from the pair distribution function (PDF) and reverse Monte Carlo (RMC) methods suggest the formation of a highly disordered structure with a high cavity-volume-fraction for low-Pt content NPs. The NP conduction band features, as extracted from X-ray absorption near-edge spectra at the Pd and Pt L III -edge, suggest that the Pd conduction band is filled by Pt valence electrons. This behaviour is consistent with observations of the hydrogen storage capacity of these NPs. The broadening of the valence band width and the down-shift of the d-band centre away from the Fermi level upon Pt substitution also provided evidence for enhanced stability of the hydride (ΔH) features of the Pd1-x Pt x solid-solution NPs with a Pt content of 8-21 atomic percent.

  5. Influence of Ni doping on PtNi nanoparticles: Synthesis, electronic/atomic structure and photocatalyst investigations

    Science.gov (United States)

    Varshney, Mayora; Sharma, Aditya; Shin, Hyun-Joon; Lee, Hyun Hwi; Jeon, Tae-Yeol; Lee, Byeong-Hyeon; Chae, Keun-Hwa; Won, Sung Ok

    2017-11-01

    Carbon-supported Pt and PtNi nanoparticles (NPs) were synthesized using a borohydride reduction method. Structural properties were studied by synchrotron X-ray diffraction (XRD) and the size/shape of the NPs was determined by transmission electron microscope (TEM). X-ray absorption spectroscopy with its two amendments; X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), has been employed to investigate the local electronic/atomic structure surrounding the Pt and Ni atoms. XANES results, at Pt L3-edge and Ni K-edge, have shown fractional oxidation of Pt and Ni atoms. The Pt3Ni1NPs have exhibited a lower bond distance of Pt-Ni shell and higher coordination number of Pt-Ni shells, indicating the alloy formation between Pt and Ni. We further have demonstrated that the Pt and PtNi NPs can serve as effective photocatalysts towards the degradation of water pollutant dye (methyl orange (MO)). By considering the interband charge-transfer of Pt (5d →6sp), a tentative mechanism is proposed to understand the photocatalytic degradation of MO dye molecules by Pt/PtNi NPs under the light irradiation.

  6. Catalytic Activity and Stability of Oxides: The Role of Near-Surface Atomic Structures and Compositions

    KAUST Repository

    Feng, Zhenxing

    2016-05-05

    Conspectus Electrocatalysts play an important role in catalyzing the kinetics for oxygen reduction and oxygen evolution reactions for many air-based energy storage and conversion devices, such as metal–air batteries and fuel cells. Although noble metals have been extensively used as electrocatalysts, their limited natural abundance and high costs have motivated the search for more cost-effective catalysts. Oxides are suitable candidates since they are relatively inexpensive and have shown reasonably high activity for various electrochemical reactions. However, a lack of fundamental understanding of the reaction mechanisms has been a major hurdle toward improving electrocatalytic activity. Detailed studies of the oxide surface atomic structure and chemistry (e.g., cation migration) can provide much needed insights for the design of highly efficient and stable oxide electrocatalysts. In this Account, we focus on recent advances in characterizing strontium (Sr) cation segregation and enrichment near the surface of Sr-substituted perovskite oxides under different operating conditions (e.g., high temperature, applied potential), as well as their influence on the surface oxygen exchange kinetics at elevated temperatures. We contrast Sr segregation, which is associated with Sr redistribution in the crystal lattice near the surface, with Sr enrichment, which involves Sr redistribution via the formation of secondary phases. The newly developed coherent Bragg rod analysis (COBRA) and energy-modulated differential COBRA are uniquely powerful ways of providing information about surface and interfacial cation segregation at the atomic scale for these thin film electrocatalysts. In situ ambient pressure X-ray photoelectron spectroscopy (APXPS) studies under electrochemical operating conditions give additional insights into cation migration. Direct COBRA and APXPS evidence for surface Sr segregation was found for La1–xSrxCoO3−δ and (La1–ySry)2CoO4±δ/La1–xSrxCoO3

  7. Atomic structure and electrochemical potential of Li[sub 1+x]V[sub 3]O[sub 8

    Energy Technology Data Exchange (ETDEWEB)

    Benedek, R.; Thackeray, M.M. (Chemical Technology Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)); Yang, L.H. (Condensed Matter Physics Division, Lawrence Livermore National Laboratory, University of California, Livermore, California 94551 (United States))

    1999-09-01

    The atomic configurations and total energies of both monoclinic phases of Li[sub 1+x]V[sub 3]O[sub 8], a candidate electrode material in rechargeable Li batteries, are calculated as a function of [ital x] within local-density-functional theory, using the plane-wave pseudopotential method. The predicted structures at the most standard compositions, 1+x=1.2 and 1+x=4, agree closely with x-ray-diffraction measurements of atomic structure. As Li is inserted into the low-Li compound, Li(2) is half filled and then S[sub t](3) is half filled, where the Li sites are labeled as in de Picciotto [ital et al.] This is followed by the onset of a two-phase region. Calculations of the electrochemical potential as a function of lithiation are in excellent overall agreement with experiment. thinsp [copyright] [ital 1999] [ital The American Physical Society

  8. Pressure/temperature fluid cell apparatus for the neutron powder diffractometer instrument: probing atomic structure in situ.

    Science.gov (United States)

    Wang, Hsiu-Wen; Fanelli, Victor R; Reiche, Helmut M; Larson, Eric; Taylor, Mark A; Xu, Hongwu; Zhu, Jinlong; Siewenie, Joan; Page, Katharine

    2014-12-01

    This contribution describes a new local structure compatible gas/liquid cell apparatus for probing disordered materials at high pressures and variable temperatures in the Neutron Powder Diffraction instrument at the Lujan Neutron Scattering Center, Los Alamos National Laboratory. The new sample environment offers choices for sample canister thickness and canister material type. Finite element modeling is utilized to establish maximum allowable working pressures of 414 MPa at 15 K and 121 MPa at 600 K. High quality atomic pair distribution function data extraction and modeling have been demonstrated for a calibration standard (Si powder) and for supercritical and subcritical CO2 measurements. The new sample environment was designed to specifically target experimental studies of the local atomic structures involved in geologic CO2 sequestration, but will be equally applicable to a wide variety of energy applications, including sorption of fluids on nano/meso-porous solids, clathrate hydrate formation, catalysis, carbon capture, and H2 and natural gas uptake/storage.

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

    Directory of Open Access Journals (Sweden)

    Akihiko Nakatsuka

    2015-09-01

    Full Text Available Single crystals of the title compound, the post-perovskite-type CaIrO3 [calcium iridium(IV trioxide], have been grown from a CaCl2 flux at atmospheric pressure. The crystal structure consists of an alternate stacking of IrO6 octahedral layers and CaO8 hendecahedral layers along [010]. Chains formed by edge-sharing of IrO6 octahedra (point-group symmetry 2/m.. run along [100] and are interconnected along [001] by sharing apical O atoms to build up the IrO6 octahedral layers. Chains formed by face-sharing of CaO8 hendecahedra (point-group symmetry m2m run along [100] and are interconnected along [001] by edge-sharing to build up the CaO8 hendecahedral layers. The IrO6 octahedral layers and CaO8 hendecahedral layers are interconnected by sharing edges. The present structure refinement using a high-power X-ray source confirms the atomic positions determined by Hirai et al. (2009 [Z. Kristallogr. 224, 345–350], who had revised our previous report [Sugahara et al. (2008. Am. Mineral. 93, 1148–1152]. However, the displacement ellipsoids of the Ir and Ca atoms based on the present refinement can be approximated as uniaxial ellipsoids elongating along [100], unlike those reported by Hirai et al. (2009. This suggests that the thermal vibrations of the Ir and Ca atoms are mutually suppressed towards the Ir...Ca direction across the shared edge because of the dominant repulsion between the two atoms.

  10. 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.

  11. Deformation-Induced Atomic Disordering and Reordering in Alloys with L12 Structure

    Science.gov (United States)

    Pantyukhova, O. D.; Starenchenko, S. V.; Solov'ev, A. N.; Solov'eva, Yu. V.; Starenchenko, V. A.

    2017-10-01

    The paper presents a mathematical model of thermal and strain hardening of alloys having L12 superstructure which allows calculating the atomic long-range order (LRO) parameter depending on the deformation degree under various temperature and loading conditions. The observed non-monotonic change in the atomic LRO parameter during plastic deformation occurs due to the two types of competitive processes. These processes are caused by the motion and accumulation of the deformation defects and their healing due to the migration of point defects of different nature. The competitiveness between these two types of processes leads to the periodical destruction and reconstruction of the atomic LRO parameter, while the equilibrium between them can stabilize it after which it continues to be stable despite the deformation.

  12. The application of an atomic effective potential to the electronic structure and bonding of Si2

    Science.gov (United States)

    Moskowitz, Jules W.; Topiol, Sid; Snyder, Lawrence C.

    1980-07-01

    A series of computations has been carried out on the ground (3Σ-g) and first excited state (1Σ+g) of Si2(R=4.244 a0) both with and without the use of an atomic effective or pseudopotential. A Gaussian double-zeta basis set was utilized and partial electronic correlation was introduced into the wave function by means of the generalized valence bond (GVB) approximation. In all cases, the all electron and effective potential computations are in good agreement. The computations indicate that the stability of the ground (3Σ-g) state is due to the tendency of silicon to prefer the divalent s2p2 atomic configuration rather than the tetrahedral sp3 atomic configuration. In contrast to the C2 carbon analog, the first excited (1Σ+g) state of Si2 is shown to possess a relatively weak π bond.

  13. 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.

  14. Additive Mixing and Conformal Coating of Noniridescent Structural Colors with Robust Mechanical Properties Fabricated by Atomization Deposition.

    Science.gov (United States)

    Li, Qingsong; Zhang, Yafeng; Shi, Lei; Qiu, Huihui; Zhang, Suming; Qi, Ning; Hu, Jianchen; Yuan, Wei; Zhang, Xiaohua; Zhang, Ke-Qin

    2018-02-15

    Artificial structural colors based on short-range-ordered amorphous photonic structures (APSs) have attracted great scientific and industrial interest in recent years. However, the previously reported methods of self-assembling colloidal nanoparticles lack fine control of the APS coating and fixation on substrates and poorly realize three-dimensional (3D) conformal coatings for objects with irregular or highly curved surfaces. In this paper, atomization deposition of silica colloidal nanoparticles with poly(vinyl alcohol) as the additive is proposed to solve the above problems. By finely controlling the thicknesses of APS coatings, additive mixing of noniridescent structural colors is easily realized. Based on the intrinsic omnidirectional feature of atomization, a one-step 3D homogeneous conformal coating is also readily realized on various irregular or highly curved surfaces, including papers, resins, metal plates, ceramics, and flexible silk fabrics. The vivid coatings on silk fabrics by atomization deposition possess robust mechanical properties, which are confirmed by rubbing and laundering tests, showing great potential in developing an environmentally friendly coloring technique in the textile industry.

  15. Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-01

    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.

  16. 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.

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

    OpenAIRE

    Heyrovska, Raji

    2008-01-01

    Two dimensional layers of graphene are currently drawing a great attention in fundamental and applied nanoscience. Graphene consists of interconnected hexagons of carbon atoms as in graphite. This article presents for the first time the structures of graphene at the atomic level and shows how it differs from that of benzene, due to the difference in the double bond and resonance bond based radii of carbon. The carbon atom of an aliphatic compound such as methane has a longer covalent single b...

  18. 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. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

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

    DEFF Research Database (Denmark)

    Brodersen, Ditlev Egeskov; Etzerodt, Michael; Madsen, Peder Søndergaard

    1998-01-01

    The S100 family consists of small acidic proteins, belonging to the EF-hand class of calcium-binding proteins. They are primarily regulatory proteins, involved in cell growth, cell structure regulation and signal transduction. Psoriasin (S100A7) is an 11.7 kDa protein that is highly upregulated......-substituted psoriasin has been determined by multiple anomalous wavelength dispersion (MAD) phasing and refined to atomic resolution (1.05 A). The structure represents the most accurately determined structure of a calcium-binding protein. Although the overall structure of psoriasin is similar to those of other S100...... proteins, several important differences exist, mainly in the N-terminal EF-hand motif that contains a distorted loop and lacks a crucial calcium-binding residue. It is these minor differences that may account for the different specificities among members of this family. CONCLUSIONS: The structure of human...

  20. Correlated atomic motions in the negative thermal expansion material ZrW2O8: A local structure study

    Science.gov (United States)

    Cao, D.; Bridges, F.; Kowach, G. R.; Ramirez, A. P.

    2003-07-01

    Recent studies of zirconium tungstate, ZrW2O8, show an isotropic negative thermal expansion (NTE) over a wide temperature range. It has been proposed that the low-energy phonon vibrational modes, observed in both specific heat and phonon density-of-states measurements, are responsible for this unusual NTE. We have carried out x-ray-absorption fine-structure (XAFS) experiments at both the W LIII edge and Zr K edge to study the detailed local structure in ZrW2O8. Our XAFS results show a very small temperature dependence of the broadening parameter, σ, for the W-Zr atom pair and the W-O-Zr linkage; consequently, the displacements of the W, O, and Zr atoms must be correlated. The data show a much larger temperature dependence of σ for the nearest W1-W2 pair as well as for the nearest Zr-Zr pair. These combined results indicate that it is the correlated motion of a WO4 tetrahedron and its three nearest ZrO6 octahedra that leads to the NTE effect in this material instead of primarily transverse vibrations of the middle O atom in the W-O-Zr linkage. The data for both W-W and Zr-Zr atom pairs also indicate a hardening of the effective spring constant near 100 K, which is consistent with the shift of the lowest mode with T in the phonon density of states. A simple model is developed to explain the NTE in terms of the local structure results; it also provides a natural explanation for the lack of a soft-mode phase transition.

  1. 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…

  2. 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.

  3. Hybrid platforms of graphane-graphene 2D structures: prototypes for atomically precise nanoelectronics.

    Science.gov (United States)

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

    2014-11-21

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

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

    NARCIS (Netherlands)

    Lisowski, W.F.; Keim, Enrico G.; van den Berg, A.H.J.; Smithers, M.A.; Smithers, Mark 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

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

    NARCIS (Netherlands)

    Sun, Z.|info:eu-repo/dai/nl/314075674

    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

  6. Aromatization process of hydrocarbons containing 2 to 4 carbon atoms in the presence of MFI structure zeolite

    Energy Technology Data Exchange (ETDEWEB)

    Alario, F.; Deves, J.M.

    1993-05-21

    The invention describes an aromatization process of hydrocarbons comprising 2 to 4 carbon atoms per molecule in the presence of a composite catalyst which contains: a MFI structure zeolite containing an element chosen among alkaline or alkaline-earth metals, with a structure made of Silicon, Aluminium and / or Gallium; a matrix; platinum metals and additive metal chosen among Stain, Germanium, Indium, Copper, Iron, Molybdenum, Gallium, Thallium, Gold, Silver, Ruthenium, Chrome, Tungsten and Lead at least; an halogen chosen among Fluorine, Chlorine, Bromine and Iodine at least; Gallium and Zinc possibly; alkaline or alkaline-earth metal in the matrix preferentially. The invention describes also catalyst preparation and use for hydrocarbons aromatization reactions.

  7. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ali, Mubarak, E-mail: mubarak74@comsats.edu.pk, E-mail: mubarak74@mail.com [COMSATS Institute of Information Technology, Department of Physics (Pakistan); Lin, I-Nan [Tamkang University, Department of Physics (China)

    2017-01-15

    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.

  9. Identifying the Atomic-Level Effects of Metal Composition on the Structure and Catalytic Activity of Peptide-Templated Materials.

    Science.gov (United States)

    Merrill, Nicholas A; McKee, Erik M; Merino, Kyle C; Drummy, Lawrence F; Lee, Sungsik; Reinhart, Benjamin; Ren, Yang; Frenkel, Anatoly I; Naik, Rajesh R; Bedford, Nicholas M; Knecht, Marc R

    2015-12-22

    Bioinspired approaches for the formation of metallic nanomaterials have been extensively employed for a diverse range of applications including diagnostics and catalysis. These materials can often be used under sustainable conditions; however, it is challenging to control the material size, morphology, and composition simultaneously. Here we have employed the R5 peptide, which forms a 3D scaffold to direct the size and linear shape of bimetallic PdAu nanomaterials for catalysis. The materials were prepared at varying Pd:Au ratios to probe optimal compositions to achieve maximal catalytic efficiency. These materials were extensively characterized at the atomic level using transmission electron microscopy, extended X-ray absorption fine structure spectroscopy, and atomic pair distribution function analysis derived from high-energy X-ray diffraction patterns to provide highly resolved structural information. The results confirmed PdAu alloy formation, but also demonstrated that significant surface structural disorder was present. The catalytic activity of the materials was studied for olefin hydrogenation, which demonstrated enhanced reactivity from the bimetallic structures. These results present a pathway to the bioinspired production of multimetallic materials with enhanced properties, which can be assessed via a suite of characterization methods to fully ascertain structure/function relationships.

  10. Templated Atom-Precise Galvanic Synthesis and Structure Elucidation of a [Ag 24 Au(SR) 18 ] − Nanocluster

    KAUST Repository

    Bootharaju, Megalamane Siddaramappa

    2015-11-27

    Synthesis of atom-precise alloy nanoclusters with uniform composition is challenging when the alloying atoms are similar in size (for example, Ag and Au). A galvanic exchange strategy has been devised to produce a compositionally uniform [Ag24Au(SR)18]- cluster (SR: thiolate) using a pure [Ag25(SR)18]- cluster as a template. Conversely, the direct synthesis of Ag24Au cluster leads to a mixture of [Ag25-xAux(SR)18]-, x=1-8. Mass spectrometry and crystallography of [Ag24Au(SR)18]- reveal the presence of the Au heteroatom at the Ag25 center, forming Ag24Au. The successful exchange of the central Ag of Ag25 with Au causes perturbations in the Ag25 crystal structure, which are reflected in the absorption, luminescence, and ambient stability of the particle. These properties are compared with those of Ag25 and Ag24Pd clusters with same ligand and structural framework, providing new insights into the modulation of cluster properties with dopants at the single-atom level.

  11. Structural, electronic and magnetic properties of transition metal atom-doped ZnS dilute magnetic semiconductors: A first-principles study

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Zhu-Hua [College of Physics and Information Technology, Shaanxi Normal University, Xian, 710119, Shaanxi (China); Zhang, Jian-Min, E-mail: jmzhang@snnu.edu.cn [College of Physics and Information Technology, Shaanxi Normal University, Xian, 710119, Shaanxi (China); Xu, Ke-Wei [State Key Laboratory for Mechanical Behavior of Materials, Xian Jiaotong University, Xian, 710049, Shaanxi (China)

    2016-11-01

    The spin-polarized first-principles calculations are performed to study the structural, electronic and magnetic properties of a single and two identical transition metal (TM) atoms X (X = V, Cr, Mn, Fe, Co and Ni) doped ZnS dilute magnetic semiconductors (DMS). The single V-, Cr-, Fe- and Ni-doped ZnS systems exhibit the magnetic half-metallic (HM) characters, while Mn- and Co-doped ZnS systems display magnetic semiconducting characters. For two identical TM atoms doped ZnS systems, the two identical V, Cr and Ni atoms are in a ferromagnetic (FM) coupling under the double-exchange (DE) mechanism, leading V-, Cr- and Ni-doped ZnS systems to be HM with FM coupling. While two identical Mn- and Co-doped ZnS systems are semiconductors with antiferromagnetic (AFM) coupling consisting with the superexchange (SE) mechanism. Specifically, two identical Fe atoms display a competition between the SE and DE mechanisms. The Zn{sub 70}Fe{sub 2}S{sub 72} system is metal with AFM coupling at the nearest separation of two Fe atoms while HM with FM coupling at the farther separations of two Fe atoms. - Graphical abstract: The 3 × 2 × 3 supercell containing 72 formula units of zincblende ZnS. Red (Green) balls represent the S (Zn) atoms. One TM atom or two identical TM atoms X (X = V, Cr, Mn, Fe, Co or Ni) to substitute for one Zn atom at position 0 or two Zn atoms at positions 0 and i (i = 1, 2, 3 or 4). - Highlights: • A single V, Cr, Fe or Ni (Mn or Co) atoms doped ZnS are magnetic HM (magnetic semiconductor). • Two V, Cr or Ni (two Mn or Co) atoms doped ZnS are FM HM (AFM semiconductor). • Two Fe atoms doped ZnS are AFM metal (FM HM) at the nearest (farther) separations.

  12. Confirmation of disordered structure of ultrasmall CdSe nanoparticles from X-ray atomic pair distribution function analysis.

    Science.gov (United States)

    Yang, Xiaohao; Masadeh, Ahmad S; McBride, James R; Božin, Emil S; Rosenthal, Sandra J; Billinge, Simon J L

    2013-06-14

    The atomic pair distribution function (PDF) analysis of X-ray powder diffraction data has been used to study the structure of small and ultra-small CdSe nanoparticles. A method is described that uses a wurtzite and zinc-blende mixed phase model to account for stacking faults in CdSe particles. The mixed-phase model successfully describes the structure of nanoparticles larger than 2 nm yielding a stacking fault density of about 30%. However, for ultrasmall nanoparticles smaller than 2 nm, the models cannot fit the experimental PDF showing that the structure is significantly modified from that of larger particles and the bulk. The observation of a significant change in the average structure at ultra-small size is likely to explain the unusual properties of the ultrasmall particles such as their white light emitting ability.

  13. Mott theory predicted thermoelectric properties based on electronic structure of Bi and Sb atoms substituted PbTe material

    Science.gov (United States)

    Vora-ud, Athorn

    2017-11-01

    In this work, thermoelectric properties of Bi and Sb atoms substituted PbTe material were predicted by Mott theory through electronic structure calculation. This calculation has been carried by the first-principles DV-Xα molecular orbital method based on Hartree-Fock-Slater approximation. The Pb14Te13, Pb13SbTe13 and Pb13BiTe13 small clusters with a cubic rocksalt structure (Fm-3m; 225) were designed to be performed PbTe, Pb0.75Sb0.25Te and Pb0.75Bi0.25Te materials, respectively. The electronic structure showed that the high symmetry crystal structure, spin energy levels, partial spin density of states and electron charge density. The energy gap and Fermi level have been obtained from energy levels and density of state to be evaluated of electrical conductivity and Seebeck coefficient within Mott's theory predication.

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

    Energy Technology Data Exchange (ETDEWEB)

    Humphreys, C.J., E-mail: colin.humphreys@msm.cam.ac.uk [Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS (United Kingdom); Griffiths, J.T., E-mail: jg641@cam.ac.uk [Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS (United Kingdom); Tang, F., E-mail: ft274@cam.ac.uk [Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS (United Kingdom); Oehler, F., E-mail: fabrice.oehler@lpn.cnrs.fr [CNRS/C2N, Paris Sud University, Route de Nozay, 91460 Marcoussis (France); Findlay, S.D., E-mail: scott.findlay@monash.edu [School of Physics and Astronomy, Monash University, Victoria 3800 (Australia); Zheng, C., E-mail: changlin.zheng@monash.edu [Monash Centre for Electron Microscopy, Monash University, Victoria 3800 (Australia); Etheridge, J., E-mail: joanne.etheridge@mcem.monash.edu [Department of Materials Science and Engineering, Monash University, Victoria 3800 (Australia); Martin, T.L., E-mail: tomas.martin@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Bagot, P.A.J., E-mail: paul.bagot@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Moody, M.P., E-mail: michael.moody@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Sutherland, D., E-mail: danny.sutherland@manchester.ac.uk [School of Physics and Astronomy, Photon Science Institute, University of Manchester, Manchester M13 9PL (United Kingdom); Dawson, P., E-mail: philip.dawson@manchester.ac.uk [School of Physics and Astronomy, Photon Science Institute, University of Manchester, Manchester M13 9PL (United Kingdom); Schulz, S., E-mail: stefan.schulz@tyndall.ie [Tyndall National Institute, Lee Maltings Complex, Dyke Parade, Cork (Ireland); and others

    2017-05-15

    Highlights: • We have studied the atomic structure of polar and non-polar InGaN quantum wells. • The non-polar (11-20) InGaN quantum wells contain indium-rich clusters, unlike the polar (0001) quantum wells. • The electrons and holes in the quantum wells are localised by different mechanisms. - Abstract: 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 20 meV. The holes are localised near the bottom QW interface, by indium fluctuations in the random alloy, with a localisation energy of typically 60 meV. 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.

  15. Communication: Hot-atom abstraction dynamics of hydrogen from tungsten surfaces: The role of surface structure

    Science.gov (United States)

    Galparsoro, Oihana; Busnengo, Heriberto Fabio; Juaristi, Joseba Iñaki; Crespos, Cédric; Alducin, Maite; Larregaray, Pascal

    2017-09-01

    Adiabatic and non-adiabatic quasiclassical molecular dynamics simulations are performed to investigate the role of the crystal face on hot-atom abstraction of H adsorbates by H scattering from covered W(100) and W(110). On both cases, hyperthermal diffusion is strongly affected by the energy dissipated into electron-hole pair excitations. As a result, the hot-atom abstraction is highly reduced in favor of adsorption at low incidence energy and low coverages, i.e., when the mean free path of the hyperthermal H is typically larger. Qualitatively, this reduction is rather similar on both surfaces, despite at such initial conditions, the abstraction process involves more subsurface penetration on W(100) than on W(110).

  16. Atomic structure and magnetic properties of the pseudobinary alloys Fe/sub 3/(Al,Si)

    Energy Technology Data Exchange (ETDEWEB)

    Schneeweiss, O.; Zemcik, T.; Zak, T. (Ceskoslovenska Akademie Ved, Brno. Ustav Fyzikalni Metalurgie); Mager, S. (Akademie der Wissenschaften der DDR, Dresden. Zentralinstitut fuer Festkoerperphysik und Werkstofforschung)

    1983-09-16

    The influence of substitution of Al by Si on the atomic order, saturation magnetic polarization, and electrical resistivity is studied in Fe/sub 3/Al/sub 1-x/Si/sub x/, 0 <= x <= 1, alloys. The changes in the hyperfine parameters of the /sup 57/Fe Moessbauer spectra indicate that the degree of DO/sub 3/ order after order anneal is rised, accompanied by a separation of the Fe/sub 3/Si and Fe/sub 3/Al types of local surroundings. The most significant changes of isomer shifts, magnetic hyperfine fields, saturation magnetic polarization, and electrical resistivity due to atomic order are observed near the Fe/sub 3/Al and Fe/sub 3/Al/sub 0.25/Si/sub 0.75/ compositions.

  17. Atomic structure of sensitive battery materials and interfaces revealed by cryo-electron microscopy.

    Science.gov (United States)

    Li, Yuzhang; Li, Yanbin; Pei, Allen; Yan, Kai; Sun, Yongming; Wu, Chun-Lan; Joubert, Lydia-Marie; Chin, Richard; Koh, Ai Leen; Yu, Yi; Perrino, John; Butz, Benjamin; Chu, Steven; Cui, Yi

    2017-10-27

    Whereas standard transmission electron microscopy studies are unable to preserve the native state of chemically reactive and beam-sensitive battery materials after operation, such materials remain pristine at cryogenic conditions. It is then possible to atomically resolve individual lithium metal atoms and their interface with the solid electrolyte interphase (SEI). We observe that dendrites in carbonate-based electrolytes grow along the (preferred), , or directions as faceted, single-crystalline nanowires. These growth directions can change at kinks with no observable crystallographic defect. Furthermore, we reveal distinct SEI nanostructures formed in different electrolytes. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  18. Morphological and structural study of gas atomized Zr-Cu-based glass-forming alloys

    Energy Technology Data Exchange (ETDEWEB)

    Zambon, A.; Badan, B

    2004-07-15

    Zr-Cu-based glass-forming alloys were processed in a laboratory scale gas atomizer, operated in sonic conditions with nitrogen or helium as the atomizing medium. Powders of rather wide size distributions were obtained, in the under 212 {mu}m range, which afforded to carry out comparative phase analyses on particles which underwent quite different cooling conditions. X-ray diffraction examinations as well as light microscopy, transmission electron microscopy, differential thermal analysis (DTA) and microhardness determinations were used to investigate the powders belonging to different size ranges. Amorphous, partially crystalline and fully crystalline powders were obtained from each atomization batch. Light microscopy afforded to evaluate the morphometric details such as the secondary dendrite arm spacing in the crystalline particles, which were correlated with the estimated cooling rates computed by means of a simplified computer code. X-ray diffraction, TEM examinations and electron diffraction confirmed that conditions were established for the development of amorphous or nanocrystalline particles, in particular in the 'under 38 {mu}m' and in the 38-45 {mu}m size ranges. Microhardness determinations showed an extremely high hardness, of the order of 1000-1100 HV{sub 0.05} in the case of fully amorphous particles, which could be encountered mainly in the smaller size ranges, while in the case of crystalline powders the hardness was around a half of such value mainly in the larger, fully crystalline ones.

  19. 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.

  20. Microfabricated Waveguide Atom Traps.

    Energy Technology Data Exchange (ETDEWEB)

    Jau, Yuan-Yu [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-09-01

    A nanoscale , microfabricated waveguide structure can in - principle be used to trap atoms in well - defined locations and enable strong photon-atom interactions . A neutral - atom platform based on this microfabrication technology will be prealigned , which is especially important for quantum - control applications. At present, there is still no reported demonstration of evanescent - field atom trapping using a microfabricated waveguide structure. We described the capabilities established by our team for future development of the waveguide atom - trapping technology at SNL and report our studies to overcome the technical challenges of loading cold atoms into the waveguide atom traps, efficient and broadband optical coupling to a waveguide, and the waveguide material for high - power optical transmission. From the atomic - physics and the waveguide modeling, w e have shown that a square nano-waveguide can be utilized t o achieve better atomic spin squeezing than using a nanofiber for first time.

  1. Atomic Structures of [0bar{1}10] Symmetric Tilt Grain Boundaries in Hexagonal Close-Packed (hcp) Crystals

    Science.gov (United States)

    Wang, Jian; Beyerlein, Irene J.

    2012-10-01

    Molecular dynamics simulation and interface defect theory are used to determine the relaxed equilibrium atomic structures of symmetric tilt grain boundaries (STGBs) in hexagonal close-packed (hcp) crystals with a [0bar{1}10] tilt axis. STGBs of all possible rotation angles θ from 0 deg to 90 deg are found to have an ordered atomic structure. They correspond either to a coherent, defect-free boundary or to a tilt wall containing an array of distinct and discrete intrinsic grain boundary dislocations (GBDs). The STGBs adopt one of six base structures, PB^{(i)} , i = 1, …, 6, and the Burgers vector of the GBDs is related to the interplanar spacing of the base structure on which it lies. The base structures correspond to the basal plane ( θ = 0 deg, PB^{(1)} ); one of four minimum-energy, coherent boundaries, (bar{2}111),(bar{2}112),(bar{2}114) , and (bar{2}116)( {PB^{(2)} - PB^{(5)} } ) ; and the ( {11bar{2}0} ) plane ( θ = 90 deg, PB^{(6)} ). Based on these features, STGBs can be classified into one of six possible structural sets, wherein STGBs belonging to the same set i contain the same base boundary structure PB^{(i)} and an array of GBDs with the same Burgers vector b_{{GB}}^{(i)} , which vary only in spacing and sign with θ. This classification is shown to apply to both Mg and Ti, two metals with different c/ a ratios and employing different interatomic potentials in simulation. We use a simple model to forecast the misorientation range of each set for hcp crystals of general c/ a ratio, the predictions of which are shown to agree well with the molecular dynamics (MD) simulations for Mg and Ti.

  2. 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.

  3. 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.

  4. 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.

  5. All-atom molecular dynamics simulations of lung surfactant protein B: Structural features of SP-B promote lipid reorganization.

    Science.gov (United States)

    Khatami, Mohammad Hassan; Saika-Voivod, Ivan; Booth, Valerie

    2016-12-01

    Lung surfactant protein B (SP-B), a 79 residue, hydrophobic protein from the saposin superfamily, plays an essential role in breathing. Because of the extreme hydrophobicity of SP-B, the experimental structure of this protein has not yet been determined. Here, we run all-atom molecular dynamics simulations using the OPLS-AA force field in GROMACS to study SP-B's structure and mechanisms for promoting lipid reorganization. Firstly, we find that the final structures indicate the need for some fine-tuning of the homology-based secondary structure predictions. Secondly, we find energetically feasible structures 1) with SP-B's helices in the plane of the bilayer, 2) with SP-B's helices inclined with respect to the bilayer, and 3) with SP-B in a closed structure interacting peripherally with the bilayer. Interestingly, SP-B structures that were bent at the hinge region between the pairs of helices promoted and/or stabilized defects in the lipid bilayer. Finally, particular salt bridge patterns and structural plasticity in the central loop and adjacent region of SP-B appeared to be involved in SP-B's lipid reorganization abilities. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. 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}.

  7. Carbon nanotubes randomly decorated with gold clusters: from nano2hybrid atomic structures to gas sensing prototypes.

    Science.gov (United States)

    Charlier, J-C; Arnaud, L; Avilov, I V; Delgado, M; Demoisson, F; Espinosa, E H; Ewels, C P; Felten, A; Guillot, J; Ionescu, R; Leghrib, R; Llobet, E; Mansour, A; Migeon, H-N; Pireaux, J-J; Reniers, F; Suarez-Martinez, I; Watson, G E; Zanolli, Z

    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(2)hybrids is quantified for the detection of toxic species like NO(2), CO, C(2)H(5)OH and C(2)H(4).

  8. Molecular structure of poly(methyl methacrylate) surface II: Effect of stereoregularity examined through all-atom molecular dynamics.

    Science.gov (United States)

    Jha, Kshitij C; Zhu, He; Dhinojwala, Ali; Tsige, Mesfin

    2014-11-04

    Utilizing all-atom molecular dynamics (MD), we have analyzed the effect of tacticity and temperature on the surface structure of poly(methyl methacrylate) (PMMA) at the polymer-vacuum interface. We quantify these effects primarily through orientation, measured as the tilt with respect to the surface normal, and the surface number densities of the α-methyl, ester-methyl, carbonyl, and backbone methylene groups. Molecular structure on the surface is a complex interplay between orientation and number densities and is challenging to capture through sum frequency generation (SFG) spectroscopy alone. Independent quantification of the number density and orientation of chemical groups through all-atom MD presents a comprehensive model of stereoregular PMMA on the surface. SFG analysis presented in part I of this joint publication measures the orientation of molecules that are in agreement with MD results. We observe the ester-methyl groups as preferentially oriented, irrespective of tacticity, followed by the α-methyl and carbonyl groups. SFG spectroscopy also points to ester-methyl being dominant on the surface. The backbone methylene groups show a very broad angular distribution, centered along the surface plane. The surface number density ratios of ester-methyl to α-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to α-methyl. These subtle trends in the relative angular orientation and number densities that influence the variation of surface structure with tacticity are highlighted in this article. A more planar conformation of the syndiotactic PMMA along the surface (x-y plane) can be visualized through the trajectories from all-atom MD. Results from conformation tensor calculations for chains with any of their segments contributing to the surface validate the visual observation.

  9. Temperature Effects on Tensile and Compressive Mechanical Behaviors of C-S-H Structure via Atomic Simulation

    Directory of Open Access Journals (Sweden)

    Hao Xin

    2017-01-01

    Full Text Available An atomic scale model of amorphous calcium silicate hydrate (C-S-H with Ca/Si ratio of 1.67 is constructed. Effects of temperature on mechanical properties of C-S-H structure under tensile and compressive loading in the layered direction are investigated via molecular dynamics simulations. Results from present simulations show that (1 the tensile strength and Young’s modulus of C-S-H structure significantly decrease with the increase of the temperature; (2 the water layer plays an important role in the mechanical properties of C-S-H structure; (3 the compressive strength is stronger than tensile strength, which corresponds with the characteristic of cement paste.

  10. Role of support-nanoalloy interactions in the atomic-scale structural and chemical ordering for tuning catalytic sites.

    Science.gov (United States)

    Yang, Lefu; Shan, Shiyao; Loukrakpam, Rameshwori; Petkov, Valeri; Ren, Yang; Wanjala, Bridgid N; Engelhard, Mark H; Luo, Jin; Yin, Jun; Chen, Yongsheng; Zhong, Chuan-Jian

    2012-09-12

    The understanding of the atomic-scale structural and chemical ordering in supported nanosized alloy particles is fundamental for achieving active catalysts by design. This report shows how such knowledge can be obtained by a combination of techniques including X-ray photoelectron spectroscopy and synchrotron radiation based X-ray fine structure absorption spectroscopy and high-energy X-ray diffraction coupled to atomic pair distribution function analysis, and how the support-nanoalloy interaction influences the catalytic activity of ternary nanoalloy (platinum-nickel-cobalt) particles on three different supports: carbon, silica, and titania. The reaction of carbon monoxide with oxygen is employed as a probe to the catalytic activity. The thermochemical processing of this ternary composition, in combination with the different support materials, is demonstrated to be capable of fine-tuning the catalytic activity and stability. The support-nanoalloy interaction is shown to influence structural and chemical ordering in the nanoparticles, leading to support-tunable active sites on the nanoalloys for oxygen activation in the catalytic oxidation of carbon monoxide. A nickel/cobalt-tuned catalytic site on the surface of nanoalloy is revealed for oxygen activation, which differs from the traditional oxygen-activation sites known for oxide-supported noble metal catalysts. The discovery of such support-nanoalloy interaction-enabled oxygen-activation sites introduces a very promising strategy for designing active catalysts in heterogeneous catalysis.

  11. 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

    2017-02-01

    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.

  12. 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

    2015-01-20

    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.

  13. 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.

  14. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yiqi, E-mail: zhangyiqi@mail.xjtu.edu.cn [Key Laboratory for Physical Electronics and Devices of the Ministry of Education & Shaanxi Key Lab of Information Photonic Technique, Xi’an Jiaotong University, Xi’an 710049 (China); Liu, Xing [Key Laboratory for Physical Electronics and Devices of the Ministry of Education & Shaanxi Key Lab of Information Photonic Technique, Xi’an Jiaotong University, Xi’an 710049 (China); Belić, Milivoj R., E-mail: milivoj.belic@qatar.tamu.edu [Science Program, Texas A& M University at Qatar, P.O. Box 23874 Doha (Qatar); Wu, Zhenkun [Key Laboratory for Physical Electronics and Devices of the Ministry of Education & Shaanxi Key Lab of Information Photonic Technique, Xi’an Jiaotong University, Xi’an 710049 (China); Zhang, Yanpeng, E-mail: ypzhang@mail.xjtu.edu.cn [Key Laboratory for Physical Electronics and Devices of the Ministry of Education & Shaanxi Key Lab of Information Photonic Technique, Xi’an Jiaotong University, Xi’an 710049 (China)

    2015-12-15

    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.

  16. Dependencies of photoelectric properties of SiC/Si structures grown by the method of atoms substitution on synthesis time

    Science.gov (United States)

    Grashchenko, A. S.; Kukushkin, S. A.; Osipov, A. V.; Feoktistov, N. A.

    2017-07-01

    This paper is dedicated to an exploration of the photoelectric properties of Si-SiC structures grown by the substitution method on silicon substrates of (001) orientation. For the samples with the synthesis times of 40, 60, 90, 120 and 900 s, magnitudes of the saturation currents are determined and the coefficients of efficiency are calculated. The obtained dependencies of the photoelectric characteristics on the synthesis time are explained using the theory of formation of dilatation dipoles during the synthesis by the method of atoms substitution.

  17. In situ study of atomic structure transformations of Pt-Ni nanoparticle catalysts during electrochemical potential cycling.

    Science.gov (United States)

    Tuaev, Xenia; Rudi, Stefan; Petkov, Valeri; Hoell, Armin; Strasser, Peter

    2013-07-23

    When exposed to corrosive anodic electrochemical environments, Pt alloy nanoparticles (NPs) undergo selective dissolution of the less noble component, resulting in catalytically active bimetallic Pt-rich core-shell structures. Structural evolution of PtNi6 and PtNi3 NP catalysts during their electrochemical activation and catalysis was studied by in situ anomalous small-angle X-ray scattering to obtain insight in element-specific particle size evolution and time-resolved insight in the intraparticle structure evolution. Ex situ high-energy X-ray diffraction coupled with pair distribution function analysis was employed to obtain detailed information on the atomic-scale ordering, particle phases, structural coherence lengths, and particle segregation. Our studies reveal a spontaneous electrochemically induced formation of PtNi particles of ordered Au3Cu-type alloy structures from disordered alloy phases (solid solutions) concomitant with surface Ni dissolution, which is coupled to spontaneous residual Ni metal segregation during the activation of PtNi6. Pt-enriched core-shell structures were not formed using the studied Ni-rich nanoparticle precursors. In contrast, disordered PtNi3 alloy nanoparticles lose Ni more rapidly, forming Pt-enriched core-shell structures with superior catalytic activity. Our X-ray scattering results are confirmed by STEM/EELS results on similar nanoparticles.

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

    Science.gov (United States)

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

    2015-08-01

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

  19. 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.

  20. Solid state NMR of isotope labelled murine fur: a powerful tool to study atomic level keratin structure and treatment effects

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Wai Ching Veronica; Narkevicius, Aurimas; Chow, Wing Ying; Reid, David G.; Rajan, Rakesh [University of Cambridge, Department of Chemistry (United Kingdom); Brooks, Roger A. [University of Cambridge, Department of Trauma and Orthopaedic Surgery, Addenbrooke’s Hospital (United Kingdom); Green, Maggie [University of Cambridge, Central Biomedical Resources, School of Clinical Medicine (United Kingdom); Duer, Melinda J., E-mail: mjd13@cam.ac.uk [University of Cambridge, Department of Chemistry (United Kingdom)

    2016-10-15

    We have prepared mouse fur extensively {sup 13}C,{sup 15}N-labelled in all amino acid types enabling application of 2D solid state NMR techniques which establish covalent and spatial proximities within, and in favorable cases between, residues. {sup 13}C double quantum–single quantum correlation and proton driven spin diffusion techniques are particularly useful for resolving certain amino acid types. Unlike 1D experiments on isotopically normal material, the 2D methods allow the chemical shifts of entire spin systems of numerous residue types to be determined, particularly those with one or more distinctively shifted atoms such as Gly, Ser, Thr, Tyr, Phe, Val, Leu, Ile and Pro. Also the partial resolution of the amide signals into two signal envelopes comprising of α-helical, and β-sheet/random coil components, enables resolution of otherwise overlapped α-carbon signals into two distinct cross peak families corresponding to these respective secondary structural regions. The increase in resolution conferred by extensive labelling offers new opportunities to study the chemical fate and structural environments of specific atom and amino acid types under the influence of commercial processes, and therapeutic or cosmetic treatments.

  1. Structure and Function of Photosystem I-[FeFe] Hydrogenase Protein Fusions: An All-Atom Molecular Dynamics Study.

    Science.gov (United States)

    Harris, Bradley J; Cheng, Xiaolin; Frymier, Paul

    2016-02-04

    All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein-protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H2ase shows that these fusion complexes approach stable equilibrium conformations during the MD simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.

  2. Atomic-Scale Topographic and Electronic Structure of Graphene Films on Ultraflat Insulating Materials

    Science.gov (United States)

    Gutierrez, Christopher; Zhao, Liuyan; Ghahari, Fereshte; Dean, Cory; Rim, Kwang; Hone, James; Flynn, George; Kim, Philip; Pasupathy, Abhay

    2011-03-01

    Graphene, a unique two-dimensional material, has attracted much attention for its exotic electronic properties. But owing to its nature as a single monolayer, many of these interesting properties depend heavily on the substrate on which the graphene rests. Scanning tunneling microscope (STM) experiments offer the unique ability to investigate the effect of the substrate on the surface roughness (via topography maps) as well as the local electronic properties (via spectroscopy maps) of graphene. In this talk we will present such experimental results of graphene on atomically flat insulating substrates such as mica and boron nitride, as well as suspended graphene sheets. We will describe experiments performed both on exfoliated graphene flakes as well as large-area graphene films grown by chemical vapor deposition (CVD).

  3. Atomic-scale structure of biogenic materials by total X-ray diffraction: a study of bacterial and fungal MnOx.

    Science.gov (United States)

    Petkov, V; Ren, Y; Saratovsky, I; Pastén, P; Gurr, S J; Hayward, M A; Poeppelmeier, K R; Gaillard, J-F

    2009-02-24

    Biogenic materials are produced by microorganisms and are typically found in a nanophase state. As such, they are difficult to characterize structurally. In this report, we demonstrate how high-energy X-ray diffraction and atomic pair distribution function analysis can be used to determine the atomic-scale structures of MnO(x) produced by bacteria and fungi. These structures are well-defined, periodic, and species-specific, built of Mn-O(6) octahedra forming birnessite-type layers and todorokite-type tunnels, respectively. The inherent structural diversity of biogenic material may offer opportunities for practical applications.

  4. Structure and orbital ordering of ultrathin LaVO{sub 3} probed by atomic resolution electron microscopy and Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lindfors-Vrejoiu, Ionela; Engelmayer, Johannes; Loosdrecht, Paul H.M. van [II. Physikalisches Institut, Koeln Univ. (Germany); Jin, Lei; Jia, Chun-Lin [Peter Gruenberg Institut (PGI-5) and Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C), Forschungszentrum Juelich GmbH (Germany); Himcinschi, Cameliu [Institut fuer Theoretische Physik, TU Bergakademie Freiberg (Germany); Hensling, Felix; Waser, Rainer; Dittmann, Regina [Peter Gruenberg Institut (PGI-7), Forschungszentrum Juelich GmbH (Germany)

    2017-03-15

    Orbital ordering has been less investigated in epitaxial thin films, due to the difficulty to evidence directly the occurrence of this phenomenon in thin film samples. Atomic resolution electron microscopy enabled us to observe the structural details of the ultrathin LaVO{sub 3} films. The transition to orbital ordering of epitaxial layers as thin as ∼4 nm was probed by temperature-dependent Raman scattering spectroscopy of multilayer samples. From the occurrence and temperature dependence of the 700 cm{sup -1} Raman active mode it can be inferred that the structural phase transition associated with orbital ordering takes place in ultrathin LaVO{sub 3} films at about 130 K. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  5. Resonant structures in the low-energy electron continuum for single ionization of atoms in the tunnelling regime

    Energy Technology Data Exchange (ETDEWEB)

    Rudenko, A; Zrost, K; Schroeter, C D; Jesus, V L B de; Feuerstein, B; Moshammer, R; Ullrich, J [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, D-67119 Heidelberg (Germany)

    2004-12-28

    We present high-resolution fully differential experimental data on single ionization of He, Ne and Ar by ultra-short (25 fs, 6 fs) 795 nm laser pulses at intensities 0.15-2.0 x 10{sup 15} W cm{sup -2}. We show that the ATI-like pattern can survive deep in the tunnelling regime and that the atomic structure plays an important role in the formation of the low-energy photoelectron spectra even at high intensities. The absence of ponderomotive shifts, the splitting of the peaks and their degeneration for few-cycle pulses indicate that the observed structures originate from a resonant process. (letter to the editor)

  6. Atomic Resolution Structure of the Double Mutant (K53,56M) of Bovine Pancreatic Phospholipase A2

    Energy Technology Data Exchange (ETDEWEB)

    Sekar,K.; Yogavel, M.; Gayathri, D.; Velmurugan, D.; Krishna, R.; Poi, M.; Dauter, Z.; Dauter, M.; Tsai, M.

    2006-01-01

    The structure of the double mutant K53,56M has previously been refined at 1.9 Angstroms resolution using room-temperature data. The present paper reports the crystal structure of the same mutant K53,56M refined against 1.1 Angstroms data collected using synchrotron radiation. A total of 116 main-chain atoms from 29 residues and 44 side chains are modeled in alternate conformations. Most of the interfacial binding residues are found to be disordered and alternate conformations could be recognized. The second calcium ion-binding site residue Glu92 adopts two alternate conformations. The minor and major conformations of Glu92 correspond to the second calcium ion bound and unbound states.

  7. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Gunay, H. Burak; Ghods, Pouria [Carleton University, Department of Civil and Environmental Engineering, Ottawa (Canada); Isgor, O. Burkan, E-mail: burkan_isgor@carleton.ca [Carleton University, Department of Civil and Environmental Engineering, Ottawa (Canada); Carpenter, Graham J.C. [CanmetMATERIALS, NRCan, Ottawa (Canada); Wu, Xiaohua [Natural Research Council of Canada, Information and Communications Technologies, Ottawa (Canada)

    2013-06-01

    The atomic structure of oxide films formed on carbon steel that are exposed to highly alkaline simulated concrete pore solutions was investigated using Electron Energy Loss Spectroscopy (EELS). In particular, the effect of chloride exposure on film structure was studied in two types of simulated pore solutions: saturated calcium hydroxide (CH) and a solution prepared to represent typical concrete pore solutions (CP). It was shown that the films that form on carbon steel in simulated concrete pore solutions contained three indistinct layers. The inner oxide film had a structure similar to that of Fe{sup II}O, which is known to be unstable in the presence of chlorides. The outer oxide film mainly resembled Fe{sub 3}O{sub 4} (Fe{sup II}O·Fe{sub 2}{sup III}O{sub 3}) in the CH solution and α-Fe{sub 2}{sup III}O{sub 3}/Fe{sub 3}O{sub 4} in the CP solution. The composition of the transition layer between the inner and outer layers of the oxide film was mainly composed of Fe{sub 3}O{sub 4} (Fe{sup II}O·Fe{sub 2}{sup III}O{sub 3}). In the presence of chloride, the relative amount of the Fe{sup III}/Fe{sup II} increased, confirming that chlorides induce valence state transformation of oxides from Fe{sup II} to Fe{sup III}, and the difference between the atomic structures of oxide film layers diminished.

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

    NARCIS (Netherlands)

    Li, Z.; Young, N.P.; Di Vece, M.|info:eu-repo/dai/nl/248753355; 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

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

    NARCIS (Netherlands)

    Grodzinska, D.

    2012-01-01

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

  11. Characterizing Crystalline-Vitreous Structures: From Atomically Resolved Silica to Macroscopic Bubble Rafts

    Science.gov (United States)

    Burson, Kristen M.; Schlexer, Philomena; Bu¨chner, Christin; Lichtenstein, Leonid; Heyde, Markus; Freund, Hans-Joachim

    2015-01-01

    A two-part experiment using bubble rafts to analyze amorphous structures is presented. In the first part, the distinctions between crystalline and vitreous structures are examined. In the second part, the interface between crystalline and amorphous regions is considered. Bubble rafts are easy to produce and provide excellent analogy to recent…

  12. Structural, electronic and photocatalytic properties of atomic defective BiI3 monolayers

    Science.gov (United States)

    Yan, Huang; Ziyu, Hu; Xu, Gong; Xiaohong, Shao

    2018-01-01

    The structural, electronic and photocatalytic properties of five vacancy-containing 2D BiI3 monolayers are investigated by the first-principle calculations. The electronic structures show that the five structures are stable and have comparable binding energies to that of the pristine BiI3 monolayer, and the defects can tune the band gaps. Optical spectra indicate that the five structures retain high absorption capacity for visible light. The spin-orbit coupling (SOC) effect is found to play an important role in the band edge of defective structures, and the VBi and VBi-I3 defective BiI3 monolayers can make absolute band edges straddle water redox potentials more easily.

  13. Facile synthesis of analogous graphene quantum dots with sp2 hybridized carbon atom dominant structures and their photovoltaic application

    Science.gov (United States)

    Huang, Zhengcheng; Shen, Yongtao; Li, Yu; Zheng, Wenjun; Xue, Yunjia; Qin, Chengqun; Zhang, Bo; Hao, Jingxiang; Feng, Wei

    2014-10-01

    Graphene quantum dot (GQD) is an emerging class of zero-dimensional nanocarbon material with many novel applications. It is of scientific importance to prepare GQDs with more perfect structures, that is, GQDs containing negligible oxygenous defects, for both optimizing their optical properties and helping in their photovoltaic applications. Herein, a new strategy for the facile preparation of ``pristine'' GQDs is reported. The method we presented is a combination of a bottom-up synthetic and a solvent-induced interface separation process, during which the target products with highly crystalline structure were selected by the organic solvent. The obtained organic soluble GQDs (O-GQDs) showed a significant difference in structure and composition compared with ordinary aqueous soluble GQDs, thus leading to a series of novel properties. Furthermore, O-GQDs were applied as electron-acceptors in a poly(3-hexylthiophene) (P3HT)-based organic photovoltaic device. The performance highlights that O-GQD has potential to be a novel electron-acceptor material due to the sp2 hybridized carbon atom dominant structure and good solubility in organic solvents.Graphene quantum dot (GQD) is an emerging class of zero-dimensional nanocarbon material with many novel applications. It is of scientific importance to prepare GQDs with more perfect structures, that is, GQDs containing negligible oxygenous defects, for both optimizing their optical properties and helping in their photovoltaic applications. Herein, a new strategy for the facile preparation of ``pristine'' GQDs is reported. The method we presented is a combination of a bottom-up synthetic and a solvent-induced interface separation process, during which the target products with highly crystalline structure were selected by the organic solvent. The obtained organic soluble GQDs (O-GQDs) showed a significant difference in structure and composition compared with ordinary aqueous soluble GQDs, thus leading to a series of novel

  14. Magnetic structure and ferroelectric activity in orthorhombic YMnO3: Relative roles of magnetic symmetry breaking and atomic displacements

    Science.gov (United States)

    Solovyev, I. V.; Valentyuk, M. V.; Mazurenko, V. V.

    2012-10-01

    We discuss the relative roles played by the magnetic inversion symmetry breaking and the ferroelectric (FE) atomic displacements in the multiferroic state of YMnO3. For these purposes we derive a realistic low-energy model, using results of first-principles electronic structure calculations and experimental parameters of the crystal structure below and above the FE transition. Then, we solve this model in the mean-field Hartree-Fock approximation. We argue that the multiferroic state in YMnO3 has a magnetic origin, and the centrosymmetric Pbnm structure is formally sufficient for explaining the main details of the noncentrosymmetric magnetic ground state. The relativistic spin-orbit interaction lifts the degeneracy, caused by the frustration of isotropic exchange interactions in the ab plane, and stabilizes a twofold periodic noncollinear magnetic state, which is similar to the E state apart from the spin canting. The noncentrosymmetric atomic displacements in the P21nm phase reduce the spin canting, but do not change the symmetry of the magnetic state. The effect of the P21nm distortion on the FE polarization ΔPa, parallel to the orthorhombic a axis, is twofold: (i) It gives rise to ionic contributions, associated with the oxygen and yttrium sites; (ii) it affects the electronic polarization, mainly through the change of the spin canting. The relatively small value of ΔPa, observed in the experiment, is caused by a partial cancellation of the electronic and ionic contributions, as well as different contributions in the ionic part, which takes place for the experimental P21nm structure. The twofold periodic magnetic state competes with the fourfold periodic one and, even in the displaced P21nm phase, these two states continue to coexist in a narrow energy range. Finally, we theoretically optimize the crystal structure. For these purposes we employ the LSDA+U approach and assume the collinear E-type antiferromagnetic alignment. Then, we use the obtained structural

  15. Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography

    Science.gov (United States)

    Chang, Juan; Liu, Xiangan; Rochat, Ryan H.; Baker, Matthew L.; Chiu, Wah

    2014-01-01

    The past few decades have seen tremendous advances in single particle electron cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of non-icosahedrally arranged proteins in viruses by employing either single particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course has been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic and biochemical states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures “in situ”. Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future. PMID:22297510

  16. Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography.

    Science.gov (United States)

    Chang, Juan; Liu, Xiangan; Rochat, Ryan H; Baker, Matthew L; Chiu, Wah

    2012-01-01

    The past few decades have seen tremendous advances in single-particle electron -cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of nonicosahedrally arranged proteins in viruses by employing either single-particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course have been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures "in situ". Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future.

  17. Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Azim, N. [University of Punjab, New Campus, Lahore-54590 (Pakistan); Deery, E.; Warren, M. J. [University of Kent, Stacey Building, Canterbury CT2 7NJ (United Kingdom); Wolfenden, B. A. A.; Erskine, P.; Cooper, J. B., E-mail: jon.cooper@ucl.ac.uk; Coker, A.; Wood, S. P. [UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF (United Kingdom); Akhtar, M. [University of Punjab, New Campus, Lahore-54590 (Pakistan)

    2014-03-01

    The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step in the biosynthesis of tetrapyrroles in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. Two near-atomic resolution structures of PBGD from B. megaterium are reported that demonstrate the time-dependent accumulation of partially oxidized forms of the cofactor, including one that possesses a tetrahedral C atom in the terminal pyrrole ring. The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.

  18. 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

    2017-05-01

    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. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  19. First-principles studies of BN sheets with absorbed transition metal single atoms or dimers: stabilities, electronic structures, and magnetic properties.

    Science.gov (United States)

    Ma, Dongwei; Lu, Zhansheng; Ju, Weiwei; Tang, Yanan

    2012-04-11

    BN sheets with absorbed transition metal (TM) single atoms, including Fe, Co, and Ni, and their dimers have been investigated by using a first-principles method within the generalized gradient approximation. All of the TM atoms studied are found to be chemically adsorbed on BN sheets. Upon adsorption, the binding energies of the Fe and Co single atoms are modest and almost independent of the adsorption sites, indicating the high mobility of the adatoms and isolated particles to be easily formed on the surface. However, Ni atoms are found to bind tightly to BN sheets and may adopt a layer-by-layer growth mode. The Fe, Co, and Ni dimers tend to lie (nearly) perpendicular to the BN plane. Due to the wide band gap of the pure BN sheet, the electronic structures of the BN sheets with TM adatoms are determined primarily by the distribution of TM electronic states around the Fermi level. Very interesting spin gapless semiconductors or half-metals can be obtained in the studied systems. The magnetism of the TM atoms is preserved well on the BN sheet, very close to that of the corresponding free atoms and often weakly dependent on the adsorption sites. The present results indicate that BN sheets with adsorbed TM atoms have potential applications in fields such as spintronics and magnetic data storage due to the special spin-polarized electronic structures and magnetic properties they possess.

  20. Atomic force microscopy: High resolution dynamic imaging of cellular and molecular structure in health and disease.

    Science.gov (United States)

    Taatjes, Douglas J; Quinn, Anthony S; Rand, Jacob H; Jena, Bhanu P

    2013-10-01

    The atomic force microscope (AFM), invented in 1986, and a member of the scanning probe family of microscopes, offers the unprecedented ability to image biological samples unfixed and in a hydrated environment at high resolution. This opens the possibility to investigate biological mechanisms temporally in a heretofore unattainable resolution. We have used AFM to investigate: (1) fundamental issues in cell biology (secretion) and, (2) the pathological basis of a human thrombotic disease, the antiphospholipid syndrome (APS). These studies have incorporated the imaging of live cells at nanometer resolution, leading to discovery of the "porosome," the universal secretory portal in cells, and a molecular understanding of membrane fusion from imaging the interaction and assembly of proteins between opposing lipid membranes. Similarly, the development of an in vitro simulacrum for investigating the molecular interactions between proteins and lipids has helped define an etiological explanation for APS. The prime importance of AFM in the success of these investigations will be presented in this manuscript, as well as a discussion of the limitations of this technique for the study of biomedical samples. Copyright © 2013 Wiley Periodicals, Inc.

  1. Structural and nanomechanical properties of paperboard coatings studied by peak force tapping atomic force microscopy.

    Science.gov (United States)

    Sababi, Majid; Kettle, John; Rautkoski, Hille; Claesson, Per M; Thormann, Esben

    2012-10-24

    Paper coating formulations containing starch, latex, and clay were applied to paperboard and have been investigated by scanning electron microscopy and Peak Force tapping atomic force microscopy. A special focus has been on the measurement of the variation of the surface topography and surface material properties with a nanometer scaled spatial resolution. The effects of coating composition and drying conditions were investigated. It is concluded that the air-coating interface of the coating is dominated by close-packed latex particles embedded in a starch matrix and that the spatial distribution of the different components in the coating can be identified due to their variation in material properties. Drying the coating at an elevated temperature compared to room temperature changes the surface morphology and the surface material properties due to partial film formation of latex. However, it is evident that the chosen elevated drying temperature and exposure time is insufficient to ensure complete film formation of the latex which in an end application will be needed.

  2. Structural dynamics of single molecules studied with high-speed atomic force microscopy.

    Science.gov (United States)

    Henderson, Robert M

    2015-03-01

    Atomic force microscopy (AFM) is a scanning probe technique that has been in use in biology to generate sub-nanometre resolution images in near-physiological environments for over 20 years. Most AFM work uses instruments that take several minutes to generate each image but instruments that can produce real-time images have recently become available and there is now a reasonable body of work published on this technique. The importance of this high-speed AFM is that dynamic events of individual macromolecules can be studied. This review focuses on specific examples that demonstrate the potential of the technique. It covers four areas in which high-speed AFM has been used to elucidate mechanisms that are either unstudied or not clearly understood. These areas are: protein-protein interactions; DNA-protein interactions; quantification of biological processes; the use of DNA origami scaffolds as nanostructures to build and study dynamic molecular events. High-speed AFM shares advantages and disadvantages with conventional AFM, but it compares well in quality of data generated and in ease of use with other currently available techniques of high-resolution biological imaging. As the instruments become more widespread, the value of high-speed AFM and its potential to complement other techniques in molecular and cell biology should become more appreciated.

  3. Dislocation core structure and dynamics in two atomic models of {alpha}-zirconium

    Energy Technology Data Exchange (ETDEWEB)

    Khater, H.A., E-mail: hassan.khater@upc.edu [Department of Engineering, University of Liverpool, Brownlow Hill, Liverpool L69 3GH (United Kingdom); Bacon, D.J. [Department of Engineering, University of Liverpool, Brownlow Hill, Liverpool L69 3GH (United Kingdom)

    2010-05-15

    Properties of basal and first order prism plane dislocations with Burgers vector 1/3 <112-bar 0> in {alpha}-Zr have been investigated by computer simulation. Results for a recent interatomic potential (MA07) are assessed and compared with an older one (AWB95). The elastic constants have been calculated with the inner relaxations allowed for and the energy and vector of metastable stacking faults have been determined and compared with published ab initio estimates. The core of the screw dislocation spreads principally in the prism plane in the MA07 model, in contrast to basal plane dissociation in the AWB95 model, and the prism-to-basal ratio of the Peierls stress for the screw is 0.28 with the MA07 model, compared with 3.31 with the AWB95 model. Simulation of the dynamics of dislocation motion under applied stress reveal how the drag coefficient varies with slip system and temperature. The results for the MA07 model are consistent with the known slip geometry of Zr, suggesting that it offers significant advantages for large-scale atomic simulation of dislocation behaviour.

  4. Structural and chemical analysis of annealed plasma-enhanced atomic layer deposition aluminum nitride films

    Energy Technology Data Exchange (ETDEWEB)

    Broas, Mikael, E-mail: mikael.broas@aalto.fi; Vuorinen, Vesa [Department of Electrical Engineering and Automation, Aalto University, P.O. Box 13500, FIN-00076 Aalto, Espoo (Finland); Sippola, Perttu; Pyymaki Perros, Alexander; Lipsanen, Harri [Department of Micro- and Nanosciences, Aalto University, P.O. Box 13500, FIN-00076 Aalto, Espoo (Finland); Sajavaara, Timo [Department of Physics, University of Jyväskylä, P.O. Box 35, FIN-40014 Jyväskylä (Finland); Paulasto-Kröckel, Mervi [Department of Electrical Engineering and Automation, Aalto University. P.O. Box 13500, FIN-00076 Aalto, Espoo (Finland)

    2016-07-15

    Plasma-enhanced atomic layer deposition was utilized to grow aluminum nitride (AlN) films on Si from trimethylaluminum and N{sub 2}:H{sub 2} plasma at 200 °C. Thermal treatments were then applied on the films which caused changes in their chemical composition and nanostructure. These changes were observed to manifest in the refractive indices and densities of the films. The AlN films were identified to contain light element impurities, namely, H, C, and excess N due to nonideal precursor reactions. Oxygen contamination was also identified in the films. Many of the embedded impurities became volatile in the elevated annealing temperatures. Most notably, high amounts of H were observed to desorb from the AlN films. Furthermore, dinitrogen triple bonds were identified with infrared spectroscopy in the films. The triple bonds broke after annealing at 1000 °C for 1 h which likely caused enhanced hydrolysis of the films. The nanostructure of the films was identified to be amorphous in the as-deposited state and to become nanocrystalline after 1 h of annealing at 1000 °C.

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

    CERN Document Server

    Gidofalvi, Gergely

    2014-01-01

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

  6. Charge inhomogeneities in the colossal magnetoresistant manganites from the local atomic structure

    Energy Technology Data Exchange (ETDEWEB)

    Billinge, S. J. L.; Petkov, V.; Proffen, T.; Kwei, G. H.; Sarrao, J. L.; Shastri, S. D.; Kycia, S.

    2000-01-12

    The authors have measured atomic pair distribution functions (PDF) of La{sub 1{minus}x}Ca{sub x}MnO{sub 3} using high energy x-ray diffraction. This approach yields accurate PDFs with very high real-space resolution. It also avoids potential pitfalls from the more usual neutron measurements that magnetic scattering is present in the measurement, that the neutron scattering length of manganese is negative leading to partial cancellation of PDF peaks, and that inelasticity effects might distort the resulting PDF. They have used this to address the following questions which do not have a satisfactory answer: (1) What are the amplitudes and natures of the local Jahn-Teller and polaronic distortions in the CMR region. (2) Is the ground-state of the ferromagnetic metallic phase delocalized or polaronic. (3) As one moves away from the ground-state, by raising temperature or decreasing doping, towards the metal insulator transition, how does the state of the material evolve?

  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, Nicholas F. [Univ. of California, Berkeley, CA (United States)

    1995-09-01

    We investigated the surface bonding of various adsorbates (0, S, C2H3 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. The effect of thermal treatment on the atomic structure of PtCu core-shell nanoparticles in PtCu/C electrocatalysts

    Science.gov (United States)

    Shemet, D. B.; Pryadchenko, V. V.; Srabionyan, V. V.; Belenov, S. B.; Mikheykin, A. S.; Avakyan, L. A.; Guterman, V. E.; Bugaev, L. A.

    2017-05-01

    Nanocatalysts PtCu/C with core-shell structure of PtCu nanoparticles were synthesized by the method of sequential chemical reduction of Cu2+ and Pt(IV) in carbon suspension, prepared on the basis of ethylene glycol-water solvent. The characterization of atomic structure of “as prepared” PtCu nanoparticles and obtained after thermal treatment at 350 °C was performed by Pt L 3- and Cu K-edge extended X-ray absorption fine structure (EXAFS), complemented with TEM and XRD studies. The processing of EXAFS was performed by the technique that enables to reduce the effect of correlations among fitting parameters on the determined values of local structure parameters of the absorbing atoms, which have the nearest surrounding consisting both Pt and Cu atoms.

  9. Atomic force microscopy imaging and 3-D reconstructions of serial thin sections of a single cell and its interior structures

    Energy Technology Data Exchange (ETDEWEB)

    Chen Yong [College of Medicine, University of Illinois, Chicago, IL 60612 (United States) and Department of Chemistry, Jinan University, Shipai Street, Guangzhou 510632 (China)]. E-mail: drychen@uic.edu; Cai Jiye [Department of Chemistry, Jinan University, Shipai Street, Guangzhou 510632 (China)]. E-mail: tjycai@jnu.edu.cn; Zhao Tao [Department of Chemistry, Jinan University, Shipai Street, Guangzhou 510632 (China); Wang Chenxi [Department of Physics, Jinan University, Guangzhou 510632 (China); Dong Shuo [Department of BME, Capital University of Medical Sciences, Beijing (China); Luo Shuqian [Department of BME, Capital University of Medical Sciences, Beijing (China); Chen, Zheng W. [College of Medicine, University of Illinois, Chicago, IL 60612 (United States); Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States)

    2005-06-15

    The thin sectioning has been widely applied in electron microscopy (EM), and successfully used for an in situ observation of inner ultrastructure of cells. This powerful technique has recently been extended to the research field of atomic force microscopy (AFM). However, there have been no reports describing AFM imaging of serial thin sections and three-dimensional (3-D) reconstruction of cells and their inner structures. In the present study, we used AFM to scan serial thin sections approximately 60 nm thick of a mouse embryonic stem (ES) cell, and to observe the in situ inner ultrastructure including cell membrane, cytoplasm, mitochondria, nucleus membrane, and linear chromatin. The high-magnification AFM imaging of single mitochondria clearly demonstrated the outer membrane, inner boundary membrane and cristal membrane of mitochondria in the cellular compartment. Importantly, AFM imaging on six serial thin sections of a single mouse ES cell showed that mitochondria underwent sequential changes in the number, morphology and distribution. These nanoscale images allowed us to perform 3-D surface reconstruction of interested interior structures in cells. Based on the serial in situ images, 3-D models of morphological characteristics, numbers and distributions of interior structures of the single ES cells were validated and reconstructed. Our results suggest that the combined AFM and serial-thin-section technique is useful for the nanoscale imaging and 3-D reconstruction of single cells and their inner structures. This technique may facilitate studies of proliferating and differentiating stages of stem cells or somatic cells at a nanoscale.

  10. Evaluation of Structure and Assembly of Xyloglucan from Tamarind Seed (Tamarindus indica L.) with Atomic Force Microscopy.

    Science.gov (United States)

    Kozioł, Arkadiusz; Cybulska, Justyna; Pieczywek, Piotr M; Zdunek, Artur

    The role of xyloglucan (XG) in the cell wall of plants and its technological usability depends on several factors, pertaining to molecular structure. Therefore, the goal of this study was to evaluate the nano-structure and self-assembly of XG by atomic force microscopy (AFM). As the model, a non-modified xyloglucan from a tamarind seed (Tamarindus indica L.) was used. Samples were minimally processed, i.e., treated with low-power ultrasound and studied on the surface of mica in ambient butanol. AFM topographic images revealed rod-like nanomolecules of xyloglucan with a mean height of 2.3 ± 0.5 nm and mean length of 640 ± 360 nm. The AFM study also showed that XG chains possessed a helical structure with a period of 115.8 ± 29.2 nm. This study showed possible-bending of molecules with a mean angle of 127.8 ± 25.6°. The xyloglucan molecules were able to aggregate as cross-like and a parallel like assemblies, and possibly as rope-like structures. The self-assembled bundles of xyloglucan chains were often complexed at an angle of 114.2 ± 36.3°.

  11. 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.

  12. Facile synthesis of analogous graphene quantum dots with sp(2) hybridized carbon atom dominant structures and their photovoltaic application.

    Science.gov (United States)

    Huang, Zhengcheng; Shen, Yongtao; Li, Yu; Zheng, Wenjun; Xue, Yunjia; Qin, Chengqun; Zhang, Bo; Hao, Jingxiang; Feng, Wei

    2014-11-07

    Graphene quantum dot (GQD) is an emerging class of zero-dimensional nanocarbon material with many novel applications. It is of scientific importance to prepare GQDs with more perfect structures, that is, GQDs containing negligible oxygenous defects, for both optimizing their optical properties and helping in their photovoltaic applications. Herein, a new strategy for the facile preparation of "pristine" GQDs is reported. The method we presented is a combination of a bottom-up synthetic and a solvent-induced interface separation process, during which the target products with highly crystalline structure were selected by the organic solvent. The obtained organic soluble GQDs (O-GQDs) showed a significant difference in structure and composition compared with ordinary aqueous soluble GQDs, thus leading to a series of novel properties. Furthermore, O-GQDs were applied as electron-acceptors in a poly(3-hexylthiophene) (P3HT)-based organic photovoltaic device. The performance highlights that O-GQD has potential to be a novel electron-acceptor material due to the sp(2) hybridized carbon atom dominant structure and good solubility in organic solvents.

  13. Ab initio density functional theory study on the atomic and electronic structure of GaP/Si(001) heterointerfaces

    Science.gov (United States)

    Romanyuk, O.; Supplie, O.; Susi, T.; May, M. M.; Hannappel, T.

    2016-10-01

    The atomic and electronic band structures of GaP/Si(001) heterointerfaces were investigated by ab initio density functional theory calculations. Relative total energies of abrupt interfaces and mixed interfaces with Si substitutional sites within a few GaP layers were derived. It was found that Si diffusion into GaP layers above the first interface layer is energetically unfavorable. An interface with Si/Ga substitution sites in the first layer above the Si substrate is energetically the most stable one in thermodynamic equilibrium. The electronic band structure of the epitaxial GaP/Si(001) heterostructure terminated by the (2 ×2 ) surface reconstruction consists of surface and interface electronic states in the common band gap of two semiconductors. The dispersion of the states is anisotropic and differs for the abrupt Si-Ga, Si-P, and mixed interfaces. Ga 2 p , P 2 p , and Si 2 p core-level binding-energy shifts were computed for the abrupt and the lowest-energy heterointerface structures. Negative and positive core-level shifts due to heterovalent bonds at the interface are predicted for the abrupt Si-Ga and Si-P interfaces, respectively. The distinct features in the heterointerface electronic structure and in the core-level shifts open new perspectives in the experimental characterization of buried polar-on-nonpolar semiconductor heterointerfaces.

  14. Atomic force microscopy imaging and 3-D reconstructions of serial thin sections of a single cell and its interior structures

    Science.gov (United States)

    Chen, Yong; Cai, Jiye; Zhao, Tao; Wang, Chenxi; Dong, Shuo; Luo, Shuqian; Chen, Zheng W.

    2010-01-01

    The thin sectioning has been widely applied in electron microscopy (EM), and successfully used for an in situ observation of inner ultrastructure of cells. This powerful technique has recently been extended to the research field of atomic force microscopy (AFM). However, there have been no reports describing AFM imaging of serial thin sections and three-dimensional (3-D) reconstruction of cells and their inner structures. In the present study, we used AFM to scan serial thin sections approximately 60nm thick of a mouse embryonic stem (ES) cell, and to observe the in situ inner ultrastructure including cell membrane, cytoplasm, mitochondria, nucleus membrane, and linear chromatin. The high-magnification AFM imaging of single mitochondria clearly demonstrated the outer membrane, inner boundary membrane and cristal membrane of mitochondria in the cellular compartment. Importantly, AFM imaging on six serial thin sections of a single mouse ES cell showed that mitochondria underwent sequential changes in the number, morphology and distribution. These nanoscale images allowed us to perform 3-D surface reconstruction of interested interior structures in cells. Based on the serial in situ images, 3-D models of morphological characteristics, numbers and distributions of interior structures of the single ES cells were validated and reconstructed. Our results suggest that the combined AFM and serial-thin-section technique is useful for the nanoscale imaging and 3-D reconstruction of single cells and their inner structures. This technique may facilitate studies of proliferating and differentiating stages of stem cells or somatic cells at a nanoscale. PMID:15850704

  15. Characterization of ion-irradiation-induced nanodot structures on InP surfaces by atom probe tomography

    Energy Technology Data Exchange (ETDEWEB)

    Gnaser, Hubert, E-mail: gnaser@rhrk.uni-kl.de [Fachbereich Physik and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, D-67663 Kaiserslautern (Germany); Institut für Oberflächen- und Schichtanalytik GmbH (IFOS), Trippstadter Strasse 120, D-67663 Kaiserslautern (Germany); Radny, Tobias [Fachbereich Physik and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, D-67663 Kaiserslautern (Germany)

    2015-12-15

    Surfaces of InP were bombarded by 1.9 keV Ar{sup +} ions under normal incidence. The total accumulated ion fluence the samples were exposed to was varied from 1×10{sup 17} cm{sup −2} to 3×10{sup 18} cm{sup −2} and ion flux densities f of (0.4−2)×10{sup 14} cm{sup −2} s{sup −1} were used. Nanodot structures were found to evolve on the surface from these ion irradiations, their dimensions however, depend on the specific bombardment conditions. The resulting surface morphology was examined by atomic force microscopy (AFM). As a function of ion fluence, the mean radius, height, and spacing of the dots can be fitted by power-law dependences. In order to determine possible local compositional changes in these nanostructures induced by ion impact, selected samples were prepared for atom probe tomography (APT). The results indicate that by APT the composition of individual InP nanodots evolving under ion bombardment could be examined with atomic spatial resolution. At the InP surface, the values of the In/P concentration ratio are distinctly higher over a distance of ~1 nm and amount to 1.3–1.8. However, several aspects critical for the analyses were identified: (i) because of the small dimensions of these nanostructures a successful tip preparation proved very challenging. (ii) The elemental compositions obtained from APT were found to be influenced pronouncedly by the laser pulse energy; typically, low energies result in the correct stoichiometry whereas high ones lead to an inhomogeneous evaporation from the tips and deviations from the nominal composition. (iii) Depending again on the laser energy, a prolific emission of P{sub n} cluster ions was observed, with n≤11. - Highlights: • Nanodot formation on InP surfaces under Ar{sup +} ion irradiation. • Atom probe tomography of InP: influence of laser pulse energy. • Compositional analysis of individual nanodots with nm spatial resolution. • Abundant emission of P{sub n} cluster ions (n≤11).

  16. All-Atom Multiscale Molecular Dynamics Theory and Simulation of Self-Assembly, Energy Transfer and Structural Transition in Nanosystems

    Science.gov (United States)

    Espinosa Duran, John Michael

    The study of nanosystems and their emergent properties requires the development of multiscale computational models, theories and methods that preserve atomic and femtosecond resolution, to reveal details that cannot be resolved experimentally today. Considering this, three long time scale phenomena were studied using molecular dynamics and multiscale methods: self-assembly of organic molecules on graphite, energy transfer in nanosystems, and structural transition in vault nanoparticles. Molecular dynamics simulations of the self-assembly of alkoxybenzonitriles with different tail lengths on graphite were performed to learn about intermolecular interactions and phases exhibited by self-organized materials. This is important for the design of ordered self-assembled organic photovoltaic materials with greater efficiency than the disordered blends. Simulations revealed surface dynamical behaviors that cannot be resolved experimentally today due to the lack of spatiotemporal resolution. Atom-resolved structures predicted by simulations agreed with scanning tunneling microscopy images and unit cell measurements. Then, a multiscale theory based on the energy density as a field variable is developed to study energy transfer in nanoscale systems. For applications like photothermal microscopy or cancer phototherapy is required to understand how the energy is transferred to/from nanosystems. This multiscale theory could be applied in this context and here is tested for cubic nanoparticles immersed in water for energy being transferred to/from the nanoparticle. The theory predicts the energy transfer dynamics and reveals phenomena that cannot be described by current phenomenological theories. Finally, temperature-triggered structural transitions were revealed for vault nanoparticles using molecular dynamics and multiscale simulations. Vault is a football-shaped supramolecular assembly very distinct from the commonly observed icosahedral viruses. It has very promising

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

    Science.gov (United States)

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

    2015-01-01

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

  18. Theoretical and experimental investigation of the atomic and electronic structures at the 4 H -SiC(0001 )/SiO2 interface

    Science.gov (United States)

    Ono, Tomoya; Kirkham, Christopher James; Saito, Shoichiro; Oshima, Yoshifumi

    2017-09-01

    Density functional theory calculations are carried out to investigate the atomic and electronic structures of the 4 H -SiC(0001 )/SiO2 interface. We find two characteristic interface atomic structures in scanning transmission electron microscopy images: One is an interface in which the density of atoms at the first interfacial SiC bilayer is greater than that in the SiC substrate, while the other is an interface where the density of atoms at the first interfacial SiC bilayer is lower. Density functional theory calculations reveal that the difference in the scanning transmission electron microscopy images is a reflection of the atomic structures of these two interfaces. In addition, it has been reported that the floating states, which appear at the conduction band edge of a 4 H -SiC(0001 )/SiO2 interface, affect the electronic structure of the interface and cause marked scattering of the electrons flowing along the interface [S. Iwase, C. J. Kirkham, and T. Ono, Phys. Rev. B 95, 041302(R) (2017), 10.1103/PhysRevB.95.041302]. Interestingly, we find that the floating states do not appear at the conduction band edge of one of the two interfaces. These results provide physical insights into understanding and controlling the electronic structure and carrier mobility of electronic devices using wide-band-gap semiconductors.

  19. 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.

  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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-06-24

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

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

    NARCIS (Netherlands)

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

    This paper presents the results of investigations of Ag-ZnO interfaces, produced by internal oxidation of an Ag-Zn alloy. ZnO precipitates with the wurtzite structure were found exhibiting mainly one orientation relation with the Ag matrix. However, closely related ORs were found, rotated by small

  3. Atomic Structure Studies of Semiconductor-Electrolyte, Metal and Vacuum Interfaces.

    Science.gov (United States)

    1982-01-12

    Channeling Studies of Metal Interaction with Silicon R. Haight, T. Itoh, T. Narusawa, W.M. Gibson and A. Hiraki Epitaxial Growth of Germanium on Si(lll...Stages of Metal-Silicide Formation (Invited Paper) A. Hiraki , T. Narusawa and W.M. Gibson 44 American Physical Society, Dallas, TX, March 1982 Structure

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

    NARCIS (Netherlands)

    Snijders, P.C.

    2006-01-01

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

  5. Structural information, resolution, and noise in high-resolution atomic force microscopy topographs.

    Science.gov (United States)

    Fechner, Peter; Boudier, Thomas; Mangenot, Stéphanie; Jaroslawski, Szymon; Sturgis, James N; Scheuring, Simon

    2009-05-06

    AFM has developed into a powerful tool in structural biology, providing topographs of proteins under close-to-native conditions and featuring an outstanding signal/noise ratio. However, the imaging mechanism exhibits particularities: fast and slow scan axis represent two independent image acquisition axes. Additionally, unknown tip geometry and tip-sample interaction render the contrast transfer function nondefinable. Hence, the interpretation of AFM topographs remained difficult. How can noise and distortions present in AFM images be quantified? How does the number of molecule topographs merged influence the structural information provided by averages? What is the resolution of topographs? Here, we find that in high-resolution AFM topographs, many molecule images are only slightly disturbed by noise, distortions, and tip-sample interactions. To identify these high-quality particles, we propose a selection criterion based on the internal symmetry of the imaged protein. We introduce a novel feature-based resolution analysis and show that AFM topographs of different proteins contain structural information beginning at different resolution thresholds: 10 A (AqpZ), 12 A (AQP0), 13 A (AQP2), and 20 A (light-harvesting-complex-2). Importantly, we highlight that the best single-molecule images are more accurate molecular representations than ensemble averages, because averaging downsizes the z-dimension and "blurs" structural details.

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

    DEFF Research Database (Denmark)

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

    1999-01-01

    The dissolution at 400 degrees C of an antimony layer deposited at room temperature on a Cu(111) substrate leads to a surface alloy with a p(root 3x root 3)R 30 degrees x 30 degrees superstructure and a Sb composition of 1/3.We present here a structural study of this Sb-Cu compound by surface X...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-25

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

  8. Exploring electronic structure of one-atom thick polycrystalline graphene films: A nano angle resolved photoemission study

    Science.gov (United States)

    Avila, José; Razado, Ivy; Lorcy, Stéphane; Fleurier, Romain; Pichonat, Emmanuelle; Vignaud, Dominique; Wallart, Xavier; Asensio, María C.

    2013-01-01

    The ability to produce large, continuous and defect free films of graphene is presently a major challenge for multiple applications. Even though the scalability of graphene films is closely associated to a manifest polycrystalline character, only a few numbers of experiments have explored so far the electronic structure down to single graphene grains. Here we report a high resolution angle and lateral resolved photoelectron spectroscopy (nano-ARPES) study of one-atom thick graphene films on thin copper foils synthesized by chemical vapor deposition. Our results show the robustness of the Dirac relativistic-like electronic spectrum as a function of the size, shape and orientation of the single-crystal pristine grains in the graphene films investigated. Moreover, by mapping grain by grain the electronic dynamics of this unique Dirac system, we show that the single-grain gap-size is 80% smaller than the multi-grain gap recently reported by classical ARPES. PMID:23942471

  9. Local Atomic Structure and Superconductivity of NEODYMIUM(2-X) Cerium(x) COPPEROXIDE(4-Y): a Pair-Distribution Study

    Science.gov (United States)

    Billinge, Simon John Laird

    1992-01-01

    We have carried out a detailed Pair Distribution Function Analysis of powder diffraction data from samples of Nd_{2-x}Ce _{x}CuO _{4-y} with x = 0.165 and x = 0.2. The former is superconducting with an almost full Meissner fraction, and T_{c} = 22K. The latter is isostructural, but exhibits no superconductivity. A "real space refinement" of the PDF has been carried out to extract quantitative information about the local atomic structure of the material. Two main observations were made. The local structure is significantly different from the average crystal structure (T ^' structure) of this material. The differences are explained by displacements of oxygen. The second result was that the local structure changes with the appearance of superconductivity. This was the first observation of such a change in this material. These changes are explained by an increase in the degree of local order of the above mentioned oxygen displacements. The displacements are inhomogeneously distributed throughout the sample and interspersed with regions of undistorted crystal. We argue that this is best explained as the direct observation of the presence of polarons, or bipolarons in the structure. We speculate that the driving force that could give rise to these polarons is a strong coupling of the lattice with the O p_{z} states which lie just below the Fermi surface in the undistorted material. The effective mass of the (bi)polarons, calculated using values estimated from the experiment, was such as to give the bipolarons a condensation temperature of 17K. This is the same order of magnitude as the observed T _{c}. Thus it is plausible that the superconductivity is due to a bipolaronic condensation. The density of polarons is too small to account for all of the chemically doped carriers. Thus it appears that they form the minority of carriers. They coexist with a majority of high mobility, wide band, electronic states, of sigma character.

  10. The structure and function of cell membranes studied by atomic force microscopy.

    Science.gov (United States)

    Shi, Yan; Cai, Mingjun; Zhou, Lulu; Wang, Hongda

    2018-01-01

    The cell membrane, involved in almost all communications of cells and surrounding matrix, is one of the most complicated components of cells. Lack of suitable methods for the detection of cell membranes in vivo has sparked debates on the biochemical composition and structure of cell membranes over half a century. The development of single molecule techniques, such as AFM, SMFS, and TREC, provides a versatile platform for imaging and manipulating cell membranes in biological relevant environments. Here, we discuss the latest developments in AFM and the progress made in cell membrane research. In particular, we highlight novel structure models and dynamic processes, including the mechanical properties of the cell membranes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. From atomic structures to neuronal functions of g protein-coupled receptors.

    Science.gov (United States)

    Palczewski, Krzysztof; Orban, Tivadar

    2013-07-08

    G protein-coupled receptors (GPCRs) are essential mediators of signal transduction, neurotransmission, ion channel regulation, and other cellular events. GPCRs are activated by diverse stimuli, including light, enzymatic processing of their N-termini, and binding of proteins, peptides, or small molecules such as neurotransmitters. GPCR dysfunction caused by receptor mutations and environmental challenges contributes to many neurological diseases. Moreover, modern genetic technology has helped identify a rich array of mono- and multigenic defects in humans and animal models that connect such receptor dysfunction with disease affecting neuronal function. The visual system is especially suited to investigate GPCR structure and function because advanced imaging techniques permit structural studies of photoreceptor neurons at both macro and molecular levels that, together with biochemical and physiological assessment in animal models, provide a more complete understanding of GPCR signaling.

  12. High-speed atomic force microscopy reveals structural dynamics of α -synuclein monomers and dimers

    Science.gov (United States)

    Zhang, Yuliang; Hashemi, Mohtadin; Lv, Zhengjian; Williams, Benfeard; Popov, Konstantin I.; Dokholyan, Nikolay V.; Lyubchenko, Yuri L.

    2018-03-01

    α-Synuclein (α-syn) is the major component of the intraneuronal inclusions called Lewy bodies, which are the pathological hallmark of Parkinson's disease. α-Syn is capable of self-assembly into many different species, such as soluble oligomers and fibrils. Even though attempts to resolve the structures of the protein have been made, detailed understanding about the structures and their relationship with the different aggregation steps is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. Here we report the structural flexibility of α-syn monomers and dimers in an aqueous solution environment as probed by single-molecule time-lapse high-speed AFM. In addition, we present the molecular basis for the structural transitions using discrete molecular dynamics (DMD) simulations. α-Syn monomers assume a globular conformation, which is capable of forming tail-like protrusions over dozens of seconds. Importantly, a globular monomer can adopt fully extended conformations. Dimers, on the other hand, are less dynamic and show a dumbbell conformation that experiences morphological changes over time. DMD simulations revealed that the α-syn monomer consists of several tightly packed small helices. The tail-like protrusions are also helical with a small β-sheet, acting as a "hinge". Monomers within dimers have a large interfacial interaction area and are stabilized by interactions in the non-amyloid central (NAC) regions. Furthermore, the dimer NAC-region of each α-syn monomer forms a β-rich segment. Moreover, NAC-regions are located in the hydrophobic core of the dimer.

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

    Energy Technology Data Exchange (ETDEWEB)

    Tao, Meng; Zhang, Qiming

    2013-11-24

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

  14. Atomic-resolution structural information from scattering experiments on macromolecules in solution.

    Science.gov (United States)

    Köfinger, Jürgen; Hummer, Gerhard

    2013-05-01

    The pair-distance distribution function (PDDF) contains all structural information probed in an elastic scattering experiment of macromolecular solutions. However, in small-angle x-ray scattering (SAXS) or small-angle neutron scattering (SANS) experiments only their Fourier transform is measured over a restricted range of scattering angles. We therefore developed a mathematically simple and computationally efficient method to calculate the PDDFs as well as accurate scattering intensities from molecular dynamics simulations. The calculated solution scattering intensities are in excellent agreement with SAXS and wide-angle x-ray scattering (WAXS) experiments for a series of proteins. The corresponding PDDFs are remarkably rich in features reporting on the detailed protein structure. Using an inverse Fourier transform method, most of these features can be recovered if scattering intensities are measured up to a momentum transfer of q≈2-3Å(-1). Our results establish that high-precision solution scattering experiments utilizing x-ray free-electron lasers and third generation synchrotron sources can resolve subnanometer structural detail, well beyond size, shape, and fold.

  15. Control of triplet state generation in heavy atom-free BODIPY-anthracene dyads by media polarity and structural factors

    KAUST Repository

    Filatov, Mikhail A.

    2018-02-12

    A family of heavy atom-free BODIPY-anthracene dyads (BADs) exhibiting triplet excited state formation from charge-transfer states is reported. Four types of BODIPY scaffolds, different in the alkyl substitution pattern, and four anthracene derivatives have been used to access BADs. The fluorescence and intersystem crossing (ISC) in these dyads depend on donor-acceptor couplings and can be accurately controlled by the substitution or media polarity. Under conditions that do not allow charge transfer (CT), the dyads exhibit fluorescence with high quantum yields. Formation of charge-transfer states triggers ISC and the formation of long-lived triplet excited states in the dyads. The excited state properties were studied by steady-state techniques and ultrafast pump-probe spectroscopy to determine the parameters of the observed processes. Structural information for various BADs was derived from single crystal X-ray structure determinations alongside DFT molecular geometry optimization, revealing the effects of mutual orientation of subunits on the photophysical properties. The calculations showed that alkyl substituents on the BODIPY destabilize CT states in the dyads, thus controlling the charge transfer between the subunits. The effect of the dyad structure on the ISC efficiency was considered at M06-2X level of theory and a correlation between mutual orientation of the subunits and the energy gap between singlet and triplet CT states was studied using multireference CASSCF method.

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

    Science.gov (United States)

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

    2006-02-28

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

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

    Science.gov (United States)

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

    2006-02-01

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

  18. Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin.

    Science.gov (United States)

    Hagiwara, Yoshinori; Wada, Kei; Irikawa, Teppei; Sato, Hideaki; Unno, Masaki; Yamamoto, Ken; Fukuyama, Keiichi; Sugishima, Masakazu

    2016-10-01

    Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the reduction of biliverdin (BV) to produce phycocyanobilin, a linear tetrapyrrole pigment used for light harvesting and light sensing. Spectroscopic and HPLC analyses inidicate that BV bound to the I86D mutant of PcyA is fully protonated (BVH+ ) and can accept an electron, but I86D is unable to donate protons for the reduction; therefore, compared to the wild-type PcyA, the I86D mutant stabilizes BVH+ . To elucidate the structural basis of the I86D mutation, we determined the atomic-resolution structure of the I86D-BVH+ complex and the protonation states of the essential residues Asp105 and Glu76 in PcyA. Our study revealed that Asp105 adopted a fixed conformation in the I86D mutant, although it had dual conformations in wild-type PcyA which reflected the protonation states of BV. Taken together with biochemical/spectroscopic results, our analysis of the I86D-BVH+ structure supports the hypothesis that flexibility of Asp105 is essential for the catalytic activity of PcyA. © 2016 Federation of European Biochemical Societies.

  19. Atomic and electronic structure of a copper/graphene interface as prepared and 1.5 years after

    Science.gov (United States)

    Boukhvalov, D. W.; Bazylewski, P. F.; Kukharenko, A. I.; Zhidkov, I. S.; Ponosov, Yu. S.; Kurmaev, E. Z.; Cholakh, S. O.; Lee, Y. H.; Chang, G. S.

    2017-12-01

    We report the results of X-ray spectroscopy and Raman measurements of as-prepared graphene on a high quality copper surface and the same materials after 1.5 years under different conditions (ambient and low humidity). The obtained results were compared with density functional theory calculations of the formation energies and electronic structures of various structural defects in graphene/Cu interfaces. For evaluation of the stability of the carbon cover, we propose a two-step model. The first step is oxidation of the graphene, and the second is perforation of graphene with the removal of carbon atoms as part of the carbon dioxide molecule. Results of the modeling and experimental measurements provide evidence that graphene grown on high-quality copper substrate becomes robust and stable in time (1.5 years). However, the stability of this interface depends on the quality of the graphene and the number of native defects in the graphene and substrate. The effect of the presence of a metallic substrate with defects on the stability and electronic structure of graphene is also discussed

  20. Atomic scale insight into the amorphous structure of Cu doped GeTe phase-change material

    Science.gov (United States)

    Zhang, Linchuan; Sa, Baisheng; Zhou, Jian; Song, Zhitang; Sun, Zhimei

    2014-10-01

    GeTe shows promising application as a recording material for phase-change nonvolatile memory due to its fast crystallization speed and extraordinary amorphous stability. To further improve the performance of GeTe, various transition metals, such as copper, have been doped in GeTe in recent works. However, the effect of the doped transition metals on the stability of amorphous GeTe is not known. Here, we shed light on this problem for the system of Cu doped GeTe by means of ab initio molecular dynamics calculations. Our results show that the doped Cu atoms tend to agglomerate in amorphous GeTe. Further, base on analyzing the pair correlation functions, coordination numbers and bond angle distributions, remarkable changes in the local structure of amorphous GeTe induced by Cu are obviously seen. The present work may provide some clues for understanding the effect of early transition metals on the local structure of amorphous phase-change compounds, and hence should be helpful for optimizing the structure and performance of phase-change materials by doping transition metals.

  1. Effect of Alkali Metal Atoms Doping on Structural and Nonlinear Optical Properties of the Gold-Germanium Bimetallic Clusters

    Directory of Open Access Journals (Sweden)

    Xiaojun Li

    2017-07-01

    Full Text Available A new series of alkali-based complexes, AM@GenAu (AM = Li, Na, and K, have been theoretically designed and investigated by means of the density functional theory calculations. The geometric structures and electronic properties of the species are systematically analyzed. The adsorption of alkali metals maintains the structural framework of the gold-germanium bimetallic clusters, and the alkali metals prefer energetically to be attached on clusters’ surfaces or edges. The high chemical stability of Li@Ge12Au is revealed by the spherical aromaticity, the hybridization between the Ge atoms and Au-4d states, and delocalized multi-center bonds, as well as large binding energies. The static first hyperpolarizability (βtot is related to the cluster size and geometric structure, and the AM@GenAu (AM = Na and K clusters exhibit the much larger βtot values up to 13050 a.u., which are considerable to establish their strong nonlinear optical (NLO behaviors. We hope that this study will promote further application of alkali metals-adsorbed germanium-based semiconductor materials, serving for the design of remarkable and tunable NLO materials.

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

    Science.gov (United States)

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

    2016-03-22

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

  3. Atomic scale insight into the amorphous structure of Cu doped GeTe phase-change material

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Linchuan; Sa, Baisheng [Department of Materials Science and Engineering, College of Materials, Xiamen University, Xiamen 361005 (China); Zhou, Jian; Sun, Zhimei, E-mail: zmsun@buaa.edu.cn [School of Materials Science and Engineering, and Center for Integrated Computational Materials Engineering, International Research Institute for Multidisciplinary Science, Beihang University, Beijing 100191 (China); Song, Zhitang [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Micro-System and Information Technology, CAS, 200050 Shanghai (China)

    2014-10-21

    GeTe shows promising application as a recording material for phase-change nonvolatile memory due to its fast crystallization speed and extraordinary amorphous stability. To further improve the performance of GeTe, various transition metals, such as copper, have been doped in GeTe in recent works. However, the effect of the doped transition metals on the stability of amorphous GeTe is not known. Here, we shed light on this problem for the system of Cu doped GeTe by means of ab initio molecular dynamics calculations. Our results show that the doped Cu atoms tend to agglomerate in amorphous GeTe. Further, base on analyzing the pair correlation functions, coordination numbers and bond angle distributions, remarkable changes in the local structure of amorphous GeTe induced by Cu are obviously seen. The present work may provide some clues for understanding the effect of early transition metals on the local structure of amorphous phase-change compounds, and hence should be helpful for optimizing the structure and performance of phase-change materials by doping transition metals.

  4. Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1

    Energy Technology Data Exchange (ETDEWEB)

    White, Mark Andrew, E-mail: white@xray.utmb.edu [Sealy Center for Structural and Molecular Biophysics, UTMB Galveston, TX 77555 (United States); Department of Biochemistry and Molecular Biology, UTMB Galveston, TX 77555 (United States); Mast, Natalia [Department of Pharmacology and Toxicology, UTMB Galveston, TX 77555 (United States); Bjorkhem, Ingemar [Department of Clinical Chemistry, Karolinska Institute, S-141 88 Huddinge (Sweden); Johnson, Eric F. [Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037 (United States); Stout, C. David [Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 (United States); Pikuleva, Irina A. [Department of Pharmacology and Toxicology, UTMB Galveston, TX 77555 (United States); Sealy Center for Structural and Molecular Biophysics, UTMB Galveston, TX 77555 (United States)

    2008-05-01

    Crystallization and analysis of the MIRAS heavy-atom structure solution of human cytochrome P450 46A1 using NaI and CsCl quick soaks. Human cytochrome P450 46A1 (CYP46A1) is one of the key enzymes in cholesterol homeostasis in the brain. The crystallization and heavy-atom structure solution of an active truncated CYP46A1 in complex with the high-affinity substrate analogue cholesterol-3-sulfate (CH-3S) is reported. The 2.6 Å structure of CYP46A1–CH-3S was solved using both anion and cation heavy-atom salts. In addition to the native anomalous signal from the haem iron, an NaI anion halide salt derivative and a complementary CsCl alkali-metal cation salt derivative were used. The general implications of the use of halide and alkali-metal quick soaks are discussed. The importance of using isoionic strength buffers, the titration of heavy-atom salts into different ionic species and the role of concentration are considered. It was observed that cation/anion-binding sites will occasionally overlap, which could negatively impact upon mixed RbBr soaks used for multiple anomalous scatterer MAD (MMAD). The use of complementary cation and anion heavy-atom salt derivatives is a convenient and powerful tool for MIR(AS) structure solution.

  5. Local atomic structure of CeO{sub 2}/ZrO{sub 2} catalyst support determined by pulsed neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Dmowski, W.; Louca, D.; Egami, T. [Univ. of Pennsylvania, Philadelphia, PA (United States); Brezny, R. [W.R. Grace & Co.-Conn, Columbia, MD (United States)

    1997-12-31

    The capability of CeO{sub 2}/ZrO{sub 2} mixture as a catalyst support in automobile exhaust three-way catalytic converters depends critically upon processing conditions of the mixture. In order to understand this dependence the atomic structure of various forms of CeO{sub 2}/ZrO{sub 2} fine powder was studied using pulsed neutron scattering and the atomic pair-distribution analysis. The results indicate that a sample with the highest oxygen storage capacity has an inhomogeneous structure, and is segregated into two nano-phases with severe local lattice distortion. It is suggested that distortion in the local atomic structure, particularly at the interfaces, facilitate the oxygen transport at the oxide/metal interface.

  6. Hierarchical, Dual-Scale Structures of Atomically Thin MoS2 for Tunable Wetting.

    Science.gov (United States)

    Choi, Jonghyun; Mun, Jihun; Wang, Michael Cai; Ashraf, Ali; Kang, Sang-Woo; Nam, SungWoo

    2017-03-08

    Molybdenum disulfide (MoS2), a well-known solid lubricant for low friction surface coatings, has recently drawn attention as an analogue two-dimensional (2D) material beyond graphene. When patterned to produce vertically grown, nanoflower-structures, MoS2 shows promise as a functional material for hydrogen evolution catalysis systems, electrodes for alkali metal-ion batteries, and field-emission arrays. Whereas the wettability of graphene has been substantially investigated, that of MoS2 structures, especially nanoflowers, has remained relatively unexplored despite MoS2 nanoflower's potential in future applications. Here, we demonstrate that the wettability of MoS2 can be controlled by multiscale modulation of surface roughness through (1) tuning of the nanoflower structures by chemical vapor deposition synthesis and (2) tuning of microscale topography via mechanical strain. This multiscale modulation offers broadened tunability (80-155°) compared to single-scale tuning (90-130°). In addition, surface adhesion, determined from contact angle hysteresis (CAH), can also be tuned by multiscale surface roughness modulation, where the CAH is changed in range of 20-40°. Finally, the wettability of crumpled MoS2 nanoflowers can be dynamically and reversibly controlled through applied strain (∼115-150° with 0-200% strain), and remains robust over 1000 strain cycles. These studies on the tunable wettability of MoS2 will contribute to future MoS2-based applications, such as tunable wettability coatings for desalination and hydrogen evolution.

  7. The atomic structure of low-index surfaces of the intermetallic compound InPd

    Science.gov (United States)

    McGuirk, G. M.; Ledieu, J.; Gaudry, É.; de Weerd, M.-C.; Hahne, M.; Gille, P.; Ivarsson, D. C. A.; Armbrüster, M.; Ardini, J.; Held, G.; Maccherozzi, F.; Bayer, A.; Lowe, M.; Pussi, K.; Diehl, R. D.; Fournée, V.

    2015-08-01

    The intermetallic compound InPd (CsCl type of crystal structure with a broad compositional range) is considered as a candidate catalyst for the steam reforming of methanol. Single crystals of this phase have been grown to study the structure of its three low-index surfaces under ultra-high vacuum conditions, using low energy electron diffraction (LEED), X-ray photoemission spectroscopy (XPS), and scanning tunneling microscopy (STM). During surface preparation, preferential sputtering leads to a depletion of In within the top few layers for all three surfaces. The near-surface regions remain slightly Pd-rich until annealing to ˜580 K. A transition occurs between 580 and 660 K where In segregates towards the surface and the near-surface regions become slightly In-rich above ˜660 K. This transition is accompanied by a sharpening of LEED patterns and formation of flat step-terrace morphology, as observed by STM. Several superstructures have been identified for the different surfaces associated with this process. Annealing to higher temperatures (≥750 K) leads to faceting via thermal etching as shown for the (110) surface, with a bulk In composition close to the In-rich limit of the existence domain of the cubic phase. The Pd-rich InPd(111) is found to be consistent with a Pd-terminated bulk truncation model as shown by dynamical LEED analysis while, after annealing at higher temperature, the In-rich InPd(111) is consistent with an In-terminated bulk truncation, in agreement with density functional theory (DFT) calculations of the relative surface energies. More complex surface structures are observed for the (100) surface. Additionally, individual grains of a polycrystalline sample are characterized by micro-spot XPS and LEED as well as low-energy electron microscopy. Results from both individual grains and "global" measurements are interpreted based on comparison to our single crystals findings, DFT calculations and previous literature.

  8. The atomic structure of low-index surfaces of the intermetallic compound InPd

    Energy Technology Data Exchange (ETDEWEB)

    McGuirk, G. M.; Ledieu, J.; Gaudry, É.; Weerd, M.-C.; Fournée, V. de, E-mail: vincent.fournee@univ-lorraine.fr [Institut Jean Lamour (UMR 7198 CNRS-Université de Lorraine), Parc de Saurupt, F-54011 Nancy Cedex (France); Hahne, M.; Gille, P. [Department of Earth and Environmental Sciences, Crystallography Section, Ludwig-Maximilians-Universität München, Theresienstrasse 41, D-80333 München (Germany); Ivarsson, D. C. A.; Armbrüster, M. [Faculty of Natural Sciences, Institute of Chemistry, Materials for Innovative Energy Concepts, Technische Universität Chemnitz, D-09107 Chemnitz (Germany); Ardini, J.; Held, G. [Department of Chemistry, University of Reading, Reading RG6 6AD (United Kingdom); Diamond Light Source Ltd, Didcot OX11 0DE (United Kingdom); Maccherozzi, F. [Diamond Light Source Ltd, Didcot OX11 0DE (United Kingdom); Bayer, A. [Lehrstuhl für Physikalische Chemie II, Universität Erlangen-Nürnberg, Egerlandstraße 3, D-91058 Erlangen (Germany); Lowe, M. [Surface Science Research Centre and Department of Physics, The University of Liverpool, Liverpool L69 3BX (United Kingdom); Pussi, K. [Department of Mathematics and Physics, Lappeenranta University of Technology, P.O. Box 20, FIN-53851 Lappeenranta (Finland); Diehl, R. D. [Department of Physics, Penn State University, University Park, Pennsylvania 16802 (United States)

    2015-08-21

    The intermetallic compound InPd (CsCl type of crystal structure with a broad compositional range) is considered as a candidate catalyst for the steam reforming of methanol. Single crystals of this phase have been grown to study the structure of its three low-index surfaces under ultra-high vacuum conditions, using low energy electron diffraction (LEED), X-ray photoemission spectroscopy (XPS), and scanning tunneling microscopy (STM). During surface preparation, preferential sputtering leads to a depletion of In within the top few layers for all three surfaces. The near-surface regions remain slightly Pd-rich until annealing to ∼580 K. A transition occurs between 580 and 660 K where In segregates towards the surface and the near-surface regions become slightly In-rich above ∼660 K. This transition is accompanied by a sharpening of LEED patterns and formation of flat step-terrace morphology, as observed by STM. Several superstructures have been identified for the different surfaces associated with this process. Annealing to higher temperatures (≥750 K) leads to faceting via thermal etching as shown for the (110) surface, with a bulk In composition close to the In-rich limit of the existence domain of the cubic phase. The Pd-rich InPd(111) is found to be consistent with a Pd-terminated bulk truncation model as shown by dynamical LEED analysis while, after annealing at higher temperature, the In-rich InPd(111) is consistent with an In-terminated bulk truncation, in agreement with density functional theory (DFT) calculations of the relative surface energies. More complex surface structures are observed for the (100) surface. Additionally, individual grains of a polycrystalline sample are characterized by micro-spot XPS and LEED as well as low-energy electron microscopy. Results from both individual grains and “global” measurements are interpreted based on comparison to our single crystals findings, DFT calculations and previous literature.

  9. Atomic force microscopy studies on circular DNA structural changes by vincristine and aspirin.

    Science.gov (United States)

    Xiao, Zhongdang; Cao, Lili; Zhu, Dan; Lu, Zuhong

    2011-01-01

    In this chapter, we have presented materials and methods to study the interaction between DNA and small molecule drugs by AFM. The detailed AFM imaging of the circular DNA after incubation with -various concentrations of vincristine and aspirin have been demonstrated. The immobilization of DNA fragments on mica surface as well as the force between tip and sample plays an important role for successful imaging of DNA-drug complexes. How to quantitatively describe the conformations and structures of circular DNA molecules and their changes is also introduced. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

  10. Atomic and electronic structure of free niobium nanoclusters: Simulation of the M{sub 4,5}-XANES spectrum of Nb{sub 13}{sup +}

    Energy Technology Data Exchange (ETDEWEB)

    Kravtsova, Antonina N., E-mail: akravtsova@sfedu.ru [Research Center for Nanoscale Structure of Matter, Southern Federal University, Sorge str. 5, 344090 Rostov-on-Don (Russian Federation); Lomachenko, Kirill A. [Research Center for Nanoscale Structure of Matter, Southern Federal University, Sorge str. 5, 344090 Rostov-on-Don (Russian Federation); Department of Chemistry and NIS Centre of Excellence, University of Turin, Via P. Giuria 7, 10125 Turin (Italy); Soldatov, Alexander V., E-mail: soldatov@sfedu.ru [Research Center for Nanoscale Structure of Matter, Southern Federal University, Sorge str. 5, 344090 Rostov-on-Don (Russian Federation); Meyer, Jennifer; Niedner-Schatteburg, Gereon [Technische Universität Kaiserslautern, Fachbereich Chemie und Forschungszentrum OPTIMAS, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern (Germany); Peredkov, Sergey [Helmholtz-Zentrum Berlin für Materialien und Energie, Wilhelm-Conrad-Röntgen-Campus Adlershof, Elektronenspeicherring BESSY II, Albert-Einstein-Straße 15, Berlin (Germany); Eberhardt, Wolfgang [Technische Universität Berlin, IOAP, Straße des 17. Juni 135, 10623 Berlin (Germany); Neeb, Matthias, E-mail: matthias.neeb@helmholtz-berlin.de [Helmholtz-Zentrum Berlin für Materialien und Energie, Wilhelm-Conrad-Röntgen-Campus Adlershof, Elektronenspeicherring BESSY II, Albert-Einstein-Straße 15, Berlin (Germany)

    2014-08-15

    Highlights: • M{sub 4,5}-XANES spectra have been calculated for several structural models of free Nb{sub 13}{sup +} cluster. • Theoretical M{sub 4,5}-XANES have been compared with the experimental spectrum of free Nb{sub 13}{sup +}. • Icosahedral structure of Nb{sub 13}{sup +} shows better agreement with experiment than the “amorphous” one. • Distance between Nb atoms in the icosahedral cluster is distinctly reduced as compared to the bulk phase. - Abstract: The atomic and electronic structure of free niobium nanoclusters has been studied on the basis of X-ray absorption near-edge structure (XANES) spectroscopy and density functional theory. M{sub 4,5}-XANES spectra have been calculated for several structural models of the 13-atomic niobium cluster. The calculations have been done on the basis of both full multiple scattering theory within the muffin-tin approximation for a potential and full-potential finite difference method. The comparison of the experimental M{sub 4,5}-edge XANES spectrum (Peredkov et al., J. Electron Spectros. Relat. Phenomena 184 (2011) 113–118) with the simulated X-ray absorption spectra of Nb{sub 13}{sup +} hints to a highly-symmetric icosahedral structure of the cluster. An internuclear distance of 2.2 ± 0.1 Å between neighboring “surface” atoms of the icosahedron and 2.09 Å between the central “bulk” atom and “surface” atoms, respectively, has been found upon comparison of the experimental and theoretical XANES spectra.

  11. Characterizing low-coordinated atoms at the periphery of MgO-supported Au islands using scanning tunneling microscopy and electronic structure calculations

    Science.gov (United States)

    Lin, Xiao; Nilius, Niklas; Sterrer, Martin; Koskinen, Pekka; Häkkinen, Hannu; Freund, Hans-Joachim

    2010-04-01

    The perimeter of oxide-supported metal particles is suggested to be of pivotal importance for various catalytic processes. To elucidate the underlying effects, the electronic properties of edge and corner atoms of planar Au clusters on MgO/Ag(001) thin films have been analyzed with scanning tunneling microscopy and electronic structure calculations. The low-coordinated perimeter atoms are characterized by a high density of s -derived states at the Fermi level. Those states accommodate transfer electrons from the MgO/Ag substrate, which render the perimeter atoms negatively charged. In contrast, the inner atoms of the island are not affected by the charge transfer and remain neutral. This combination of charge accumulation and high state-density explains the specific relevance of the cluster perimeter in adsorption and reaction processes.

  12. Cohesion strength and atomic structure of W-Cu graded interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Liang, C.P.; Fan, J.L.; Gong, H.R., E-mail: gonghr@csu.edu.cn

    2017-04-15

    W-Cu graded interface is a solution to big differences of properties between W and Cu, while the number and composition of graded layers in the literature are quite different. The present first principles calculation reveals that W-rich graded interfaces possess higher strength and lower interface energy than Cu-rich counterparts. It shows that the differences of thermal expansion and Young’s modulus between overlayer and substrate are decisive factors in the design of Cu-rich and W-rich graded interfaces, respectively. A graded structure of W{sub 8}Cu{sub 1}/W{sub 7}Cu{sub 2}/W{sub 6}Cu{sub 3}/Cu{sub 6}W{sub 3}/Cu{sub 8}W{sub 1} is therefore suggested theoretically.

  13. N-linear algebraic maps for chemical structure codification: a suitable generalization for atom-pair approaches?

    Science.gov (United States)

    Garcia-Jacas, Cesar R; Marrero-Ponce, Yovani; Barigye, Stephen J; Valdes-Martini, Jose R; Rivera-Borroto, Oscar M; Olivero-Verbel, Jesus

    2014-01-01

    The present manuscript introduces, for the first time, a novel 3D-QSAR alignment free method (QuBiLS-MIDAS) based on tensor concepts through the use of the three-linear and four-linear algebraic forms as specific cases of n-linear maps. To this end, the k(th) three-tuple and four-tuple spatial-(dis)similarity matrices are defined, as tensors of order 3 and 4, respectively, to represent 3Dinformation among "three and four" atoms of the molecular structures. Several measures (multi-metrics) to establish (dis)-similarity relations among "three and four" atoms are discussed, as well as, normalization schemes proposed for the n-tuple spatial-(dis)similarity matrices based on the simple-stochastic and mutual probability algebraic transformations. To consider specific interactions among atoms, both for the global and local indices, n-tuple path and length cut-off constraints are introduced. This algebraic scaffold can also be seen as a generalization of the vector-matrix-vector multiplication procedure (which is a matrix representation of the traditional linear, quadratic and bilinear forms) for the calculation of molecular descriptors and is thus a new theoretical approach with a methodological contribution. A variability analysis based on Shannon's entropy reveals that the best distributions are achieved with the ternary and quaternary measures corresponding to the bond and dihedral angles. In addition, the proposed indices have superior entropy behavior than the descriptors calculated by other programs used in chemo-informatics studies, such as, DRAGON, PADEL, Mold2, and so on. A principal component analysis shows that the novel 3D n-tuple indices codify the same information captured by the DRAGON 3D-indices, as well as, information not codified by the latter. A QSAR study to obtain deeper criteria on the contribution of the novel molecular parameters was performed for the binding affinity to the corticosteroid-binding globulin, using Cramer's steroid database. The

  14. Widespread Perturbation of Function, Structure, and Dynamics by a Conservative Single-Atom Substitution in Thymidylate Synthase.

    Science.gov (United States)

    Sapienza, Paul J; Lee, Andrew L

    2016-10-11

    Thymidylate synthase (TSase) is responsible for synthesizing the sole de novo source of dTMP in all organisms. TSase is a drug target, and as such, it has been well studied in terms of both structure and reaction mechanism. Cysteine 146 in Escherichia coli TSase is universally conserved because it serves as the nucleophile in the enzyme mechanism. Here we use the C146S mutation to probe the role of the sulfur atom in early events in the catalytic cycle beyond serving as the nucleophile. Surprisingly, the single-atom substitution severely decreases substrate binding affinity, and the unfavorable ΔΔG° bind is comprised of roughly equal enthalpic and entropic components at 25 °C. Chemical shifts in the free and dUMP-bound states show the mutation causes perturbations throughout TSase, including regions important for complex stability, in agreement with a less favorable enthalpy change. We measured the nuclear magnetic resonance methyl symmetry axis order parameter (S 2 axis ), a proxy for conformational entropy, for TSase at all vertices of the dUMP binding/C146S mutation thermodynamic cycle and found that the calculated TΔΔS° conf is similar in sign and magnitude to the calorimetric TΔΔS°. Further, we ascribed minor resonances in wild-type-dUMP spectra to a state with a covalent bond between Sγ of C146 and C6 of dUMP and find S 2 axis values are unaffected by covalent bond formation, indicating this reaction step is neutral with respect to ΔS° conf . Lastly, the C146S mutation allowed us to measure cofactor analog binding by isothermal titration calorimetry without the confounding heat signature of covalent bond formation. Raltitrexed binds free and singly bound TSase with similar affinities, yet the two binding events have different enthalpy changes, providing further evidence of communication between the two active sites.

  15. Exploring the subsurface atomic structure of the epitaxially grown phase-change material Ge2Sb2Te5

    Science.gov (United States)

    Kellner, J.; Bihlmayer, G.; Deringer, V. L.; Liebmann, M.; Pauly, C.; Giussani, A.; Boschker, J. E.; Calarco, R.; Dronskowski, R.; Morgenstern, M.

    2017-12-01

    Scanning tunneling microscopy (STM) and spectroscopy (STS) in combination with density functional theory (DFT) calculations are employed to study the surface and subsurface properties of the metastable phase of the phase-change material Ge2Sb2Te5 as grown by molecular beam epitaxy. The (111) surface is covered by an intact Te layer, which nevertheless permits the detection of the more disordered subsurface layer made of Ge and Sb atoms. Centrally, we find that the subsurface layer is significantly more ordered than expected for metastable Ge2Sb2Te5 . First, we show that vacancies are nearly absent within the subsurface layer. Secondly, the potential fluctuation, tracked by the spatial variation of the valence band onset, is significantly less than expected for a random distribution of atoms and vacancies in the subsurface layer. The strength of the fluctuation is compatible with the potential distribution of charged acceptors without being influenced by other types of defects. Thirdly, DFT calculations predict a partially tetrahedral Ge bonding within a disordered subsurface layer, exhibiting a clear fingerprint in the local density of states as a peak close to the conduction band onset. This peak is absent in the STS data implying the absence of tetrahedral Ge, which is likely due to the missing vacancies required for structural relaxation around the shorter tetrahedral Ge bonds. Finally, isolated defect configurations with a low density of 10-4nm-2 are identified by comparison of STM and DFT data, which corroborates the significantly improved order in the epitaxial films driven by the buildup of vacancy layers.

  16. Effect of two kinds of iron drops on the discoloration, atomic absorption and structural changes of primary teeth enamel

    Directory of Open Access Journals (Sweden)

    Mehran M.

    2009-03-01

    Full Text Available "nBackground and Aim: Black staining after taking iron drops on the primary teeth is always concern of parents. There is not an exact explanation for the mechanism of iron black staining. The purpose of this study was to compare tooth discolorations, atomic absorption and structural changes of primary teeth enamel caused by two kinds of iron drops[ Kharazmi(Iran and Fer-in-sol(USA]. "nMaterials and Methods: In this ex-vivo study, 93 sound primary teeth in normal color range were divided into five groups. Two groups of samples were immersed into the Artificial Caries Challenge(ACC for two weeks before getting exposured to iron drops: Group 1 Control(NS: sound enamel teeth which were kept in Normal Saline environment(NS(13teeth. Group 2 (NS-KH: NS, kharazmi iron drop (20 teeth. Group 3 (ACC-KH: ACC, Kharazmi iron drop (20teeth. Group 4 (NS-F-in-S: NS, Fer-in-Sol iron drop (20teeth. Group 5 (ACC-F-in-S: ACC, Fer-in-Sol iron drop. Visual tooth discolorations were determined by a specialist in operative dentistry who was not aware of experimental groups. The iron concentration was measured by ICP system (Vista-pro, Australia and the structural changes were studied by SEM (Philips, Netherland. The data of discoloration were studied with Kruskal-Wallis test and multiple comparison using Bonferroni type test, and with the data of atomic absorption were studied with oneway ANOVA test and Tukey HSD test. "nResults: The discoloration in the teeth immersed into the ACC (ACC-KH, ACC-F-in-S was more severe than the sound enamel surface (NS-KH, NS-F-IN-S (p<0.001 and Kharazmi iron drop caused more discoloration in the teeth immersed into the ACC (p=0.018. The teeth immersed into the ACC, absorbed more iron than the sound enamel surface (p<0.001 and also the teeth immersed into the ACC absorbed more Kharazmi iron drop (p<0.001. In the Scanning Electron Microscopy study, at low magnification in the sound teeth the perikymata was arranged regular. At low

  17. The effect of deposition energy of energetic atoms on the growth and structure of ultrathin amorphous carbon films studied by molecular dynamics simulations

    KAUST Repository

    Wang, N

    2014-05-16

    The growth and structure of ultrathin amorphous carbon films was investigated by molecular dynamics simulations. The second-generation reactive-empirical-bond-order potential was used to model atomic interactions. Films with different structures were simulated by varying the deposition energy of carbon atoms in the range of 1-120 eV. Intrinsic film characteristics (e.g. density and internal stress) were determined after the system reached equilibrium. Short- and intermediate-range carbon atom ordering is examined in the context of atomic hybridization and ring connectivity simulation results. It is shown that relatively high deposition energy (i.e., 80 eV) yields a multilayer film structure consisting of an intermixing layer, bulk film and surface layer, consistent with the classical subplantation model. The highest film density (3.3 g cm-3), sp3 fraction (∼43%), and intermediate-range carbon atom ordering correspond to a deposition energy of ∼80 eV, which is in good agreement with experimental findings. © 2014 IOP Publishing Ltd.

  18. Structure and Nanomechanics of Model Membranes by Atomic Force Microscopy and Spectroscopy: Insights into the Role of Cholesterol and Sphingolipids

    Directory of Open Access Journals (Sweden)

    Berta Gumí-Audenis

    2016-12-01

    Full Text Available Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs. Atomic force microscope (AFM is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information.

  19. Structural and mechanical properties of the proliferative zone of the developing murine growth plate cartilage assessed by atomic force microscopy.

    Science.gov (United States)

    Prein, Carina; Warmbold, Niklas; Farkas, Zsuzsanna; Schieker, Matthias; Aszodi, Attila; Clausen-Schaumann, Hauke

    2016-03-01

    The growth plate (GP) is a dynamic tissue driving bone elongation through chondrocyte proliferation, hypertrophy and matrix production. The extracellular matrix (ECM) is the major determinant of GP biomechanical properties and assumed to play a pivotal role for chondrocyte geometry and arrangement, thereby guiding proper growth plate morphogenesis and bone elongation. To elucidate the relationship between morphology and biomechanics during cartilage morphogenesis, we have investigated age-dependent structural and elastic properties of the proliferative zone of the murine GP by atomic force microscopy (AFM) from the embryonic stage to adulthood. We observed a progressive cell flattening and arrangement into columns from embryonic day 13.5 until postnatal week 2, correlating with an increasing collagen density and ECM stiffness, followed by a nearly constant cell shape, collagen density and ECM stiffness from week 2 to 4 months. At all ages, we found marked differences in the density and organization of the collagen network between the intracolumnar matrix, and the intercolumnar matrix, associated with a roughly two-fold higher stiffness of the intracolumnar matrix compared to the intercolumnar matrix. This difference in local ECM stiffness may force the cells to arrange in a columnar structure upon cell division and drive bone elongation during embryonic and juvenile development. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2016-07-13

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

  1. Ab initio calculations on structural and electronic transport properties of six-atom GaN clusters

    Science.gov (United States)

    Song, Jinfeng; Long, Xiaojiang; Hao, Yanjun; Zhu, Jun; Guo, Yundong

    2017-11-01

    The structural and electronic transport properties of GaxNy (x + y = 6) clusters are investigated in the framework of density functional theory (DFT). To get their most stable structures, a strategy of particle swarm optimization (PSO) algorithm is adopted. It is found that the most stable cluster’s binding energy and HOMO-LUMO gap energy decrease with Ga atom’s number in cluster increasing. The electronic transport properties of the clusters connected with two Al(100) electrodes are obtained by a method of combining nonequilibrium Green’s function (NEGF) with DFT. Equilibrium conductance of all six-atom GaN cluster is low (less than 0.65 G0), and Ga2N4 has the highest one (0.635 G0). Significant negative differential resistance (NDR) phenomenon is observed in configurations with cluster Ga2N4, Ga3N3 and Ga5N1, and these three clusters have almost the same current value in voltage region from 0.8 V to 1.3 V.

  2. Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jae-Mun; Hutson, Anne M.; Estes, Mary K.; Prasad, B.V. Venkataram (Baylor)

    2008-07-28

    Members of Norovirus, a genus in the family Caliciviridae, are causative agents of epidemic diarrhea in humans. Susceptibility to several noroviruses is linked to human histo-blood type, and its determinant histo-blood group antigens (HBGAs) are regarded as receptors for these viruses. Specificity for these carbohydrates is strain-dependent. Norwalk virus (NV) is the prototype genogroup I norovirus that specifically recognizes A- and H-type HBGA, in contrast to genogroup II noroviruses that exhibit a more diverse HBGA binding pattern. To understand the structural basis for how HBGAs interact with the NV capsid protein, and how the specificity is achieved, we carried out x-ray crystallographic analysis of the capsid protein domain by itself and in complex with A- and H-type HBGA at a resolution of {approx}1.4 {angstrom}. Despite differences in their carbohydrate sequence and linkage, both HBGAs bind to the same surface-exposed site in the capsid protein and project outward from the capsid surface, substantiating their possible role in initiating cell attachment. Precisely juxtaposed polar side chains that engage the sugar hydroxyls in a cooperative hydrogen bonding and a His/Trp pair involved in a cation-p interaction contribute to selective and specific recognition of A- and H-type HBGAs. This unique binding epitope, confirmed by mutational analysis, is highly conserved, but only in the genogroup I noroviruses, suggesting that a mechanism by which noroviruses infect broader human populations is by evolving different sites with altered HBGA specificities.

  3. Electric polarization switching in an atomically thin binary rock salt structure

    Science.gov (United States)

    Martinez-Castro, Jose; Piantek, Marten; Schubert, Sonja; Persson, Mats; Serrate, David; Hirjibehedin, Cyrus F.

    2018-01-01

    Inducing and controlling electric dipoles is hindered in the ultrathin limit by the finite screening length of surface charges at metal-insulator junctions1-3, although this effect can be circumvented by specially designed interfaces4. Heterostructures of insulating materials hold great promise, as confirmed by perovskite oxide superlattices with compositional substitution to artificially break the structural inversion symmetry5-8. Bringing this concept to the ultrathin limit would substantially broaden the range of materials and functionalities that could be exploited in novel nanoscale device designs. Here, we report that non-zero electric polarization can be induced and reversed in a hysteretic manner in bilayers made of ultrathin insulators whose electric polarization cannot be switched individually. In particular, we explore the interface between ionic rock salt alkali halides such as NaCl or KBr and polar insulating Cu2N terminating bulk copper. The strong compositional asymmetry between the polar Cu2N and the vacuum gap breaks inversion symmetry in the alkali halide layer, inducing out-of-plane dipoles that are stabilized in one orientation (self-poling). The dipole orientation can be reversed by a critical electric field, producing sharp switching of the tunnel current passing through the junction.

  4. Electrosynthesis of Biomimetic Manganese-Calcium Oxides for Water Oxidation Catalysis--Atomic Structure and Functionality.

    Science.gov (United States)

    González-Flores, Diego; Zaharieva, Ivelina; Heidkamp, Jonathan; Chernev, Petko; Martínez-Moreno, Elías; Pasquini, Chiara; Mohammadi, Mohammad Reza; Klingan, Katharina; Gernet, Ulrich; Fischer, Anna; Dau, Holger

    2016-02-19

    Water-oxidizing calcium-manganese oxides, which mimic the inorganic core of the biological catalyst, were synthesized and structurally characterized by X-ray absorption spectroscopy at the manganese and calcium K edges. The amorphous, birnesite-type oxides are obtained through a simple protocol that involves electrodeposition followed by active-site creation through annealing at moderate temperatures. Calcium ions are inessential, but tune the electrocatalytic properties. For increasing calcium/manganese molar ratios, both Tafel slopes and exchange current densities decrease gradually, resulting in optimal catalytic performance at calcium/manganese molar ratios of close to 10 %. Tracking UV/Vis absorption changes during electrochemical operation suggests that inactive oxides reach their highest, all-Mn(IV) oxidation state at comparably low electrode potentials. The ability to undergo redox transitions and the presence of a minor fraction of Mn(III) ions at catalytic potentials is identified as a prerequisite for catalytic activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Perceptual atoms: proximal motion vector-structures and the perception of object motion in depth

    Directory of Open Access Journals (Sweden)

    Hershenson Maurice

    2003-01-01

    Full Text Available A framework is proposed for analyzing the perception of motion in depth produced by simple proximal motion patterns of two to four points. The framework includes input structure, perceptual system constraints, and a depth scaling mechanism. The input is relational stimulation described by two proximal dimensions, orientation and separation, that can change or remain constant over the course of a motion pattern. Combinations of change or no-change in these dimensions yield four basic patterns of proximal stimulation: parallel, circular, perspective, and parallax. These primary patterns initiate automatic processing mechanisms - a unity constraint that treats pairs of points as connected and a rigidity constraint that treats the connection as rigid. When the constraints are activated by perspective or parallax patterns, the rigid connection between the points also appears to move in depth. A scaling mechanism governs the degree to which the objects move in depth in order to maintain the perceived rigidity. Although this framework is sufficient to explain perceptions produced by three- and four-point motion patterns in most cases, some patterns require additional configurational factors to supplement the framework. Nevertheless, perceptual qualities such as shrinking, stretching, bending, and folding emerge from the application of the same processing constraints and depth scaling factors as those that produce the perception of rigid objects moving in depth.

  6. Unified field theory from the classical wave equation: Preliminary application to atomic and nuclear structure

    Energy Technology Data Exchange (ETDEWEB)

    Múnera, Héctor A., E-mail: hmunera@hotmail.com [Centro Internacional de Física (CIF), Apartado Aéreo 4948, Bogotá, Colombia, South America (Colombia); Retired professor, Department of Physics, Universidad Nacional de Colombia, Bogotá, Colombia, South America (Colombia)

    2016-07-07

    It is postulated that there exists a fundamental energy-like fluid, which occupies the flat three-dimensional Euclidean space that contains our universe, and obeys the two basic laws of classical physics: conservation of linear momentum, and conservation of total energy; the fluid is described by the classical wave equation (CWE), which was Schrödinger’s first candidate to develop his quantum theory. Novel solutions for the CWE discovered twenty years ago are nonharmonic, inherently quantized, and universal in the sense of scale invariance, thus leading to quantization at all scales of the universe, from galactic clusters to the sub-quark world, and yielding a unified Lorentz-invariant quantum theory ab initio. Quingal solutions are isomorphic under both neo-Galilean and Lorentz transformations, and exhibit nother remarkable property: intrinsic unstability for large values of ℓ (a quantum number), thus limiting the size of each system at a given scale. Unstability and scale-invariance together lead to nested structures observed in our solar system; unstability may explain the small number of rows in the chemical periodic table, and nuclear unstability of nuclides beyond lead and bismuth. Quingal functions lend mathematical basis for Boscovich’s unified force (which is compatible with many pieces of evidence collected over the past century), and also yield a simple geometrical solution for the classical three-body problem, which is a useful model for electronic orbits in simple diatomic molecules. A testable prediction for the helicoidal-type force is suggested.

  7. Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts

    Science.gov (United States)

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

    2015-04-01

    An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the

  8. Effects of the c-Si/a-SiO2 interfacial atomic structure on its band alignment: an ab initio study.

    Science.gov (United States)

    Zheng, Fan; Pham, Hieu H; Wang, Lin-Wang

    2017-12-13

    The crystalline-Si/amorphous-SiO2 (c-Si/a-SiO2) interface is an important system used in many applications, ranging from transistors to solar cells. The transition region of the c-Si/a-SiO2 interface plays a critical role in determining the band alignment between the two regions. However, the question of how this interface band offset is affected by the transition region thickness and its local atomic arrangement is yet to be fully investigated. Here, by controlling the parameters of the classical Monte Carlo bond switching algorithm, we have generated the atomic structures of the interfaces with various thicknesses, as well as containing Si at different oxidation states. A hybrid functional method, as shown by our calculations to reproduce the GW and experimental results for bulk Si and SiO2, was used to calculate the electronic structure of the heterojunction. This allowed us to study the correlation between the interface band characterization and its atomic structures. We found that although the systems with different thicknesses showed quite different atomic structures near the transition region, the calculated band offset tended to be the same, unaffected by the details of the interfacial structure. Our band offset calculation agrees well with the experimental measurements. This robustness of the interfacial electronic structure to its interfacial atomic details could be another reason for the success of the c-Si/a-SiO2 interface in Si-based electronic applications. Nevertheless, when a reactive force field is used to generate the a-SiO2 and c-Si/a-SiO2 interfaces, the band offset significantly deviates from the experimental values by about 1 eV.

  9. New clues to the local atomic structure of short-range ordered ferric arsenate from extended X-ray absorption fine structure spectroscopy.

    Science.gov (United States)

    Mikutta, Christian; Mandaliev, Petar N; Kretzschmar, Ruben

    2013-04-02

    Short-range ordered ferric arsenate (FeAsO4 · xH2O) is a secondary As precipitate frequently encountered in acid mine waste environments. Two distinct structural models have recently been proposed for this phase. The first model is based on the structure of scorodite (FeAsO4 · 2H2O) where isolated FeO6 octahedra share corners with four adjacent arsenate (AsO4) tetrahedra in a three-dimensional framework (framework model). The second model consists of single chains of corner-sharing FeO6 octahedra being bridged by AsO4 bound in a monodentate binuclear (2)C complex (chain model). In order to rigorously test the accuracy of both structural models, we synthesized ferric arsenates and analyzed their local (absorption fine structure (EXAFS) spectroscopy. We found that both As and Fe K-edge EXAFS spectra were most compatible with isolated FeO6 octahedra being bridged by AsO4 tetrahedra (RFe-As = 3.33 ± 0.01 Å). Our shell-fit results further indicated a lack of evidence for single corner-sharing FeO6 linkages in ferric arsenate. Wavelet-transform analyses of the Fe K-edge EXAFS spectra of ferric arsenates complemented by shell fitting confirmed Fe atoms at an average distance of ∼5.3 Å, consistent with crystallographic data of scorodite and in disagreement with the chain model. A scorodite-type local structure of short-range ordered ferric arsenates provides a plausible explanation for their rapid transformation into scorodite in acid mining environments.

  10. Surfactant-Free Synthesis of Single Crystalline SnS2 and Effect of Surface Atomic Structure on the Photocatalytic Property

    Directory of Open Access Journals (Sweden)

    Mengyi Li

    2014-01-01

    Full Text Available Sheetlike tin disulfide (SnS2 single crystal exposed with well-defined {001} facets and flowerlike SnS2 mainly exposed with {010} facets were prepared through a surfactant-free solvothermal process. Photocatalytic degradation of methyl orange (MO under visible light irradiation indicated that the sheetlike SnS2 showed a much higher activity than flowerlike SnS2. Theoretical and experimental results revealed that the band structure derived from the surface atomic structure played a more important role than the surface energy in the photocatalytic property. The present work has provided a deep insight into the important role of the surface energy and band structure, both of which are derived from the surface atomic structure, in the photocatalytic activity.

  11. Using an Advanced Computational Laboratory Experiment to Extend and Deepen Physical Chemistry Students' Understanding of Atomic Structure

    Science.gov (United States)

    Hoffman, Gary G.

    2015-01-01

    A computational laboratory experiment is described, which involves the advanced study of an atomic system. The students use concepts and techniques typically covered in a physical chemistry course but extend those concepts and techniques to more complex situations. The students get a chance to explore the study of atomic states and perform…

  12. Deciphering the structure, growth and assembly of amyloid-like fibrils using high-speed atomic force microscopy.

    Directory of Open Access Journals (Sweden)

    Pierre-Emmanuel Milhiet

    Full Text Available Formation of fibrillar structures of proteins that deposit into aggregates has been suggested to play a key role in various neurodegenerative diseases. However mechanisms and dynamics of fibrillization remains to be elucidated. We have previously established that lithostathine, a protein overexpressed in the pre-clinical stages of Alzheimer's disease and present in the pathognomonic lesions associated with this disease, form fibrillar aggregates after its N-terminal truncation. In this paper we visualized, using high-speed atomic force microscopy (HS-AFM, growth and assembly of lithostathine protofibrils under physiological conditions with a time resolution of one image/s. Real-time imaging highlighted a very high velocity of elongation. Formation of fibrils via protofibril lateral association and stacking was also monitored revealing a zipper-like mechanism of association. We also demonstrate that, like other amyloid ß peptides, two lithostathine protofibrils can associate to form helical fibrils. Another striking finding is the propensity of the end of a growing protofibril or fibril to associate with the edge of a second fibril, forming false branching point. Taken together this study provides new clues about fibrillization mechanism of amyloid proteins.

  13. Variations in atomic structural features of a supercooled Pd-Ni-Cu-P glass forming liquid during in situ vitrification

    Energy Technology Data Exchange (ETDEWEB)

    Georgarakis, Konstantinos [WPI Advanced Institute for Materials Research, Tohoku University, Aoba-Ku, Sendai 980-8577 (Japan); SIMAP-CNRS, Institut Polytechnique de Grenoble, BP 75, 38402 St-Martin-d' Heres (France); Louzguine-Luzgin, Dmitri V., E-mail: dml@wpi-aimr.tohoku.ac.jp [WPI Advanced Institute for Materials Research, Tohoku University, Aoba-Ku, Sendai 980-8577 (Japan); Antonowicz, Jerzy [Faculty of Physics, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw (Poland); Vaughan, Gavin [European Synchrotron Radiation Facility, 38042 Grenoble (France); Yavari, Alain R. [WPI Advanced Institute for Materials Research, Tohoku University, Aoba-Ku, Sendai 980-8577 (Japan); SIMAP-CNRS, Institut Polytechnique de Grenoble, BP 75, 38402 St-Martin-d' Heres (France); European Synchrotron Radiation Facility, 38042 Grenoble (France); Egami, Takeshi [WPI Advanced Institute for Materials Research, Tohoku University, Aoba-Ku, Sendai 980-8577 (Japan); Joint Institute for Neutron Sciences, Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996 (United States); Joint Institute for Neutron Sciences, Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996 (United States); Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Inoue, Akihisa [WPI Advanced Institute for Materials Research, Tohoku University, Aoba-Ku, Sendai 980-8577 (Japan)

    2011-01-15

    In situ vitrification in a synchrotron beam during cooling of a Pd{sub 42.5}Cu{sub 30}Ni{sub 7.5}P{sub 20} melt allowed continuous acquisition of X-ray diffraction spectra in the supercooled liquid region between the liquidus temperature T{sub l} and the glass transition temperature T{sub g} for the first time in a metallic liquid alloy. These and subsequent acquisitions on reheating allowed determination of the structural changes in the supercooled and glassy states using the real space atomic pair distribution function PDF(R) and radial distribution function RDF(R). The nearest neighbor (NN) distance in the first coordination shell has a low R peak (pre-peak) that appears and increases on cooling from the liquidus temperature to the glass transition temperature in the supercooled liquid region. In this temperature range reversible expansion of the NN distances in the first coordination shell is observed. The slope of the expansion changes discontinuously at the glass transition. This behavior is explained by the theory of local topological fluctuations.

  14. From average to local structure: a Rietveld and an atomic pair distribution function (PDF) study of selenium clusters in zeolite-NdY.

    Science.gov (United States)

    Abeykoon, A M Milinda; Donner, Wolfgang; Brunelli, Michela; Castro-Colin, Miguel; Jacobson, Allan J; Moss, Simon C

    2009-09-23

    The structure of Se particles in the approximately 13 A diameter alpha-cages of zeolite NdY has been determined by Rietveld refinement and pair distribution function (PDF) analysis of X-ray data. With the diffuse scattering subtracted an average structure comprised of an undistorted framework containing nanoclusters of 20 Se atoms is observed. The intracluster correlations and the cluster-framework correlations which give rise to diffuse scattering were modeled by using PDF analysis.

  15. Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy.

    Science.gov (United States)

    Yan, Si; Guo, Changmiao; Hou, Guangjin; Zhang, Huilan; Lu, Xingyu; Williams, John Charles; Polenova, Tatyana

    2015-11-24

    Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

  16. Integrated Surface and Mechanical Characterization of Freestanding Biological and Other Nano-Structures Using Atomic Force Microscopy

    Science.gov (United States)

    Wang, Xin

    This dissertation is focused on surface and mechanical characterization of freestanding biological and other nano-structures using atomic force microscopy including two parts: cell mechanics and nano-structure mechanics. The main purpose of this work is to investigate how the nano- / micro-scale mechanical properties affect macro-scale function. In cancer cells, efficacy of drug delivery is oftentimes declined due to the thick dendritic network of oligosaccharide mucin chains on the cell surface. AFM is used to measure the force needed to pierce the mucin layer to reach the cell surface. A pool of ovarian, pancreatic, lung, colorectal and breast cancer cells are characterized. The studies offer additional support for the development of clinical and pharmaceutical approaches to combat mucin over-expression in tumors during cancer chemotherapy. Macroscopic adhesion-aggregation and subsequent transportation of microorganisms in porous medium are closely related to the microscopic deformation and adhesion mechanical properties. The classical Tabor's parameter is modified. Multiple bacterial strains are characterized in terms of aggregates size, aggregation index and transportation kinetics. AFM is employed to obtain the microscopic coupled adhesion-deformation properties. The strong correlation between Tabor's parameter and aggregation-deposition-transportation suggests the AFM characterization is capable of making reliable predication of macroscopic behavior. A novel "nano-cheese-cutter" is fabricated on tipless AFM cantilever to measure elastic modulus and interfacial adhesion of a 1-D freestanding nano-structure. A single electrospun fiber is attached to the free end of AFM cantilever, while another fiber is similarly prepared on a mica substrate in an orthogonal direction. An external load is applied to deform the two fibers into complementary V-shapes. This work is extended to investigate the interfacial adhesion energy between dissimilar materials. SWCNT thin

  17. Projected atomic structure of a large-angle (001). sigma. = 5 (theta = 36. 9/sup 0/) twist boundary in gold: diffraction analysis and theoretical predictions

    Energy Technology Data Exchange (ETDEWEB)

    Budai, J.; Bristowe, P.D.; Sass, S.L.

    1982-09-01

    The projected atomic structure of a large angle (001) ..sigma.. = 5 (theta = 36.9/sup 0/) twist boundary in Au was determined using x-ray diffraction techniques. The extra reflections resulting from the periodic structure of the boundary were studied using synchrotron radiation. The observed structure factor rules are consistent with the boundary existing in the exact (no translation away from) coincidence configuration. The projected structure was determined using a variable coordinate and reliability factor analysis which was simplified by the low value of ..sigma.., the boundary symmetry and the assumption of a thin boundary region. The structure thus determined consists of groups of atoms which have undergone large rotations about 0-elements in the planes immediately adjacent to the boundary. The structure is made up of separate patches of median fcc structure in analogy with small angle boundaries. Various structures calculated by computer relaxation techniques using interatomic potentials are also presented and compared with the diffraction results. These structures also show rotational relaxations about 0-elements but the degree of the rotation is much smaller than was determined by diffraction leading to a distortion of the median fcc structure. Consequently, there is only limited correspondence between the computer results and experimental observations.

  18. The projected atomic structure of a large angle (001). sigma. = 5 (0 = 36. 9) twist boundary in gold: Diffraction analysis and theoretical predictions

    Energy Technology Data Exchange (ETDEWEB)

    Budai, J.; Bristowe, P.D.; Sass, S.L.

    1983-05-01

    The projected atomic structure of a large angle (001) ..sigma.. = 5 (0 = 36.9) twist boundary in Au was determined using X-ray diffraction techniques. The extra reflections resulting from the periodic structure of the boundary were studied using synchrotron radiation. The observed structure factor rules are consistent with the boundary existing in the exact (no translation away from) coincidence configuration. The projected structure was determined using a variable coordinate and reliability factor analysis which was simplified by the low value of ..sigma.., the boundary symmetry and the assumption o a thin boundary region. The structure thus determined consists of groups of atoms which have undergone large rotations about ''0'' elements in the planes immediately adjacent to the boundary. The structure is made up of separate patches of median f.c.c. structure in analogy with small angle boundaries. Various structures calculated by computer relaxation techniques using interatomic potentials are also presented and compared with the diffraction results. These structures also show rotational relaxations about ''0'' -elements but the degree of the rotation is much smaller than was determined by diffraction leading to a distortion of the median f.c.c. structure. Consequently, there is only limited correspondence between the computer results and experimental observations.

  19. The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

    2014-09-01

    Full Text Available The structure of a protein provides insight into its physiological interactions with other components of the cellular soup. Methods that predict putative structures from sequences typically yield multiple, closely-ranked possibilities. A critical component in the process is the model quality assessing program (MQAP, which selects the best candidate from this pool of structures. Here, we present a novel MQAP based on the physical properties of sidechain atoms. We propose a method for assessing the quality of protein structures based on the electrostatic potential difference (EPD of Cβ atoms in consecutive residues. We demonstrate that the EPDs of Cβ atoms on consecutive residues provide unique signatures of the amino acid types. The EPD of Cβ atoms are learnt from a set of 1000 non-homologous protein structures with a resolution cuto of 1.6 Å obtained from the PISCES database. Based on the Boltzmann hypothesis that lower energy conformations are proportionately sampled more, and on Annsen's thermodynamic hypothesis that the native structure of a protein is the minimum free energy state, we hypothesize that the deviation of observed EPD values from the mean values obtained in the learning phase is minimized in the native structure. We achieved an average specificity of 0.91, 0.94 and 0.93 on hg_structal, 4state_reduced and ig_structal decoy sets, respectively, taken from the Decoys `R' Us database. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.

  20. The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v2; ref status: indexed, http://f1000r.es/2cf

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

    2013-11-01

    Full Text Available The structure of a protein provides insight into its physiological interactions with other components of the cellular soup. Methods that predict putative structures from sequences typically yield multiple, closely-ranked possibilities. A critical component in the process is the model quality assessing program (MQAP, which selects the best candidate from this pool of structures. Here, we present a novel MQAP based on the physical properties of sidechain atoms. We propose a method for assessing the quality of protein structures based on the electrostatic potential difference (EPD of Cβ atoms in consecutive residues. We demonstrate that the EPDs of Cβ atoms on consecutive residues provide unique signatures of the amino acid types. The EPD of Cβ atoms are learnt from a set of 1000 non-homologous protein structures with a resolution cuto of 1.6 Å obtained from the PISCES database. Based on the Boltzmann hypothesis that lower energy conformations are proportionately sampled more, and on Annsen's thermodynamic hypothesis that the native structure of a protein is the minimum free energy state, we hypothesize that the deviation of observed EPD values from the mean values obtained in the learning phase is minimized in the native structure. We achieved an average specificity of 0.91, 0.94 and 0.93 on hg_structal, 4state_reduced and ig_structal decoy sets, respectively, taken from the Decoys `R' Us database. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.

  1. Atomic and electronic structures of the (√(13)×√(13))R13.9° of silicene sheet on Ag(1 1 1)

    Energy Technology Data Exchange (ETDEWEB)

    Tchalala, Mohamed Rachid [Institut des Sciences Moléculaires d’Orsay, ISMO-CNRS, Bât. 210, Université Paris-Sud, F-91405 Orsay (France); Laboratoire de Chimie de Coordination et Catalyse, Département de Chimie, Faculté des Sciences-Semlalia, Université Cadi Ayyad, Marrakech 40001 (Morocco); Enriquez, Hanna [Institut des Sciences Moléculaires d’Orsay, ISMO-CNRS, Bât. 210, Université Paris-Sud, F-91405 Orsay (France); Yildirim, Handan; Kara, Abdelkader [Department of Physics, University of Central Florida, Orlando, FL 32816 (United States); Mayne, Andrew J.; Dujardin, Gérald [Institut des Sciences Moléculaires d’Orsay, ISMO-CNRS, Bât. 210, Université Paris-Sud, F-91405 Orsay (France); Ali, Mustapha Ait [Laboratoire de Chimie de Coordination et Catalyse, Département de Chimie, Faculté des Sciences-Semlalia, Université Cadi Ayyad, Marrakech 40001 (Morocco); Oughaddou, Hamid, E-mail: Hamid.Oughaddou@u-psud.fr [Institut des Sciences Moléculaires d’Orsay, ISMO-CNRS, Bât. 210, Université Paris-Sud, F-91405 Orsay (France); Département de Physique, Université de Cergy-Pontoise, F-95031 Cergy-Pontoise Cedex (France)

    2014-06-01

    Using scanning tunneling microscopy, low energy electron diffraction measurements, and ab initio calculations based on density functional theory, we present atomic models of the (√(13)×√(13))R13.9° silicene superstructure grown on Ag(1 1 1). The STM images reveal two co-existing atomic arrangements with two different orientations of the silicene sheet relative to the Ag(1 1 1) surface. DFT calculations with and without the inclusion of van der Waals interactions show corrugated Si atomic positions for both orientations implying a significant interaction with Ag(1 1 1) surface. The electronic structure of both silicene and Ag(1 1 1) surface are sufficiently affected that new interface states emerge close to the Fermi level.

  2. Ab Initio Structure Determination of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A(2) at Atomic and High Resolution Using ACORN

    Energy Technology Data Exchange (ETDEWEB)

    Velmurugan,D.; Rajakannan, V.; Gayathri, D.; Banumathi, S.; Yamane, T.; Dauter, Z.; Dauter, M.; Sekar, K.

    2006-01-01

    Atomic resolution (0.97 Angstroms) data were collected for the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A{sub 2} at 100 K and data extending to 1.0 Angstroms resolution were used for the present study. Accuracy of the data at high resolution allowed the structure to be solved using the program ACORN, with a random single-atom start in an ab initio manner. The phases obtained from ACORN are of good quality and revealed most of the amino acid residues. Single wavelength Anomalous Diffraction (SAD) data were also used to locate the position of the sulphurs and ACORN was run with these atomic positions as a source of phasing information. The effect of truncating the data to 1.4 and 1.45 Angstroms for input to ACORN is also examined. Larger fragments are required to trigger successful phase refinement at these lower resolutions.

  3. Single atom microscopy.

    Science.gov (United States)

    Zhou, Wu; Oxley, Mark P; Lupini, Andrew R; Krivanek, Ondrej L; Pennycook, Stephen J; Idrobo, Juan-Carlos

    2012-12-01

    We show that aberration-corrected scanning transmission electron microscopy operating at low accelerating voltages is able to analyze, simultaneously and with single atom resolution and sensitivity, the local atomic configuration, chemical identities, and optical response at point defect sites in monolayer graphene. Sequential fast-scan annular dark-field (ADF) imaging provides direct visualization of point defect diffusion within the graphene lattice, with all atoms clearly resolved and identified via quantitative image analysis. Summing multiple ADF frames of stationary defects produce images with minimized statistical noise and reduced distortions of atomic positions. Electron energy-loss spectrum imaging of single atoms allows the delocalization of inelastic scattering to be quantified, and full quantum mechanical calculations are able to describe the delocalization effect with good accuracy. These capabilities open new opportunities to probe the defect structure, defect dynamics, and local optical properties in 2D materials with single atom sensitivity.

  4. Structure of the alkali-metal-atom + strontium molecular ions: Towards photoassociation and formation of cold molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Aymar, M.; Dulieu, O. [Laboratoire Aime Cotton, CNRS, UPR3321, Ba circumflex t. 505, Univ Paris-Sud, 91405 Orsay Cedex (France); Guerout, R. [Laboratoire Kastler-Brossel, CNRS, ENS, Univ Pierre et Marie Curie case 74, Campus Jussieu, F-75252 Paris Cedex 05 (France)

    2011-08-14

    The potential energy curves, permanent and transition dipole moments, and the static dipolar polarizability, of molecular ions composed of one alkali-metal atom and a strontium ion are determined with a quantum chemistry approach. The molecular ions are treated as effective two-electron systems and are treated using effective core potentials including core polarization, large gaussian basis sets, and full configuration interaction. In the perspective of upcoming experiments aiming at merging cold atom and cold ion traps, possible paths for radiative charge exchange, photoassociation of a cold lithium or rubidium atom and a strontium ion are discussed, as well as the formation of stable molecular ions.

  5. Corrugation in the Weakly Interacting Hexagonal-BN/Cu(111) System: Structure Determination by Combining Noncontact Atomic Force Microscopy and X-ray Standing Waves.

    Science.gov (United States)

    Schwarz, Martin; Riss, Alexander; Garnica, Manuela; Ducke, Jacob; Deimel, Peter S; Duncan, David A; Thakur, Pardeep Kumar; Lee, Tien-Lin; Seitsonen, Ari Paavo; Barth, Johannes V; Allegretti, Francesco; Auwärter, Willi

    2017-09-26

    Atomically thin hexagonal boron nitride (h-BN) layers on metallic supports represent a promising platform for the selective adsorption of atoms, clusters, and molecular nanostructures. Specifically, scanning tunneling microscopy (STM) studies revealed an electronic corrugation of h-BN/Cu(111), guiding the self-assembly of molecules and their energy level alignment. A detailed characterization of the h-BN/Cu(111) interface including the spacing between the h-BN sheet and its support-elusive to STM measurements-is crucial to rationalize the interfacial interactions within these systems. To this end, we employ complementary techniques including high-resolution noncontact atomic force microscopy, STM, low-energy electron diffraction, X-ray photoelectron spectroscopy, the X-ray standing wave method, and density functional theory. Our multimethod study yields a comprehensive, quantitative structure determination including the adsorption height and the corrugation of the sp(2) bonded h-BN layer on Cu(111). Based on the atomic contrast in atomic force microscopy measurements, we derive a measurable-hitherto unrecognized-geometric corrugation of the h-BN monolayer. This experimental approach allows us to spatially resolve minute height variations in low-dimensional nanostructures, thus providing a benchmark for theoretical modeling. Regarding potential applications, e.g., as a template or catalytically active support, the recognition of h-BN on Cu(111) as a weakly bonded and moderately corrugated overlayer is highly relevant.

  6. On the relationship between the population of the fine structure levels of the ground electronic state of atomic oxygen and the translational temperature

    Science.gov (United States)

    Sharma, R.; Zygelman, B.; von Esse, F.; Dalgarno, A.

    1994-08-01

    Using a recent calculation of the cross sections for fine structure changing collisions during an encounter between two oxygen atoms in the ground electronic state, we determine the population of the fine structure levels of oxygen as a function of altitude for four model atmospheres representing conditions at 0 deg longitude, 45 deg latitude, at midday and midnight, and high and low solar and geomagnetic activity. We include the effect of electron impacts. The fine structure levels are shown to be in local thermodynamic equilibrium (LTE) at the local neutral atom translational temperature for altitudes up to 350 km and 400 km for midnight and midday, respectively, at low activity, and up to at least 600 km at high activity. At higher altitudes spotaneous emission causes deviation from LTE and overpopulates the lowest (J = 2) level at the expense of the other two levels.

  7. The influence of atomic order on the magnetic and structural properties of the ferromagnetic shape memory compound Ni sub 2 MnGa

    CERN Document Server

    Kreissl, M; Stephens, T; Ziebeck, K R A

    2003-01-01

    The effect of atomic order on the martensitic phase transition and magnetic properties of stoichiometric Ni sub 2 MnGa has been investigated in a sample quenched from 1000 deg C. Magnetization, resistivity and x-ray diffraction measurements indicate that the structural phase transition occurs at approx 103 K, substantially lower than the value reported for samples quenched from 800 deg C and ordered in the Heusler L2 sub 1 structure. A small reduction in the ferromagnetic moment was also observed, although the Curie temperature remained largely unaffected. The electronic Sommerfeld coefficient obtained from heat capacity measurements is enhanced but smaller than that observed for the 800 deg C quenched sample. The results are consistent with band structure calculations and the electronic changes brought about by atomic disorder.

  8. Effect of additional elements on compositional modulated atomic layered structure of hexagonal Co{sub 80}Pt{sub 20} alloy films with superlattice diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Hinata, Shintaro [Department of Electronic Engineering, Graduate School of Engineering, Tohoku University, 6-6-05, Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Research Fellowship Division Japan Society for the Promotion of Science (JSPS), Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083 (Japan); Yamane, Akira; Saito, Shin [Department of Electronic Engineering, Graduate School of Engineering, Tohoku University, 6-6-05, Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan)

    2016-05-15

    The effect of additional element on compositionally modulated atomic layered structure of hexagonal Co{sub 80}Pt{sub 20} alloy films with superlattice diffraction was investigated. In this study it is found that the addition of Cr or W element to Co{sub 80}Pt{sub 20} alloy film shows less deterioration of hcp stacking structure and compositionally modulated atomic layer stacking structure as compared to Si or Zr or Ti with K{sub u} of around 1.4 or 1.0 × 10{sup 7} erg/cm{sup 3} at 5 at.% addition. Furthermore, for O{sub 2} addition of O{sub 2} ≥ 5.0 × 10{sup −3} Pa to CoPt alloy, compositionally modulated atomic layer stacking structure will be deteriorated with enhancement of formation of hcp stacking structure which leads higher K{sub u} of 1.0 × 10{sup 7} erg/cm{sup 3}.

  9. A theoretical investigation of the structural and electronic properties of 55-atom nanoclusters: The examples of Y–Tc and Pt

    Energy Technology Data Exchange (ETDEWEB)

    Batista, Krys E. A.; Piotrowski, Maurício J., E-mail: mauriciomjp@gmail.com [Department of Physics, Federal University of Pelotas, P.O. Box 354, 96010 − 900, Pelotas, RS (Brazil); Chaves, Anderson S.; Da Silva, Juarez L. F., E-mail: juarez-dasilva@iqsc.usp.br [São Carlos Institute of Chemistry, University of São Paulo, P.O. Box 780, 13560 − 970, São Carlos, SP (Brazil)

    2016-02-07

    Several studies have found that the Pt{sub 55} nanocluster adopts a distorted reduced core structure, DRC{sub 55}, in which there are 8–11 atoms in the core and 47–44 atoms in the surface, instead of the compact and high-symmetry icosahedron structure, ICO{sub 55}, with 13 and 42 atoms in the core and surface, respectively. The DRC structure has also been obtained as the putative global minimum configuration (GMC) for the Zn{sub 55} (3d), Cd{sub 55} (4d), and Au{sub 55} (5d) systems. Thus, the DRC{sub 55} structure has been reported only for systems with a large occupation of the d-states, where the effects of the occupation of the valence anti-bonding d-states might play an important role. Can we observe the DRC structure for 55-atom transition-metal systems with non-occupation of the anti-bonding d-states? To address this question, we performed a theoretical investigation of the Y {sub 55}, Zr{sub 55}, Nb{sub 55}, Mo{sub 55}, Tc{sub 55}, and Pt{sub 55} nanoclusters, employing density functional theory calculations. For the putative GMCs, we found that the Y {sub 55} adopts the ICO{sub 55} structure, while Nb{sub 55} and Mo{sub 55} adopt a bulk-like fragment based on the hexagonal close-packed structure and Tc{sub 55} adopts a face-centered cubic fragment; however, Zr{sub 55} adopts a DRC{sub 55} structure, like Zn{sub 55}, Cd{sub 55}, Pt{sub 55}, and Au{sub 55}. Thus we can conclude that the preference for DRC{sub 55} structure is not related to the occupation of the anti-bonding d-states, but to a different effect, in fact, a combination of structural and electronic effects. Furthermore, we obtained that the binding energy per atom follows the occupation of the bonding and anti-bonding model, i.e., the stability of the studied systems increases from Y to Tc with a small oscillation for Mo, which also explains the equilibrium bond lengths. We obtained a larger magnetic moment for Y {sub 55} (31 μ{sub B}) which can be explained by the localization of the d

  10. Atomic Resolution Structural and Chemical Imaging Revealing the Sequential Migration of Ni, Co, and Mn upon the Battery Cycling of Layered Cathode.

    Science.gov (United States)

    Yan, Pengfei; Zheng, Jianming; Zhang, Ji-Guang; Wang, Chongmin

    2017-06-14

    Layered lithium transition metal oxides (LTMO) are promising candidate cathode materials for next-generation high-energy density lithium ion battery. The challenge for using this category of cathode is the capacity and voltage fading, which is believed to be associated with the layered structure disordering, a process that is initiated from the surface or solid-electrolyte interface and facilitated by transition metal (TM) reduction and oxygen vacancy formation. However, the atomic level dynamic mechanism of such a layered structure disordering is still not fully clear. In this work, utilizing atomic resolution electron energy loss spectroscopy (EELS), we map, for the first time at atomic scale, the spatial evolution of Ni, Co and Mn in a cycled LiNi1/3Mn1/3Co1/3O2 layered cathode. In combination with atomic level structural imaging, we discovered the direct correlation of TM ions migration behavior with lattice disordering, featuring the residing of TM ions in the tetrahedral site and a sequential migration of Ni, Co, and Mn upon the increased lattice disordering of the layered structure. This work highlights that Ni ions, though acting as the dominant redox species in many LTMO, are labile to migrate to cause lattice disordering upon battery cycling, while the Mn ions are more stable as compared with Ni and Co and can act as pillar to stabilize layered structure. Direct visualization of the behavior of TM ions during the battery cycling provides insight for designing of cathode with high structural stability and correspondingly a superior performance.

  11. Atomic Resolution Structural and Chemical Imaging Revealing the Sequential Migration of Ni, Co, and Mn upon the Battery Cycling of Layered Cathode

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Pengfei; Zheng, Jianming; Zhang, Ji-Guang; Wang, Chongmin

    2017-05-11

    Layered lithium transition metal oxides (LTMO) are promising candidate cathode materials for next generation high energy density lithium ion battery. The challenge for using this category of cathode is the capacity and voltage fading, which is believed to be associated with the layered structure disordering, a process that is initiated from the surface or solid-electrolyte interface and facilitated by transition metal (TM) reduction and oxygen vacancy formation. However, the atomic level dynamic mechanism of such a layered structure disordering is still not fully clear. In this work, utilizing atomic resolution electron energy loss spectroscopy (EELS), we map, for the first time at atomic scale, the spatial evolution of Ni, Co and Mn in a cycled LiNi1/3M1/3Co1/3O2 layered cathode. In combination with atomic level structural imaging, we discovered the direct correlation of TM ions migration behavior with lattice disordering, featuring the residing of TM ions in the tetrahedral site and a sequential migration of Ni, Co, and Mn upon the increased lattice disordering of the layered structure. This work highlights that Ni ions, though acting as the dominant redox species in many LTMO, are labile to migrate to cause lattice disordering upon battery cycling; while the Mn ions are more stable as compared with Ni and Co and can act as pillar to stabilize layered structure. Direct visualization of the behavior of TM ions during the battery cycling provides insight for designing of cathode with structural stability and correspondingly a superior performance.

  12. Atomic force microscopy for biomechanical and structural analysis of human dermis: a complementary tool for medical diagnosis and therapy monitoring.

    Science.gov (United States)

    Peñuela, Leonardo; Negro, Carola; Massa, Michela; Repaci, Erica; Cozzani, Emanuele; Parodi, Aurora; Scaglione, Silvia; Quarto, Rodolfo; Raiteri, Roberto

    2017-11-20

    Skin mechanical properties are usually measured considering the entire skin thickness and very little is known about the mechanical behavior of individual skin layers. We propose atomic force microscopy (AFM) as a tool to quantify nanoscale changes in the biomechanical properties and ultrastructure of human papillary dermis exposed to different mechanical and physical stimuli. Samples from three human skin biopsies were studied: one stretched by obesity, one subjected to a high level of sun-exposure, and normal skin as control. Slices of the papillary dermis layer were harvested at controlled depths from each skin biopsy and 25 μm2 areas of each slice were imaged and D-periodicity of collagen fibers measured by AFM, together with their stiffness. Standard histological analysis was also carried out in order to correlate biochemical properties and their distribution with stiffness and topography. We obtained similar stiffness values between the sample affected by obesity and the control sample at any depth level into the dermis, while the sun-exposed sample presented a significant lower stiffness. Additionally, all samples presented an increase in the stiffness at higher depths into the papillary dermis layer. Collagen fibers close to the epidermis of sample affected either by obesity and sun-exposure- the former even more than the latter - are thicker and present a larger D-period than those in the control sample. Our results open the possibility to use structural and mechanical analysis based on AFM as a complementary tool for medical diagnosis and therapy monitoring. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  13. Multidimensional characterisation of biomechanical structures by combining Atomic Force Microscopy and Focused Ion Beam: A study of the rat whisker.

    Science.gov (United States)

    Adineh, Vahid Reza; Liu, Boyin; Rajan, Ramesh; Yan, Wenyi; Fu, Jing

    2015-07-01

    Understanding the heterogeneity of biological structures, particularly at the micro/nano scale can offer insights valuable for multidisciplinary research in tissue engineering and biomimicry designs. Here we propose to combine nanocharacterisation tools, particularly Focused Ion Beam (FIB) and Atomic Force Microscopy (AFM) for three dimensional mapping of mechanical modulus and chemical signatures. The prototype platform is applied to image and investigate the fundamental mechanics of the rat face whiskers, a high-acuity sensor used to gain detailed information about the world. Grazing angle FIB milling was first applied to expose the interior cross section of the rat whisker sample, followed by a "lift-out" method to retrieve and position the target sample for further analyses. AFM force spectroscopy measurements revealed a non-uniform pattern of elastic modulus across the cross section, with a range from 0.8GPa to 13.5GPa. The highest elastic modulus was found at the outer cuticle region of the whisker, and values gradually decreased towards the interior cortex and medulla regions. Elemental mapping with EDS confirmed that the interior of the rat whisker is dominated by C, O, N, S, Cl and K, with a significant change of elemental distribution close to the exterior cuticle region. Based on these data, a novel comprehensive three dimensional (3D) elastic modulus model was constructed, and stress distributions under realistic conditions were investigated with Finite Element Analysis (FEA). The simulations could well account for the passive whisker deflections, with calculated resonant frequency as well as force-deflection for the whiskers being in good agreement with reported experimental data. Limitations and further applications are discussed for the proposed FIB/AFM approach, which holds good promise as a unique platform to gain insights on various heterogeneous biomaterials and biomechanical systems. Copyright © 2015 Acta Materialia Inc. Published by Elsevier

  14. Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.

    Science.gov (United States)

    Malinska, Maura; Dauter, Zbigniew

    2016-06-01

    In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.

  15. Atomic polarizabilities

    Energy Technology Data Exchange (ETDEWEB)

    Safronova, M. S. [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States); Mitroy, J. [School of Engineering, Charles Darwin University, Darwin NT 0909 (Australia); Clark, Charles W. [Joint Quantum Institute, National Institute of Standards and Technology and the University of Maryland, Gaithersburg, Maryland 20899-8410 (United States); Kozlov, M. G. [Petersburg Nuclear Physics Institute, Gatchina 188300 (Russian Federation)

    2015-01-22

    The atomic dipole polarizability governs the first-order response of an atom to an applied electric field. Atomic polarization phenomena impinge upon a number of areas and processes in physics and have been the subject of considerable interest and heightened importance in recent years. In this paper, we will summarize some of the recent applications of atomic polarizability studies. A summary of results for polarizabilities of noble gases, monovalent, and divalent atoms is given. The development of the CI+all-order method that combines configuration interaction and linearized coupled-cluster approaches is discussed.

  16. An Atomic X-ray Absorption Fine Structure Study of the Influence of Hydrogen Chemisorption and Support on the Electronic Structure of Supported Pt Particles

    NARCIS (Netherlands)

    Koningsberger, D.C.; Ramaker, D.E.; Dorssen, G.E. van; Mojet, B.L.

    2000-01-01

    The physical principles of atomic XAFS (AXAFS) are presented along with important details on how to isolate the AXAFS contribution from the experimental XAFS data. Intuitive illustrations are given showing how various interactions of the absorber atom with its neighbours influence the AXAFS

  17. Ultracold atoms on atom chips

    DEFF Research Database (Denmark)

    Krüger, Peter; Hofferberth, S.; Haller, E.

    2005-01-01

    Miniaturized potentials near the surface of atom chips can be used as flexible and versatile tools for the manipulation of ultracold atoms on a microscale. The full scope of possibilities is only accessible if atom-surface distances can be reduced to microns. We discuss experiments in this regime...

  18. Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of C(alpha atoms.

    Directory of Open Access Journals (Sweden)

    Rupali A Gadkari

    Full Text Available BACKGROUND: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C(alpha atoms which are modeled with modest accuracy. METHODOLOGY/PRINCIPAL FINDINGS: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C(alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C(alpha. We extend the method further to recognize potential protein-protein interface residues. CONCLUSION/ SIGNIFICANCE: Our approach to identify buried and exposed residues solely from the positions of C(alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C(alpha positions and all-atom models suggested that, recognition of interfacial residues using C(alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only (alpha positions are available as, for example, in the cases of integration of cryo

  19. On the size and structure of helium snowballs formed around charged atoms and clusters of noble gases.

    Science.gov (United States)

    Bartl, Peter; Leidlmair, Christian; Denifl, Stephan; Scheier, Paul; Echt, Olof

    2014-09-18

    Helium nanodroplets doped with argon, krypton, or xenon are ionized by electrons and analyzed in a mass spectrometer. HenNgx(+) ions containing up to seven noble gas (Ng) atoms and dozens of helium atoms are identified;