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1

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

E-print Network

LETTERS Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy identification of all the atoms in a material with unknown three-dimensional structure would con- stitute a very. The results demon- strate that atom-by-atom structural and chemical analysis of all radiation

Pennycook, Steve

2

Atomic structure of clusters through chemical reactions  

SciTech Connect

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.

Riley, S.J.

1991-01-01

3

Structural and chemical characterization of complex nanomaterials at atomic resolution  

NASA Astrophysics Data System (ADS)

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

Sanchez, Sergio I.

4

Deducing chemical structure from crystallographically determined atomic coordinates  

PubMed Central

An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

2011-01-01

5

Atomic Structure  

NSDL National Science Digital Library

In this activity students explore the structure and properties of atoms. They construct models of atoms with properties of particular mass and charge; create models of atoms with different stabilities by adding or subtracting neutrons, protons, and electrons to a model atom; and determine that the same element may have varying number of neutrons and these form isotopes.Students will be able to:

The Concord Consortium

2011-12-11

6

Determining Chemically and Spatially Resolved Atomic Profile of Low Contrast Interface Structure with High Resolution  

PubMed Central

We present precise measurements of atomic distributions of low electron density contrast at a buried interface using soft x-ray resonant scattering. This approach allows one to construct chemically and spatially highly resolved atomic distribution profile upto several tens of nanometer in a non-destructive and quantitative manner. We demonstrate that the method is sensitive enough to resolve compositional differences of few atomic percent in nano-scaled layered structures of elements with poor electron density differences (0.05%). The present study near the edge of potential impurities in soft x-ray range for low-Z system will stimulate the activity in that field. PMID:25726866

Nayak, Maheswar; Pradhan, P. C.; Lodha, G. S.

2015-01-01

7

Determining Chemically and Spatially Resolved Atomic Profile of Low Contrast Interface Structure with High Resolution  

NASA Astrophysics Data System (ADS)

We present precise measurements of atomic distributions of low electron density contrast at a buried interface using soft x-ray resonant scattering. This approach allows one to construct chemically and spatially highly resolved atomic distribution profile upto several tens of nanometer in a non-destructive and quantitative manner. We demonstrate that the method is sensitive enough to resolve compositional differences of few atomic percent in nano-scaled layered structures of elements with poor electron density differences (0.05%). The present study near the edge of potential impurities in soft x-ray range for low-Z system will stimulate the activity in that field.

Nayak, Maheswar; Pradhan, P. C.; Lodha, G. S.

2015-03-01

8

Predicting the chemical composition and structure of Aspergillus nidulans hyphal wall surface by atomic force microscopy  

Microsoft Academic Search

In fungi, cell wall plays an important role in growth and development. Major macromolecular constituents of the aspergilli\\u000a cell wall are glucan, chitin, and protein. We examined the chemical composition and structure of the Aspergillus nidulans hyphal wall surface by an atomic force microscope (AFM). To determine the composition of the cell wall surface, the adhesion\\u000a forces of commercially available

Hyun-uk Lee; Jong Bae Park; Haeseong Lee; Keon-Sang Chae; Dong-Min Han; Kwang-Yeop Jahng

2010-01-01

9

Quantitative Statistical Analysis of Atomic Scale Structural and Chemical Variations in Complex Oxides Interfaces  

NASA Astrophysics Data System (ADS)

Grain boundaries (GBs) are known to have far-reaching effects on the electrical and mechanical properties of materials. Understanding the atomic scale mechanisms behind these effects requires an accurate determination of the interplay between GB structure and composition. Based on the analysis of a range of grain boundaries using aberration corrected scanning transmission electron microscopy (STEM), a general structural units model has been derived for the structure of grain boundaries in various dense packing cubic materials including FCC metals, perovskites and fluorites. The similarities in the observed grain boundary structures of these materials originate from related space (and point) group symmetries of the parent structures. The presence of structural variations away from the general structural units model may be caused by frustrations of certain symmetry operations that result from the incorporation of point defects (vacancies and impurities). A clear understanding of the similarity and variation in grain boundary atomic structures will not only provide a means to infer the structure-property relationships in broad classes of materials, but also enables us eventually to effectively manipulate the GB structures to achieve better materials properties. To understand these chemical induced variations, and further quantify exactly how atomic scale variations at the boundary plane extend to the practical mesoscale operating length of the system, statistical analysis has been applied to the aberration corrected STEM Z-contrast images acquired from a series of undoped and doped SrTiO3 GBs. In order to understand the effects of oxygen vacancies incorporation, in-situ characterization of GB atomic structures were performed using the Environmental TEM under the reduced gas and heating environment. This analysis of GB similarity and variation provides insights into the structure-composition relationship in GBs to understand the influence of nonstoichiometry and dopant segregations. It also helps to determine experimentally the energetics behind the formation of grain boundary structures to predict GB formation in various materials.

Yang, Hao

10

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

NASA Technical Reports Server (NTRS)

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

Kahn, L. R.

1981-01-01

11

Atomic Structure: Investigating Atoms  

NSDL National Science Digital Library

Science Objects are two hour on-line interactive inquiry-based content modules that help teachers better understand the science content they teach. This Science Object is the first of three Science Objects in the Atomic Structure SciPack. It discusses the

National Science Teachers Association (NSTA)

2010-05-24

12

Atomic and Molecular Structure in Chemical Education: A Critical Analysis from Various Perspectives of Science Education  

NASA Astrophysics Data System (ADS)

With the development during the past few decades of chemical education (and in general of science education) as a research discipline, the place of structural theories and concepts has undergone strong criticism. The main reason for this criticism is the difficulty students encounter in dealing with these concepts. An explanation of this difficulty occurs if one examines the relevant concepts from different perspectives of science education, some of which many researchers consider as conflicting theories. The perspectives employed in this paper are (i) the Piagetian developmental perspective, (ii) the Ausbelian theory of meaningful learning, (iii) the information processing theory, and (iv) the alternative conceptions movement. The implications for teaching and curriculums are discussed with respect to the following: (a) Atoms and molecules as structural units of matter; (b) classification of substances according to their electrical character; (c) teaching introductory chemistry in three cycles: macro, representational and submicro; (d) the historical method of teaching; and (e) the modern quantum mechanical structural theories.

Tsaparlis, Georgios

1997-08-01

13

Probing Atomic and Electronic Structure of Catalysts by Combination of In Situ and Ex Situ Chemical Imaging  

E-print Network

Probing Atomic and Electronic Structure of Catalysts by Combination of In Situ and Ex Situ Chemical Karim, Robert Dagle, Ja Hun Kwak, Janos Szanyi, Charles Peden Purpose Understand the structural capabilities that enable this understanding Directly relate structural information with the catalytic

14

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

PubMed

Resolving individual atoms has always been the ultimate goal of surface microscopy. The scanning tunneling microscope images atomic-scale features on surfaces, but resolving single atoms within an adsorbed molecule remains a great challenge because the tunneling current is primarily sensitive to the local electron density of states close to the Fermi level. We demonstrate imaging of molecules with unprecedented atomic resolution by probing the short-range chemical forces with use of noncontact atomic force microscopy. The key step is functionalizing the microscope's tip apex with suitable, atomically well-defined terminations, such as CO molecules. Our experimental findings are corroborated by ab initio density functional theory calculations. Comparison with theory shows that Pauli repulsion is the source of the atomic resolution, whereas van der Waals and electrostatic forces only add a diffuse attractive background. PMID:19713523

Gross, Leo; Mohn, Fabian; Moll, Nikolaj; Liljeroth, Peter; Meyer, Gerhard

2009-08-28

15

Second Exam All atoms, chemical bonding and structures must be complete and correct for full credit. Please print and sign  

E-print Network

1 BIOL 213 Second Exam All atoms, chemical bonding and structures must be complete and correct. Explain the GU/AG rule in Group III intron removal, and the role of the spliceosome. #12;4 (10 pt) 7 can be processed in several ways. Identify five (5) co-translational or post-translational protein

Summers, Max D.

16

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

NASA Astrophysics Data System (ADS)

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 B?-sites and Fe0.20Ti0.80 at B??-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.

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

2014-02-01

17

Atomic-scale chemical imaging and quantification of metallic alloy structures by energy-dispersive X-ray spectroscopy.  

PubMed

Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L2(1) phase with Ni0.48Co0.52 at A-sites, Al at B(?)-sites and Fe0.20Ti0.80 at B(??)-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

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

2014-01-01

18

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

SciTech Connect

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 B?-sites and Fe0.20Ti0.80 at B??-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.

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

2014-02-04

19

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

PubMed Central

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 B?-sites and Fe0.20Ti0.80 at B??-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

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

2014-01-01

20

Atomic Structure: Properties of Atoms  

NSDL National Science Digital Library

Science Objects are two hour on-line interactive inquiry-based content modules that help teachers better understand the science content they teach. This Science Object is the second of three Science Objects in the Atomic Structure SciPack. It explores the

National Science Teachers Association (NSTA)

2010-05-24

21

Atomic Structure: Energy in Atoms  

NSDL National Science Digital Library

Science Objects are two hour on-line interactive inquiry-based content modules that help teachers better understand the science content they teach. This Science Object is the third of three Science Objects in the Atomic Structure SciPack. It investigates

National Science Teachers Association (NSTA)

2010-05-24

22

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

NASA Technical Reports Server (NTRS)

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.

Kahn, L. R.

1982-01-01

23

Atomic Structure Timeline  

NSDL National Science Digital Library

Lee Buescher is a microbiology and chemistry instructor at Watertown High School in Watertown, WI. He maintains the Atomic Structure Timeline page. The timeline follows major discoveries and advancements throughout history related to atomic structure. From Democritus to Bohr to modern day scientists, the descriptions and links explain the individual and what they accomplished.

Buescher, Lee.

24

Strain and structure heterogeneity in MoS2 atomic layers grown by chemical vapour deposition  

NASA Astrophysics Data System (ADS)

Monolayer molybdenum disulfide (MoS2) has attracted tremendous attention due to its promising applications in high-performance field-effect transistors, phototransistors, spintronic devices and nonlinear optics. The enhanced photoluminescence effect in monolayer MoS2 was discovered and, as a strong tool, was employed for strain and defect analysis in MoS2. Recently, large-size monolayer MoS2 has been produced by chemical vapour deposition, but has not yet been fully explored. Here we systematically characterize chemical vapour deposition-grown MoS2 by photoluminescence spectroscopy and mapping and demonstrate non-uniform strain in single-crystalline monolayer MoS2 and strain-induced bandgap engineering. We also evaluate the effective strain transferred from polymer substrates to MoS2 by three-dimensional finite element analysis. Furthermore, our work demonstrates that photoluminescence mapping can be used as a non-contact approach for quick identification of grain boundaries in MoS2.

Liu, Zheng; Amani, Matin; Najmaei, Sina; Xu, Quan; Zou, Xiaolong; Zhou, Wu; Yu, Ting; Qiu, Caiyu; Birdwell, A. Glen; Crowne, Frank J.; Vajtai, Robert; Yakobson, Boris I.; Xia, Zhenhai; Dubey, Madan; Ajayan, Pulickel M.; Lou, Jun

2014-11-01

25

Theories of Atomic Structure  

Microsoft Academic Search

IN a letter to NATURE (March 11, p. 41) S. C. Bradford stated: ``The great objection to Langmuir's theory of atomic structure is the difficulty of accepting his hypothesis of stationary eletrons.'' The cases cited are all discussed in G. N. Lewis's paper, ``The Atom and the Molecule'' (Journ. Amer. Chem. Soc, xxxviii., p. 762, April, 1916), so it is

Irving Langmuir

1920-01-01

26

Chemical identification of individual surface atoms by atomic force microscopy.  

PubMed

Scanning probe microscopy is a versatile and powerful method that uses sharp tips to image, measure and manipulate matter at surfaces with atomic resolution. At cryogenic temperatures, scanning probe microscopy can even provide electron tunnelling spectra that serve as fingerprints of the vibrational properties of adsorbed molecules and of the electronic properties of magnetic impurity atoms, thereby allowing chemical identification. But in many instances, and particularly for insulating systems, determining the exact chemical composition of surfaces or nanostructures remains a considerable challenge. In principle, dynamic force microscopy should make it possible to overcome this problem: it can image insulator, semiconductor and metal surfaces with true atomic resolution, by detecting and precisely measuring the short-range forces that arise with the onset of chemical bonding between the tip and surface atoms and that depend sensitively on the chemical identity of the atoms involved. Here we report precise measurements of such short-range chemical forces, and show that their dependence on the force microscope tip used can be overcome through a normalization procedure. This allows us to use the chemical force measurements as the basis for atomic recognition, even at room temperature. We illustrate the performance of this approach by imaging the surface of a particularly challenging alloy system and successfully identifying the three constituent atomic species silicon, tin and lead, even though these exhibit very similar chemical properties and identical surface position preferences that render any discrimination attempt based on topographic measurements impossible. PMID:17330040

Sugimoto, Yoshiaki; Pou, Pablo; Abe, Masayuki; Jelinek, Pavel; Pérez, Rubén; Morita, Seizo; Custance, Oscar

2007-03-01

27

Atom Probe Tomography Frontiers in Chemical Imaging  

E-print Network

Atom Probe Tomography Frontiers in Chemical Imaging Seminar Series Presented by... M.K. Miller overview of the history of the atom probe tomography (APT) technique and instruments will be presented, from the early field ion microscopy experiments in which images of individual atoms were obtained

28

Influence of krypton atoms on the structure of hydrogenated amorphous carbon deposited by plasma enhanced chemical vapor deposition  

SciTech Connect

Hydrogenated amorphous carbon (a-C:H) films were prepared by plasma enhanced chemical vapor deposition using methane (CH{sub 4}) plus krypton (Kr) mixed atmosphere. The depositions were performed as function of the bias voltage and krypton partial pressure. The goal of this work was to study the influence of krypton gas on the physical properties of a-C:H films deposited on the cathode electrode. Krypton concentration up to 1.6 at. %, determined by Rutherford Back-Scattering, was obtained at high Kr partial pressure and bias of -120 V. The structure of the films was analyzed by means of optical transmission spectroscopy, multi-wavelength Raman scattering and Fourier Transform Infrared spectroscopy. It was verified that the structure of the films remains unchanged up to a concentration of Kr of about 1.0 at. %. A slight graphitization of the films occurs for higher concentration. The observed variation in the film structure, optical band gap, stress, and hydrogen concentration were associated mainly with the subplantation process of hydrocarbons radicals, rather than the krypton ion energy.

Oliveira, M. H. Jr. [Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas-UNICAMP, C. P. 6165, Campinas, Sao Paulo 13083-970 (Brazil); Institut de Ciencia dels Materials, Universitat de Valencia, E-46071 Valencia (Spain); Viana, G. A.; Marques, F. C. [Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas-UNICAMP, C. P. 6165, Campinas, Sao Paulo 13083-970 (Brazil); Lima, M. M. Jr. de; Cros, A.; Cantarero, A. [Institut de Ciencia dels Materials, Universitat de Valencia, E-46071 Valencia (Spain)

2010-12-15

29

Exploring Conceptual Frameworks of Models of Atomic Structures and Periodic Variations, Chemical Bonding, and Molecular Shape and Polarity: A Comparison of Undergraduate General Chemistry Students with High and Low Levels of Content Knowledge  

ERIC Educational Resources Information Center

The purpose of the study was to explore students' conceptual frameworks of models of atomic structure and periodic variations, chemical bonding, and molecular shape and polarity, and how these conceptual frameworks influence their quality of explanations and ability to shift among chemical representations. This study employed a purposeful sampling…

Wang, Chia-Yu; Barrow, Lloyd H.

2013-01-01

30

Orientation dependences of atomic structures in chemically heterogeneous Cu50Ta50/Ta glass-crystal interfaces  

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations based on an angular-dependent potential were performed to examine the structural properties of chemically heterogeneous interfaces between amorphous Cu50Ta50 and crystalline Ta. Several phenomena, namely, layering, crystallization, intermixing, and composition segregation, were observed in the Cu50Ta50 region adjacent to the Ta layers. These interfacial behaviors are found to depend on the orientation of the underlying Ta substrate: Layering induced by Ta(110) extends the farthest into Cu50Ta50, crystallization in the Cu50Ta50 region is most significant for interface against Ta(100), while inter-diffusion is most pronounced for Ta(111). It turns out that the induced layering behavior is dominated by the interlayer distances of the underlying Ta layers, while the degree of inter-diffusion is governed by the openness of the Ta crystalline layers. In addition, composition segregations are observed in all interface models, corresponding to the immiscible nature of the Cu-Ta system. Furthermore, Voronoi polyhedra ?0,5,2,6? and ?0,4,4,6? are found to be abundant in the vicinity of the interfaces for all models, whose presence is believed to facilitate the structural transition between amorphous and body centered cubic.

Yang, Guiqin; Gao, Xiaoze; Li, Jinfu; Kong, Lingti

2015-01-01

31

3-Dimensional atomic scale structure of the ionic liquid-graphite interface elucidated by AM-AFM and quantum chemical simulations  

NASA Astrophysics Data System (ADS)

In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition.In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01219d

Page, Alister J.; Elbourne, Aaron; Stefanovic, Ryan; Addicoat, Matthew A.; Warr, Gregory G.; Voïtchovsky, Kislon; Atkin, Rob

2014-06-01

32

Atomic and electronic structure of carbon strings.  

PubMed

This paper presents an extensive study of various string and tubular structures formed by carbon atomic chains. Our study is based on first-principles pseudopotential plane wave and finite-temperature ab initio molecular dynamics calculations. Infinite- and finite-length carbon chains exhibit unusual mechanical and electronic properties such as large cohesive energy, axial strength, high conductance, and overall structural stability even at high temperatures. They are suitable for structural and chemical functionalizations. Owing to their flexibility and reactivity they can form linear chain, ring, helix, two-dimensional rectangular and honeycomb grids, three-dimensional cubic networks, and tubular structures. Metal-semiconductor heterostructures and various quantum structures, such as multiple quantum wells and double-barrier resonant tunnelling structures, can be formed from the junctions of metallic carbon and semiconducting BN linear chains. Analysis of atomic and electronic structures of these periodic, finite, and doped structures reveals fundamentally and technologically interesting features, such as structural instabilities and chiral currents. The double covalent bonding of carbon atoms depicted through self-consistent charge density analysis underlies the chemical, mechanical, and electronic properties. PMID:21690699

Tongay, S; Dag, S; Durgun, E; Senger, R T; Ciraci, S

2005-06-29

33

Atomic Structure and Valence: Level II, Unit 10, Lesson 1; Chemical Bonding: Lesson 2; The Table of Elements: Lesson 3; Electrolysis: Lesson 4. Advanced General Education Program. A High School Self-Study Program.  

ERIC Educational Resources Information Center

This self-study program for high-school level contains lessons on: Atomic Structure and Valence, Chemical Bonding, The Table of Elements, and Electrolysis. Each of the lessons concludes with a Mastery Test to be completed by the student. (DB)

Manpower Administration (DOL), Washington, DC. Job Corps.

34

Morphology and atomic structure of hydrogen-terminated Si(110)-(1 × 1) surfaces prepared by a wet chemical process  

NASA Astrophysics Data System (ADS)

We have measured the macroscopic and microscopic surface morphology of hydrogen-terminated Si(110)-(1 × 1) [H:Si(110)-(1 × 1)] surfaces prepared by an improved wet chemical process. The observations were performed by high-resolution electron-energy-loss spectroscopy (HREELS), low-energy-electron diffraction (LEED), and scanning tunneling microscopy (STM). At macroscopic scale, it was found that the surface is a mono-hydride terminated surface with a two-dimensional p2mg space group, thus, being a well-defined H:Si(110)-(1 × 1) surface. At microscopic scale, elongated terraces were observed along the [1 1 bar0] direction reflecting surface anisotropy. The terraces extend in frames with sizes up to a few micrometers. We discussed the macroscopic and microscopic surface morphology by combining our LEED and STM results.

Matsushita, Stephane Yu; Kawamoto, Erina; Haga, Kenya; Yamada, Taro; Suto, Shozo

2015-02-01

35

Chemical evolution STRUCTURE OF GALAXIES  

E-print Network

Outline Absorption Chemical evolution STRUCTURE OF GALAXIES 8. Absorption; chemical evolution Piet Piet van der Kruit, Kapteyn Astronomical Institute Absorption; chemical evolution #12;Outline Absorption Chemical evolution Outline Absorption Holmberg's analysis Analysis of Disney et al. Edge

Kruit, Piet van der

36

RADIOACTIVE CHEMICAL ELEMENTS IN THE ATOMIC TABLE.  

SciTech Connect

In the 1949 Report of the Atomic Weights Commission, a series of new elements were added to the Atomic Weights Table. Since these elements had been produced in the laboratory and were not discovered in nature, the atomic weight value of these artificial products would depend upon the production method. Since atomic weight is a property of an element as it occurs in nature, it would be incorrect to assign an atomic weight value to that element. As a result of that discussion, the Commission decided to provide only the mass number of the most stable (longest-lived) known isotope as the number to be associated with these entries in the Atomic Weights Table. As a function of time, the mass number associated with various elements has changed as longer-lived isotopes of a particular elements has been found in nature, or as improved half-life values of an element's isotopes might cause a shift in the longest-lived isotope from one mass number to another. In the 1957 Report of the Atomic Weights Commission, it was decided to discontinue the listing of the mass number in the Atomic Weights Table on the grounds that the kind of information supplied by the mass number is inconsistent with the primary purpose of the Table, i.e., to provide accurate values of ''these constants'' for use in chemical calculations. In addition to the Table of Atomic Weights, the Commission included an auxiliary Table of Radioactive Elements for the first time, where the entry would be the isotope of that element which was most stable, i.e., it had the longest known half-life. In their 1973 report, the Commission noted that the users of the Atomic Weights Table were dissatisfied with the omission of values in the Table for some elements and it was decided to reintroduce the mass number for elements. In their 1983 report, the Commission decided that radioactive elements were considered to lack a characteristic terrestrial isotopic composition, from which an atomic weight value could be calculated to five or more figure accuracy, without prior knowledge of the sample. These elements were again listed in the table with no further information, is., no mass number or atomic weight value. For the elements, which have no stable or long-lived isotopes, the data on radioactive half-lives and relative atomic masses for the nuclides of interest have been evaluated. The values of the half-lives their uncertainties are listed. The uncertainties are given in the last digit quoted of the half-life vale and shown in parentheses. The criteria for consideration of entries in this Table continue to be the same as it has been for over fifty years. It is the same criteria, which are used for all data that are evaluated for inclusion in the Atomic Weight's Table. If a report of data is published in a peer-reviewed journal, that data is evaluated and considered for inclusion in the appropriate table of the biennial report of the Atomic Weights Commission. As better data might become available in the future, the information that is contained in either of the tables may be modified. The information contained in the Table of Radioactive Elements should enable the user to calculate the atomic weight for any sample of radioactive material, which might have a variety of isotopic compositions. The atomic mass values have been taken from the 2003 Atomic Mass Table. Most of these half-lives have already been documented in various sources.

HOLDEN, N.E.

2005-08-13

37

Atomic Structure of Carbon Nanomaterials  

E-print Network

Materials #12;Atomistic model of pyrolytic carbons Jean-Marc Leyssale et al. APPLIED PHYSICS LETTERS 95Atomic Structure of Carbon Nanomaterials: Physics and Characterization Jian-Min (Jim) Zuo;Outline of This Talk I. Structure of carbon nanomaterials II. Electron diffraction III. Growth

Zuo, Jian-Min "Jim"

38

Elastic and structural properties and buckling behavior of single-walled carbon nanotubes under chemical adsorption of atomic oxygen and hydroxyl  

NASA Astrophysics Data System (ADS)

Atomic decoration of carbon nanotubes (CNTs) is an effective way to alter the key properties of pristine CNTs. Elastic properties and axial buckling behavior of atomic oxygen and hydroxyl chemisorbed single-walled CNTs are explored employing molecular dynamics (MD) simulations. Our results demonstrate that the structure of chemisorbed CNTs changes compared to pristine CNT which considerably depends on the distribution pattern of chemisorbed oxygen and -hydroxyl. The results also demonstrate that chemisorption of atomic oxygen and -hydroxyl reduces Young's modulus and critical strain while increases the critical force of CNTs. Buckling mode shape of chemisorbed CNTs depends on the distribution pattern.

Ansari, R.; Ajori, S.; Ameri, A.

2014-11-01

39

Atomic Structure in Black Hole  

E-print Network

We propose that any black hole has atomic structure in its inside and has no horizon as a model of black holes. Our proposal is founded on a mean field approximation of gravity. The structure of our model consists of a (charged) singularity at the center and quantum fluctuations of fields around the singularity, namely, it is quite similar to that of atoms. Any properties of black holes, e.g. entropy, can be explained by the model. The model naturally quantizes black holes. In particular, we find the minimum black hole, whose structure is similar to that of the hydrogen atom and whose Schwarzschild radius is approximately 1.1287 times the Planck length. Our approach is conceptually similar to the Bohr's model of the atomic structure, and the concept of the minimum Schwarzschild radius is similar to that of the Bohr radius. The model predicts that black holes carry baryon number, and the baryon number is rapidly violated. This baryon number violation can be used as verification of the model.

Yukinori Nagatani

2006-11-27

40

Relativistic calculation of atomic structures  

Microsoft Academic Search

The current state of the art in relativistic calculation of atomic structures is surveyed. The theory is modelled on the practice in non-relativistic calculations, using many-particle wave functions built from Dirac central field spinors. The Hamiltonian includes quantum electrodynamic effects in the form of the Breit approximation for the interaction energy of two electrons. Within the limits for which this

I. P. Grant

1970-01-01

41

The atomic structure of transition metal clusters  

SciTech Connect

Chemical reactions are used to probe the atomic (geometrical) structure of isolated clusters of transition metal atoms. The number of adsorbate molecules that saturate a cluster, and/or the binding energy of molecules to cluster surfaces, are determined as a function of cluster size. Systematics in these properties often make it possible to propose geometrical structures consistent with the experimental observations. We will describe how studies of the reactions of cobalt and nickel clusters with ammonia, water, and nitrogen provide important and otherwise unavailable structural information. Specifically, small (less than 20 atoms) clusters of cobalt and nickel atoms adopt entirely different structures, the former having packing characteristic of the bulk and the latter having pentagonal symmetry. These observations provide important input for model potentials that attempt to describe the local properties of transition metals. In particular, they point out the importance of a proper treatment of d-orbital binding in these systems, since cobalt and nickel differ so little in their d-orbital occupancy.

Riley, S.J.

1995-08-01

42

Chemical Bonding: The Classical Description sharing or transferring electrons between atoms  

E-print Network

Chemical Bonding: The Classical Description sharing or transferring electrons between atoms LEWIS Structure (w/o quantum mechanics) Chapter. 3 Two or more atoms approach -> their electrons interact and form new arrangements of electrons with lower total potential energy than isolated atoms covalent ionic

Ihee, Hyotcherl

43

COMBUSTION DRIVEN ATOMIC FLUORINE GENERATORS FOR DF CHEMICAL LASERS Abstract -Conventional high pressure corabustors delivering atomic fluorine for DF chemical  

E-print Network

COMBUSTION DRIVEN ATOMIC FLUORINE GENERATORS FOR DF CHEMICAL LASERS Abstract - Conventional high pressure corabustors delivering atomic fluorine for DF chemical lasers have been designed and tested been obtained between the maximum laser power and the predicted best conditions of atomic fluorine

Paris-Sud XI, Université de

44

Atomic structure of titania nanosheet with vacancies  

PubMed Central

Titania nanosheets are two-dimensional single crystallites of titanium oxide with a thickness of one titanium or two oxygen atoms, and they show attractive material properties, such as photocatalytic reactions. Since a titania (Ti0.87O2) nanosheet is synthesized by the delamination of a parent layered K0.8Ti1.73Li0.27O4 crystal using a soft chemical procedure, substantial Ti vacancies are expected to be included and affect the material properties. The atomic arrangement of a titania nanosheet with vacancies has not been revealed owing to the difficulties of direct observation. Here, we have directly visualized the atomic arrangement and Ti vacancies of a titania nanosheet using advanced lower-voltage transmission electron microscopy (TEM). Analyses of the results of first-principles calculations and TEM image simulations for various Ti vacancy structure models indicate that two particular oxygen atoms around each Ti vacancy are desorbed, suggesting the sites where atomic reduction first occurs. PMID:24077611

Ohwada, Megumi; Kimoto, Koji; Mizoguchi, Teruyasu; Ebina, Yasuo; Sasaki, Takayoshi

2013-01-01

45

Chemical control of electrical contact to sp2 carbon atoms  

PubMed Central

Carbon-based nanostructures are attracting tremendous interest as components in ultrafast electronics and optoelectronics. The electrical interfaces to these structures play a crucial role for the electron transport, but the lack of control at the atomic scale can hamper device functionality and integration into operating circuitry. Here we study a prototype carbon-based molecular junction consisting of a single C60 molecule and probe how the electric current through the junction depends on the chemical nature of the foremost electrode atom in contact with the molecule. We find that the efficiency of charge injection to a C60 molecule varies substantially for the considered metallic species, and demonstrate that the relative strength of the metal-C bond can be extracted from our transport measurements. Our study further suggests that a single-C60 junction is a basic model to explore the properties of electrical contacts to meso- and macroscopic sp2 carbon structures. PMID:24736561

Frederiksen, Thomas; Foti, Giuseppe; Scheurer, Fabrice; Speisser, Virginie; Schull, Guillaume

2014-01-01

46

Physical Construction of the Chemical Atom: Is it Convenient to Go All the Way Back?  

NASA Astrophysics Data System (ADS)

In this paper we present an analysis of chemistry texts (mainly textbooks) published during the first half of the 20th century. We show the evolution of the explanations therein in terms of atoms and of atomic structure, when scientists were interpreting phenomena as evidence of the discontinuous, corpuscular structure of matter. In this process of evidence construction, new contributions from physicists and physical chemists that were incorporated to chemical research acquired ‘chemical’ meaning, since they were related to research questions that genuinely came from chemistry. Conversely, the core ideas of 19th-century chemical atomism, among which we must highlight valence and Mendeleev’s periodic system, provided ‘clues’ for imagining an atom in terms of the elements adjusted to their chemical behaviour, which changed periodically as a function of atomic mass. With this, chemistry ceased to be a descriptive science and began to be a ‘law-based’, theoretical science. Little by little, chemistry teaching became the teaching of the internal structure of atoms, which were arranged in the Periodic Table according to criteria and ‘construction rules’ related to quantum mechanics. We pose the question: ‘how can we now teach general chemistry in a way that does not disregard current knowledge about the structure of the atom yet, at the same time, gives priority to chemical criteria, thus making such structure useful to interpret chemical change?’.

Izquierdo-Aymerich, Mercè; Adúriz-Bravo, Agustín

2009-04-01

47

Noncontiguous atom matching structural similarity function.  

PubMed

Measuring similarity between molecules is a fundamental problem in cheminformatics. Given that similar molecules tend to have similar physical, chemical, and biological properties, the notion of molecular similarity plays an important role in the exploration of molecular data sets, query-retrieval in molecular databases, and in structure-property/activity modeling. Various methods to define structural similarity between molecules are available in the literature, but so far none has been used with consistent and reliable results for all situations. We propose a new similarity method based on atom alignment for the analysis of structural similarity between molecules. This method is based on the comparison of the bonding profiles of atoms on comparable molecules, including features that are seldom found in other structural or graph matching approaches like chirality or double bond stereoisomerism. The similarity measure is then defined on the annotated molecular graph, based on an iterative directed graph similarity procedure and optimal atom alignment between atoms using a pairwise matching algorithm. With the proposed approach the similarities detected are more intuitively understood because similar atoms in the molecules are explicitly shown. This noncontiguous atom matching structural similarity method (NAMS) was tested and compared with one of the most widely used similarity methods (fingerprint-based similarity) using three difficult data sets with different characteristics. Despite having a higher computational cost, the method performed well being able to distinguish either different or very similar hydrocarbons that were indistinguishable using a fingerprint-based approach. NAMS also verified the similarity principle using a data set of structurally similar steroids with differences in the binding affinity to the corticosteroid binding globulin receptor by showing that pairs of steroids with a high degree of similarity (>80%) tend to have smaller differences in the absolute value of binding activity. Using a highly diverse set of compounds with information about the monoamine oxidase inhibition level, the method was also able to recover a significantly higher average fraction of active compounds when the seed is active for different cutoff threshold values of similarity. Particularly, for the cutoff threshold values of 86%, 93%, and 96.5%, NAMS was able to recover a fraction of actives of 0.57, 0.63, and 0.83, respectively, while the fingerprint-based approach was able to recover a fraction of actives of 0.41, 0.40, and 0.39, respectively. NAMS is made available freely for the whole community in a simple Web based tool as well as the Python source code at http://nams.lasige.di.fc.ul.pt/. PMID:24044748

Teixeira, Ana L; Falcao, Andre O

2013-10-28

48

Development of a chemical oxygen - iodine laser with production of atomic iodine in a chemical reaction  

SciTech Connect

The alternative method of atomic iodine generation for a chemical oxygen - iodine laser (COIL) in chemical reactions with gaseous reactants is investigated experimentally. The influence of the configuration of iodine atom injection into the laser cavity on the efficiency of the atomic iodine generation and small-signal gain is studied. (lasers)

Censky, M; Spalek, O; Jirasek, V; Kodymova, J [Institute of Physics, Czech Academy of Sciences, Prague (Czech Republic); Jakubec, I [Institute of Inorganic Chemistry, Czech Academy of Sciences, Rez (Czech Republic)

2009-11-30

49

The Structure of the Helium Atom  

Microsoft Academic Search

Models for the Helium Atom.-(1) Bohr's model is unsatisfactory because it gives too great a value for the ionizing potential and is not in accord with the optical and magnetic properties of helium. Now the chemical evidence suggests that each electron in an atom has its own separate orbit, and that these orbits are closely interrelated. Accordingly two new models

Irving Langmuir

1921-01-01

50

Chemical structure and dynamics: Annual report 1993  

SciTech Connect

The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

Colson, S.D.

1994-07-01

51

A source of atomic oxygen for a chemical CO laser  

Microsoft Academic Search

A supersonic chemical CO laser employing a CS2\\/O2 mixture is proposed in which the equilibrium products of the combustion of sulfur in oxygen are used as a source of atomic oxygen. Theoretical calculations are presented which show that supersonic flows containing about 15 percent of oxygen atoms can be generated by this method over a wide range of pressures and

T. V. Bystrova; Iu. L. Chizhov

1985-01-01

52

The Atomic Structure of Oxide\\/Oxide Interface  

Microsoft Academic Search

The physical and chemical properties of thin or ultrathin oxide film deposited on another oxide bulk or thin film usually differ strongly from the bulk. The properties of the heterostructures ultimately rely on the structure and the chemistry of the oxide\\/oxide interface. Data in the literature indicated that atomically abrupt interfaces between oxides show abnormal electronic and magnetic properties. This

Qi-Hui Wu

2011-01-01

53

Local atomic structures in Zr-Ni metallic glasses  

NASA Astrophysics Data System (ADS)

Local atomic structures of ZrNi ( x=33.3, 36, 50 at%) binary metallic glasses were investigated by means of extended X-ray absorption fine structure (EXAFS) probe. Structural parameters show that the Zr-Ni bond length, R, keeps a constant value of 2.62 Å, regardless of alloy compositions. This result implies that there is a strongly chemical interaction between Zr and Ni atoms, leading to significant chemical short-range orders (CSROs) in the present metallic glasses. Further analysis indicates that the SRO structures in these metallic glasses are extremely similar with those in their crystalline counterparts. It is interesting to note that the CSROs in the eutectic Zr 64Ni 36 metallic glass consist of Zr 2Ni-like and ZrNi-like CSROs.

Liu, X. J.; Hui, X. D.; Chen, G. L.; Liu, T.

2009-06-01

54

Unraveling the Atomic Structure of Ultrafine Iron Clusters  

PubMed Central

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. PMID:23251781

Wang, Hongtao; Li, Kun; Yao, Yingbang; Wang, Qingxiao; Cheng, Yingchun; Schwingenschlögl, Udo; Zhang, Xi Xiang; Yang, Wei

2012-01-01

55

Digital Resource Package for Teaching Atomic Structure  

NSDL National Science Digital Library

This digital resource package is a collection of online sources to help K-12 teachers create lessons on the Chemistry subject of atomic structures. Topics include The History of the Atom, Reference Material, Tutorials, Simulations, Questions and Activities, Periodic Tables, and resources for more advanced learners.

Laura Moin

56

Chemical Analysis of Impurity Boron Atoms in Diamond Using Soft X-ray Emission Spectroscopy  

SciTech Connect

To analyze the local structure and/or chemical states of boron atoms in boron-doped diamond, which can be synthesized by the microwave plasma-assisted chemical vapor deposition method (CVD-B-diamond) and the temperature gradient method at high pressure and high temperature (HPT-B-diamond), we measured the soft X-ray emission spectra in the CK and BK regions of B-diamonds using synchrotron radiation at the Advanced Light Source (ALS). X-ray spectral analyses using the fingerprint method and molecular orbital calculations confirm that boron atoms in CVD-B-diamond substitute for carbon atoms in the diamond lattice to form covalent B-C bonds, while boron atoms in HPT-B-diamond react with the impurity nitrogen atoms to form hexagonal boron nitride. This suggests that the high purity diamond without nitrogen impurities is necessary to synthesize p-type B-diamond semiconductors.

Muramatsu, Yasuji; Iihara, Junji; Takebe, Toshihiko; Denlinger, Jonathan D.

2008-03-29

57

Some Experiments in Atomic Structure  

ERIC Educational Resources Information Center

The role of spectral color slides in laboratory situations is discussed, then experiments for secondary school students concerning color and wave length, evidence of quantization, and the ionization energy of the hydrogen atom are outlined. Teaching guidelines for creating a set of spectrograms and photographic specifications are provided. (DT)

Logan, Kent R.

1974-01-01

58

Introduction to Atomic Structure: Demonstrations and Labs.  

ERIC Educational Resources Information Center

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

Ciparick, Joseph D.

1988-01-01

59

Atom structures of relation algebras Ian Hodkinson \\Lambda  

E-print Network

Atom structures of relation algebras Ian Hodkinson \\Lambda October 24, 1995 Abstract We study atom structures of relation algebras. We prove that the class of atom structures that arise from representable is not determined by its atom structure, by exhibiting two (countable) relation algebras with the same atom

Hodkinson, Ian

60

About the atomic structures of icosahedral quasicrystals  

NASA Astrophysics Data System (ADS)

This paper is a survey of the crystallographic methods that have been developed these last twenty five years to decipher the atomic structures of the icosahedral stable quasicrystals since their discovery in 1982 by D. Shechtman. After a brief recall of the notion of quasiperiodicity and the natural description of Z-modules in 3-dim as projection of regular lattices in N>3-dim spaces, we give the basic geometrical ingredients useful to describe icosahedral quasicrystals as irrational 3-dim cuts of ordinary crystals in 6-dim space. Atoms are described by atomic surfaces (ASs) that are bounded volumes in the internal (or perpendicular) 3-dim space and the intersections of which with the physical space are the actual atomic positions. The main part of the paper is devoted to finding the major properties of quasicrystalline icosahedral structures. As experimentally demonstrated, they can be described with a surprisingly few high symmetry ASs located at high symmetry special points in 6-dim space. The atomic structures are best described by aggregations and intersections of high symmetry compact interpenetrating atomic clusters. We show here that the experimentally relevant clusters are derived from one generic cluster made of two concentric triacontahedra scaled by ? and an external icosidodecahedron. Depending on which ones of the orbits of this cluster are eventually occupied by atoms, the actual atomic clusters are of type Bergman, Mackay, Tsai and others….

Quiquandon, Marianne; Gratias, Denis

2014-01-01

61

Sublattice Resolution Structural and Chemical Analysis of Individual CdSe Nanocrystals Using Atomic Number Contrast Scanning Transmission Electron Microscopy and Electron  

E-print Network

effects and the large surface-to-volume ratio. For instance, a 25 Ã? diameter CdS nanocrystal has a band embedded in MEH-PPV polymer films.The atomic column-resolved Z-STEM image provides information both distribution of the oxygen signal in the EELS measurement suggests a thin oxide layer on the nanocrystal

Pennycook, Steve

62

Organic structure determination using atomic-resolution scanning probe microscopy.  

PubMed

Nature offers a huge and only partially explored variety of small molecules with potential pharmaceutical applications. Commonly used characterization methods for natural products include spectroscopic techniques such as nuclear magnetic resonance spectroscopy and mass spectrometry. In some cases, however, these techniques do not succeed in the unambiguous determination of the chemical structure of unknown compounds. To validate the usefulness of scanning probe microscopy as an adjunct to the other tools available for organic structure analysis, we used the natural product cephalandole A, which had previously been misassigned, and later corrected. Our results, corroborated by density functional theory, demonstrate that direct imaging of an organic compound with atomic-resolution force microscopy facilitates the accurate determination of its chemical structure. We anticipate that our method may be developed further towards molecular imaging with chemical sensitivity, and will become generally useful in solving certain classes of natural product structures. PMID:20861896

Gross, Leo; Mohn, Fabian; Moll, Nikolaj; Meyer, Gerhard; Ebel, Rainer; Abdel-Mageed, Wael M; Jaspars, Marcel

2010-10-01

63

Local atomic structure in thin films of silicon nitride and silicon diimide produced by remote plasma-enhanced chemical-vapor deposition  

Microsoft Academic Search

We have grown thin films of silicon nitride by remote plasma-enhanced chemical-vapor deposition and have studied the chemical bonding by infrared absorption, x-ray photoelectron spectroscopy, Rutherford backscattering, and Auger-electron spectroscopy. Films were grown using two different gases as the source of nitrogen, N2 and NH3. We have found that films grown from N2 and deposited at substrate temperatures in excess

D. V. Tsu; G. Lucovsky; M. J. Mantini

1986-01-01

64

Electronic Structure and Chemical Reactivity  

NASA Astrophysics Data System (ADS)

A general theme of this survey is the electronic density as a source and carrier of the information about molecular structure and reactivity. First, the classical rules of the electronic structure and chemical reactivity are reexamined, stressing the continuity of ideas in chemistry and exposing the interrelations between their original, mostly intuitive basis, and more rigorous foundations within the Density Functional Theory (DFT). The conceptual advantages of the DFT approach are stressed and a distinction is made between changes in the ground-state density ([`]horizontal' displacements) and in a division of the fixed molecular density ([`]vertical' displacements). The molecular charge sensitivities for the global equilibrium (of the mutually open subsystems) and the constrained equilibrium (of the mutually closed subsystems) are summarized and expressed in terms of the principal second derivatives of the system energy. The DFT treatment of a wide variety of molecular responses, to be eventually used as reactivity indices, is briefly surveyed. A wealth of reactivity concepts originating from the DFT rooted charge sensitivity analysis is reviewed, including both the electronic and external potential related quantities. This overview also covers general criteria for the equilibrium distribution of electrons in molecular systems and their fragments, explicit relations between alternative sets of the conjugate state-parameters, reflecting the transformations between displacements (perturbations) of the controlled state variables into the equilibrium linear responses of their respective energy conjugates, and the DFT characterization of the embedded molecular fragments, e.g., atoms-in-molecules, reactants, etc. Recent developments in a [`]thermodynamic'-like approach to molecules and their constituent fragments are then summarized, with the entropic representation description provided by the information theory, and the elements of the [`]communication' system approach to the chemical bond multiplicities. In particular, the Hirshfeld partitioning of molecular one-electron densities (probabilities) is summarized and its minimum entropy deficiency basis is stressed. The same entropic principle can be used to derive the [`]stockholder' rule of dividing the joint many-electron probabilities and the local softness (Fukui function) characteristics of the electronic gas in the molecular/reactive systems and their constituent fragments. For example, the proportionality relations between the charge responses of subsystems in the molecular/reactive system and their [`]promolecular' reference, respectively, directly follow from the relevant minimum entropy deficiency principles formulated in terms of the local softness or Fukui function descriptors of molecular fragments. The charge sensitivities of the Hirshfeld fragments are examined and the surprisal analysis of molecular densities is advocated as an attractive interpretative tool, supplementary to the familiar density difference diagrams. The local equalization rules of the subsystem information-distance densities at the corresponding global value, which are satisfied by the Hirshfeld molecular fragments, are then emphasized. These local measures of the information distance with respect to the separated subsystems of the relevant promolecular reference are semi-quantitatively related to the molecular density difference function. The entropy representation [`]forces' driving the charge transfer (CT) between reactants in the donor-acceptor systems are defined. These CT affinities combine the familiar Fukui functions of the subsystems with the information-distance densities, i.e., the entropy representation [`]intensive' conjugates of the subsystem electron densities ([`]extensive' local state variables), and exactly vanish for the [`]stockholder' densities of reactants.

Nalewajski, Roman F.

65

Chemical Principles Revisited: Updating the Atomic Theory in General Chemistry.  

ERIC Educational Resources Information Center

Presents a descriptive overview of recent achievements in atomic structure to provide instructors with the background necessary to enhance their classroom presentations. Topics considered include hadrons, quarks, leptons, forces, and the unified fields theory. (JN)

Whitman, Mark

1984-01-01

66

Atomic Structure Schrdinger equation has approximate solutions for multi-  

E-print Network

Atomic Structure Schrödinger equation has approximate solutions for multi- electron atoms, which indicate that all atoms are like hydrogen Atomic Structure Schrödinger equation has approximate solutions 3s 3p 3d Energy hydrogen multi-electron #12;Atomic Structure · orbitals are populated by electrons

Zakarian, Armen

67

Quantum Structures of the Hydrogen Atom  

E-print Network

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

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

2014-05-28

68

Structural cluster analysis of chemical reactions in solution  

NASA Astrophysics Data System (ADS)

We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.

Gallet, Grégoire A.; Pietrucci, Fabio

2013-08-01

69

Making Matter: The Atomic Structure of Materials  

NSDL National Science Digital Library

The Institut Laue Langevin provides the Making Matter: The Atomic Structure of Materials Website. This site offers information as well as 3D structures of inorganic materials (such as salt) in the Inorganic Crystal Structure Database. Sections included at the site are Close Packing, Compounds, Bonding, and Gems & Minerals, among others. This site provides spectacular 3D images (.gif and VRML format) of inorganic materials and is well worth the visit.

70

Atomic-scale chemical quantification of oxide interfaces using energy-dispersive X-ray spectroscopy  

SciTech Connect

Atomic-scale quantification of chemical composition across oxide interfaces is important for understanding physical properties of epitaxial oxide nanostructures. Energy-dispersive X-ray spectroscopy (EDS) in an aberration-corrected scanning transmission electron microscope was used to quantify chemical composition across the interface of ferromagnetic La{sub 0.7}Sr{sub 0.3}MnO{sub 3} and antiferromagnetic BiFeO{sub 3} quantum structure. This research demonstrates that chemical composition at atomic columns can be quantified by Gaussian peak-fitting of EDS compositional profiles across the interface. Cation diffusion was observed at both A- and B-sublattice sites; and asymmetric chemical profiles exist across the interface, consistent with the previous studies.

Lu, Ping; Van Benthem, Mark [Sandia National Laboratories, P.O. Box 5800, MS 1411, Albuquerque, New Mexico 87185-1411 (United States)] [Sandia National Laboratories, P.O. Box 5800, MS 1411, Albuquerque, New Mexico 87185-1411 (United States); Xiong, Jie; Jia, Quanxi [Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2013-04-29

71

Chemical bonding and atomic structure in Y2O3:ZrO2-SrTiO3 layered heterostructures.  

PubMed

Repeating boundaries: the buried interfaces in artificial heterostructures produced by sequential deposition of nanosized units are critical to their properties. With density functional theory it was shown that in Y(2)O(3):ZrO(2) (YSZ) and SrTiO(3) (STO) heterostructures reconstruction of the interfaces between the component units is required to access the most favorable structure. PMID:22374790

Dyer, Matthew S; Darling, George R; Claridge, John B; Rosseinsky, Matthew J

2012-04-01

72

Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality  

E-print Network

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.

Mikhail M. Labushev

2012-06-20

73

Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality  

E-print Network

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.

Labushev, Mikhail M

2012-01-01

74

Atomic Structure Calculations from the Los Alamos Atomic Physics Codes  

DOE Data Explorer

The well known Hartree-Fock method of R.D. Cowan, developed at Los Alamos National Laboratory, is used for the atomic structure calculations. Electron impact excitation cross sections are calculated using either the distorted wave approximation (DWA) or the first order many body theory (FOMBT). Electron impact ionization cross sections can be calculated using the scaled hydrogenic method developed by Sampson and co-workers, the binary encounter method or the distorted wave method. Photoionization cross sections and, where appropriate, autoionizations are also calculated. Original manuals for the atomic structure code, the collisional excitation code, and the ionization code, are available from this website. Using the specialized interface, you will be able to define the ionization stage of an element and pick the initial and final configurations. You will be led through a series of web pages ending with a display of results in the form of cross sections, collision strengths or rates coefficients. Results are available in tabular and graphic form.

Cowan, R. D.

75

Nuclear structure effects in light muonic atoms  

E-print Network

Nuclear structure corrections to energy levels of light muonic atoms are derived with particular attention to the correct nuclear mass dependence. The obtained result for the 2P-2S transition of 1.717(19) meV serves for determination of the nuclear charge radius from the spectroscopic measurement in muonic deuterium.

Pachucki, Krzysztof

2015-01-01

76

Nuclear structure effects in light muonic atoms  

E-print Network

Nuclear structure corrections to energy levels of light muonic atoms are derived with particular attention to the correct nuclear mass dependence. The obtained result for the 2P-2S transition of 1.717(19) meV serves for determination of the nuclear charge radius from the spectroscopic measurement in muonic deuterium.

Krzysztof Pachucki; Albert Wienczek

2015-03-04

77

Structural materials: understanding atomic scale microstructures  

SciTech Connect

With the ability to locate and identify atoms in three dimensions, atom-probe tomography (APT) has revolutionized our understanding of structure-property relationships in materials used for structural applications. The atomic-scale details of clusters, second phases, and microstructural defects that control alloy properties have been investigated, providing an unprecedented level of detail on the origins of aging behavior, strength, creep, fracture toughness, corrosion, and irradiation resistance. Moreover, atomic-scale microscopy combined with atomistic simulation and theoretical modeling of material behavior can guide new alloy design. In this article, selected examples highlight how APT has led to a deeper understanding of materials structures and therefore properties, starting with the phase transformations controlling the aging and strengthening behavior of complex Al-, Fe-, and Ni-based alloys systems. The chemistry of interfaces and structural defects that play a crucial role in high-temperature strengthening, fracture, and corrosion resistance are also discussed, with particular reference to Zr- and Al-alloys and FeAl intermetallics.

Marquis, E A [University of Oxford; Miller, Michael K [ORNL; Blavette, D [Universite de Rouen, France; Ringer, S. P. [University of Sydney, Australia; Sudbrack, C [Northwestern University, Evanston; Smith, G.D.W. [University of Oxford

2009-01-01

78

Atomic Resolution Imaging and Quantification of Chemical Functionality of Surfaces  

SciTech Connect

The work carried out from 2006-2014 under DoE support was targeted at developing new approaches to the atomic-scale characterization of surfaces that include species-selective imaging and an ability to quantify chemical surface interactions with site-specific accuracy. The newly established methods were subsequently applied to gain insight into the local chemical interactions that govern the catalytic properties of model catalysts of interest to DoE. The foundation of our work was the development of three-dimensional atomic force microscopy (3D-AFM), a new measurement mode that allows the mapping of the complete surface force and energy fields with picometer resolution in space (x, y, and z) and piconewton/millielectron volts in force/energy. From this experimental platform, we further expanded by adding the simultaneous recording of tunneling current (3D-AFM/STM) using chemically well-defined tips. Through comparison with simulations, we were able to achieve precise quantification and assignment of local chemical interactions to exact positions within the lattice. During the course of the project, the novel techniques were applied to surface-oxidized copper, titanium dioxide, and silicon oxide. On these materials, defect-induced changes to the chemical surface reactivity and electronic charge density were characterized with site-specific accuracy.

Schwarz, Udo [Yale University

2014-12-10

79

Chemical reactions of excited nitrogen atoms for short wavelength chemical lasers. Final technical report  

SciTech Connect

Accomplishments of this program include the following: (1) Scalable, chemical generation of oxygen atoms by reaction of fluorine atoms and water vapor. (2) Production of nitrogen atom densities of 1 {times} 10{sup 1}5 cm{sup {minus}3} with 5% electrical efficiency by injecting trace amounts of fluorine into microwave discharged nitrogen. (3) Production of cyanide radicals by reaction of high densities of N atoms with cyanogen. (4) Production of carbon atoms by reaction of nitrogen atoms with cyanogen or with fluorine atoms and hydrogen cyanide. (5) Confirmation that the reaction of carbon atoms and carbonyl sulfide produces CS(a{sup 3} {Pi}{sub r}), as predicted by conservation of electron spin and orbital angular momenta and as proposed by others under another SWCL program. (6) Production of cyanide radicals by injection of cyanogen halides into active nitrogen and use as spectroscopic calibration source. (7) Demonstration that sodium atoms react with cyanogen chloride, bromide and iodide and with cyanuric trifluoride to produce cyanide radicals. (8) Demonstration of the potential utility of the fluorine atom plus ammonia reaction system in the production of NF(b{sup l}{Sigma}{sup +}) via N({sup 2}D) + F{sub 2}.

Not Available

1989-12-15

80

Beyond the Isotropic Atom Model in Crystal Structure Prediction of Rigid Molecules: Atomic Multipoles versus  

E-print Network

Beyond the Isotropic Atom Model in Crystal Structure Prediction of Rigid Molecules: Atomic ABSTRACT: The lattice energies of predicted and known crystal structures for 50 small organic molecules is described by atom-centered multipoles. In comparison to previous predictions using atomic point charge

de Gispert, Adrià

81

Localized description of band structure effects on Li atom interaction with graphene  

Microsoft Academic Search

We study theoretically the localized aspects of the interaction between an Li atom and graphene. To this end, we use an ab initio calculation of the Hamiltonian terms within the Anderson model that allows us to take into account the chemical properties of Li and C atoms and the two-dimensional band structure of graphene. In this way, physical magnitudes of

Marcelo A. Romero; A. Iglesias-García; E. C. Goldberg

2011-01-01

82

"atomicphysicsproof" --2003/10/7 --page 1 --#11 ATOMIC STRUCTURE  

E-print Network

"atomicphysicsproof" -- 2003/10/7 -- page 1 -- #11 1 ATOMIC STRUCTURE 1.1 Ground state. The study of atomic structure continues to be an exciting field, with increasingly precise measurements of phosphorus One of the most important topics in atomic physics is the description of atomic energy levels

Budker, Dmitry

83

Automated extraction of chemical structure information from digital raster images  

PubMed Central

Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles. PMID:19196483

Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

2009-01-01

84

Atomic spin structure of antiferromagnetic domain walls  

Microsoft Academic Search

The search for uncompensated magnetic moments on antiferromagnetic surfaces is of great technological importance as they are responsible for the exchange-bias effect that is widely used in state-of-the-art magnetic storage devices. We have studied the atomic spin structure of phase domain walls in the antiferromagnetic Fe monolayer on W(001) by means of spin-polarized scanning tunnelling microscopy and Monte Carlo simulations.

M. Bode; E. Y. Vedmedenko; K. von Bergmann; A. Kubetzka; P. Ferriani; S. Heinze; R. Wiesendanger

2006-01-01

85

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

E-print Network

It has been shown recently that chemical bond lengths, in general, like those in the components of nucleic acids, caffeine related compounds, all essential amino acids, methane, benzene, graphene and fullerene are sums of the radii of adjacent atoms constituting the bond. Earlier, the crystal ionic distances in all alkali halides and lengths of many partially ionic bonds were also accounted for by the additivity of ionic as well as covalent radii. Here, the atomic structures of riboflavin and its reduced form are presented based on the additivity of the same set of atomic radii as for other biological molecules.

Raji Heyrovska

2008-06-21

86

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

E-print Network

It has been shown recently that chemical bond lengths, in general, like those in the components of nucleic acids, caffeine related compounds, all essential amino acids, methane, benzene, graphene and fullerene are sums of the radii of adjacent atoms constituting the bond. Earlier, the crystal ionic distances in all alkali halides and lengths of many partially ionic bonds were also accounted for by the additivity of ionic as well as covalent radii. Here, the atomic structures of riboflavin and its reduced form are presented based on the additivity of the same set of atomic radii as for other biological molecules.

Heyrovska, Raji

2008-01-01

87

Synthesis, atomic structures and properties of carbon and boron nitride fullerene materials  

Microsoft Academic Search

Carbon (C) and boron nitride (BN) fullerene materials (clusters, onions, intercalation, nanopolyhedra, nanotubes and nanocapsules) were synthesized by polymer pyrolysis, chemical reaction, arc-melting and electron-beam irradiation. Atomic structure and formation mechanism were investigated by high-resolution electron microscopy, energy dispersive spectroscopy and electron energy-loss spectroscopy. Fullerene clusters and atomic clouds (atom hopping) were formed on the surface of the C and

Takeo Oku; Takanori Hirano; Masaki Kuno; Takafumi Kusunose; Koichi Niihara; Katsuaki Suganuma

2000-01-01

88

Markov logic networks for optical chemical structure recognition.  

PubMed

Optical chemical structure recognition is the problem of converting a bitmap image containing a chemical structure formula into a standard structured representation of the molecule. We introduce a novel approach to this problem based on the pipelined integration of pattern recognition techniques with probabilistic knowledge representation and reasoning. Basic entities and relations (such as textual elements, points, lines, etc.) are first extracted by a low-level processing module. A probabilistic reasoning engine based on Markov logic, embodying chemical and graphical knowledge, is subsequently used to refine these pieces of information. An annotated connection table of atoms and bonds is finally assembled and converted into a standard chemical exchange format. We report a successful evaluation on two large image data sets, showing that the method compares favorably with the current state-of-the-art, especially on degraded low-resolution images. The system is available as a web server at http://mlocsr.dinfo.unifi.it. PMID:25068386

Frasconi, Paolo; Gabbrielli, Francesco; Lippi, Marco; Marinai, Simone

2014-08-25

89

An Atomic Environment Potential for use in Protein Structure Prediction  

E-print Network

An Atomic Environment Potential for use in Protein Structure Prediction Christopher M. Summa1 of a knowledge-based atomic environment potential for the modeling of protein structural energetics. An analysis of the probabilities of atomic interactions in a dataset of high- resolution protein structures shows

Summa, Christopher M.

90

Galactic Chemical Evolution Redux: Atomic Numbers 6 < Z < 15  

E-print Network

Motivated by the inability of Galactic chemical evolution models to reproduce some of the observed solar neighbourhood distribution of elements (and isotopes) with atomic numbers 6 < Z < 15, we have revisited the relevant stellar and Galactic models as part of an ambitious new program aimed at resolving these long-standing discrepancies. Avoiding the use of (traditional) parametric models for low- and intermediate-mass stellar evolution, we have generated a new, physically self-consistent, suite of stellar models and integrated the nucleosynthetic outputs into GEtool, our semi-analytical galactic chemical evolution software package. The predicted temporal evolution of several light- and intermediate-mass elements (and their isotopes) in the solar neighbourhood - from carbon to phosphorus - demonstrate the efficacy of the new yields in reconciling theory and observation.

B. K. Gibson; Y. Fenner; A. Kiessling

2005-02-15

91

Atomic structure and hierarchical assembly of a cross-? amyloid fibril  

PubMed Central

The cross-? amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of ?-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-? amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale—including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy—we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent ?-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils. PMID:23513222

Fitzpatrick, Anthony W. P.; Debelouchina, Galia T.; Bayro, Marvin J.; Clare, Daniel K.; Caporini, Marc A.; Bajaj, Vikram S.; Jaroniec, Christopher P.; Wang, Luchun; Ladizhansky, Vladimir; Müller, Shirley A.; MacPhee, Cait E.; Waudby, Christopher A.; Mott, Helen R.; De Simone, Alfonso; Knowles, Tuomas P. J.; Saibil, Helen R.; Vendruscolo, Michele; Orlova, Elena V.; Griffin, Robert G.; Dobson, Christopher M.

2013-01-01

92

Atomic Structure and the Periodic Table  

NSDL National Science Digital Library

Any online chemistry textbook that contains a photograph of Max Planck and Albert Einstein on its first page definitely sets the right tone, and Stephen Lower's textbook certainly falls into that category. Over the past several years Lower has been working on this textbook, and for students looking for a bit of refresher on the world of the structure of atoms and the periodic table, this is the right place in which to spend a bit of time. Through the use of short and concise chapters, the textbook provides six different lesson titles which cover the world of quantum physics, the Bohr atom, and the periodic properties of the elements. Within each chapter, users will also find illustrations and a "What you need to know" section that effectively summarizes the key principles and concepts in each section.

Lower, Stephen

93

Atomic spin structure of antiferromagnetic domain walls.  

PubMed

The search for uncompensated magnetic moments on antiferromagnetic surfaces is of great technological importance as they are responsible for the exchange-bias effect that is widely used in state-of-the-art magnetic storage devices. We have studied the atomic spin structure of phase domain walls in the antiferromagnetic Fe monolayer on W(001) by means of spin-polarized scanning tunnelling microscopy and Monte Carlo simulations. The domain wall width only amounts to 6-8 atomic rows. Although walls oriented along <100> directions are found to be fully compensated, detailed analysis of <110>-oriented walls reveals an uncompensated perpendicular magnetic moment. Our result represents a major advance in the field of antiferromagnetism, and may lead to a better understanding of the magnetic interaction between ferromagnetic and antiferromagnetic materials. PMID:16680147

Bode, M; Vedmedenko, E Y; von Bergmann, K; Kubetzka, A; Ferriani, P; Heinze, S; Wiesendanger, R

2006-06-01

94

On the atomic structure of Zr-Ni and Zr-Ni-Al metallic glasses  

NASA Astrophysics Data System (ADS)

Using real space pair distribution functions derived from high precision x-ray diffraction data, the local atomic structure of Zr-Ni and Zr-Ni-Al metallic glasses was investigated. Unlike Zr-Cu metallic glasses, the structure of Zr-Ni metallic glasses cannot be approached with an ideal solution model, due to strong attractive interactions between Zr and Ni atoms, which promote chemical short range order. Addition of Al can be beneficial for the glass forming ability of Zr-Ni metallic glasses. The atomic size of Al, being intermediate to those of Zr and Ni and the strongly attractive interactions between Zr-Al and Zr-Ni atoms can lead to highly negative volumes of mixing ?Vmix, and to denser atomic structures, reduced atomic mobility in the liquid and easier suppression of crystallization in the undercooled liquid state

Georgarakis, K.; Yavari, A. R.; Aljerf, M.; Louzguine-Luzgin, D. V.; Stoica, M.; Vaughan, G.; Inoue, A.

2010-07-01

95

Chemical Etiology of Nucleic Acid Structure  

NSDL National Science Digital Library

Systematic chemical studies indicate that the capability of Watson-Crick base-pairing is widespread among potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. A comparison of RNA and such alternatives with regard to chemical properties that are fundamental to the biological function of RNA provides chemical facts that may contain clues to RNA's origin.

Albert Eschenmoser (The Scripps Research Institute; )

1999-06-25

96

CHEMISTRY 1060 CHEMICAL STRUCTURE and REACTIVITY  

E-print Network

graded problems Course outline: Review and extension: Names, ionic compounds and Structure: Ionic solids Enthalpy, Bond Energies, Born-Haber Cycle BondingCHEMISTRY 1060 CHEMICAL STRUCTURE and REACTIVITY A Summer Program for high-ability High

Simons, Jack

97

An Atomic Resolution Structure for Human Fibroblast Growth Factor 1  

E-print Network

An Atomic Resolution Structure for Human Fibroblast Growth Factor 1 Matthew J. Bernett. The backbone atoms of each structurally conserved region of the symmetry-related subdomains in FGF-1 overlay and Biochemistry, Florida State University, Tallahassee, Florida ABSTRACT A 1.10-Ã? atomic resolution X

Blaber, Michael

98

Classifying chemical elements and particles: from the atomic to the sub-atomic world  

E-print Network

This paper presents two facets. First, we show that the periodic table of chemical elements can be described, understood and modified (as far as its format is concerned) on the basis of group theory and more specifically by using the group SO(4,2)xSU(2). Second, we show that "periodic tables" also exist in the sub-atomic and sub-nuclear worlds and that group theory is of paramount importance for these tables. In that sense, this paper may be considered as an excursion, for non specialists, into nuclear and particle physics.

Maurice R. Kibler

2008-01-08

99

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

NASA Astrophysics Data System (ADS)

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

100

Atomic fidelity of subunit-based chemically-synthesized antimalarial vaccine components.  

PubMed

The tri-dimensional (3D) structure determined by NMR of functionally relevant High Activity Binding Peptides (HABPs) of chemically-synthesized malarial proteins, involved in invasion to target cells, is practically identical, at the atomic level, to their corresponding recombinantly produced proteins, determined by X-ray crystallography. Both recombinant proteins as well as these chemically-synthesized HABPs bind to host-cell receptors through channels or troughs formation, stabilized by hydrogen bonding; most of them are located on distant segments to the highly polymorphic, highly antigenic, strain specific amino acid sequences the parasite uses to evade immune pressure. When these immunologically silent conserved HABPs are specifically modified, they become highly immunogenic and capable of inducing protective immune responses, supporting the specifically modified minimal subunit-based, multiepitopic, chemically-synthesized vaccines concept. PMID:19961869

Patarroyo, Manuel E; Cifuentes, Gladys; Martínez, Nora L; Patarroyo, Manuel A

2010-01-01

101

Atomic and electronic structure of gadolinium oxide  

NASA Astrophysics Data System (ADS)

Rare earth gadolinium oxide film has been studied by X-ray absorption fine structure (XAFS) at Gd L3-edge and energy electron loss spectroscopy (EELS) spectroscopies. XAFS data showed that the nearest Gd coordination shells consist of six oxygen atoms at ~2.308(2) Å and six gadolinium atoms at ~3.57(2) Å corresponding to Gd2O3 with a space group of Ia-3. EELS analysis of the film revealed excitations at the energies of 14.2, 19.9 eV which are due to electron transition from the valence band to the conductive one; excitations at the energies of 22.2-23.5 eV originated from valence electrons plasmon oscillations (bulk plasmons); and the excitation at 5.5 eV resulted from the electron transition at defects. When the photon energy changed from 1.5 to 5.0 eV the refractive index increased from 1.92 to 2.15.

Viktorovich Perevalov, Timofey; Evgenievich Dolbak, Andrey; Aleksandrovich Shvets, Vasilii; Alekseevich Gritsenko, Vladimir; Ivanovna Asanova, Tatijana; Borisovich Erenburg, Simon

2014-01-01

102

Electronic Structure of Superheavy Atoms. Revisited  

E-print Network

The electronic structure of an atom with Z 137 is inconsistent and physically meaningless because the formula for the lower energy level of the Dirac Hamiltonian formally gives imaginary eigenvalues. But a strict mathematical consideration shows that difficulties with the electronic spectrum for Z > 137 do not arise if the Dirac Hamiltonian is correctly defined as a self-adjoint operator, see [1]. In this article, we brie y summarize the main physical results of that consideration in a form suitable for physicists with some additional new details and numerical calculations of the electronic spectra. [1] B.L. Voronov, D.M. Gitman, and I.V. Tyutin, Theor. Math. Phys. 150(1) (2007) 34

D. M. Gitman; A. D. Levin; I. V. Tyutin; B. L. Voronov

2012-05-01

103

Atomic-Scale Chemical Imaging via Combination of Scanning Tunneling and Electron Energy Loss Spectroscopies  

E-print Network

Atomic-Scale Chemical Imaging via Combination of Scanning Tunneling and Electron Energy Loss spectroscopy and benchmark against high-resolution electron energy loss spectroscopy Directly probe visualization of chemical reaction pathways to provide mechanistic understanding for catalytically important

104

Arithmetic Aspects of Atomic Structures Charles L. Fefferman  

E-print Network

Arithmetic Aspects of Atomic Structures Charles L. Fefferman Department of Mathematics, Princeton success to explain the hydrogen atom, one of the early challenges of quantum mechanics was to study larger atoms. The problems encountered in this pro­ cess were numerous, and the quest for an understanding

Seco, Luis A.

105

Sharing chemical relationships does not reveal structures.  

PubMed

In this study, we propose a new, secure method of sharing useful chemical information from small-molecule libraries, without revealing the structures of the libraries' molecules. Our method shares the relationship between molecules rather than structural descriptors. This is an important advance because, over the past few years, several groups have developed and published new methods of analyzing small-molecule screening data. These methods include advanced hit-picking protocols, promiscuous active filters, economic optimization algorithms, and screening visualizations, which can identify patterns in the data that might otherwise be overlooked. Application of these methods to private data requires finding strategies for sharing useful chemical data without revealing chemical structures. This problem has been examined in the context of ADME prediction models, with results from information theory suggesting it is impossible to share useful chemical information without revealing structures. In contrast, we present a new strategy for encoding the relationships between molecules instead of their structures, based on anonymized scaffold networks and trees, that safely shares enough chemical information to be useful in analyzing chemical data, while also sufficiently blinding structures from discovery. We present the details of this encoding, an analysis of the usefulness of the information it conveys, and the security of the structures it encodes. This approach makes it possible to share data across institutions, and may securely enable collaborative analysis that can yield insight into both specific projects and screening technology as a whole. PMID:24289228

Matlock, Matthew; Swamidass, S Joshua

2014-01-27

106

MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES  

SciTech Connect

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.

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

2000-09-01

107

Atomic Structure of Benzene Which Accounts for Resonance Energy  

E-print Network

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

Raji Heyrovska

2008-07-09

108

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy  

NASA Astrophysics Data System (ADS)

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip–sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin–streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2?Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

109

Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic Representations  

E-print Network

Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic the secondary structure level to the atomic level. Our technique represents -helices and -strands as vectors of vectors. The second step in our algorithm is based on the atomic coordinates of the protein structures

Brutlag, Doug

110

Theory of rotational transition in atom-diatom chemical reaction  

NASA Astrophysics Data System (ADS)

Rotational transition in atom-diatom chemical reaction is theoretically studied. A new approximate theory (which we call IOS-DW approximation) is proposed on the basis of the physical idea that rotational transition in reaction is induced by the following two different mechanisms: rotationally inelastic half collision in both initial and final arrangement channels, and coordinate transformation in the reaction zone. This theory gives a fairy compact expression for the state-to-state transition probability. Introducing the additional physically reasonable assumption that reaction (particle rearrangement) takes place in a spatially localized region, we have reduced this expression into a simpler analytical form which can explicitly give overall rotational state distribution in reaction. Numerical application was made to the H+H2 reaction and demonstrated its effectiveness for the simplicity. A further simplified most naive approximation, i.e., independent events approximation was also proposed and demonstrated to work well in the test calculation of H+H2. The overall rotational state distribution is expressed simply by a product sum of the transition probabilities for the three consecutive processes in reaction: inelastic transition in the initial half collision, transition due to particle rearrangement, and inelastic transition in the final half collision.

Nakamura, Masato; Nakamura, Hiroki

1989-05-01

111

A Variational Monte Carlo Approach to Atomic Structure  

ERIC Educational Resources Information Center

The practicality and usefulness of variational Monte Carlo calculations to atomic structure are demonstrated. It is found to succeed in quantitatively illustrating electron shielding, effective nuclear charge, l-dependence of the orbital energies, and singlet-tripetenergy splitting and ionization energy trends in atomic structure theory.

Davis, Stephen L.

2007-01-01

112

Atomic structure of highly ordered pyrolytic graphite doped with boron  

E-print Network

substitute for the carbon atom in the graphite structure and promote the graphitization of pyrolytic graphiteAtomic structure of highly ordered pyrolytic graphite doped with boron Eunkyung Kim, Ilwhan Oh 3 September 2001; accepted 3 September 2001 Abstract Boron-doped carbon was prepared by the high

Kwak, Juhyoun

113

Atomic scale structure of ionic and semiconducting solid solutions  

Microsoft Academic Search

Experimental studies of the atomic scale structure of ionic and semiconducting solid solutions have shown that the bond-length mismatch is partially accommodated by microscopic lattice distortions and that the values of the nearest-neighbour bond lengths are intermediate between those of the corresponding pure compounds and the average Vegard value. Here the authors investigate theoretically the atomic scale structure of alloys

A. Baldereschi; M. Peressi

1993-01-01

114

Atomic and electronic structures of an extremely fragile liquid  

PubMed Central

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid. PMID:25520236

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T.; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-01-01

115

Atomic and electronic structures of an extremely fragile liquid  

NASA Astrophysics Data System (ADS)

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T.; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-12-01

116

Atomic and electronic structures of an extremely fragile liquid.  

PubMed

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia-Thornton number-number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr-O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr-O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid. PMID:25520236

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-01-01

117

Ability to Control a Titanium-Alloy Structure by Atomic-Emission Spectroscopy  

NASA Astrophysics Data System (ADS)

The effect of material structure on the analytical signal was studied using atomic emission spectroscopy with spark excitation of solids. A method for assessing the structure of the titanium alloy was proposed. It consisted of repeated analysis of a series of samples before and after heat treatment with excitation and recording of the spectrum under identical conditions followed by statistical processing of the results. The effects on the alloy structure of two heattreatment regimes, quenching and annealing, were studied. Atomic-emission spectroscopy with inductively coupled plasma was used to control the homogeneity of the chemical composition in the test samples.

Molchan, N. V.; Polkin, I. S.; Fertikov, V. I.

2014-05-01

118

Teaching Atomic Structure Using Cooperative Learning  

NSDL National Science Digital Library

This lesson plan focuses on the concepts of atomic number, mass number, isotope, and nuclear atom. A student quiz is included as an assessment instrument. This resource is from PUMAS - Practical Uses of Math and Science - a collection of brief examples created by scientists and engineers showing how math and science topics taught in K-12 classes have real world applications.

2012-08-03

119

ChemTeacher Resource: Atomic Structure  

NSDL National Science Digital Library

This applet allows students to build atoms by combining different amounts of protons, neutrons, and electrons. The atomic number, charge, and radioactivity are displayed after each additional particle is added. Questions throughout the applet allow students to check their understanding of the concepts with instantaneous feedback.

The Concord Consortium

2011-01-01

120

Atomic force microscopy of bamboo-shaped multiwalled carbon nanotube structures  

Microsoft Academic Search

Atomic force microscopy (AFM) was employed for the morphology measurements of bamboo-shaped multiwalled carbon nanotubes (BS-MWNTs) grown by thermal chemical vapor deposition on Fe catalyst deposited SiO2\\/Ti substrates. Greater diameters and compartment distances of the bamboo structures were observed for the BS-MWNTs grown at 950 °C than for those grown at 850 °C.

J. W. Jang; C. E. Lee; T. J. Lee; C. J. Lee; S. J. Noh

2003-01-01

121

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

E-print Network

Recent rsearches have shown that the lengths of the chemical bonds, whether completely or partially covalent or ionic, are sums of the radii of the adjacent atoms and/or ions. On investigating the bond length data for the molecular components of nucleic acids, all were found (for the first time) to be effectively the sums of the covalent radii of the adjacent atoms. This work shows that the bond lengths in caffeine and related molecules are likewise sums of the covalent radii of C, N, O and H. This has enabled arriving at the atomic structures of these molecules, also for the first time.

Raji Heyrovska; Saraswathi Narayan

2008-01-28

122

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

E-print Network

Recent rsearches have shown that the lengths of the chemical bonds, whether completely or partially covalent or ionic, are sums of the radii of the adjacent atoms and/or ions. On investigating the bond length data for the molecular components of nucleic acids, all were found (for the first time) to be effectively the sums of the covalent radii of the adjacent atoms. This work shows that the bond lengths in caffeine and related molecules are likewise sums of the covalent radii of C, N, O and H. This has enabled arriving at the atomic structures of these molecules, also for the first time.

Heyrovska, Raji

2008-01-01

123

Atomic-Structural Synergy for Catalytic CO Oxidation over Palladium-Nickel Nanoalloys  

SciTech Connect

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 a 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.

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

2014-05-05

124

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

PubMed

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. PMID:24794852

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

2014-05-14

125

Chemical structure and dynamics. Annual report 1995  

SciTech Connect

The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

Colson, S.D.; McDowell, R.S.

1996-05-01

126

Annual Report 2000. Chemical Structure and Dynamics  

SciTech Connect

This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

Colson, Steven D.; McDowell, Robin S.

2001-04-15

127

Chemical structure and dynamics: Annual report 1996  

SciTech Connect

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.

Colson, S.D.; McDowell, R.S.

1997-03-01

128

Cheminoes: A Didactic Game to Learn Chemical Relationships between Valence, Atomic Number, and Symbol  

ERIC Educational Resources Information Center

Cheminoes is a didactic game that enables the meaningful learning of some relations between concepts such as chemical element, valence, atomic number, and chemical symbol for the first 36 chemical elements of the periodic system. Among the students who have played the game, their opinions of the activity were positive, considering the game to be a…

Moreno, Luis F.; Hincapié, Gina; Alzate, María Victoria

2014-01-01

129

Local structure, chemical bond parameters and hyperfine magnetic interactions of 57Fe and doped 119Sn atoms in the orthoferrites TlFeO3 and TlFe0.99Sn0.01O3  

NASA Astrophysics Data System (ADS)

Mössbauer spectroscopy has been applied to study the magnetic hyperfine interactions of 57Fe and 119Sn probe atoms within TlFeO3 and TlFe0.99Sn0.01O3 ferrites. According to the magnetic measurements, the magnetic ordering temperature TN (= 560 K) for TlFeO3 is much lower than that for any other orthoferrites RFeO3 (R = rare earth). It is suggested that such difference in TN may be explained by different characteristics of the Tl-O and R-O chemical bonds involved and the induced competition with the Fe-O bonds. The effects of covalency and overlap distortion on the spin and charge densities at 57Fe nuclei are discussed in relation with the hyperfine interactions observed. By using cluster molecular orbital (MO) calculations, it was shown that the low value of the hyperfine magnetic field HFe(= 538 kOe) at 57Fe nuclei in TlFeO3 is strongly associated with a decrease of the covalent mixing parameter (b?)2 = 0.048 and (b?)2 = 0.009 values, which characterize the Fe-O bond covalence. It was elucidated that the value of super-transferred hyperfine field (HSTHF) at 119Sn nuclei in TlFe0.99Sn0.01O3 is sensitive mainly to the angle of the Sn-O-Fe bonds.

Presniakov, I. A.; Sobolev, A. V.; Baranov, A. V.; Demazeau, G.; Rusakov, V. S.

2006-10-01

130

Extracting chemical information from plane wave calculations by a 3D 'fuzzy atoms' analysis  

NASA Astrophysics Data System (ADS)

Bond order and valence indices have been calculated by the method of the three-dimensional 'fuzzy atoms' analysis, using the numerical molecular orbitals obtained from plane wave DFT calculations, i.e., without introducing any external atom-centered functions. Weight functions of both Hirshfeld and Becke types have been applied. The results are rather close to the similar 'fuzzy atoms' ones obtained by using atom-centered basis sets and agree well with the chemical expectations, stressing the power of the genuine chemical concepts.

Bakó, I.; Stirling, A.; Seitsonen, A. P.; Mayer, I.

2013-03-01

131

Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures  

USGS Publications Warehouse

New crystal-structure refinements of Pca21 boracite, Mg3ClB7O13, and R??{lunate}c ericaite, Fe2.4Mg0.6ClB7O13, show that some boron and oxygen atoms are involved in the 'ferro' transitions as well as the metal and halogen atoms. The atomic displacements associated with the polarity changes are as large as 0.6A??. ?? 1972.

Dowty, E.; Clark, J.R.

1972-01-01

132

The chemical environment about Cd atoms in Cd chemical bath treated CuInSe 2 and CuGaSe 2  

Microsoft Academic Search

Recent reports in the literature have concluded that chemical bath deposited Cd (CBD-Cd) has beneficial effects on Cu(In, Ga)Se2 solar cell performance. Before detailed mechanisms explaining why this is so can be proposed, a key question that must be answered is where in the lattice the Cd atoms reside. We have used near-edge X-ray absorption fine structure (XANES) to selectively

P. Fons; K. Sakurai; A. Yamada; K. Matsubara; K. Iwata; T. Baba; Y. Kimura; H. Nakanishi; S. Niki

2003-01-01

133

Electronic structures and chemical bonding of actinyl nitrates dihydrates  

NASA Astrophysics Data System (ADS)

The electronic structures and chemical bonding of actinyl nitrates [AnO2 (NO3)2 · 2H2O, An=U, Np and Pu] was studied using the discrete-variational Dirac-Fock-Slater MO method. The strength of both the covalent and the ionic bonds decreases with atomic number of the actinide. This change arises from variations in both the occupancy and the energy of the HOMO. Changes in the energies of the HOMO and LUMO correspond to changes in the stability of the hexavalent state in the actinyl nitrates. The characteristics of each ligand bonds were also analyzed.

Hirata, Masaru; Tachimori, Shoichi; Sekine, Rika; Onoe, Jun; Nakamatsu, Hirohide

134

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

NASA Astrophysics Data System (ADS)

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

McBriarty, Martin E.

135

REVIEWS OF TOPICAL PROBLEMS: Atomic structure of the amorphous nonstoichiometric silicon oxides and nitrides  

NASA Astrophysics Data System (ADS)

In addition to amorphous SiO2 and Si3N4, the two key dielectric film materials used in modern silicon devices, the fabrication technology of nonstoichiometric SiOxNy, SiNx, and SiOx compounds is currently under development. Varying the chemical composition of these compounds allows a wide range of control over their physical — specifically, optical and electrical — properties. The development of technology for synthesizing such films requires a detailed understanding of their atomic structure. Current views on the atomic structure of nonstoichiometric silicon nitrides and oxides are reviewed and summarized.

Gritsenko, V. A.

2008-07-01

136

Presentation of Atomic Structure in Turkish General Chemistry Textbooks  

ERIC Educational Resources Information Center

Research in science education has recognized the importance of teaching atomic structure within a history and philosophy of science perspective. The objective of this study is to evaluate general chemistry textbooks published in Turkey based on the eight criteria developed in previous research. Criteria used referred to the atomic models of…

Niaz, Mansoor; Costu, Bayram

2009-01-01

137

Resonance enhanced multiphoton ionisation probing of H atoms in a hot lament chemical vapour deposition reactor  

E-print Network

Resonance enhanced multiphoton ionisation probing of H atoms in a hot Ðlament chemical vapour multiphoton ionisation (MPI) spectroscopy, resonance enhanced at the two photon energy by the state, to detect

Bristol, University of

138

Rutherford and Bohr describe atomic structure 1913  

NSDL National Science Digital Library

This page is from PBS A Science Odyssey: People and Discoveries. It describes Bohr's contribution to theories of the atom and its relationship to others' such as Rutherford's. Links to relevant pages are provided. An image of Bohr's conception drawn in his notebook is included.

1998-01-01

139

Extended Xray Absorption Fine Structure Spectroscopy (EXAFS) Provides details on how x rays are absorbed by an atom at energies near X18A,B,X19A Provides details on how xrays are absorbed by an atom at energies near  

E-print Network

to determine the chemical state and local atomic structure for a selected atomic species · Used in a varietyExtended Xray Absorption Fine Structure Spectroscopy (EXAFS) · Provides details on how x rays are absorbed by an atom at energies near X18A,B,X19A· Provides details on how xrays are absorbed by an atom

Ohta, Shigemi

140

Nanoscale structure and transport : from atoms to devices  

E-print Network

Nanoscale structures present both unique physics and unique theoretical challenges. Atomic-scale simulations can find novel nanostructures with desirable properties, but the search can be difficult if the wide range of ...

Evans, Matthew Hiram

2005-01-01

141

A Jigsaw Classroom - Illustrated by the Teaching of Atomic Structure.  

ERIC Educational Resources Information Center

Discusses an approach to teaching the structure of atoms using a teaching technique referred to as a jigsaw classroom. Reports that the jigsaw classroom involves arranging students in various types of groups for cooperative learning. (Author/MM)

Eilks, Ingo; Leerhoff, Gabriele

2001-01-01

142

Relating Dynamic Properties to Atomic Structure in Metallic Glasses  

SciTech Connect

Atomic packing in metallic glasses is not completely random but displays various degrees of structural ordering. While it is believed that local structures profoundly affect the properties of glasses, a fundamental understanding of the structure–property relationship has been lacking. In this article, we provide a microscopic picture to uncover the intricate interplay between structural defects and dynamic properties of metallic glasses, from the perspective of computational modeling. Computational methodologies for such realistic modeling are introduced. Exploiting the concept of quasi-equivalent cluster packing, we quantify the structural ordering of a prototype metallic glass during its formation process, with a new focus on geometric measures of subatomic “voids.” Atomic sites connected with the voids are found to be crucial in terms of understanding the dynamic, including vibrational and atomic transport, properties. Normal mode analysis is performed to reveal the structural origin of the anomalous boson peak (BP) in the vibration spectrum of the glass, and its correlation with atomic packing cavities. Through transition-state search on the energy landscape of the system, such structural disorder is found to be a facilitating factor for atomic diffusion, with diffusion energy barriers and diffusion pathways significantly varying with the degree of structural relaxation/ordering. The implications of structural defects for the mechanical properties of metallic glasses are also discussed.

Sheng, H.W.; Ma, E.; Kramer, Matthew J.

2012-07-18

143

Laser Isotope Separation in Atomic Vapour:. PhotoChemical Method VS. PhotoIonization One  

Microsoft Academic Search

Two methods of laser isotope separation in atomic vapour are compared. The first of them is a well developed Photo-ionization method. The other method is based on isotope-selective excitation of long-living atomic states and subsequent chemical reaction of excited atom with special reagents. It is shown that this method has some principal advantages compared to Photo-ionization method.

P. A. Bokhan; N. V. Fateyev; D. E. Zakrevskiy; V. V. Buchanov; M. A. Kazaryan

2010-01-01

144

Atomic Structure of Graphene on SiO 2  

Microsoft Academic Search

We employ scanning probe microscopy to reveal atomic structures and nanoscale\\u000amorphology of graphene-based electronic devices (i.e. a graphene sheet\\u000asupported by an insulating silicon dioxide substrate) for the first time.\\u000aAtomic resolution STM images reveal the presence of a strong spatially\\u000adependent perturbation, which breaks the hexagonal lattice symmetry of the\\u000agraphitic lattice. Structural corrugations of the graphene sheet

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

2007-01-01

145

Atomic structure of highly-charged ions. Final report  

SciTech Connect

Atomic properties of multiply charged ions have been investigated using excitation of energetic heavy ion beams. Spectroscopy of excited atomic transitions has been applied from the visible to the extreme ultraviolet wavelength regions to provide accurate atomic structure and transition rate data in selected highly ionized atoms. High-resolution position-sensitive photon detection has been introduced for measurements in the ultraviolet region. The detailed structures of Rydberg states in highly charged beryllium-like ions have been measured as a test of long-range electron-ion interactions. The measurements are supported by multiconfiguration Dirac-Fock calculations and by many-body perturbation theory. The high-angular-momentum Rydberg transitions may be used to establish reference wavelengths and improve the accuracy of ionization energies in highly charged systems. Precision wavelength measurements in highly charged few-electron ions have been performed to test the most accurate relativistic atomic structure calculations for prominent low-lying excited states. Lifetime measurements for allowed and forbidden transitions in highly charged few-electron ions have been made to test theoretical transition matrix elements for simple atomic systems. Precision lifetime measurements in laser-excited alkali atoms have been initiated to establish the accuracy of relativistic atomic many-body theory in many-electron systems.

Livingston, A. Eugene

2002-05-23

146

The effect of doping three Al and N atoms on the chemical shielding tensor parameters of the boron phosphide nanotubes: A DFT study  

NASA Astrophysics Data System (ADS)

In this work, an armchair model of the (4,4) boron phosphide nanotubes (BPNTs) with a 1-nm length and consisting of 32 B and 32 P atoms is considered to study the influence of doping three atoms of aluminum in sites of boron (B 3AlPNTs) and three atoms of nitrogen in sites of phosphors (BP 3NNTs) on the electrostatic structure properties. The mouths of nanotubes are capped by hydrogen atoms in order to saturate the dangling bonds of the boundaries and to decrease the calculation time. The structures of BPNTs, B 3AlPNTs and BP 3NNTs are optimized by performing the level of density functional theory (DFT) using 6-31G * basis set. The optimized structures are used for calculating the chemical shielding (CS) tensors and nuclear magnetic resonance parameters such as isotropic chemical shielding (CS I) and anisotropic chemical shielding (CS A). The results reveal that in both models of B 3AlPNTs and BP 3NNTs by doping N atoms the chemical shielding parameters of P and B atoms, which are directly connected to the Al and N atoms decreased and the other sites significantly changed.

Rezaei-Sameti, Mahdi

2012-01-01

147

Chemical Structure and Dynamics annual report 1997  

SciTech Connect

The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

Colson, S.D.; McDowell, R.S.

1998-03-01

148

Quantum chemical studies of protein structure  

PubMed Central

Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions. PMID:16147526

Oldfield, Eric

2004-01-01

149

Structure and Local Chemical Properties of Boron-Terminated Tetravacancies in Hexagonal Boron Nitride  

NASA Astrophysics Data System (ADS)

Imaging and spectroscopy performed in a low-voltage scanning transmission electron microscope are used to characterize the structure and chemical properties of boron-terminated tetravacancies in hexagonal boron nitride. We confirm earlier theoretical predictions about the structure of these defects and identify new features in the electron energy-loss spectra of B atoms using high resolution chemical maps, highlighting differences between these areas and pristine sample regions. We correlate our experimental data with calculations which help explain our observations.

Cretu, Ovidiu; Lin, Yung-Chang; Koshino, Masanori; Tizei, Luiz H. G.; Liu, Zheng; Suenaga, Kazutomo

2015-02-01

150

Atomic Calligraphy: The Direct Writing of Nanoscale Structures using MEMS  

E-print Network

We present a micro-electromechanical system (MEMS) based method for the resist free patterning of nano-structures. Using a focused ion beam (FIB) to customize larger MEMS machines, we fabricate apertures as small as 50 nm on plates that can be moved with nanometer precision over an area greater than 20x20 {\\mu}m^2. Depositing thermally evaporated gold atoms though the apertures while moving the plate results in the deposition of nanoscale metal patterns. Adding a shutter only microns above the aperture, enables high speed control of not only where but also when atoms are deposited. Using a shutter, different sized apertures can be selectively opened and closed for nano-structure fabrication with features ranging from nano- to micrometers in scale. The ability to evaporate materials with high precision, and thereby fabricate circuits and structures in situ, enables new kinds of experiments based on the interactions of a small number of atoms and eventually even single atoms.

Matthias Imboden; Han Han; Jackson Chang; Flavio Pardo; Cristian A. Bolle; Evan Lowell; David J. Bishop

2013-04-04

151

Atomic structure and dynamics of metal dopant pairs in graphene.  

PubMed

We present an atomic resolution structural study of covalently bonded dopant pairs in the lattice of monolayer graphene. Two iron (Fe) metal atoms that are covalently bonded within the graphene lattice are observed and their interaction with each other is investigated. The two metal atom dopants can form small paired clusters of varied geometry within graphene vacancy defects. The two Fe atoms are created within a 10 nm diameter predefined location in graphene by manipulating a focused electron beam (80 kV) on the surface of graphene containing an intentionally deposited Fe precursor reservoir. Aberration-corrected transmission electron microscopy at 80 kV has been used to investigate the atomic structure and real time dynamics of Fe dimers embedded in graphene vacancies. Four different stable structures have been observed; two variants of an Fe dimer in a graphene trivacancy, an Fe dimer embedded in two adjacent monovacancies and an Fe dimer trapped by a quadvacancy. According to spin-sensitive DFT calculations, these dimer structures all possess magnetic moments of either 2.00 or 4.00 ?B. The dimer structures were found to evolve from an initial single Fe atom dopant trapped in a graphene vacancy. PMID:24945707

He, Zhengyu; He, Kuang; Robertson, Alex W; Kirkland, Angus I; Kim, Dongwook; Ihm, Jisoon; Yoon, Euijoon; Lee, Gun-Do; Warner, Jamie H

2014-07-01

152

Atomic structure of GTP cyclohydrolase I  

Microsoft Academic Search

Background: Tetrahydrobiopterin serves as the cofactor for enzymes involved in neurotransmitter biosynthesis and as a regulatory factor in immune cell proliferation and the biosynthesis of melanin. The biosynthetic pathway to tetrahydrobiopterin consists of three steps starting from GTP. The initial reaction is catalyzed by GTP cyclohydrolase I (GTP-CH-I) and involves the chemically complex transformation of the purine into the pterin

Herbert Nar; Robert Huber; Winfried Meining; Cornelia Schmid; Sevil Weinkauf; Adelbert Bacher

1995-01-01

153

Computational Atomic Structure and Search for New Physics  

NASA Astrophysics Data System (ADS)

The overarching goal of this dissertation is to examine constraints on extensions to the Standard Model (SM) through atomic-structure computations. More specifically, atomic parity-nonconserving (PNC) amplitudes and intrinsic electric dipole moments (EDM) are examined for sources of physics beyond the SM. Precision calculations of these properties in the trivalent thallium atom, will help set new constraints on searches beyond the SM. To this end, the first half of the dissertation is devoted to improving atomic structure calculations. In particular, we numerically investigate the effectiveness of two convergence methods for coupled-cluster (CC) method. Further we explore the feasibility of transferring high-precision CC methods, developed for monovalent atoms, to trivalent systems. Here we showcase calculations of various properties of the trivalent atomic boron as a prototype for future precision computations for thallium. In the second half of the dissertation, we consider "dark force" extensions to the SM. We introduce "dark forces" by considering the parity-odd as well as simultaneous parity-and time-reversal-violating interactions between atomic electrons and nucleons. Here we hypothesize the exchange of a "dark sector" light gauge-boson particle between atomic electrons and nucleons, as the source of the "dark force". Furthermore, using the latest experimental upper limits on mercury EDM and error bars on the cesium PNC experiments, we place constraints on the coupling strengths of such "dark forces" with ordinary matter.

Gharibnejad, Heman

154

Chemical Vapor Generation with Slurry Sampling: A Review of Applications to Atomic and Mass Spectrometry  

Microsoft Academic Search

A critical review of published analytical methods and techniques for chemical vapor generation (CVG) with slurry sample introduction for detection by atomic and mass spectrometry is presented. Instrumentation used for the reaction as well as separation and transport of the species, influence of chemical and physical factors, and the efficiency of the process are considered. A brief comparison of detection

HENRYK MATUSIEWICZ; RALPH E. STURGEON

2011-01-01

155

Chemical Vapor Generation with Slurry Sampling: A Review of Applications to Atomic and Mass Spectrometry  

Microsoft Academic Search

A critical review of published analytical methods and techniques for chemical vapor generation (CVG) with slurry sample introduction for detection by atomic and mass spectrometry is presented. The nstrumentation used for the reaction as well as separation and transport of the species, influence of chemical and physical factors, and efficiency of the process are considered. A brief comparison of detection

Henryk Matusiewicz; Ralph E. Sturgeon

2012-01-01

156

Chemical vapor deposition and atomic layer deposition of metal oxide and nitride thin films  

Microsoft Academic Search

Processes for depositing thin films with various electronic, optical, mechanical, and chemical properties are indispensable in many industries today. Of the many deposition methods available, chemical vapor deposition (CVD) has proved over time to be one of the most flexible, efficient, and cost-effective. Atomic layer deposition (ALD) is a newer process that is gaining favor as a method for depositing

Jeffrey Thomas Barton

2003-01-01

157

Chemical structure and dynamics. Annual report 1994  

SciTech Connect

The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

Colson, S.D.

1995-07-01

158

Annual Report 1998: Chemical Structure and Dynamics  

SciTech Connect

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

SD Colson; RS McDowell

1999-05-10

159

Understanding chemical expansion in perovskite-structured oxides.  

PubMed

In this work, chemical expansion in perovskite oxides was characterized in detail, motivated, inter alia, by a desire to understand the lower chemical expansion coefficients observed for perovskites in comparison to fluorite-structured oxides. Changes in lattice parameter and in local atomic arrangements taking place during compositional changes of perovskites, i.e., stoichiometric expansion, were investigated by developing an empirical model and through molecular dynamics and density functional theory atomistic simulations. An accurate empirical expression for predicting lattice constants of perovskites was developed, using a similar approach to previous reports. From this equation, analytical expressions relating chemical expansion coefficients to separate contributions from the cation and anion sublattices, assuming Shannon ionic radii, were developed and used to isolate the effective radius of an oxygen vacancy, rV. Using both experimental and simulated chemical expansion coefficient data, rV for a variety of perovskite compositions was estimated, and trends in rV were studied. In most cases, rV was slightly smaller than or similar to the radius of an oxide ion, but larger than in the fluorite structured materials. This result was in good agreement with the atomistic simulations, showing contractive relaxations of the closest oxide ions towards the oxygen vacancy. The results indicate that the smaller chemical expansion coefficients of perovskites vs. fluorites are largely due to the smaller change in cation radii in perovskites, given that the contraction around the oxygen vacancy appears to be less in this structure. Limitations of applicability for the model are discussed. PMID:25785684

Marrocchelli, Dario; Perry, Nicola H; Bishop, Sean R

2015-04-01

160

Atomic structures of tubulin and FtsZ  

Microsoft Academic Search

The recently published atomic structures of tubulin and FtsZ are a research milestone. The N-terminal GTP-binding domains of tubulin and FtsZ are virtually identical in structure, as expected from the substantial sequence identity. Sequence identity is absent from the C-terminal domains, but they also have virtually identical structures. A surprising finding is that the N-terminal GTP-binding domain is structurally homologous

Harold P Erickson

1998-01-01

161

Physical Construction of the Chemical Atom: Is It Convenient to Go All the Way Back?  

ERIC Educational Resources Information Center

In this paper we present an analysis of chemistry texts (mainly textbooks) published during the first half of the 20th century. We show the evolution of the explanations therein in terms of atoms and of atomic structure, when scientists were interpreting phenomena as evidence of the discontinuous, corpuscular structure of matter. In this process…

Izquierdo-Aymerich, Merce; Aduriz-Bravo, Agustin

2009-01-01

162

Determination of the atomic structure of scanning probe microscopy tungsten tips by field ion microscopy  

E-print Network

Determination of the atomic structure of scanning probe microscopy tungsten tips by field ion of scanning probe microscopy SPM experiments usually need to make an assumption about the atomic tip structure ago that FIM could also be used to machine structures atom by atom.7 We have used such atomically

Grütter, Peter

163

Editorial . Quantum fluctuations and coherence in optical and atomic structures  

Microsoft Academic Search

From simple interference fringes, over molecular wave packets, to nonlinear optical patterns - the fundamental interaction between light and matter leads to the formation of structures in many areas of atomic and optical physics. Sophisticated technology in experimental quantum optics, as well as modern computational tools available to theorists, have led to spectacular achievements in the investigation of quantum structures.

Jürgen Eschner; Alessandra Gatti; Agnès Maître; Giovanna Morigi

2003-01-01

164

Atomic-scale structure and composition of tungsten carbide reinforced diamondlike carbon films  

NASA Astrophysics Data System (ADS)

This study presents the true atomic-scale structure and composition of hard/lubricious nanocomposite diamondlike carbon (DLC) films. Nanocrystalline tungsten carbide (˜2-4 nm precipitates) in mixed sp3/sp2 amorphous C-H matrices was characterized using the combination of three-dimensional atom probe (3DAP) tomography and transmission electron microscopy. Excellent correspondence in structural and chemical layering was observed (alternating ˜25 nm thick carbon-rich and tungsten-rich layers) with 3DAP also revealing C32+ and C2H4+ species in the carbon-rich layers and W2+, WC2+, C+, and C2+ species in the tungsten-rich layers. 3D morphology and chemical partitioning of the WC nanoprecipitates in the tungsten-rich layers are also discussed.

Scharf, T. W.; Romanes, M. C.; Mahdak, K. C.; Hwang, J. Y.; Banerjee, R.; Evans, R. D.; Doll, G. L.

2008-10-01

165

Highly Scalable, Atomically Thin WSe2 Grown via Metal-Organic Chemical Vapor Deposition.  

PubMed

Tungsten diselenide (WSe2) is a two-dimensional material that is of interest for next-generation electronic and optoelectronic devices due to its direct bandgap of 1.65 eV in the monolayer form and excellent transport properties. However, technologies based on this 2D material cannot be realized without a scalable synthesis process. Here, we demonstrate the first scalable synthesis of large-area, mono and few-layer WSe2 via metal-organic chemical vapor deposition using tungsten hexacarbonyl (W(CO)6) and dimethylselenium ((CH3)2Se). In addition to being intrinsically scalable, this technique allows for the precise control of the vapor-phase chemistry, which is unobtainable using more traditional oxide vaporization routes. We show that temperature, pressure, Se:W ratio, and substrate choice have a strong impact on the ensuing atomic layer structure, with optimized conditions yielding >8 ?m size domains. Raman spectroscopy, atomic force microscopy (AFM), and cross-sectional transmission electron microscopy (TEM) confirm crystalline monoto-multilayer WSe2 is achievable. Finally, TEM and vertical current/voltage transport provide evidence that a pristine van der Waals gap exists in WSe2/graphene heterostructures. PMID:25625184

Eichfeld, Sarah M; Hossain, Lorraine; Lin, Yu-Chuan; Piasecki, Aleksander F; Kupp, Benjamin; Birdwell, A Glen; Burke, Robert A; Lu, Ning; Peng, Xin; Li, Jie; Azcatl, Angelica; McDonnell, Stephen; Wallace, Robert M; Kim, Moon J; Mayer, Theresa S; Redwing, Joan M; Robinson, Joshua A

2015-02-24

166

Study of amorphous alloy structures with medium range atomic ordering.  

PubMed

Structures with atomic medium range order (MRO) extending as small as approximately 2 nm in amorphous alloys can be observed under suitable defocus conditions as clear lattice fringe images by means of axial-beam high-resolution electron microscopy (HREM). In this article, our studies of local structure observation in some metal-metalloid amorphous alloys with the "selected-defocus method" are introduced. Also introduced are an HREM image simulation study of amorphous alloy structures and a nano-probe (1-1.5 nm) electron diffraction analysis of MRO structure. A multislice image simulation study for suitable structure models (1) with a random atomic distribution, (2) with MRO regions having different sizes, distributions, and specimen thicknesses, is a necessary step to verify the MRO observation in amorphous alloys. It was demonstrated that not only HREM information but also nano-diffraction information are necessary in order to understand local structures of amorphous alloys. PMID:9523762

Hirotsu, Y; Ohkubo, T; Matsushita, M

1998-02-15

167

Structural and kinetic aspects of chemical reactions in DNA duplexes. Information on DNA local structure obtained from chemical ligation data.  

PubMed Central

Chemical ligation of oligonucleotides in double-stranded helices has been considered in its structural-kinetic aspect. A study was made of (i) two series of DNA duplexes with various arrangements of reacting groups in the ligation junction induced by mispairing or by alteration of furanose structure (the replacement of dT unit with rU, aU, IU, xU, dxT ones) and of (ii) eight synthetic water-soluble carbodiimides with different substituents at N1 and N3 atoms. We assumed that some information on the local structure of modified sites in the duplex can be obtained from kinetic parameters of oligonucleotide coupling reaction. The ratio of kinetic constants k3/(k2 + k3) for productive and nonproductive decomposition of the activated phosphomonoester derivative apparently reflects the reaction site structure: for a given duplex this parameter is virtually independent of the condensing agent composition. Based on the analysis of the chemical ligation kinetics a suggestion has been made about the conformation of some modified units in the double helix. Images PMID:2057363

Dolinnaya, N G; Tsytovich, A V; Sergeev, V N; Oretskaya, T S; Shabarova, Z A

1991-01-01

168

Structural and Chemical Transformations in Nanocrystals  

NASA Astrophysics Data System (ADS)

Structural and Chemical transformation of nanocrystals from one state to another can proceed rapidly and with remarkably simplified kinetics compared to bulk solid state transformations. We have investigated the Wurtzite to rock salt pressure induced solid-solid structural transformation in CdSe nanorods of 4 nm diameter as a function of rod length. Rods of length less than 10 nm transform reversibly, while rods greater than 10 nm in length fracture during the structural transformation. Two other recent examples we have investigated are the formation of hollow nanocrystals via addition reactions and cation exchange reactions. Hollow nanocrystals of many transition metal oxides and sulfides have been studied, and from these we are learning how to predict the shell thickness. Cation exchange from CdSe to Ag2Se proceeds completely, but is reversible, and the number of anions per nanocrystal remains invariant. Above a critical size, the nanocrystals retain non-equilibrium shapes over multiple cycles of cation exchange.

Alivisatos, P.

2007-12-01

169

Electronic structure of atomically resolved carbon nanotubes  

NASA Astrophysics Data System (ADS)

Carbon nanotubes can be considered as single graphene sheets wrapped up into cylinders. Theoretical studies have shown that nanotubes can be either metallic or semiconducting, depending on minor differences in wrapping angle and diameter. We have obtained scanning tunneling microscopy and spectroscopy results on individual nanotubes which verify this prediction( J.W.G.Wildöer, L.C. Venema, A.G. Rinzler, R.E. Smalley, and C. Dekker, Nature, aimed for publication in Januari 1998). The combination of spectroscopy measurements and atomically resolved images allow to relate the electronic spectra to the wrapping angle and diameter. Tubes with various wrapping angles appear to be either metallic or semiconducting. Carbon nanotubes are expected to be one-dimensional conductors. Sharp peaks in the tunneling density of states that can be associated with the onsets of one-dimensional subbands are indeed observed. Furthermore, we are able to control the length of carbon nanotubes by STM nanostructuring( L.C. Venema, J.W.G. Wildöer, H.J. Temminck Tuinstra, A.G. Rinzler, R.E. Smalley and C. Dekker, Appl. Phys. Lett. (1997)). By applying voltage pulses to the STM tip above a nanotube, the tube can cut into a shorter section. In this way the electronic properties of nanotubes of various lengths can be investigated. footnotetext[0] email: venema@qt.tn.tudelft.nl Work done in collaboration with J.W.G. Wildöer, A.G. Rinzler, R.E. Smalley and C. Dekker.

Venema, Liesbeth

1998-03-01

170

Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts  

PubMed Central

Structured non-coding RNAs underline fundamental cellular processes, but determining their 3D structures remains challenging. We demonstrate herein that integrating NMR 1H chemical shift data with Rosetta de novo modeling can consistently return high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 blind targets, Chemical-Shift-ROSETTA for RNA (CS-ROSETTA-RNA) recovered the experimental structures with high accuracy (0.6 to 2.0 Å all-heavy-atom rmsd) in 18 cases. PMID:24584194

Sripakdeevong, Parin; Cevec, Mirko; Chang, Andrew T.; Erat, Michèle C.; Ziegeler, Melanie; Zhao, Qin; Fox, George E.; Gao, Xiaolian; Kennedy, Scott D.; Kierzek, Ryszard; Nikonowicz, Edward P.; Schwalbe, Harald; Sigel, Roland K. O.; Turner, Douglas H.; Das, Rhiju

2014-01-01

171

A 4096 atom model of amorphous silicon: Structure and dynamics  

Microsoft Academic Search

We present structural and lattice dynamical information for a 4096 atom model of amorphous silicon. The structural model was obtained, similarly to previously published smaller models, using periodic boundary conditions, the Wooten-Winer-Weaire bond-switching algorithm, and the Broughton-Li relaxation with respect to the Stillinger-Weber potential. The structure is dynamically stable and there is no evidence in the radial distribution function of

Joseph L. Feldman; Scott R. Bickham; Brian N. Davidson; Frederick Wooten

1997-01-01

172

Atom interferometric measurement of the fine structure constant  

NASA Astrophysics Data System (ADS)

Atom interferometers are among the most accurate and precise devices for precision measurements. They are used to realize atomic clocks, to measure the size of the earth's gravitational acceleration with ppb accuracy as well as its gradient and are also applied as rotation sensors. Atom interferometers may also be used in the field of fundamental physics to measure the fine structure constant or to test General Relativity. The HYPER project is currently under study to perform some of the above mentioned measurements with space based atom interferometers. A state-of-the-art ground based atom interferometer at Stanford has been used to measure the fine structure constant with an accuracy of ˜ 7ppb [1]. The experiment is based on measuring the recoil velocity which a 133Cs atom acquires when absorbing a single photon. The absorption of the photon momentum shifts the optical resonance frequency (335 THz ) by ˜ 7.5 kHz which we have measured with an accuracy of ˜ 100 ? Hz. The goal of this presentation is to interpret the experience with the Stanford interferometer in the light of space based operation. We first briefly describe the basic principles of atom interferometry and then give a description of the experimental setup. We present the physical origin of interferometer noise and of the leading systematic effects and point out how they are controlled or cancelled. We finally try to estimate the performance of the very same setup as-is under space based conditions, i.e. we re-estimate the size of interferometer phase noise and of the leading systematic effects: these include vibrational noise, residual acceleration, gravity gradients, magnetic field and magnetic field gradients, electric fields, and rotational effects (Sagnac effect). [1] A. Wicht, J. Hensley, E. Sarajlic and S. Chu, ``A preliminary measurement of the fine structure constant based on atom interferometry'', Physica Scripta 102, 82-88, (2002).

Wicht, A.; Sarajlic, E.; Chu, S.; Laemmerzahl, C.

173

Chemical mapping of mammalian cells by atom probe tomography  

PubMed Central

In atom probe tomography (APT), a technique that has been used to determine 3D maps of ion compositions of metals and semiconductors at sub-nanometer resolution, controlled emissions of ions can be induced from needle-shaped specimens in the vicinity of a strong electric field. Detection of these ions in the plane of a position sensitive detector provides two-dimensional compositional information while the sequence of ion arrival at the detector provides information in the third dimension. However, the applicability of APT to imaging unstained cells has not been explored. Here, we report the use of APT to obtain 3D spatial distributions of cellular ions and metabolites from unstained, freeze-dried mammalian cells. Multiple peaks were reliably obtained in the mass spectrum from tips with diameters of ~ 50 nm and heights of ~ 200 nm, with mass-to-charge ratios (m/z) ranging from 1 to 80. Peaks at m/z 12, 23, 28 and 39, corresponding to carbon, sodium, carbonyl and potassium ions respectively, showed distinct patterns of spatial distribution within the cell. Our studies establish that APT could become a powerful tool for mapping the sub-cellular distribution of atomic species, such as labeled metabolites, at 3D spatial resolutions as high as ~ 1 nm. PMID:22245777

Narayan, Kedar; Prosa, Ty; Fu, Jing; Kelly, Thomas F; Subramaniam, Sriram

2012-01-01

174

Atomic-scale observation of the grain-boundary structure of Yb-doped and heat-treated silicon nitride ceramics  

E-print Network

and the latter to control crack propagation. The IGFs strength is controlled by its chemical composition and its the chemical bonding strength.4,9,21­24 Previous studies in a similar material showed that postsintering heat boundaries 1 nm in thickness , which surround ev- ery Si3N4 grain, their atomic structure and chemical compo

Ritchie, Robert

175

Vortex-ring-fractal Structure of Atom and Molecule  

NASA Astrophysics Data System (ADS)

This chapter is an attempt to attain a new and profound model of the nature's structure using a vortex-ring-fractal theory (VRFT). Scientists have been trying to explain some phenomena in Nature that have not been explained so far. The aim of this paper is the vortex-ring-fractal modeling of elements in the Mendeleev's periodic table, which is not in contradiction to the known laws of nature. We would like to find some acceptable structure model of the hydrogen as a vortex-fractal-coil structure of the proton and a vortex-fractal-ring structure of the electron. It is known that planetary model of the hydrogen atom is not right, the classical quantum model is too abstract. Our imagination is that the hydrogen is a levitation system of the proton and the electron. Structures of helium, oxygen, and carbon atoms and a hydrogen molecule are presented too.

Osmera, Pavel

2010-06-01

176

Vortex-ring-fractal Structure of Atom and Molecule  

SciTech Connect

This chapter is an attempt to attain a new and profound model of the nature's structure using a vortex-ring-fractal theory (VRFT). Scientists have been trying to explain some phenomena in Nature that have not been explained so far. The aim of this paper is the vortex-ring-fractal modeling of elements in the Mendeleev's periodic table, which is not in contradiction to the known laws of nature. We would like to find some acceptable structure model of the hydrogen as a vortex-fractal-coil structure of the proton and a vortex-fractal-ring structure of the electron. It is known that planetary model of the hydrogen atom is not right, the classical quantum model is too abstract. Our imagination is that the hydrogen is a levitation system of the proton and the electron. Structures of helium, oxygen, and carbon atoms and a hydrogen molecule are presented too.

Osmera, Pavel [European Polytechnical Institute Kunovice, Osvobozeni 699, 686 04 Kunovice (Czech Republic)

2010-06-17

177

Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography  

SciTech Connect

Here we report the total synthesis of kaliotoxin by 'one pot' native chemical ligation of three synthetic peptides. A racemic mixture of D- and L-kaliotoxin synthetic protein molecules gave crystals in the centrosymmetric space groupP that diffracted to atomic-resolution (0.95 {angstrom}), enabling the X-ray structure of kaliotoxin to be determined by direct methods.

Pentelute, Brad L.; Mandal, Kalyaneswar; Gates, Zachary P.; Sawaya, Michael R.; Yeates, Todd O.; Kent, Stephen B.H. (UCLA); (UC)

2010-11-05

178

Solitonic fullerene structures in light atomic nuclei  

E-print Network

The Skyrme model is a classical field theory which has topological soliton solutions. These solitons are candidates for describing nuclei, with an identification between the numbers of solitons and nucleons. We have computed numerically, using two different minimization algorithms, minimum energy configurations for up to 22 solitons. We find, remarkably, that the solutions for seven or more solitons have nucleon density isosurfaces in the form of polyhedra made of hexagons and pentagons. Precisely these structures arise, though at the much larger molecular scale, in the chemistry of carbon shells, where they are known as fullerenes.

R. A. Battye; P. M. Sutcliffe

2001-02-16

179

Atomic Parity Nonconservation: Electroweak Parameters and Nuclear Structure  

E-print Network

There have been suggestions to measure atomic parity nonconservation (PNC) along an isotopic chain, by taking ratios of observables in order to cancel complicated atomic structure effects. Precise atomic PNC measurements could make a significant contribution to tests of the Standard Model at the level of one loop radiative corrections. However, the results also depend upon certain features of nuclear structure, such as the spatial distribution of neutrons in the nucleus. To examine the sensitivity to nuclear structure, we consider the case of Pb isotopes using various recent relativistic and non-relativistic nuclear model calculations. Contributions from nucleon internal weak structure are included, but found to be fairly negligible. The spread among present models in predicted sizes of nuclear structure effects may preclude using Pb isotope ratios to test the Standard Model at better than a one percent level, unless there are adequate independent tests of the nuclear models by various alternative strong and electroweak nuclear probes. On the other hand, sufficiently accurate atomic PNC experiments would provide a unique method to measure neutron distributions in heavy nuclei.

S. J. Pollock; E. N. Fortson; L. Wilets

1992-11-05

180

Editorial . Quantum fluctuations and coherence in optical and atomic structures  

NASA Astrophysics Data System (ADS)

From simple interference fringes, over molecular wave packets, to nonlinear optical patterns - the fundamental interaction between light and matter leads to the formation of structures in many areas of atomic and optical physics. Sophisticated technology in experimental quantum optics, as well as modern computational tools available to theorists, have led to spectacular achievements in the investigation of quantum structures. This special issue is dedicated to recent developments in this area. It presents a selection of examples where quantum dynamics, fluctuations, and coherence generate structures in time or in space or where such structures are observed experimentally. The examples range from coherence phenomena in condensed matter, over atoms in optical structures, entanglement in light and matter, to quantum patterns in nonlinear optics and quantum imaging. The combination of such seemingly diverse subjects formed the basis of a successful European TMR network, "Quantum Structures" (visit http://cnqo.phys.strath.ac.uk/~gianluca/QSTRUCT/). This special issue partly re.ects the results and collaborations of the network, going however well beyond its scope by including contributions from a global community and from many related topics which were not addressed directly in the network. The aim of this issue is to present side by side these di.erent topics, all of which are loosely summarized under quantum structures, to highlight their common aspects, their di.erences, and the progress which resulted from the mutual exchange of results, methods, and knowledge. To guide the reader, we have organized the articles into subsections which follow a rough division into structures in material systems and structures in optical .elds. Nevertheless, in the following introduction we point out connections between the contributions which go beyond these usual criteria, thus highlighting the truly interdisciplinary nature of quantum structures. Much of the progress in atom optics has been generated by the application of concepts from wave optics to matter waves. An example is the contribution by Franke-Arnold et al. The authors investigate the coherence properties of two trapped cold atoms using concepts developed in wave optics. Nevertheless, novel features appear in this system due to the quantum statistics - as atoms may be bosons or fermions - and due to interactions. Matter waves find a spectacular manifestation in Bose-Einstein condensates (BECs) of cold dilute atomic gases. Several concepts of wave optics, like the laser, have been discussed in relation to BECs, and the .eld of atom optics with BECs is rapidly developing. The similarity between the theoretical description of a weakly interacting BEC with that of a non-linear optical system has motivated a series of experiments that led to the observation of, e.g., solitons, vortices and vortex crystallization in matter waves. In this context, the paper by Josopait et al. describes the dynamics of a Bose-Einstein condensate containing a vortex. The vortex stability is discussed as a function of the interparticle interaction, which can be tuned using Feshbach resonances, and the dynamics of the BEC reflected by an atomic mirror is investigated. Non-linear optics merges with atomic physics also in a relatively new research area which aims at quantum non-linear optics with cold atomic gases. Labeyrie et al. use a dense, laser-cooled atomic gas as a non-linear medium for light propagation, and discuss the conditions for observing optical patterns in the transmitted beam. Pattern formation in non-linear optical media is one of the numerous forms of self-organization that these systems display, including also turbulence and optical solitons. With respects to other physical systems, where these phenomena are commonly observed, optical systems are however special: at optical frequencies thermal .uctuations are negligible and do not hide the presence of quantum .uctuations, even at room temperature. Remarkably, the interplay between non-linearity and quantum noise leads to novel

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

2003-03-01

181

Method for quantitative determination and separation of trace amounts of chemical elements in the presence of large quantities of other elements having the same atomic mass  

DOEpatents

Photoionization via autoionizing atomic levels combined with conventional mass spectroscopy provides a technique for quantitative analysis of trace quantities of chemical elements in the presence of much larger amounts of other elements with substantially the same atomic mass. Ytterbium samples smaller than 10 ng have been detected using an ArF* excimer laser which provides the atomic ions for a time-of-flight mass spectrometer. Elemental selectivity of greater than 5:1 with respect to lutetium impurity has been obtained. Autoionization via a single photon process permits greater photon utilization efficiency because of its greater absorption cross section than bound-free transitions, while maintaining sufficient spectroscopic structure to allow significant photoionization selectivity between different atomic species. Separation of atomic species from others of substantially the same atomic mass is also described.

Miller, C.M.; Nogar, N.S.

1982-09-02

182

Atomic and electronic structure of Ni-Nb metallic glasses  

NASA Astrophysics Data System (ADS)

Solid state 93Nb nuclear magnetic resonance spectroscopy has been employed to investigate the atomic and electronic structures in Ni-Nb based metallic glass (MG) model system. 93Nb nuclear magnetic resonance (NMR) isotropic metallic shift of Ni60Nb35Sn5 has been found to be ˜100 ppm lower than that of Ni60Nb35Zr5 MG, which is correlated with their intrinsic fracture toughness. The evolution of 93Nb NMR isotropic metallic shifts upon alloying is clearly an electronic origin, as revealed by both local hyperfine fields analysis and first-principle computations. This preliminary result indicates that, in addition to geometrical considerations, atomic form factors should be taken into a description of atomic structures for better understanding the mechanical behaviors of MGs.

Yuan, C. C.; Yang, Y.-F.; Xi, X. K.

2013-12-01

183

Various atomic structures of monolayer silicene fabricated on Ag(111)  

NASA Astrophysics Data System (ADS)

Silicene, a monolayer of silicon atoms arranged in honeycomb lattices, can be synthesized on the Ag(111) surface, where it forms several superstructures with different buckling patterns and periodicity. Using scanning tunneling microscopy (STM), we obtained high-resolution images of silicene grown on Ag(111) and revealed its five phases, i.e., 4 × 4 - ?, 4 × 4 - ?, \\sqrt{13}\\times \\sqrt{13} - ?, \\sqrt{13}\\times \\sqrt{13} - ? and \\sqrt{13}\\times \\sqrt{13} - ?, some observed for the first time. For each of the phases, we have determined its atomic structure by comparing the atomic-resolution STM images with theoretical simulation results previously reported. We thus eliminate the contradictions of previous studies on the structural models of various silicene phases supported by the Ag(111) surface.

Liu, Zhi-Long; Wang, Mei-Xiao; Xu, Jin-Peng; Ge, Jian-Feng; Le Lay, Guy; Vogt, Patrick; Qian, Dong; Gao, Chun-Lei; Liu, Canhua; Jia, Jin-Feng

2014-07-01

184

Atomic and electronic structure of Ni-Nb metallic glasses  

SciTech Connect

Solid state {sup 93}Nb nuclear magnetic resonance spectroscopy has been employed to investigate the atomic and electronic structures in Ni-Nb based metallic glass (MG) model system. {sup 93}Nb nuclear magnetic resonance (NMR) isotropic metallic shift of Ni{sub 60}Nb{sub 35}Sn{sub 5} has been found to be ?100?ppm lower than that of Ni{sub 60}Nb{sub 35}Zr{sub 5} MG, which is correlated with their intrinsic fracture toughness. The evolution of {sup 93}Nb NMR isotropic metallic shifts upon alloying is clearly an electronic origin, as revealed by both local hyperfine fields analysis and first-principle computations. This preliminary result indicates that, in addition to geometrical considerations, atomic form factors should be taken into a description of atomic structures for better understanding the mechanical behaviors of MGs.

Yuan, C. C.; Yang, Y.-F., E-mail: yifeng@iphy.ac.cn; Xi, X. K., E-mail: xi@iphy.ac.cn [Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

2013-12-07

185

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

SciTech Connect

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

Abdallah, J. Jr.; Clark, R.E.H.; Cowan, R.D.

1988-12-01

186

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

PubMed

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. PMID:25825836

van den Bedem, Henry; Fraser, James S

2015-03-31

187

Atomic structure of amorphous Al sub 90 Fe sub x Ce sub 10 minus sub x  

SciTech Connect

The atomic structure of liquid-quenched amorphous Al{sub 90}Fe{sub {ital x}}Ce{sub 10{minus}}{sub {ital x}} ({ital x}=5, 7) was studied by pulsed neutron and x-ray scattering. The atomic pair--density function determined by pulsed neutron diffraction indicates that a significant portion of Al--Fe distances are anomalously short, while some part of Al--Al distances are anomalously long. Both neutron and x-ray scattering showed the presence of a prepeak in the structure factor. These results suggest that a strong interaction between Al and Fe modifies the structure of this glass, leading to chemical and topological short-range ordering.

Hsieh, H.Y. (Department of Electrical Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6314 (US)); Toby, B.H.; Egami, T. (Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania (US)); He, Y.; Poon, S.J. (Department of Physics, The University of Virginia, Charlittesville, Virginia (US)); Shiflet, G.J. (Department of Materials Science, University of Virginia, Charlottesville, Virginia (US))

1990-12-01

188

InChI - the worldwide chemical structure identifier standard  

PubMed Central

Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the international, worldwide standard for defined chemical structures. This article will describe the extensive use and dissemination of the InChI and InChIKey structure representations by and for the world-wide chemistry community, the chemical information community, and major publishers and disseminators of chemical and related scientific offerings in manuscripts and databases. PMID:23343401

2013-01-01

189

Atomic structures at last: the ribosome in 2000  

Microsoft Academic Search

Last year, atomic structures of the 50S ribosomal subunit from Haloarcula marismortui and of the 30S ribosomal subunit from Thermus thermophilus were published. A year before that, a 7.8 Å resolution electron density map of the 70S ribosome from T. thermophilus appeared. This information is revolutionizing our understanding of protein synthesis.

V. Ramakrishnan; P. B. Moore

2001-01-01

190

On the structure of the interstellar atomic gas  

E-print Network

The interstellar atomic hydrogen is known to be a 2-phase medium in which turbul ence plays an important r\\^ole. Here we present high resolution numerical simulations describing the gas from tens of parsec down to hundreds of AU. This high resolut ion allows to probe numerically, the small scale structures which naturally arises from the turbulence and the 2-phase physics.

P. Hennebelle; E. Audit

2007-01-24

191

The relativistic hydrogen atom: a theoretical laboratory for structure functions  

E-print Network

Thanks to the Dirac equation, the hydrogen-like atom at high $Z$ offers a precise model of relativistic bound state, allowing to test properties of unpolarized and polarized structure functions analogous to the hadronic ones, in particular: Sivers effect, sum rules for the vector, axial, tensor charges and for the magnetic moment, positivity constraints, sea contributions and fracture functions

X. Artru; K. Benhizia

2006-01-17

192

Aquaporin water channels - from atomic structure to clinical medicine  

Microsoft Academic Search

The water permeability of biological membranes has been a longstanding problem in physiology, but the proteins responsible for this remained unknown until discovery of the aquaporin 1 (AQP1) water channel protein. AQP1 is selectively permeated by water driven by osmotic gradients. The atomic structure of human AQP1 has recently been defined. Each subunit of the tetramer contains an individual aqueous

Peter Agre; Landon S. King; Masato Yasui; Wm B. Guggino; Ole Petter Ottersen; Yoshinori Fujiyoshi; Andreas Engel; Søren Nielsen

2002-01-01

193

Atomic Structure of Intracellular Amorphous Calcium Phosphate Deposits  

Microsoft Academic Search

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 angstrom in longest dimension, whose probable composition

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

1975-01-01

194

Workshop on foundations of the relativistic theory of atomic structure  

SciTech Connect

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)

Not Available

1981-03-01

195

Spectroscopic Imaging STM: Atomic-Scale Visualization of Electronic Structure  

E-print Network

Chapter 3 Spectroscopic Imaging STM: Atomic-Scale Visualization of Electronic Structure and Symmetry in Underdoped Cuprates Kazuhiro Fujita, Mohammad Hamidian, Inês Firmo, Sourin Mukhopadhyay, Chung) phases of underdoped cuprates, two distinct types of electronic states are observed K. Fujita (B) · M

Davis, James C.

196

Determining parameters of the local atomic structure of Cu-Ni and Cu-Mn alloys by the method of extended electron-loss fine structure spectroscopy  

NASA Astrophysics Data System (ADS)

In this work, we consider the possibility of analyzing local atomic structure based on strongly overlapping experimental extended electron-energy-loss fine structure (EELFS) spectra of two different chemical elements. M 2,3 EELFS spectra have been obtained from the surface of Cu x Ni1 - x and Cu x Mn1 - x ( x = 0.5) alloys. The method of determining the parameters of the local atomic structure (coordination numbers, lengths of the chemical bonds, and the parameters of their dispersion) of the nearest atomic surroundings in ultrathin (1-5 nm) surface layers of two-component alloys of 3 d metals has been suggested based on the overlapping extended fine structures of the electron-energy-loss spectra. The method was tested on experimental M 2,3 EELFS spectra of the surface of testing alloys Cu50Ni50 and Cu50Mn50.

Bakieva, O. R.; Nemtsova, O. M.; Gai, D. E.

2015-01-01

197

Mobile Point Defects and Atomic Basis for Structural Transformations of a Crystal Surface  

E-print Network

Mobile Point Defects and Atomic Basis for Structural Transformations of a Crystal Surface [Articles diffusion and structural transformations proceed through mechanisms that operate on the atomic scale of impurity Pb atoms on a Ge surface catalyze atomic motions and structural changes without altering the basic

Golovchenko, Jene A.

198

Ground State Hyperfine Structure of Muonic Helium Atom  

E-print Network

On the basis of the perturbation theory in the fine structure constant $\\alpha$ and the ratio of the electron to muon masses we calculate one-loop vacuum polarization and electron vertex corrections and the nuclear structure corrections to the hyperfine splitting of the ground state of muonic helium atom $(\\mu e ^4_2He)$. We obtain total result for the ground state hyperfine splitting $\\Delta \

A. A. Krutov; A. P. Martynenko

2008-07-21

199

A quantum interface between single atoms and nanophotonic structures  

NASA Astrophysics Data System (ADS)

Strong interactions between light and atoms at the single-quantum level are an important ingredient for quantum technologies, as well as for studies of fundamental effects in quantum optics. This thesis describes the development of a novel experimental platform that allows for trapping a single rubidium atom in the evanescent mode of a nano-fabricated optical cavity with sub-wavelength dimensions. By virtue of their small size, these cavities provide extremely large atom-photon coupling strengths and good prospects for scalability and integration into complex quantum optical circuits. Positioning the atom near the nano-structure is accomplished using a scanning optical tweezer dipole trap. As a first application, we have demonstrated a coherent optical switch, where a single gate photon controls the propagation of many subsequent signal photons, with the interaction mediated by the atom and cavity. We have also shown that the optical response of the combined atom-cavity system is nonlinear at the level of one or two photons.

Thompson, Jeffrey Douglas

200

Structural plasticity: how intermetallics deform themselves in response to chemical pressure, and the complex structures that result.  

PubMed

Interfaces between periodic domains play a crucial role in the properties of metallic materials, as is vividly illustrated by the way in which the familiar malleability of many metals arises from the formation and migration of dislocations. In complex intermetallics, such interfaces can occur as an integral part of the ground-state crystal structure, rather than as defects, resulting in such marvels as the NaCd2 structure (whose giant cubic unit cell contains more than 1000 atoms). However, the sources of the periodic interfaces in intermetallics remain mysterious, unlike the dislocations in simple metals, which can be associated with the exertion of physical stresses. In this Article, we propose and explore the concept of structural plasticity, the hypothesis that interfaces in complex intermetallic structures similarly result from stresses, but ones that are inherent in a defect-free parent structure, rather than being externally applied. Using DFT-chemical pressure analysis, we show how the complex structures of Ca2Ag7 (Yb2Ag7 type), Ca14Cd51 (Gd14Ag51 type), and the 1/1 Tsai-type quasicrystal approximant CaCd6 (YCd6 type) can all be traced to large negative pressures around the Ca atoms of a common progenitor structure, the CaCu5 type with its simple hexagonal 6-atom unit cell. Two structural paths are found by which the compounds provide relief to the Ca atoms' negative pressures: a Ca-rich pathway, where lower coordination numbers are achieved through defects eliminating transition metal (TM) atoms from the structure; and a TM-rich path, along which the addition of spacer Cd atoms provides the Ca coordination environments greater independence from each other as they contract. The common origins of these structures in the presence of stresses within a single parent structure highlights the diverse paths by which intermetallics can cope with competing interactions, and the role that structural plasticity may play in navigating this diversity. PMID:25238606

Berns, Veronica M; Fredrickson, Daniel C

2014-10-01

201

Atomic disorder and amorphization of B2-structure CoZr by ball milling  

SciTech Connect

For a considerable number of intermetallic compounds it has been found that ball milling introduces atomic (chemical) disorder. Disorder due to milling was demonstrated by x-ray diffraction in AlRu, crystallizing in the B2 structure (ordered b.c.c.) by a decrease of the intensity of superlattice reflections relative to fundamental reflections. The same technique was used to investigate disordering by milling in Ni{sub 3}Al, crystallizing in the L1{sub 2} structure (ordered f.c.c.). In both cases the disorder is anti-site disorder of both components, i.e. both atomic species substitute on the wrong sublattices. Besides x-ray diffraction measurements of magnetic properties turned out to be useful in monitoring structural changes due to milling. The change in the superconducting transition temperature, measured by magnetic a.c. susceptibility, was used to demonstrate atomic disordering by milling in Nb{sub 3}Sn and Nb{sub 3}Au. The type of disorder turned out to be anti-site disorder. Such a type of disorder occurs in the same materials also at high temperatures or after irradiation by neutrons. The disordering was accompanied by an increase of the lattice parameter. An increase in high-field magnetization accompanied by a decrease of the lattice parameter during milling was found in B2 CoGa and B2 CoAl. In principle in the completely ordered state both compounds are non-magnetic, because the CO atoms are shielded from one another by Ga and Al atoms, respectively. However, when a Co atom is transferred to the wrong sublattice, it is surrounded by Co atoms as nearest neighbors and bears a magnetic moment. This explains the strong increase of the magnetization due to milling.

Zhou, G.F.; Bakker, H. [Univ. van Amsterdam (Netherlands). Van der Waals-Zeeman Lab.] [Univ. van Amsterdam (Netherlands). Van der Waals-Zeeman Lab.

1996-01-01

202

A Structure Model for Black Holes: Atomic-like Structure, Quantization and the Minimum Schwarzschild Radius  

E-print Network

A structure model for black holes is proposed by mean field approximation of gravity. The model, which consists of a charged singularity at the center and quantum fluctuation of fields around the singularity, is similar to the atomic structure. The model naturally quantizes the black hole. Especially we find the minimum black hole, whose structure is similar to the hydrogen atom and whose Schwarzschild radius becomes about 1.1287 of the Planck length.

Yukinori Nagatani

2005-01-04

203

Atomic Structure and Properties of Extended Defects in Silicon  

SciTech Connect

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.

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

1998-10-15

204

An atomic-scale analysis of catalytically-assisted chemical vapor deposition of carbon nanotubes  

E-print Network

An atomic-scale analysis of catalytically-assisted chemical vapor deposition of carbon nanotubes M Growth of carbon nanotubes during transition-metal particles catalytically-assisted thermal decomposition of various nanotube surface and edge reactions (e.g. adsorption of hydrocarbons and hydrogen onto the surface

Grujicic, Mica

205

Constant centrifugal potential approximation for atom-diatom chemical reaction dynamics  

E-print Network

Constant centrifugal potential approximation for atom-diatom chemical reaction dynamics Kengo,Myodaiji, Okazaki 444. Japan (Received 28 September 1993; accepted 8 December 1993) The constant centrifugal of such practically useful approxima- tions the constant centrifugal potential approximation (CCPA) (or the energy

Takada, Shoji

206

Local atomic structure of Ca-Mg-Zn metallic glasses  

NASA Astrophysics Data System (ADS)

The amorphous structure of four Ca60MgXZn40-X ( X=10 , 15, 20, and 25at.% ) ternary metallic glasses (MGs) has been investigated by neutron and x-ray diffraction, using Reverse Monte Carlo modeling to simulate the results. A critical analysis of the resultant models, corroborated by ab initio molecular-dynamics simulations, indicate that the glass structure for this system can be described as a mixture of Mg- and Zn-centered clusters, with Ca dominating in the first coordination shell of these clusters. A coordination number (CN) of 10 [with about 7 Ca and 3 (Mg+Zn) atoms] is most common for the Zn-centered clusters. CN=11 and 12 [with about 7-8 Ca and 4 (Mg+Zn) atoms] are most common for Mg-centered clusters. Fivefold bond configurations (pentagonal pyramids) dominate (˜60%) in the first coordination shell of the clusters, suggesting dense atomic packing. Bond-angle distributions suggest near-equilateral triangles and pentagonal bipyramids to be the most common nearest atom configurations. This is the systematic characterization of the structure of Ca-Mg-Zn MGs, a category of bulk MGs with interesting properties and intriguing applications. It is also the experimental verification of the principle of efficient packing of solute-centered clusters in ternary MGs.

Senkov, O. N.; Miracle, D. B.; Barney, E. R.; Hannon, A. C.; Cheng, Y. Q.; Ma, E.

2010-09-01

207

Metal Oxide Nanoparticle Growth on Graphene via Chemical Activation with Atomic Oxygen  

PubMed Central

Chemically interfacing the inert basal plane of graphene with other materials has limited the development of graphene-based catalysts, composite materials, and devices. Here, we overcome this limitation by chemically activating epitaxial graphene on SiC(0001) using atomic oxygen. Atomic oxygen produces epoxide groups on graphene, which act as reactive nucleation sites for zinc oxide nanoparticle growth using the atomic layer deposition precursor diethyl zinc. In particular, exposure of epoxidized graphene to diethyl zinc abstracts oxygen, creating mobile species which diffuse on the surface to form metal oxide clusters. This mechanism is corroborated with a combination of scanning probe microscopy, Raman spectroscopy, and density functional theory, and can likely be generalized to a wide variety of related surface reactions on graphene. PMID:24206242

Johns, James E.; Alaboson, Justice M. P.; Patwardhan, Sameer; Ryder, Christopher R.; Schatz, George C.

2013-01-01

208

Volcano structure in atomic resolution core-loss images.  

PubMed

A feature commonly present in simulations of atomic resolution electron energy loss spectroscopy images in the scanning transmission electron microscope is the volcano or donut structure. In the past this has been understood in terms of a geometrical perspective using a dipole approximation. It is shown that the dipole approximation for core-loss spectroscopy begins to break down as the probe forming aperture semi-angle increases, necessitating the inclusion of higher order terms for a quantitative understanding of volcano formation. Using such simulations we further investigate the mechanisms behind the formation of such structures in the single atom case and extend this to the case of crystals. The cubic SrTiO3 crystal is used as a test case to show the effects of nonlocality, probe channelling and absorption in producing the volcano structure in crystal images. PMID:18077094

D'Alfonso, A J; Findlay, S D; Oxley, M P; Allen, L J

2008-06-01

209

Degradation of High-k/Interface Layer Structures by H Atoms and Interface Engineering with O Atom Manipulation  

NASA Astrophysics Data System (ADS)

With regard to the growing numbers of H atoms in high-k/SiO2/Si systems, it is revealed through first principles calculations that degradation of high-k/interface layer structures has been found to occur from the interface layers by H atoms, even if the interface defects are terminated with H atoms by forming gas annealing. O termination is proposed to prevent this degradation. The effects of H and O atoms are verified by experimental analyses.

Kato, K.; Hirano, I.; Matsushita, D.; Nakasaki, Y.; Mitani, Y.

2011-12-01

210

Anomalous decay of an atom in structured band gap reservoirs  

E-print Network

We analyze the spontaneous emission of a two-level atom interacting with a special class of structured reservoirs of field modes with band gap edge coinciding with the atomic transition frequency. The exact time evolution of the population of the excited level is evaluated analytically through series of Fox-$H$ functions. Over estimated long time scales, inverse power law relaxations emerge, with powers decreasing continuously to 2 according to the choice of the special reservoir. No trapping of the population of the excited level emerges. The same results are recovered in presence of $N-1$ atoms, each one in the ground state, described by the Dicke model. The power of the inverse power law decay results to be independent of $N$. A critical number $N_{\\alpha}^{(\\star)}$ is evaluated, such that, for $N \\gg N_{\\alpha}^{(\\star)}$, the inverse power law decay vanishes.

Filippo Giraldi; Francesco Petruccione

2011-04-09

211

Stable atomic structure of NiTi austenite  

SciTech Connect

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

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

2014-08-01

212

Stable atomic structure of NiTi austenite  

NASA Astrophysics Data System (ADS)

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

Zarkevich, Nikolai A.; Johnson, Duane D.

2014-08-01

213

Multilayer cyclic C6 structures intercalated with metal atoms  

NASA Astrophysics Data System (ADS)

A new type of tubular inorganic metal-carbon sandwich molecule based on cyclic C6 is proposed. These consist of multiple layers of cyclic C6 with intercalated metal atoms. Structures and electronic properties of these molecules have been calculated using first-principles density functional techniques. We have evaluated all metals in the first six periods of the periodic table, except for the lanthanides, as possible components of such molecules. Our calculations show high bond energy and small energy gaps in many of these structures. We suggest that the high structural stability and high conductivity in these sandwich compounds make them very promising for use in nanoelectronic applications.

Kuzmin, Stanislav; Duley, Walter W.

2011-02-01

214

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase  

PubMed Central

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

2013-01-01

215

STRAIN-INDUCED STRUCTURAL CHANGES AND CHEMICAL REACTIONSI. THERMOMECHANICAL AND  

E-print Network

STRAIN-INDUCED STRUCTURAL CHANGES AND CHEMICAL REACTIONSÐI. THERMOMECHANICAL AND KINETIC MODELS V analysis of shear-induced chemical reac- tions is absent; likewise, the extent to which plastic ¯ow can

Meyers, Marc A.

216

Chemical potential, Teller's theorem, and the scaling of atomic and molecular energies  

PubMed Central

For atoms and homonuclear diatomic molecules, it is argued that the electronic energies have the forms [Formula: see text] and [Formula: see text] [Formula: see text], respectively,where Z is the atomic number, N is the number of electrons, and R is the internuclear distance. By using the Lieb-Simon theorem that the Thomas-Fermi theory is exact in the limit of large atomic number and the Teller theorem that molecules are not bound in the Thomas-Fermi theory, it is then shown, among other results, that the electron-electron repulsion energy for neutral systems has no term in Z2 and that the nucleus-nucleus repulsion energy for neutral molecules is probably [unk](Z5/3). For neutral atoms, it is predicted and verified that the chemical potential (electronegativity) is [unk](Z-1/3) for large Z. Tetrahedral and octahedral molecules are briefly discussed. PMID:16592908

March, Norman H.; Parr, Robert G.

1980-01-01

217

Modeling Protein Structure at Near Atomic Resolutions With Gorgon  

PubMed Central

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

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

218

Modeling protein structure at near atomic resolutions with Gorgon.  

PubMed

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

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

2011-05-01

219

Zero-Temperature Structures of Atomic Metallic Hydrogen  

NASA Astrophysics Data System (ADS)

Since the first prediction of an atomic metallic phase of hydrogen by Wigner and Huntington over 75 years ago, there have been many theoretical efforts aimed at determining the crystal structures of the zero-temperature phases. We present results from ab initio random structure searching with density functional theory performed to determine the ground state structures from 500 GPa to 5 TPa. We estimate that molecular hydrogen dissociates into a monatomic body-centered tetragonal structure near 500 GPa (rs= 1.225), which then remains stable to 2.5 TPa (rs= 0.969). At higher pressures, hydrogen stabilizes in an ...ABCABC... planar structure that is remarkably similar to the ground state of lithium, which compresses to the face-centered cubic lattice beyond 5 TPa (rs< 0.86). Our results provide a complete ab initio description of the atomic metallic crystal structures of hydrogen, resolving one of the most fundamental and long outstanding issues concerning the structures of the elements.

McMahon, Jeffrey; Ceperley, David

2011-03-01

220

Chemical structures and electrical properties of atomic layer deposited HfO2 thin films grown at an extremely low temperature (?100 °C) using O3 as an oxygen source  

NASA Astrophysics Data System (ADS)

The properties of atomic layer deposited (ALD) HfO2 films grown at low temperatures (?100 °C) were examined for potential applications in flexible display and bioelectronics. A saturated ALD growth behavior was observed even at an extremely low temperature (30 °C) due to the strong oxidizing potential of O3. However, HfO2 films grown at low temperatures showed a low film density and high impurity concentration, because the thermal energy during film growth was insufficient to remove ligands completely from Hf ions in precursor molecule. This resulted in low dielectric constant and high leakage current density of the films. Nevertheless, HfO2 film grown at 100 °C using O3 gas with a high concentration (390 g/Nm3) showed a tolerable impurity concentration with the dielectric constant of ?16 and breakdown field of ?4 MV/cm, which are approximately two-thirds of those of HfO2 film grown at 250 °C.

Kim, Jeong Hwan; Park, Tae Joo; Kim, Seong Keun; Cho, Deok-Yong; Jung, Hyung-Suk; Lee, Sang Young; Hwang, Cheol Seong

2014-02-01

221

Ab initio nanoplasmonics: The impact of atomic structure  

NASA Astrophysics Data System (ADS)

We present an ab initio study of the hybridization of localized surface plasmons in a metal nanoparticle dimer. The atomic structure, which is often neglected in theoretical studies of quantum nanoplasmonics, has a strong impact on the optical absorption properties when subnanometric gaps between the nanoparticles are considered. We demonstrate that this influences the hybridization of optical resonances of the dimer, and leads to significantly smaller electric field enhancements as compared to the standard jellium model. In addition, we show that the corrugation of the metal surface at a microscopic scale becomes as important as other well-known quantum corrections to the plasmonic response, implying that the atomic structure has to be taken into account to obtain quantitative predictions for realistic nanoplasmonic devices.

Zhang, Pu; Feist, Johannes; Rubio, Angel; García-González, Pablo; García-Vidal, F. J.

2014-10-01

222

Magnetism and surface structure of atomically controlled ultrathin metal films.  

SciTech Connect

We review the correlation of magnetism and surface structure in ultrathin metal films, including the tailoring of novel magnetic properties using atomic scale control of the nanostructure. We provide an overview of modern fabrication and characterization techniques used to create and explore these fascinating materials, and highlight important phenomena of interest. We also discuss techniques that control and characterize both the magnetic and structural properties on an atomic scale. Recent advances in the development and applications of these techniques allow nanomagnetism to be investigated in an unprecedented manner. A system cannot necessarily retain a two-dimensional structure as it enters the ultrathin region, but it can transform into a three-dimensional, discontinuous structure due to the Volmer-Weber growth mechanism. This structural transformation can give rise to superparamagnetism. During this evolution, competing factors such as interparticle interactions and the effective magnetic anisotropy govern the magnetic state. These magnetic parameters are influenced by the nanostructure of the film. In particular, controlling the magnetic anisotropy is critical for determining the magnetic properties. Surface effects play especially important roles in influencing both the magnitude and direction of the magnetic anisotropy in ultrathin films. By properly altering the surface structure, the strength and direction of the magnetic anisotropy are controlled via spin-orbit and/or dipole interactions.

Shiratsuchi, Yu.; Yamamoto, M.; Bader, S. D.; Materials Science Division; Osaka Univ.

2007-01-01

223

Atomic Cut Introduction by Resolution: Proof Structuring and Compression  

NASA Astrophysics Data System (ADS)

The careful introduction of cut inferences can be used to structure and possibly compress formal sequent calculus proofs. This paper presents CIRes, an algorithm for the introduction of atomic cuts based on various modifications and improvements of the CERes method, which was originally devised for efficient cut-elimination. It is also demonstrated that CIRes is capable of compressing proofs, and the amount of compression is shown to be exponential in the length of proofs.

Woltzenlogel Paleo, Bruno

224

Atomic structure of misfit dislocations in metal-ceramic interfaces  

Microsoft Academic Search

In this paper we present a combined experimental and theoretical study of misfit dislocations in metal?ceramic interfaces. The goal is to reveal the atomic structure of the cores of misfit dislocations and relate it to the bonding strength between the two materials. Two interfaces in the niobium-sapphire system corresponding to different interface planes between the Nb and Al2O3 crystals, (0110)Al2O3|(112)Nb

V. Vitek; G. Gutekunst; J. Mayer; M. Rühle

1995-01-01

225

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

PubMed

A new characterization of known drug, lead, and representative nondrug databases was performed taking into account several properties at the atomic and molecular levels. This characterization included atom type preferences, intrinsic structural diversity (Atom Type Diversity, ATD), and other well-known physicochemical properties, as an approach for rapid assessment of druglikeness for small molecule libraries. To characterize ATD, an elaborate united atom classification, UALOGP (United Atom Log P), with 148 atom types, was developed along with associated atomic physicochemical parameters. This classification also enabled an analysis of atom type and physicochemical property distributions (for calculated log P, molar refractivity, molecular weight, total atom count, and ATD) of drug, lead, and nondrug databases, a reassessment of the Ro5 (Rule of Five) and GVW (Ghose?Viswanadhan?Wendoloski) criteria, and development of new criteria and ranges more accurately reflecting the chemical space occupied by small molecule drugs. A relative druglikeness parameter was defined for atom types in drugs, identifying the most preferred types. The present work demonstrates that drug molecules are constitutionally more diverse relative to nondrugs, while being less diverse than leads. PMID:21480669

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

2011-05-01

226

Structure and local chemical properties of boron-terminated tetravacancies in hexagonal boron nitride.  

PubMed

Imaging and spectroscopy performed in a low-voltage scanning transmission electron microscope are used to characterize the structure and chemical properties of boron-terminated tetravacancies in hexagonal boron nitride. We confirm earlier theoretical predictions about the structure of these defects and identify new features in the electron energy-loss spectra of B atoms using high resolution chemical maps, highlighting differences between these areas and pristine sample regions. We correlate our experimental data with calculations which help explain our observations. PMID:25763963

Cretu, Ovidiu; Lin, Yung-Chang; Koshino, Masanori; Tizei, Luiz H G; Liu, Zheng; Suenaga, Kazutomo

2015-02-20

227

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

SciTech Connect

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.

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

2012-02-10

228

Sub-micron period lattice structures of magnetic microtraps for ultracold atoms on an atom chip  

NASA Astrophysics Data System (ADS)

We report on the design, fabrication and characterization of magnetic nanostructures to create a lattice of magnetic traps with sub-micron period for trapping ultracold atoms. These magnetic nanostructures were fabricated by patterning a Co/Pd multilayered magnetic film grown on a silicon substrate using high precision e-beam lithography and reactive ion etching. The Co/Pd film was chosen for its small grain size and high remanent magnetization and coercivity. The fabricated structures are designed to magnetically trap 87Rb atoms above the surface of the magnetic film with one-dimensional and two-dimensional (triangular and square) lattice geometries and sub-micron period. Such magnetic lattices can be used for quantum tunneling and quantum simulation experiments, including using geometries and periods that may be inaccessible with optical lattices.

Herrera, I.; Wang, Y.; Michaux, P.; Nissen, D.; Surendran, P.; Juodkazis, S.; Whitlock, S.; McLean, R. J.; Sidorov, A.; Albrecht, M.; Hannaford, P.

2015-03-01

229

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures  

E-print Network

Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer...

Li, Yunqi; Roy, Ambrish; Zhang, Yang

2009-08-20

230

Chemical reactivities of catalytic and noncatalytic zinc or cobalt atoms of horse liver alcohol dehydrogenase: differentiation by their thermodynamic and kinetic properties.  

PubMed Central

Horse liver alcohol dehydrogenase (EC 1.1.1.1) contains one catalytic and one noncatalytic pair of zinc atoms that can be replaced selectively with cobalt and/or 65zince. We have now prepared "hybird" metalloenzymes by specifically replacing one or both pairs of zinc atoms with 65zinc and/or cobalt. Their differential chemical reactivities serve to characterize the metal atoms at either site.The spectral and kinetic properties of the resultant 65zinc, cobalt, and hybrid enzymes, as well as those of their complexes with 1,10-phenanthroline, identify the metal atoms that are at the catalytic sites and differentiate them from those at the noncatalytic sites. All data are in complete agreement with the results of the x-ray crystal structure analysis. Remarkably, under the conditions used, chemical reactivity, as gauged by thermodynamic methods under equilibrium conditions, identifies the catalytic metal atoms as those which are reactive to 1,10-phenanthroline, while this reagnet does not affect the noncatalytic pair. Under dynamic conditions the kinetics of the metal-metal exchange reveals the converse to be true: the chemical reactivity of the noncatalytic atoms is much higher and, hence, they exchange more rapidly. The results are examined in terms of thermodynamic and kinetic properties of metal complex ions which serve as the basis of possible mechanisms underlying these observations. PMID:1061138

Sytkowski, A J; Vallee, B L

1976-01-01

231

Atomic-Scale Recognition of Surface Structure and Intercalation Mechanism of Ti3C2X.  

PubMed

MXenes represent a large family of functionalized two-dimensional (2D) transition-metal carbides and carbonitrides. However, most of the understanding on their unique structures and applications stops at the theoretical suggestion and lack of experimental support. Herein, the surface structure and intercalation chemistry of Ti3C2X are clarified at the atomic scale by aberration-corrected scanning transmission electron microscope (STEM) and density functional theory (DFT) calculations. The STEM studies show that the functional groups (e.g., OH(-), F(-), O(-)) and the intercalated sodium (Na) ions prefer to stay on the top sites of the centro-Ti atoms and the C atoms of the Ti3C2 monolayer, respectively. Double Na-atomic layers are found within the Ti3C2X interlayer upon extensive Na intercalation via two-phase transition and solid-solution reactions. In addition, aluminum (Al)-ion intercalation leads to horizontal sliding of the Ti3C2X monolayer. On the basis of these observations, the previous monolayer surface model of Ti3C2X is modified. DFT calculations using the new modeling help to understand more about their physical and chemical properties. These findings enrich the understanding of the MXenes and shed light on future material design and applications. Moreover, the Ti3C2X exhibits prominent rate performance and long-term cycling stability as an anode material for Na-ion batteries. PMID:25688582

Wang, Xuefeng; Shen, Xi; Gao, Yurui; Wang, Zhaoxiang; Yu, Richeng; Chen, Liquan

2015-02-25

232

A Distance-Dependent Atomic Knowledge-Based Potential for Improved Protein Structure Selection  

E-print Network

A Distance-Dependent Atomic Knowledge-Based Potential for Improved Protein Structure Selection Hui atomic potential to test sets obtained from the web, composed of native protein and decoy structures published atomic potentials in the task of selecting native and near-native structures. This newly developed

Lu, Hui

233

The Meshless Dynamic Relaxation Techniques for Simulating Atomic Structures of Materials  

E-print Network

1 The Meshless Dynamic Relaxation Techniques for Simulating Atomic Structures of Materials By Li could result in a change of the local atomic structure. The present paper introduces new Dynamic, to find equilibrium positions of the block of atoms containing different structural defects. The internal

Niewczas, Marek

234

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures  

E-print Network

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures Yunqi Li diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures. PLoS ONE 4(8): e6701. doi:10

Zhang, Yang

235

Imaging the Atomic Surface Structures of CeO2 Nanoparticles Yuyuan Lin,*,  

E-print Network

Imaging the Atomic Surface Structures of CeO2 Nanoparticles Yuyuan Lin,*, Zili Wu, Jianguo Wen ABSTRACT: Atomic surface structures of CeO2 nanoparticles are under debate owing to the lack of clear using aberration-corrected high-resolution elec- tron microscopy, we determined the atomic structures

Shull, Kenneth R.

236

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz  

E-print Network

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz Rhiju Das Abstract Consistently predicting biopolymer structure at atomic resolution from sequence alone remains: Das R (2013) Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz. PLo

Das, Rhiju

237

Fractional Band Filling in an Atomic Chain Structure J. N. Crain,1  

E-print Network

Fractional Band Filling in an Atomic Chain Structure J. N. Crain,1 A. Kirakosian,1 K. N. Altmann,1 [5­12]. X-ray dif- fraction from the Si(557)-Au structure shows that gold atoms are incorporated by increasing U. We have found a chain structure of gold atoms on silicon, which exhibits a 1=4-filled band. Two

Himpsel, Franz J.

238

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

E-print Network

Atomically precise self-assembly of one-dimensional structures on silicon I. Barke, T.K. Ru-magnetic surface. An interesting by-product is a memory structure with self-assembled tracks that are five atom: Low-dimensional structures; Atomic wires; Silicon surfaces; One-dimensional physics; Scanning

Himpsel, Franz J.

239

Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images  

E-print Network

Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images A. J, TN 37831-6031, U.S.A. Key words. Atomic resolution, crystal structure retrieval, incoherent imaging be used to yield important information on unexpected atomic structures. Introduction The physical

Pennycook, Steve

240

A directional representation for 3D tubular structures resulting from isotropic well-localized atoms  

E-print Network

, their interaction via convolution with the tubular structure is equivalent to a set of directional atoms at various, the directionality of our representation arises only in the presence of tubular structures. More precisely, the atoms structure is equivalent to a set of directional multiscale 3D atoms, oriented along any possible direction

Labate, Demetrio

241

Chemical modifiers in arsenic determination in biological materials by tungsten coil electrothermal atomic absorption spectrometry  

Microsoft Academic Search

Palladium, iridium, and rhodium are evaluated as possible chemical modifiers in the determination of As in digest solutions of biological materials (human hair and clam) by tungsten coil electrothermal atomic absorption spectrophotometry (TCA-AAS). The modifier in solution was applied onto the coil and thermally pre-reduced; the pre-reduction conditions, the amount of modifier, and the thermal program were optimized. Palladium was

C. G. Bruhn; V. N. Huerta; J. Y. Neira

2004-01-01

242

A collaboration of labs: The Institute for Atom-Efficient Chemical Transformations (IACT)  

ScienceCinema

The Institute for Atom-Efficient Chemical Transformations (IACT) is an Energy Frontier Research Center funded by the U.S. Department of Energy. IACT focuses on advancing the science of catalysis to improve the efficiency of producing fuels from biomass and coal. IACT is a collaborative effort that brings together a diverse team of scientists from Argonne National Laboratory, Brookhaven National Laboratory, Northwestern University, Purdue University and the University of Wisconsin. For more information, visit www.iact.anl.gov

Lobo, Rodrigo; Marshall, Chris; Cheng, Lei; Stair, Peter; Wu, Tianpan; Ray, Natalie; O'Neil, Brandon; Dietrich, Paul

2013-04-19

243

Atomic structures of peptide self-assembly mimics  

PubMed Central

Although the ?-rich self-assemblies are a major structural class for polypeptides and the focus of intense research, little is known about their atomic structures and dynamics due to their insoluble and noncrystalline nature. We developed a protein engineering strategy that captures a self-assembly segment in a water-soluble molecule. A predefined number of self-assembling peptide units are linked, and the ?-sheet ends are capped to prevent aggregation, which yields a mono-dispersed soluble protein. We tested this strategy by using Borrelia outer surface protein (OspA) whose single-layer ?-sheet located between two globular domains consists of two ?-hairpin units and thus can be considered as a prototype of self-assembly. We constructed self-assembly mimics of different sizes and determined their atomic structures using x-ray crystallography and NMR spectroscopy. Highly regular ?-sheet geometries were maintained in these structures, and peptide units had a nearly identical conformation, supporting the concept that a peptide in the regular ?-geometry is primed for self-assembly. However, we found small but significant differences in the relative orientation between adjacent peptide units in terms of ?-sheet twist and bend, suggesting their inherent flexibility. Modeling shows how this conformational diversity, when propagated over a large number of peptide units, can lead to a substantial degree of nanoscale polymorphism of self-assemblies. PMID:17093048

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

2006-01-01

244

Images of Atoms.  

ERIC Educational Resources Information Center

Recommends using a simple image, such as the fuzzy atom ball to help students develop a useful understanding of the molecular world. Explains that the image helps students easily grasp ideas about atoms and molecules and leads naturally to more advanced ideas of atomic structure, chemical bonding, and quantum physics. (Author/NB)

Wright, Tony

2003-01-01

245

Atomic Clocks and Variations of the FIne Structure Constant  

NASA Technical Reports Server (NTRS)

We describe a new test for possible variations of the fine structure constant alpha by comparisons of rates between clocks based on hyperfine transitions in alkali atoms with different atomic number Z. H-maser, Cs, and Hg(+) clocks have a different dependence on alpha via relativistic contributions of order (Z-alpha)(sup 2). Recent H-maser vs Hg(+) clock comparison data improve laboratory limits on a time variation by 100-fold to give dot-alpha less than or equal to 3.7 x 10(exp -14)/yr. Future laser cooled clocks (Be(+), Rb, Cs, Hg(+), etc.), when compared, will yield the most sensitive of all tests for dot-alpha/alpha.

Prestage, John D.; Tjoelker, Robert L.; Maleki, Lute

1995-01-01

246

Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations  

PubMed Central

Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes. PMID:24586129

Gumbart, James C.; Beeby, Morgan; Jensen, Grant J.; Roux, Benoît

2014-01-01

247

Three-dimensionality of space in the structure of the periodic table of chemical elements  

SciTech Connect

The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the number of stable systems of electrons at different levels of the periodic table of chemical elements and some characteristics of the systems. The conditions for the stability of systems of electrons and the electron system of an atom as a whole are considered. On the basis of the results obtained, comparison with other hierarchical systems (nanostructures and biological structures) is performed.

Veremeichik, T. F. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)], E-mail: tomver@online.ru

2006-07-15

248

Ordering of carbon atoms in boron carbide structure  

SciTech Connect

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.

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

249

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

E-print Network

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

Raji Heyrovska

2007-11-09

250

Molecular structure and chemical bonding in K3C60 and K6C60  

Microsoft Academic Search

We present the results of local-density-approximation-based Car-Parrinello calculations of orientationally ordered phases of K3C60 and K6C60. Our investigation focuses on the following points: the effects of alkali-mental intercalation on the structural and electronic properties of C60, the chemical bonding, the inhomogeneity of the electron distribution, and the degree of freedom of the potassium atoms in the interstitial region. The results

Wanda Andreoni; Paolo Giannozzi; Michele Parrinello

1995-01-01

251

Electronic and structural properties of Laves-phase MgZn2 of varying chemical disorder  

Microsoft Academic Search

The C14 Laves-phase MgZn2 has been investigated from 30 to 36at.%Mg . In this way chemical disorder can be monitored over a limited concentration range and the influence on electron properties can be investigated. Our studies include thermodynamic calculations of atomic configurations of Mg and Zn at off-stoichiometric compositions, electronic-transport measurements, and electronic band-structure calculations of MgZn2 . The disorder

M. Andersson; M. de Boissieu; S. Brühne; C. Drescher; W. Assmus; S. Ohahshi; A. P. Tsai; M. Mihalkovic; M. Krajcí; Ö. Rapp

2010-01-01

252

Mining the chemical quarry with joint chemical probes: an application of latent semantic structure indexing (LaSSI) and TOPOSIM (Dice) to chemical database mining.  

PubMed

In this study we use a novel similarity search technique called latent semantic structure indexing (LaSSI) with joint chemical probes as queries to mine the MDL drug data report database. LaSSI is based on latent semantic indexing developed for searching textual databases. We use atom pair and topological torsion descriptors in our calculations. The results obtained with LaSSI are compared with another in-house similarity search technique TOPOSIM. The results from the similarity searches using joint chemical probes are significantly better than searches using single chemical probes for both LaSSI and TOPOSIM. The selected molecules are closely related in activity to their queries and are ranked among the top 300 scoring molecules of the 82 860 entries in the database. Our implementation of LaSSI is very fast and efficient in finding active compounds. The results also show that LaSSI consistently retrieves more diverse chemical structures representative of the joint chemical probes in comparison to TOPOSIM. The use of multimolecule topological probes to identify compounds complements the use of searching databases with 3D pharmacophore hypotheses. PMID:11334566

Singh, S B; Sheridan, R P; Fluder, E M; Hull, R D

2001-05-10

253

Simultaneous Stark and Zeeman effects in atoms with hyperfine structure  

NASA Astrophysics Data System (ADS)

A quantum model for calculating the combined Stark and Zeeman effects of simultaneously applied electric and magnetic fields is presented. Our focus here is on atoms with hyperfine structure, such as Cesium. Matrix representations of the Stark, Zeeman, and hyperfine interaction operators are constructed using angular momentum theory and spherical tensor algebra. Matrix elements are evaluated in order to determine the energy-level dependence on the applied fields and reveal intriguing state dynamics in both parallel and orthogonal electric and magnetic fields. The fundamental physics is relevant for an advanced undergraduate or graduate quantum mechanics course.

Virgo, Wilton L.

2013-12-01

254

Magnetic and Atomic Structure Parameters of Sc-doped Barium Hexagonal Ferrites  

SciTech Connect

Scandium-doped M-type barium hexagonal ferrites of the composition BaFe12?xScxO19 are well suited for low frequency microwave device applications such as isolators and circulators. A series of Sc-doped M-type barium hexagonal ferrite powders (x = 0-1.2) were prepared by conventional ceramic processing techniques. The resulting powders were verified to be pure phase and maintain the nominal chemical stoichiometry by x-ray diffraction and energy dispersive x-ray spectroscopy, respectively. Static magnetic measurements indicated that both saturation magnetization and uniaxial magnetocrystalline anisotropy field decreased with increasing concentration of scandium. Extended x-ray absorption fine structure measurements were carried out to clarify the correlation between the magnetic and atomic structure properties. It is found that the substituted Sc has a strong preference for the bipyramidal site. Nevertheless, the substitution did not introduce additional atomic structural disorder into the barium hexagonal structure. The structural study provided important evidence to quantitatively explain the change in dc and microwave magnetic properties due to Sc ion doping.

Yang,A.; Chen, Y.; Chen, Z.; Vittoria, C.; Harris, V.

2008-01-01

255

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

E-print Network

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

Lin, Lin; Yang, Chao; He, Lixin

2012-01-01

256

Accelerating atomic orbital-based electronic structure calculation via pole expansion and selected inversion  

NASA Astrophysics Data System (ADS)

We describe how to apply the recently developed pole expansion and selected inversion (PEXSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating the charge density, the total energy, the Helmholtz free energy and the atomic forces (including both the Hellmann-Feynman force and the Pulay force) 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 PEXSI is that it has a computational complexity much lower than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEXSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEXSI 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 PEXSI are modest. This even makes it possible to perform Kohn-Sham DFT calculations for 10?000-atom nanotubes with a sequential implementation of the selected inversion algorithm. We also perform an accurate geometry optimization calculation on a truncated (8, 0) boron nitride nanotube system containing 1024 atoms. Numerical results indicate that the use of PEXSI does not lead to loss of the accuracy required in a practical DFT calculation.

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

2013-07-01

257

Accelerating atomic orbital-based electronic structure calculation via pole expansion and selected inversion.  

PubMed

We describe how to apply the recently developed pole expansion and selected inversion (PEXSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating the charge density, the total energy, the Helmholtz free energy and the atomic forces (including both the Hellmann-Feynman force and the Pulay force) 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 PEXSI is that it has a computational complexity much lower than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEXSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEXSI 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 PEXSI are modest. This even makes it possible to perform Kohn-Sham DFT calculations for 10?000-atom nanotubes with a sequential implementation of the selected inversion algorithm. We also perform an accurate geometry optimization calculation on a truncated (8, 0) boron nitride nanotube system containing 1024 atoms. Numerical results indicate that the use of PEXSI does not lead to loss of the accuracy required in a practical DFT calculation. PMID:23803312

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

2013-07-24

258

Chemical structure of vanadium-based contact formation on n-AlN  

SciTech Connect

We have investigated the chemical interaction between a Au/V/Al/V layer structure and n-type AlN epilayers using soft x-ray photoemission, x-ray emission spectroscopy, and atomic force microscopy. To understand the complex processes involved in this multicomponent system, we have studied the interface before and after a rapid thermal annealing step. We find the formation of a number of chemical phases at the interface, including VN, metallic vanadium, aluminum oxide, and metallic gold. An interaction mechanism for metal contact formation on the entire n-(Al,Ga)N system is proposed.

Pookpanratana, S.; France, R.; Blum, M.; Bell, A.; Bar, M.; Weinhardt, L.; Zhang, Y.; Hofmann, T.; Fuchs, O.; Yang, W.; Denlinger, J. D.; Mulcahy, S.; Moustakas, T. D.; Heske, Clemens

2010-05-17

259

Local atomic structure of Fontainebleau sandstone: Evidence for an amorphous phase?  

E-print Network

Local atomic structure of Fontainebleau sandstone: Evidence for an amorphous phase? K. L. Page, Th be deduced from the properties of the component grains [Darling et al., 2004]. Enhanced atomic structure of Fontainebleau sandstone have shown clear evidence for the presence of an unexpected glass-like component. Atomic

260

T~ STRUCTURE OF T~ ATOM Comparison between the classical continuum theory and the  

E-print Network

SERIESI T~ STRUCTURE OF T~ ATOM LECTURE 1 Comparison between the classical continuum theory and the quantum theory- Chief experimentalresults on the structure of the atom - General principles of the quantum theory - Examples. Physics today is everywhere based on the theory of atoms . Through experimental

261

Fabrication of nano-structural arrays by channeling pulsed atomic beams through an intensity-modulated  

E-print Network

Fabrication of nano-structural arrays by channeling pulsed atomic beams through an intensity-dimensional nano-structure arrays by passing a pulsed atomic beam through an intensity-modulated continuous-modulated optical standing wave with a time-varying atom focal length X.D. Zhu* Department of Physics, University

Zhu, Xiangdong

262

Modeling the atomic structure of amorphous steels using crystalline approximants  

SciTech Connect

Using the pair density function analysis of pulsed neutron diffraction data, the local topology of Fe-based metallic glasses with good glass forming ability was investigated upon alloying with transition metal ions of Y, Zr, or Mo. Distinct short and medium range atomic order with common characteristics in all the glasses is observed. The local order is well described by a geometrical model constructed from superposition of 'crystalline approximant' phases which is different from Frank-Kasper polyhedra clustering or dense random packing models. The mechanism responsible for the structure in the glass phase might involve a frustration-induced structural disorder of the crystalline approximant phases as they are driven away from stable stoichiometric compositions.

Kazimirov, V.Yu.; Louca, Despina; Ponnambalam, V.; Poon, S.J. [University of Virginia, Department of Physics, Charlottesville, Virginia 22904 (United States); Proffen, T. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2005-08-01

263

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

PubMed Central

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

2014-01-01

264

Quantum structural phase transition in chains of interacting atoms  

SciTech Connect

A quasi-one-dimensional system of trapped, repulsively interacting atoms (e.g., an ion chain) exhibits a structural phase transition from a linear chain to a zigzag structure, tuned by reducing the transverse trap potential or increasing the particle density. Since it is a one-dimensional transition, it takes place at zero temperature and therefore quantum fluctuations dominate. In Fishman et al.[Phys. Rev. B 77, 064111 (2008)] it was shown that the system close to the linear-zigzag instability is described by a {phi}{sup 4} model. We propose a mapping of the {phi}{sup 4} field theory to the well-known Ising chain in a transverse field, which exhibits a quantum critical point. Based on this mapping, we estimate the quantum critical point in terms of the system parameters. This estimate gives the critical value of the transverse trap frequency for which the quantum phase transition occurs and which has a finite, measurable deviation from the critical point evaluated within the classical theory. A measurement is suggested for atomic systems which can probe the critical trap frequency at sufficiently low temperatures T. We focus in particular on a trapped-ion system and estimate the implied limitations on T and on the interparticle distance. We conclude that the experimental observation of the quantum critical behavior is, in principle, accessible.

Shimshoni, Efrat [Department of Physics, Bar-Ilan University, Ramat-Gan IL-52900 (Israel); Morigi, Giovanna [Theoretische Physik, Universitaet des Saarlandes, D-66041 Saarbruecken (Germany); Department de Fisica, Universitat Autonoma de Barcelona, E-08193 Bellaterra (Spain); Fishman, Shmuel [Department of Physics, Technion, Haifa IL-32000 (Israel)

2011-03-15

265

Correlation between muonic levels and nuclear structure in muonic atoms  

E-print Network

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.

J. M. Dong; W. Zuo; H. F. Zhang; W. Scheid; J. Z. Gu; Y. Z. Wang

2011-11-02

266

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

SciTech Connect

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

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

2014-01-28

267

Quantum simulation of a triatomic chemical reaction with ultracold atoms on a waveguide  

E-print Network

We study the scaling and coordinate transformation to physically simulate quantum three-body collinear chemical reactions of the type A+BC $\\rightarrow$ AB+C by the motion of single ultracold atoms or a weakly interacting Bose-Einstein condensate on an $L$-shaped waveguide. As an example we show that the parameters to model the reaction F+HH $\\to$ H+HF with lithium are at reach with current technology. This mapping provides also an inverse scattering tool to find an unknown potential, and a way to transfer the knowledge on molecular reaction dynamics to design beam splitters for cold atoms with control of the channel outcome and vibrational excitation.

E. Torrontegui; A. Ruschhaupt; D. Guéry-Odelin; J. G. Muga

2011-02-23

268

Marine Chemical Ecology: Chemical Signals and Cues Structure Marine Populations, Communities, and Ecosystems  

PubMed Central

Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized. PMID:21141035

Hay, Mark E.

2012-01-01

269

Structures and chemical properties of silicene: unlike graphene.  

PubMed

The discovery of graphene and its remarkable and exotic properties have aroused interest in other elements and molecules that form 2D atomic layers, such as metal chalcogenides, transition metal oxides, boron nitride, silicon, and germanium. Silicene and germanene, the Si and Ge counterparts of graphene, have interesting fundamental physical properties with potential applications in technology. For example, researchers expect that silicene will be relatively easy to incorporate within existing silicon-based electronics. In this Account, we summarize the challenges and progress in the field of silicene research. Theoretical calculations have predicted that silicene possesses graphene-like properties such as massless Dirac fermions that carry charge and the quantum spin Hall effect. Researchers are actively exploring the physical and chemical properties of silicene and tailoring it for wide variety of applications. The symmetric buckling in each of the six-membered rings of silicene differentiates it from graphene and imparts a variety of interesting properties with potential technological applications. The pseudo-Jahn-Teller (PJT) distortion breaks the symmetry and leads to the buckling in silicenes. In graphene, the two sublattice structures are equivalent, which does not allow for the opening of the band gap by an external electric field. However, in silicene where the neighboring Si atoms are displaced alternatively perpendicular to the plane, the intrinsic buckling permits a band gap opening in silicene in the presence of external electric field. Silicene's stronger spin orbit coupling than graphene has far reaching applications in spintronic devices. Because silicon prefers sp(3) hybridization over sp(2), hydrogenation is much easier in silicene. The hydrogenation of silicene to form silicane opens the band gap and increases the puckering angle. Lithiation can suppress the pseudo-Jahn-Teller distortion in silicene and hence can flatten silicene's structure while opening the band gap. So far, chemists have not successfully synthesized and characterized a free-standing silicene. But recently chemists have successfully produced silicene sheets and nanoribbons over various substrates such as silver, diboride thin films, and iridium. The supporting substrate critically controls the electronic properties of silicene, and the match of the appropriate support and its use is critical in applications of silicene. PMID:24215179

Jose, Deepthi; Datta, Ayan

2014-02-18

270

Atomic structures of Zr-based metallic glasses  

NASA Astrophysics Data System (ADS)

The atomic structures of Zr-Ni and Zr-Ti-Al-Cu-Ni metallic glasses were investigated by using classical molecular dynamic (MD), reverse Monte Carlo (RMC), ab initio MD (AIMD) simulations and high resolution transmission electron microscopy (HRTEM) techniques. We focused on the short-range order (SRO) and medium-range order (MRO) in the glassy structure. It is shown that there are icosahedral, FCC-and BCC-type SROs in the Zr-based metallic glasses. A structural model, characterized by imperfect ordered packing (IOP), was proposed based on the MD simulation and confirmed by the HRTEM observation. Furthermore, the evolution from IOP to nanocrystal during the crystallization of metallic glasses was also explored. It is found that the growth from IOP to nanocrystal proceeds through three distinct stages: the formation of quasi-ordered structure with one-dimensional (1D) periodicity, then 2D periodicity, and finally the formation of 3D nanocrystals. It is also noted that these three growth steps are crosslinked.

Hui, Xidong; Liu, Xiongjun; Gao, Rui; Hou, Huaiyu; Fang, Huazhi; Liu, Zikui; Chen, Guoliang

2008-04-01

271

Atomic structure and electronic states of extended defects in silicon  

NASA Astrophysics Data System (ADS)

Defects in silicon like dislocations, grain boundaries, silicide precipitates, etc. are spatially extended and associated with a large number of electronic states in the band gap. Our knowledge on the relation between atomic structure and electronic states of these extended defects presently starts to grow by applying high-resolution electron microscopy (HRTEM) and deep level transient spectroscopy (DLTS) in combination with numerical simulations. While by means of HRTEM details of structure can be studied, DLTS has been shown to allow for a classification of extended defect states into bandlike and localized. Moreover, this method opens the perspective to distinguish between trap-like and recombination-like electrical activity. In this paper, we emphasize the particular role of nickel and copper silicide precipitates, since in their cases structural features could be successfully related to specific DLTS line characteristics. Rapid quenching from high diffusion temperatures prevents decoration of platelet-shaped NiSi 2 and Cu 3Si precipitates with other impurities. This allows to study their intrinsic electrical activity. Comparison of experimental results with numerical simulations enables identification of structural units originating electrical activity and yields first evaluations of extended defect parameters. Accordingly, e.g., in the case of as-quenched NiSi 2 it is the dislocation bounding the platelet that provides a one-dimensional distribution of deep electronic states.

Riedel, Frank; Hedemann, Henrik; Schröter, Wolfgang

2002-01-01

272

Chromosome structure investigated with the atomic-force microscope  

NASA Astrophysics Data System (ADS)

We have developed an atomic force microscope (AFM) with an integrated optical microscope. The optical microscope consists of an inverted epi-illumination system that yields images in reflection or fluorescence of the sample. With this system it is possible to quickly locate an object of interest. A high-resolution image of the object thus selected can then be obtained with the AFM that is built on top of the optical microscope. In addition, the combined microscopes enable a direct comparison between the optical image and the topography of the same object. The microscope is used to study the structure of metaphase chromosomes of eukaryotic cells. The topography of metaphase chromosomes reveal grooved structures that might indicate spiral structure of the chromatin. High resolution images reveal structures that can be ascribed to the end loops of the chromatin. The resolution of the AFM images was improved by using sharper tips obtained by carbon deposition on the Si3N4 cantilevers using a scanning electron microscope. Chromosomes which are treated to reveal the G- banding pattern in the optical microscope display a similar pattern when viewed with the AFM, as is shown by a direct comparison.

de Grooth, Bart G.; Putman, Constant A.; van der Werf, Kees O.; van Hulst, Niko F.; van Oort, Geeske; Greve, Jan

1992-05-01

273

Bayesian inference of protein structure from chemical shift data  

PubMed Central

Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction.

Bratholm, Lars A.; Christensen, Anders S.; Hamelryck, Thomas

2015-01-01

274

Note: Mechanically and chemically stable colloidal probes from silica particles for atomic force microscopy  

NASA Astrophysics Data System (ADS)

In this note we present a novel approach to prepare colloidal probes for atomic force microscopy by sintering. A central element of this procedure is the introduction of an inorganic "fixation neck" between the cantilever and a micrometer-sized silica particle that is acting as probe. This procedure overcomes previous restrictions for the probe particles, which had to be low melting point materials, such as borosilicate glass or latex particles. The here-presented colloidal probes from silica can withstand large mechanical forces. Additionally, they have high chemical resistivity due to the absence of adhesives and the well-studied surface chemistry of colloidal silica.

Kuznetsov, V.; Papastavrou, G.

2012-11-01

275

A Method for the Automatic Classification of Chemical Structures  

ERIC Educational Resources Information Center

A method has been developed for the automatic classification of chemical structures and it has been tested by applying it to the common naturally occurring amino acids. The resulting classification is reasonable from a qualitative viewpoint. (9 references) (Authors)

Adamson, George W.; Bush, Judith A.

1973-01-01

276

PREDICTING MODES OF TOXIC ACTION FROM CHEMICAL STRUCTURE: AN OVERVIEW  

EPA Science Inventory

In the field of environmental toxicology, and especially aquatic toxicology, quantitative structure activity relationships (QSARS) have developed as scientifically-credible tools for predicting the toxicity of chemicals when little or no empirical data are available. asic and fun...

277

Surface complex structures modelled with quantum chemical calculations: carbonate, phosphate,  

E-print Network

Surface complex structures modelled with quantum chemical calculations: carbonate, phosphate to provide good agree- ment with experimental observations for the oxyanions carbonate, phosphate, sulphate, the interaction of species such as carbon- ate, phosphate, sulphate, arsenate and arsenite with metal oxide

Sparks, Donald L.

278

Polarization from aligned atoms as a diagnostics of circumstellar, AGN and interstellar magnetic fields: II. Atoms with Hyperfine Structure  

E-print Network

We show that atomic alignment presents a reliable way to study topology of astrophysical magnetic fields. The effect of atomic alignment arises from modulation of the relative population of the sublevels of atomic ground state pumped by anisotropic radiation flux. As such aligned atoms precess in the external magnetic field and this affects the properties of the polarized radiation arising from both scattering and absorption by the atoms. As the result the polarizations of emission and absorption lines depend on the 3D geometry of the magnetic field as well as the direction and anisotropy of incident radiation. We consider a subset of astrophysically important atoms with hyperfine structure. For emission lines we obtain the dependencies of the direction of linear polarization on the directions of magnetic field and the incident pumping radiation. For absorption lines we establish when the polarization is perpendicular and parallel to magnetic field. For both emission and absorption lines we find the dependence on the degree of polarization on the 3D geometry of magnetic field. We claim that atomic alignment provides a unique tool to study magnetic fields in circumstellar regions, AGN, interplanetary and interstellar medium. This tool allows studying of 3D topology of magnetic fields and establish other important astrophysical parameters. We consider polarization arising from both atoms in the steady state and also as they undergo individual scattering of photons. We exemplify the utility of atomic alignment for studies of astrophysical magnetic fields by considering a case of Na alignment in a comet wake.

Huirong Yan; A. Lazarian

2006-12-13

279

Atomic Oxygen Recombination and Chemical Energy Accommodation on Alumina at High Temperature  

SciTech Connect

To develop heat shields for space vehicles, materials must be characterized in simulation conditions close to those in space environments. The most important conditions for simulating the Earth re-entry phase of space vehicles are achieved through the MESOX set-up associating a 6 kW solar radiation concentrator and a 2450 MHz microwave plasma generator. This paper presents some experimental results for the recombination coefficient {gamma} and the chemical energy accommodation coefficient {beta} in the surface-catalyzed oxygen atom recombination based on experiments performed on the MESOX set-up. This set-up allows both the experimental measurements of the recombination coefficient {gamma} using Optical Emission Spectroscopy and the chemical energy accommodation coefficient {beta} using calorimetry according to a defined protocol. Experimental results are presented for three types of alumina in the temperature range 900-2400 K, for 200 Pa total air pressure. These three alumina differ essentially from their content of sintering additives.

Balat-Pichelin, Marianne J.H.; Bedra, L.; Badie, J.-M. [Laboratoire Procedes, Materiaux et Energie Solaire, PROMES-CNRS (ex IMP-CNRS), BP5, 66125 Odeillo, Font-Romeu (France); Boubert, P. [Institut Universitaire des Systemes Thermiques Industriels, IUSTI-CNRS, 5 rue E. Fermi, 13453 Marseille (France)

2005-05-16

280

Sommerfeld Fine-Structure Formula for Two-Body Atoms  

E-print Network

For relativistic atomic two-body systems such as the hydrogen atom, positronium, and muon-proton bound states, a two-body generalisation of the single-particle Sommerfeld fine-structure formula for the relativistic bound-state energies is found. The two-body Sommerfeld bound-state energy formula is obtained from a two-body wave equation which is physically correct to order $(Z\\alpha)^4$. The two-body Sommerfeld formula makes two predictions in order $(Z\\alpha)^6$ for every bound state and every mass ratio. With $N$ the Bohr quantum number: (a) The coefficient of the $(Z\\alpha)^6/N^6$ energy term has a specified value which depends only on the masses of the bound particles, not on angular quantum numbers; (b) The coefficient of the $(Z\\alpha)^6/N^4$ energy term is a specified multiple of the {\\em square} of the coefficient of the $(Z\\alpha)^4/N^3$ energy term. Both these predictions are verified in positronium by previous calculations to order $(Z\\alpha)^6$ which used second-order perturbation theory. They are also correct in the Coulomb-Dirac limit. The effect of the two-body Sommerfeld formula on calculations of muon-proton bound-state energies is examined.

John H. Connell

2013-03-20

281

Defects in p-GaN and their atomic structure  

SciTech Connect

In this paper defects formed in p-doped GaN:Mg grown with Ga polarity will be discussed. The atomic structure of these characteristic defects (Mg-rich hexagonal pyramids and truncated pyramids) in bulk and thin GaN:Mg films grown with Ga polarity was determined at atomic resolution by direct reconstruction of the scattered electron wave in a transmission electron microscope. Small cavities were present inside the defects. The inside walls of the cavities were covered by GaN which grew with reverse polarity compared to the matrix. It was proposed that lateral overgrowth of the cavities restores matrix polarity on the defect base. Exchange of Ga and N sublattices within the defect compared to the matrix lead to a 0.6 {+-} 0.2 {angstrom} displacement between the Ga sublattices of these two areas. A [1{und 1}00]/3 shift with change from AB stacking in the matrix to BC within the entire pyramid is observed

Liliental-Weber, Z.; Tomaszewicz, T.; Zakharov, D.; Jasinski, J.; and O'Keefe, M.

2004-10-08

282

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

PubMed

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

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

2009-11-01

283

Low temperature hydrogen plasma assisted chemical vapor generation for Atomic Fluorescence Spectrometry.  

PubMed

Chemical vapor generation techniques have long been considered as important ways of sample introduction for analytical atomic spectrometry. In this paper, a low temperature plasma assisted chemical vapor generation method which avoids the massive use of consumptive chemical agents was proposed by using atmospheric pressure dielectric barrier discharge. The plasma was generated by hydrogen doped argon gas flow through a quartz tube, serving as a dielectric barrier, which had a copper wire inner electrode and a copper foil outer electrode. An alternative high voltage was applied to electrodes to ignite and sustain the plasma. Sample solutions were converted to aerosol by a nebulizer and then mixed with the plasma to generate hydrides. To confirm the utility of this method, four hydride forming elements, As, Te, Sb and Se, were determined by coupling the low temperature plasma assisted chemical vapor generation system with an atomic fluorescence spectrometer. Responses of As, Te, Sb and Se were linear in the range of 0.5-20?g mL(-1). The RSDs of As, Te, Sb and Se in the present method were less than 4.1% and the absolute detection limits for As, Te, Sb and Se were 0.6ng, 1.0ng, 1.4ng and 1.2ng, respectively. Furthermore, four arsenic species were determined after HPLC separation. The method is green and simple compared with hydride generation with tetrahydroborate and the most attractive characteristic is micro-sampling. In principle, the method offers potential advantages of miniaturization, less consumption and ease of automation. PMID:24881527

Yang, Meng; Xue, Jiao; Li, Ming; Han, Guojun; Xing, Zhi; Zhang, Sichun; Zhang, Xinrong

2014-08-01

284

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM  

E-print Network

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo important contribu- tions to modern structural biology. Bacteriophages, the most diverse and abundant previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution

Jiang, Wen

285

Spatially Resolved Electronic Structures of Atomically Precise Armchair Graphene Nanoribbons  

PubMed Central

Graphene has attracted much interest in both academia and industry. The challenge of making it semiconducting is crucial for applications in electronic devices. A promising approach is to reduce its physical size down to the nanometer scale. Here, we present the surface-assisted bottom-up fabrication of atomically precise armchair graphene nanoribbons (AGNRs) with predefined widths, namely 7-, 14- and 21-AGNRs, on Ag(111) as well as their spatially resolved width-dependent electronic structures. STM/STS measurements reveal their associated electron scattering patterns and the energy gaps over 1 eV. The mechanism to form such AGNRs is addressed based on the observed intermediate products. Our results provide new insights into the local properties of AGNRs, and have implications for the understanding of their electrical properties and potential applications. PMID:23248746

Huang, Han; Wei, Dacheng; Sun, Jiatao; Wong, Swee Liang; Feng, Yuan Ping; Neto, A. H. Castro; Wee, Andrew Thye Shen

2012-01-01

286

Atomic structure of the actin: DNase I complex  

NASA Astrophysics Data System (ADS)

The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined byo X-ray analysis at an effective resolution of 2.8 Å and 3 Å, respectively. The two structures are very similar. The actin molecule consists of two domains which can be further subdivided into two subdomains. ADP or ATP is located in the cleft between the domains with a calcium ion bound to the ?- or ?- and ?-phosphates, respectively. The motif of a five-stranded (3 sheet consisting of a (3 meander and a right handed ??? unit appears in each domain suggesting that gene duplication might have occurred. These sheets have the same topology as that found in hexokinase.

Kabsch, Wolfgang; Mannherz, Hans Georg; Suck, Dietrich; Pai, Emil F.; Holmes, Kenneth C.

1990-09-01

287

Stretched DNA structures observed with atomic force microscopy.  

PubMed Central

Double-stranded DNA molecules are occasionally found that appear to be straightened and stretched in atomic force microscope (AFM) images. Usually pBS+ plasmid and lambda DNA show relaxed structures with bends and kinks along the strands and have measured contour lengths consistent to about 5-7%; they also appear not to cross over each other, except in very high concentrations. The anomalous molecules observed here, compared with the majority of molecules in the preparation, show contour lengths increased by as much as 80% and have measured heights of about half that of normal relaxed DNA. Some molecules also appear to be in transition between stretched and relaxed forms. These observations are consistent with an uncoiling of the DNA helix without breakage of the covalent bonds in the deoxyribose-phosphate backbone. Images PMID:7937149

Thundat, T; Allison, D P; Warmack, R J

1994-01-01

288

The atomic structure of niobium and tantalum containing borophosphate glasses  

NASA Astrophysics Data System (ADS)

A complete structural study has been carried out on sodium borophosphate glass containing increasing amounts of either niobium or tantalum. A combination of high energy x-ray diffraction, neutron diffraction, extended x-ray absorption fine structure, nuclear magnetic resonance, and infrared and Raman spectroscopy has been used to discern the local atomic structure of each component and the changes with M content, where M is either niobium or tantalum. The glasses are found to consist of tetrahedral borate and phosphate with octahedral MO6. As expected, B and P play the roles of tetrahedral network formers. At low M content there are isolated MO6 units with \\mathrm {P{\\cdots }M} and \\mathrm {B{\\cdots }M} linkages that contribute to the glass network. As the M content increases, the number of \\mathrm {M{\\cdots }M} links increases, and at the highest M content each MO6 unit is connected to several others. The octahedra become significantly distorted as the niobium content increases, an effect that is not seen for tantalum.

Wetherall, K. M.; Doughty, P.; Mountjoy, G.; Bettinelli, M.; Speghini, A.; Casula, M. F.; Cesare-Marincola, F.; Locci, E.; Newport, R. J.

2009-09-01

289

The atomic structure of niobium and tantalum containing borophosphate glasses.  

PubMed

A complete structural study has been carried out on sodium borophosphate glass containing increasing amounts of either niobium or tantalum. A combination of high energy x-ray diffraction, neutron diffraction, extended x-ray absorption fine structure, nuclear magnetic resonance, and infrared and Raman spectroscopy has been used to discern the local atomic structure of each component and the changes with M content, where M is either niobium or tantalum. The glasses are found to consist of tetrahedral borate and phosphate with octahedral MO(6). As expected, B and P play the roles of tetrahedral network formers. At low M content there are isolated MO(6) units with [Formula: see text] and [Formula: see text] linkages that contribute to the glass network. As the M content increases, the number of [Formula: see text] links increases, and at the highest M content each MO(6) unit is connected to several others. The octahedra become significantly distorted as the niobium content increases, an effect that is not seen for tantalum. PMID:21832337

Wetherall, K M; Doughty, P; Mountjoy, G; Bettinelli, M; Speghini, A; Casula, M F; Cesare-Marincola, F; Locci, E; Newport, R J

2009-09-16

290

Atomic layer chemical vapor deposition of ZrO2-based dielectric films: Nanostructure and nanochemistry  

NASA Astrophysics Data System (ADS)

A 4 nm layer of ZrOx (targeted x˜2) was deposited on an interfacial layer (IL) of native oxide (SiO, t˜1.2 nm) surface on 200 mm Si wafers by a manufacturable atomic layer chemical vapor deposition technique at 300 °C. Some as-deposited layers were subjected to a postdeposition, rapid thermal annealing at 700 °C for 5 min in flowing oxygen at atmospheric pressure. The experimental x-ray diffraction, x-ray photoelectron spectroscopy, high-resolution transmission electron microscopy, and high-resolution parallel electron energy loss spectroscopy results showed that a multiphase and heterogeneous structure evolved, which we call the Zr-O/IL/Si stack. The as-deposited Zr-O layer was amorphous ZrO2-rich Zr silicate containing about 15% by volume of embedded ZrO2 nanocrystals, which transformed to a glass nanoceramic (with over 90% by volume of predominantly tetragonal-ZrO2 (t-ZrO2) and monoclinic-ZrO2 (m-ZrO2) nanocrystals) upon annealing. The formation of disordered amorphous regions within some of the nanocrystals, as well as crystalline regions with defects, probably gave rise to lattice strains and deformations. The interfacial layer (IL) was partitioned into an upper SiO2-rich Zr silicate and the lower SiOx. The latter was substoichiometric and the average oxidation state increased from Si0.86+ in SiO0.43 (as-deposited) to Si1.32+ in SiO0.66 (annealed). This high oxygen deficiency in SiOx was indicative of the low mobility of oxidizing specie in the Zr-O layer. The stacks were characterized for their dielectric properties in the Pt/{Zr-O/IL}/Si metal oxide-semiconductor capacitor (MOSCAP) configuration. The measured equivalent oxide thickness (EOT) was not consistent with the calculated EOT using a bilayer model of ZrO2 and SiO2, and the capacitance in accumulation (and therefore, EOT and kZr-O) was frequency dispersive, trends well documented in literature. This behavior is qualitatively explained in terms of the multilayer nanostructure and nanochemistry that evolves.

Dey, S. K.; Wang, C.-G.; Tang, D.; Kim, M. J.; Carpenter, R. W.; Werkhoven, C.; Shero, E.

2003-04-01

291

A neural network structure for prediction of chemical agent fate  

NASA Astrophysics Data System (ADS)

This work presents the development of a multi-input, multi-output neural network structure to predict the time dependent concentration of chemical agents as they participate in chemical reaction with environmental substrates or moisture content within these substrates. The neural network prediction is based on a computationally or experimentally produced database that includes the concentration of all chemicals presents (reactants and products) as a function of the chemical agent droplet size, wind speed, temperature, and turbulence. The utilization of this prediction structure is made userfriendly via an easy-to-use graphical user interface. Furthermore, upon the knowledge of the time-varying environmental parameters (wind speed and temperature that are usually recorded and available), the time varying concentration of all chemicals can be predicted almost instantaneously by recalling the previously trained network. The network prediction was compared with actual open air test data and the results were found to match.

Navaz, H. K.; Kehtarnavaz, N.; Jovic, Zoran

2014-05-01

292

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

NASA Astrophysics Data System (ADS)

The atomic and electronic properties of amorphous unhydrogenated (a-SiC) and hydrogenated (a-SiC:H) silicon carbides are studied using an sp3sstar 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.

Ivashchenko, V. I.; Turchi, P. E. A.; Shevchenko, V. I.; Ivashchenko, L. A.; Rusakov, G. V.

2003-06-01

293

Impacts of the 2010 Amazon drought on forest structure and function using CAO AToMS  

NASA Astrophysics Data System (ADS)

The 2010 Amazon mega-drought is thought to have had a widespread impact on forest condition, including tree mortality. However, no large-scale, high-resolution information exists on changes in forest structure, function, turnover or other processes in response to the drought. With the possibility of increasing drought frequency in the Amazon basin, it is now critical that we develop repeat, large-area studies to assess impacts and recovery. Using the Carnegie Airborne Observatory Airborne Taxonomic Mapping System (AToMS), we assessed the impacts of the 2010 drought by repeat flying of approximately 500,000 hectares of lowland humid tropical forest in the Peru Amazon. The CAO AToMS Visible-to-Near-Infrared (VNIR) and Visible-to-Shortwave-Infrared (VSWIR) imaging spectrometers recorded changes in forest canopy spectral, chemical and physiological state from 2009 to 2011. Areas of greatest functional change were observed near the Peru-Brazil border in areas under heavy forest use for selective logging. The CAO AToMS waveform Light Detection and Ranging (LiDAR) instruments measured highest rates of treefall and canopy gap formation in areas subjected to combined drought and logging, and on low fertility soils. The results provide the first spatially-explicit, large-scale and ecologically detailed information on the response of Amazonian forests to drought.

Asner, G. P.; Martin, R. E.; Knapp, D. E.; Kennedy-Bowdoin, T.; Kellner, J.

2012-12-01

294

Structural study of biotic and abiotic poorly-crystalline manganese oxides using atomic  

E-print Network

Structural study of biotic and abiotic poorly-crystalline manganese oxides using atomic pair structures. In this study, the crystal structures of their synthetic analogs includ- ing acid birnessite using atomic pair distribution function (PDF) analysis. Results unambiguously verify that these Mn

Sparks, Donald L.

295

Structural changes at grain boundaries in bcc iron induced by atomic collisions  

E-print Network

Structural changes at grain boundaries in bcc iron induced by atomic collisions F. Javier P boundaries, is to model the static microstructure for a better understanding of the atomic structure 22, 1999 Abstract Symmetrical tilt and twist grain boundary structures have been simu- lated in bcc

296

THREE-DIMENSIONAL ATOMIC STRUCTURE OF NiO ZrO2(CUBIC) INTERFACES  

E-print Network

THREE-DIMENSIONAL ATOMIC STRUCTURE OF NiO± ZrO2(CUBIC) INTERFACES E. C. DICKEY{1 , V. P. DRAVID1-dimensional atomic structure of low-energy NiO±ZrO2(cubic) interfaces is determined through a combination of electron structure of low-energy NiO±ZrO2(cubic) interfaces and the associated interfacial relaxation mechanisms

Pennycook, Steve

297

Why Can't We Predict RNA Structure At Atomic Resolution?  

E-print Network

will hasten the development of atomic accuracy methods for modeling RNA structures without extensiveChapter 4 Why Can't We Predict RNA Structure At Atomic Resolution? Parin Sripakdeevong, Kyle the performance of current structure prediction algorithms. 4.1 RNA as a Model System Predicting the three

Das, Rhiju

298

221A Lecture Notes Fine and Hyperfine Structures of the Hydrogen Atom  

E-print Network

221A Lecture Notes Fine and Hyperfine Structures of the Hydrogen Atom 1 Introduction With the usual://astron.berkeley.edu/mwhite/ darkmatter/bbn.html by our own Martin White. 2 Fine Structure The fine structure of the hydrogen atom refers Hamiltonian for the hydrogen-like atom (in the Gaussian unit), H0 = p2 2m - Ze2 r , (1) we have the n2 -fold

Murayama, Hitoshi

299

Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures  

E-print Network

We propose and analyze a scheme to interface individual neutral atoms with nanoscale solid-state systems. The interface is enabled by optically trapping the atom via the strong near-field generated by a sharp metallic ...

Chang, D. E.

300

The grasp2K relativistic atomic structure package  

NASA Astrophysics Data System (ADS)

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 Xeon, 3.06 GHz Operating system: Suse LINUX RAM: 500 MB or more Classification: 2.1 Nature of problem: Prediction of atomic spectra—atomic energy levels, oscillator strengths, and radiative decay rates—using a 'fully relativistic' approach. Solution method: Atomic orbitals are assumed to be four-component spinor eigenstates of the angular momentum operator, j=l+s, and the parity operator ?=??. Configuration state functions (CSFs) are linear combinations of Slater determinants of atomic orbitals, and are simultaneous eigenfunctions of the atomic electronic angular momentum operator, J, and the atomic parity operator, P. Approximate atomic state functions (ASFs) are linear combinations of CSFs. A variational functional may be constructed by combining expressions for the energies of one or more ASFs. Average energy level (EAL) functionals are weighted sums of energies of all possible ASFs that may be constructed from a set of CSFs; the number of ASFs is then the same as the number of CSFs. Extended optimal level (EOL) functionals are weighted sums of energies of some subset of ASFs. Radial functions may be determined by numerically solving the multiconfiguration Dirac-Hartree-Fock (MCDHF) equations that define an extremum of the variational functional by the self-consistent-field (SCF) method. Lists of CSFs are generated from a set of reference CSFs and rules for deriving other CSFs from these. Expansion coefficients are obtained using sparse-matrix methods for solving the relativistic configuration interaction (CI) problem. Transition properties for pairs of ASFs are computed from matrix elements of multipole operators of the electromagnetic field. Biorthogonal transformation methods are employed so that all matrix elements between CSFs can be evaluated using Racah algebra. Restrictions: The maximum number of radial orbitals is limited to 120 by the packing algorithm used for 32-bit integers. The maximum size of a multiconfiguration (MC) calculation, as measured by the length of the configuration state function (CSF) list, is limited by numerical st

Jönsson, P.; He, X.; Froese Fischer, C.; Grant, I. P.

2007-10-01

301

Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures D. E. Chang,1  

E-print Network

Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures D. E. Chang,1 J. D of Physics, MIT-Harvard Center for Ultracold Atoms, and Research Laboratory of Electronics, Massachusetts September 2009) We propose and analyze a scheme to interface individual neutral atoms with nanoscale solid

Heller, Eric

302

The local atomic quasicrystal structure of the icosahedral Mg25Y11Zn64 alloy  

Microsoft Academic Search

A local and medium range atomic structure model for the face centred icosahedral (fci) Mg25Y11Zn64 alloy has been established in a sphere of r = 27 Å. The model was refined by least squares techniques using the atomic pair distribution (PDF) function obtained from synchrotron powder diffraction. Three hierarchies of the atomic arrangement can be found: (i) five types of

S. Brühne; E. Uhrig; C. Gross; W. Assmus; A. S. Masadeh; S. J. L. Billinge

2005-01-01

303

The local atomic quasicrystal structure of the icosahedral Mg25Y11Zn64 alloy  

Microsoft Academic Search

A local and medium range atomic structure model for the face centred icosahedral (fci) Mg25Y11Zn64 alloy has been established in a sphere of r = 27 Å. The model was refined by least squares techniques using the atomic pair distribution (PDF) function obtained from synchrotron powder diffraction. Three hierarchies of the atomic arrangement can be found: (i) five types of

S Brühne; E Uhrig; C Gross; W Assmus; A S Masadeh

304

Atomic optical clocks and search for variation of the fine-structure constant  

Microsoft Academic Search

Theories unifying gravity and other interactions suggest the possibility of spatial and temporal variations of physical ``constants.'' Accuracy achieved for atomic optical frequency standards (optical clocks) approaches the level when possible time evolution of the fine-structure constant alpha can be studied by comparisons of rates between clocks based on different atomic transitions in different atoms. The sensitivity to variation of

V. A. Dzuba; V. V. Flambaum

2000-01-01

305

Observations on the full honeycomb structure of graphite as imaged by atomic force microscopy  

Microsoft Academic Search

Most atomic force microscopy (AFM) images of highly ordered pyrolytic graphite (HOPG) yield only every other atom with a lattice constant 2.46 Å. However, its full honeycomb structure, revealing all six carbon atoms of each hexagon, can only be obtained under certain conditions. A particular problem is the large meniscus force generated by a thin condensed layer of water when

P. Singjai; P. A. Zhdan; J. E. Castle

2000-01-01

306

Observations on the full honeycomb structure of graphite as imaged by atomic force microscopy  

Microsoft Academic Search

Most atomic force microscopy (AFM) images of highly ordered pyrolytic graphite (HOPG) yield only every other atom with a lattice constant 2.46Å. However, its full honeycomb structure, revealing all six carbon atoms of each hexagon, can only be obtained under certain conditions. A particular problem is the large meniscus force generated by a thin condensed layer of water when imaging

P. Singjai; P. A. Zhdan; J. E. Castle

2000-01-01

307

Countable models A structure M is atomic iff tpM  

E-print Network

Countable models A structure M is atomic iff tpM (a) is isolated, for all positive integers m models. Let M be a model of T. Then M is prime iff it is countable and atomic. Proof. : Assume that M is atomic. since T has countable models by the downward L¨owenheim-Skolem theorem, and M can be elementarily

Monk, Don

308

CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.  

PubMed

In this article, we propose a method for locating functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three-dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed chem-path-tracker. This software is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra's algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. This tool turned out to be very useful, fast, and user-friendly in the performed tests. The chem-path-tracker package is distributed as an independent platform and can be found at http://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker. PMID:24775806

Ribeiro, João V; Cerqueira, N M F S A; Fernandes, Pedro A; Ramos, Maria J

2014-07-01

309

Recent Strategies for Retrieving Chemical Structure Information on the Web.  

ERIC Educational Resources Information Center

Various methods for retrieving chemical structure information on the World Wide Web are discussed. Although graphical plug-in programs provide more search capabilities, users first have to obtain a copy of the programs. Tripos's WebSketch and ACD Interactive Lab adopt a different approach; using JAVA applets, users create and display a structure…

Lo, Mei Ling

1997-01-01

310

Predicting chemical activities from structures by attributed molecular graph classification  

Microsoft Academic Search

Designing Quantitative Structure-Activity Relationship (QSAR) models has been a recurrent research interest for biologists and computer scientists. An example is to predict the toxicity of chemical compounds using their structural properties as features represented by graphs. A popular method to classify these graphs is to exploit classifiers such as support vector machines (SVMs) and graph kernels to incorporate the sequential,

Qian Xu; Derek Hao Hu; Hong Xue; Qiang Yang

2010-01-01

311

Atomic scale dynamics of a solid state chemical reaction directly determined by annular dark-field electron microscopy.  

PubMed

Dynamic processes, such as solid-state chemical reactions and phase changes, are ubiquitous in materials science, and developing a capability to observe the mechanisms of such processes on the atomic scale can offer new insights across a wide range of materials systems. Aberration correction in scanning transmission electron microscopy (STEM) has enabled atomic resolution imaging at significantly reduced beam energies and electron doses. It has also made possible the quantitative determination of the composition and occupancy of atomic columns using the atomic number (Z)-contrast annular dark-field (ADF) imaging available in STEM. Here we combine these benefits to record the motions and quantitative changes in the occupancy of individual atomic columns during a solid-state chemical reaction in manganese oxides. These oxides are of great interest for energy-storage applications such as for electrode materials in pseudocapacitors. We employ rapid scanning in STEM to both drive and directly observe the atomic scale dynamics behind the transformation of Mn3O4 into MnO. The results demonstrate we now have the experimental capability to understand the complex atomic mechanisms involved in phase changes and solid state chemical reactions. PMID:25532123

Pennycook, Timothy J; Jones, Lewys; Pettersson, Henrik; Coelho, João; Canavan, Megan; Mendoza-Sanchez, Beatriz; Nicolosi, Valeria; Nellist, Peter D

2014-01-01

312

Chemical composition in relation with biomass ash structure  

NASA Astrophysics Data System (ADS)

Biomass combustion can be more complicated like combustion of fossil fuels because it is necessary to solve problems with lower ash melting temperature. It can cause a lot of problems during combustion process. Chemical composition of biomass ash has great impact on sinters and slags creation in ash because it affects structure of heated ash. In this paper was solved relation between chemical composition and structure of heated ash from three types of biomass (spruce wood, miscanthus giganteus and wheat straw). Amount of SiO2, CaO, MgO, Al2O3 and K2O was determined. Structure of heated ash was optically determined after heating to 1000 °C or 1200 °C. Results demonstrated that chemical composition has strong effect on structure and color of heated ash.

Holubcik, Michal; Jandacka, Jozef

2014-08-01

313

Nanostructured thin layers of vanadium oxides doped with cobalt, prepared by pulsed laser ablation: chemistry, local atomic structure, morphology and magnetism  

Microsoft Academic Search

Cobalt-doped vanadium oxide thin layers prepared by pulsed laser ablation are investigated from the following points of view: (1) the chemical states by X-ray photoelectron spectroscopy (XPS), (2) the local atomic order by X-ray absorption fine structure at both vanadium and cobalt K-edges, (3) the morphology of the films by atomic force microscopy (AFM) and (4) the magnetic properties by

C. M. Teodorescu; G. Socol; C. Negrila; D. Luca; D. Macovei

2010-01-01

314

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

E-print Network

Single-molecule nuclear magnetic resonance (NMR) is a crown-jewel challenge in the field of magnetic resonance spectroscopy and has important applications in chemical analysis and in quantum computing. Recently, it becomes possible to tackle this grand challenge thanks to experimental advances in preserving quantum coherence of nitrogen-vacancy (NV) center spins in diamond as a sensitive probe and theoretical proposals on atomic-scale magnetometry via dynamical decoupling control. Through decoherence measurement of NV centers under dynamical decoupling control, sensing of single $^{13}\\textbf{C}$ at nanometer distance has been realized. Toward the ultimate goal of structure analysis of single molecules, it is highly desirable to directly measure the interactions within single nuclear spin clusters. Here we sensed a single $^{13}\\textbf{C}$-$^{13}\\textbf{C}$ nuclear spin dimer located about 1 nm from the NV center and characterized the interaction between the two nuclear spins, by measuring NV center spin decoherence under various dynamical decoupling control. From the measured interaction we derived the spatial configuration of the dimer with atomic-scale resolution. These results demonstrate that central spin decoherence under dynamical decoupling control is a feasible probe for NMR structure analysis of single molecules.

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

2013-09-25

315

Atomic size and chemical effects on the local order of Zr2M ( M=Co , Ni, Cu, and Ag) binary liquids  

NASA Astrophysics Data System (ADS)

First-principles molecular dynamics simulations are performed to investigate the atomic size and chemical effects on the short-range order (SRO) in superheated and undercooled Zr-based metallic liquids, Zr2M ( M=Co , Ni, Cu, and Ag). We demonstrate that the local atomic structures in liquids are quite sensitive to the atomic size ratio and the electronic interactions between component elements. The large negative heats of mixing for Zr-M do not favor icosahedral SRO in these binary liquids, contrary to the common belief. Full icosahedral structure units are few in the superheated liquids, although the number of icosahedral clusters increases upon undercooling. Comparing Zr2Co , Zr2Ni , and Zr2Cu , all of which have very similar atomic size ratios, we find that the degree of local icosahedral order increases with decreasing interaction strength between the d electrons in Zr-Co, Zr-Ni, and Zr-Cu. A comparison of Zr2Cu and Zr2Ag alloys shows that the degree of icosahedral order increases much more in Zr2Ag than in Zr2Cu with decreasing temperature. The difference in atomic sizes of Cu and Ag may account for the subtle discrepancy in the evolution of short-range ordering in undercooled Zr2Cu and Zr2Ag liquids.

Huang, Li; Wang, C. Z.; Hao, S. G.; Kramer, M. J.; Ho, K. M.

2010-01-01

316

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

PubMed

Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost. PMID:24676684

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

2014-05-30

317

Clarkeite: New chemical and structural data  

Microsoft Academic Search

Clarkeite crystallizes during metasomatic replacement of pegmatitic uraninite by latestage, oxidizing hydrothermal fluids. Samples are zoned compositionally: Clarkeite, which is Na rich, surrounds a K-rich core (commonly with remnant uraninite) and is surrounded by more Ca-rich material-volumetrically, clarkeite is most abundant. Clarkeite is hexagonal (space group R3m) a = 3.954(4), c = 17.73(1) â« (Z = 3). The structure of

ROBERT J. FINCH; RODNEY C. EWING

1997-01-01

318

Chemical Structure of Bacteriovorax stolpii Lipid A  

Microsoft Academic Search

Bdellovibrionales is a phylogenetically diverse group of predatory prokaryotes, which consists of the two families Bdellovibrionaceae and Bacteriovoracaceae. We describe LPS and lipid A of the type strain Bacteriovorax stolpii DSM 12778, representing the first characterized endotoxin of a Bacteriovoracaceae member. It has a smooth form LPS, which was identified by SDS-polyacrylamide gel electrophoresis. The lipid A structure was\\u000a determined

Sebastian Beck; Frederic D. Müller; Eckhard Strauch; Lothar Brecker; Michael W. Linscheid

2010-01-01

319

Chemically assisted release of transition metals in graphite vaporizers for atomic spectrometry  

NASA Astrophysics Data System (ADS)

The processes associated with the vaporization of microgram samples and modifiers in a graphite tube ET AAS were investigated by the example of transition metals. The vapor absorption spectra and vaporization behavior of ?g-amounts Cd, Zn, Cu, Ag, Au, Ni, Co, Fe, Mn and Cr were studied using the UV spectrometer with CCD detector, coupled with a continuum radiation source. The pyrocoated, Ta or W lined tubes, with Ar or He as internal gases, and filter furnace were employed in the comparative experiments. It was found that the kinetics of atomic vapor release changed depending on the specific metal-substrate-gas combination; fast vaporization at the beginning was followed by slower 'tailing.' The absorption continuum, overlapped by black body radiation at longer wavelengths, accompanied the fast vaporization mode for all metals, except Cd and Zn. The highest intensity of the continuum was observed in the pyrocoated tube with Ar. For Cu and Ag the molecular bands overlapped the absorption continuum; the continuum and bands were suppressed in the filter furnace. It is concluded that the exothermal interaction of sample vapor with the material of the tube causes the energy evolution in the gas phase. The emitted heat is dispersed near the tube wall in the protective gas and partially transferred back to the surface of the sample, thus facilitating the vaporization. The increased vapor flow causes over-saturation and gas-phase condensation in the absorption volume at some distance from the wall, where the gas temperature is not affected by the reaction. The condensation is accompanied by the release of phase transition energy via black body radiation and atomic emission. The particles of condensate and molecular clusters cause the scattering of light and molecular absorption; slow decomposition of the products of the sample vapor-substrate reaction produces the 'tailing' of atomic absorption signal. The interaction of graphite with metal vapor or oxygen, formed in the decomposition of metal oxide, is the most probable source of chemical energy, which facilitates the vaporization. Intensity of the process depends on chemical properties of the sample and substrate and efficiency of mass and heat transfer by the protective gas. The discussed mechanism of chemically assisted vapor release signifies the energy exchange between all participants of the vaporization process in ET AAS including the matrix, modifier, purge gas and analyte. The finding contributes in the ET AAS theory regarding the mechanisms of vaporization and mass transfer in the presence of matrix and modifiers.

Katskov, Dmitri; Darangwa, Nicholas; Grotti, Marco

2006-05-01

320

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

SciTech Connect

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.

Paesler, M.; Sayers, D.

1988-12-01

321

From nuclei to atoms and molecules: the chemical history of the early Universe  

E-print Network

The "dark age" of the Universe is generally pointed out as the period between the recombination epoch and the horizon of current observations (z=5-6). The arrow of time in the cosmic history describes the progression from simplicity to complexity, because the present Universe is clumpy and complicated unlike the homogeneous early Universe. Thus it is crucial to know the nature of the constituents, in order to understand the conditions of the formation of the first bound objects. In this paper we analyse the chemical history of this "dark age" through the creation of the primordial nuclei to the formation of the first atoms and molecules. Then we will describe the consequences of the molecular formation on the birth of the proto-objects. In this context we will mention the important works of Dennis W. Sciama who influenced a large number of theorists -cosmologists and astronomers- on this new field of research dedicated to primordial molecules.

D. Puy; M. Signore

2001-01-10

322

Atomic detail of chemical transformation at the transition state of an enzymatic reaction.  

PubMed

Transition path sampling (TPS) has been applied to the chemical step of human purine nucleoside phosphorylase (PNP). The transition path ensemble provides insight into the detailed mechanistic dynamics and atomic motion involved in transition state passage. The reaction mechanism involves early loss of the ribosidic bond to form a transition state with substantial ribooxacarbenium ion character, followed by dynamic motion from the enzyme and a conformational change in the ribosyl group leading to migration of the anomeric carbon toward phosphate, to form the product ribose 1-phosphate. Calculations of the commitment probability along reactive paths demonstrated the presence of a broad energy barrier at the transition state. TPS identified (i) compression of the O4'...O5' vibrational motion, (ii) optimized leaving group interactions, and (iii) activation of the phosphate nucleophile as the reaction proceeds through the transition state region. Dynamic motions on the femtosecond timescale provide the simultaneous optimization of these effects and coincide with transition state formation. PMID:18946041

Saen-Oon, Suwipa; Quaytman-Machleder, Sara; Schramm, Vern L; Schwartz, Steven D

2008-10-28

323

Survey of reproductive hazards among oil, chemical, and atomic workers exposed to halogenated hydrocarbons  

SciTech Connect

Several halogenated hydrocarbons are suspected of causing adverse reproductive effects. Because of such concerns, the Oil, Chemical, and Atomic Workers International Union surveyed the reproductive histories of two groups of workers. One group worked at plants engaged in the production or use of halogenated hydrocarbons (exposed) whereas the others had no such opportunity for exposure (nonexposed). Although a low response rate precludes firm conclusions, the 1,280 completed questionnaires provide useful data for generating hypotheses in this developing field of interest. A history of diagnosed cancer was reported more frequently among exposed workers. The infant mortality rate was also significantly elevated among the offspring of exposed workers. No risk gradient was observed for episodes of infertility, fetal loss, congenital defects, or low-birthweight offspring. Concerns with nonresponse, exposure characterization, possible confounding factors, and limited statistical power are addressed. The results provide further suggestions which help to direct studies of occupational reproductive risks.

Savitz, D.A.; Harley, B.; Krekel, S.; Marshall, J.; Bondy, J.; Orleans, M.

1984-01-01

324

Atomic structure of As(2)S(3)-Ag chalcogenide glasses.  

PubMed

(As(0.4)S(0.6))(100-x)Ag(x) glasses (x = 0, 4, 8, 12 at.%) have been studied with high-energy x-ray diffraction, neutron diffraction and extended x-ray absorption spectroscopy at As and Ag K-edges. The experimental data were modelled simultaneously with the reverse Monte Carlo simulation method. Analysis of the partial pair correlation functions and coordination numbers extracted from the model atomic configurations revealed that silver preferentially bonds to sulfur in the As(2)S(3)-Ag ternary glasses, which results in the formation of homoatomic As-As bonds. Upon the addition of Ag, a small proportion of Ag-As bonds (N(AgAs)?0.3) are formed in all three ternary compositions, while the direct Ag-Ag bonds (N(AgAg)? 0.4) appear only in the glass with the highest Ag content (12 at.%). Similar to the g- As(2)S(3) binary, the mean coordination number of arsenic is close to three, and that of sulfur is close to two, in the As(2)S(3)-Ag ternary glasses. The first sharp diffraction peak on the total structure factors of As(2)S(3) binary and (As(0.4)S(0.6))(100-x)Ag(x) ternary glasses is related to the As-As and As-S correlations. PMID:21832397

Kaban, I; Jóvári, P; Wagner, T; Frumar, M; Stehlik, S; Bartos, M; Hoyer, W; Beuneu, B; Webb, M A

2009-09-30

325

Correlating atomic structure and transport in suspended graphene nanoribbons.  

PubMed

Graphene nanoribbons (GNRs) are promising candidates for next generation integrated circuit (IC) components; this fact motivates exploration of the relationship between crystallographic structure and transport of graphene patterned at IC-relevant length scales (<10 nm). We report on the controlled fabrication of pristine, freestanding GNRs with widths as small as 0.7 nm, paired with simultaneous lattice-resolution imaging and electrical transport characterization, all conducted within an aberration-corrected transmission electron microscope. Few-layer GNRs very frequently formed bonded-bilayers and were remarkably robust, sustaining currents in excess of 1.5 ?A per carbon bond across a 5 atom-wide ribbon. We found that the intrinsic conductance of a sub-10 nm bonded bilayer GNR scaled with width as GBL(w) ? 3/4(e(2)/h)w, where w is the width in nanometers, while a monolayer GNR was roughly five times less conductive. Nanosculpted, crystalline monolayer GNRs exhibited armchair-terminated edges after current annealing, presenting a pathway for the controlled fabrication of semiconducting GNRs with known edge geometry. Finally, we report on simulations of quantum transport in GNRs that are in qualitative agreement with the observations. PMID:24954396

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

2014-08-13

326

Atomic structure of intracellular amorphous calcium phosphate deposits.  

PubMed Central

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

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

1975-01-01

327

Structural Transition in Atomic Chains Driven by Transient Doping P. C. Snijders,2  

E-print Network

Structural Transition in Atomic Chains Driven by Transient Doping S. Polei,1 P. C. Snijders,2 S. C, Wisconsin 53706, USA (Received 30 April 2013; published 8 October 2013) A reversible structural transition into the surface. The periodicity of atomic chains near the step edges changes from the 1 Ã? 3 ground state to a 1 Ã?

Himpsel, Franz J.

328

ALMOST: An All Atom Molecular Simulation Toolkit for Protein Structure Determination  

E-print Network

ALMOST: An All Atom Molecular Simulation Toolkit for Protein Structure Determination Biao Fu,[d] Michele Vendruscolo,[a] and Andrea Cavalli*[a,e] Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems

Caflisch, Amedeo

329

Collapse the Zeeman structure the hydrogen atom external electric field , Zhilinski  

E-print Network

­2947/96/53~6!/4064~4!/$10.00 4064 1996 American Physical Society #12; same quadratic Zeeman effect Fig. this pattern disappearsCollapse the Zeeman structure the hydrogen atom external electric field Sadovski� â?? , Zhilinski a Zeeman a structure a weakly Rydberg n multiplet of atom parallel magnetic electric fields. The classical

Zhilinskií, Boris

330

Structural Characterization of Micromechanical Properties in Asphalt Using Atomic Force Microscopy  

E-print Network

of the requirements for the degree of MASTER OF SCIENCE December 2010 Major Subject: Civil Engineering STRUCTURAL CHARACTERIZATION OF MICROMECHANICAL PROPERTIES IN ASPHALT USING ATOMIC FORCE MICROSCOPY A Thesis by ROBERT GROVER ALLEN... J. Glover Head of Department, John Niedzwecki December 2010 Major Subject: Civil Engineering iii ABSTRACT Structural Characterization of Micromechanical Properties in Asphalt Using Atomic Force Microscopy. (December 2010) Robert...

Allen, Robert Grover

2012-02-14

331

Lens capsule structure assessed with atomic force microscopy  

PubMed Central

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 ?m, 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.

Sueiras, Vivian M.; Moy, Vincent T.

2015-01-01

332

Phosphorus-doped graphene and (8, 0) carbon nanotube: Structural, electronic, magnetic properties, and chemical reactivity  

NASA Astrophysics Data System (ADS)

Recently, doping non-carbon atoms into graphene or carbon nanotube (CNT) has attracted considerable attention due to its effectiveness to change or tailor their electronic and magnetic properties as well as chemical reactivity. In this work, we present a density functional theory study of the recently synthesized phosphorus (P) doped graphene and CNT. Particular attention is paid to studying the effects of P-doping on the structural, electronic, and magnetic properties as well as chemical reactivity of graphene or CNT. The results show that P dopant drastically changes the geometrical structure of graphene or CNT, rendering P and its neighboring C atoms protrude from the sidewall of CNT and graphene. Moreover, P-doping induces localized electronic states into graphene and CNTs, thus modifying the electronic properties by producing n-type behavior. Meanwhile, due to P doping, the graphene and CNT exhibit magnetic nature with spin net moment of 1.02 and 0.99 ?B, respectively. In order to evaluate the chemical reactivity of the two nanostructures, their interactions with several gas molecules, including NH3, H2O, O2, NO2, and NO, are further calculated. Our results may be useful not only for deeply understanding the properties of CNTs and graphenes, but also for developing various novel nanodevices.

Wang, Hong-mei; Wang, Hong-xia; Chen, Ying; Liu, Yue-jie; Zhao, Jing-xiang; Cai, Qing-hai; Wang, Xuan-zhang

2013-05-01

333

Multi-element analysis of manganese nodules by atomic absorption spectrometry without chemical separation  

USGS Publications Warehouse

Five manganese nodules, including the USGS reference nodules A-1 and P-1, were analyzed for Co, Cu, Fe, K, Mg, Mn, Na, Ni and Zn without prior chemical separation by using a simultaneous multi-element atomic absorption spectrometer with an air-cetylene flame. The nodules were prepared in three digestion matrices. One of these solutions was measured using sixteen different combinations of burner height and air/acetylene ratios. Results for A-1 and P-1 are compared to recommended values and results for all nodules are compared to those obtained with an inductively coupled plasma. The elements Co, Cu, Fe, K, Mg, Mn, Na, Ni, and Zn are simultaneously determined with a composite recovery for all elements of 100 ?? 7%, independent of the digestion matrices, heights in the flame, or flame stoichiometries examined. Individual recoveries for Co, K, and Ni are considerably poorer in two digests than this composite figure, however. The optimum individual recoveries of 100 ?? 5% and imprecisions of 1-4%, except for zinc, are obtained when Co, K, Mn, Na and Ni are determined simultaneously in a concentrated digest, and in another analytical sequence, when Cu, Fe, Mg, Mn and Zn are measured simultaneously after dilution. Determination of manganese is equally accurate in the two sequences; its measurement in both assures internal consistency between the two measurement sequences. This approach improves analytical efficiency over that for conventional atomic absorption methods, while minimizing loss of accuracy or precision for individual elements. ?? 1982.

Kane, J.S.; Harnly, J.M.

1982-01-01

334

Entangling strings of neutral atoms in 1D atomic pipeline structures  

E-print Network

We study a string of neutral atoms with nearest neighbor interaction in a 1D beam splitter configuration, where the longitudinal motion is controlled by a moving optical lattice potential. The dynamics of the atoms crossing the beam splitter maps to a 1D spin model with controllable time dependent parameters, which allows the creation of maximally entangled states of atoms by crossing a quantum phase transition. Furthermore, we show that this system realizes protected quantum memory, and we discuss the implementation of one- and two-qubit gates in this setup.

U. Dorner; P. Fedichev; D. Jaksch; M. Lewenstein; P. Zoller

2003-04-09

335

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

PubMed

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 characteristics and the competing roles of network forming and network modifying SiOm and TiOn units in the mixed hybrid oxides. PMID:24848713

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

2014-06-25

336

Precision physics of simple atoms: QED tests, nuclear structure and fundamental constants  

E-print Network

Quantum electrodynamics is the first successful and still the most successful quantum field theory. Simple atoms, being essentially QED systems, allow highly accurate theoretical predictions. Because of their simple spectra, such atoms have been also efficiently studied experimentally frequently offering the most precisely measured quantities. Our review is devoted to comparison of theory and experiment in the field of precision physics of light simple atoms. In particular, we consider the Lamb shift in the hydrogen atom, the hyperfine structure in hydrogen, deuterium, helium-3 ion, muonium and positronium, as well as a number of other transitions in positronium. Additionally to a spectrum of unperturbed atoms, we consider annihilation decay of positronium and the g factor of bound particles in various two-body atoms. Special attention is paid to the uncertainty of the QED calculations due to the uncalculated higher-order corrections and effects of the nuclear structure. We also discuss applications of simple atoms to determination of several fundamental constants.

Savely G. Karshenboim

2005-09-01

337

Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3.  

PubMed

The electronic structure, chemical bonding, geometry, and effects produced by Sr-doping in CaCO(3) have been studied on the basis of density-functional theory using the VASP simulation package and molecular-orbital theory utilizing the CLUSTERD computer code. Two calcium carbonate structures which occur naturally in anhydrous crystalline forms, calcite and aragonite, were considered in the present investigation. The obtained diagrams of density of states show similar patterns for both materials. The spatial structures are computed and analyzed in comparison to the available experimental data. The electronic properties and atomic displacements because of the trace element Sr-incorporation are discussed in a comparative manner for the two crystalline structures. PMID:17654648

Stashans, Arvids; Chamba, Gaston; Pinto, Henry

2008-02-01

338

Sensing signatures mediated by chemical structure of molecular solids in laser-induced plasmas.  

PubMed

Laser ablation of organic compounds has been investigated for almost 30 years now, either in the framework of pulse laser deposition for the assembling of new materials or in the context of chemical sensing. Various monitoring techniques such as atomic and molecular fluorescence, time-of-flight mass spectrometry, and optical emission spectroscopy have been used for plasma diagnostics in an attempt to understand the spectral signature and potential origin of gas-phase ions and fragments from organic plasmas. Photochemical and photophysical processes occurring within these systems are generally much more complex than those suggested by observation of optical emission features. Together with laser ablation parameters, the structural and chemical-physical properties of molecules seem to be closely tied to the observed phenomena. The present manuscript, for the first time, discusses the role of molecular structure in the optical emission of organic plasmas. Factors altering the electronic distribution within the organic molecule have been found to have a direct impact on its ensuing optical emissions. The electron structure of an organic molecule, resulting from the presence, nature, and position of its atoms, governs the breakage of the molecule and, as a result, determines the extent of atomization and fragmentation that has proved to directly impact the emissions of CN radicals and C2 dimers. Particular properties of the molecule respond more positively depending on the laser irradiation wavelength, thereby redirecting the ablation process through photochemical or photothermal decomposition pathways. It is of paramount significance for chemical identification purposes how, despite the large energy stored and dissipated by the plasma and the considerable number of transient species formed, the emissions observed never lose sight of the original molecule. PMID:25668318

Serrano, Jorge; Moros, Javier; Laserna, J Javier

2015-03-01

339

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

NASA Astrophysics Data System (ADS)

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.

Bhushan, Bharat; Latorre, Carmen; Wei, Guohua

340

Atomic-scale clarification of structural transition of MoS? upon sodium intercalation.  

PubMed

Two-dimensional (2D) transition-metal dichalcogenides hold enormous potential for applications in electronic and optoelectronic devices. Their distinctive electronic and chemical properties are closely related to the structure and intercalation chemistry. Herein, the controversial phase transition from semiconductive 2H to metallic 1T phase and occupancy of the intercalated sodium (Na) upon electrochemical Na intercalation into MoS2 are clarified at the atomic scale by aberration-corrected scanning transmission electron microscope. In addition, a series of other complicated phase transitions along with lattice distortion, structural modulation, and even irreversible structural decomposition are recognized in MoS2 depending on the content of Na ion intercalation. It is shown that x = 1.5 in Na(x)MoS2 is a critical point for the reversibility of the structural evolution. Our findings enrich the understanding of the phase transitions and intercalation chemistry of the MoS2 and shed light on future material design and applications. PMID:25363475

Wang, Xuefeng; Shen, Xi; Wang, Zhaoxiang; Yu, Richeng; Chen, Liquan

2014-11-25

341

The Carbon Atom Model and the Structure of Diamond  

Microsoft Academic Search

Electron orbits in the neutral carbon atom.-The atomic model of carbon used is assumed to have four 21 orbits. The dimensions of these orbits are computed by a method outlined in a previous paper using various assumptions as to screening, viz.: (a) spherical distribution of charge about the nucleus; (b) orientation in orbital planes with random phase relations; (c) orientation

R. B. Lindsay

1927-01-01

342

Effects of Wet Chemical and Trimethyl Aluminum Treatments on the Interface Properties in Atomic Layer Deposition of Al2O3 on InAs  

NASA Astrophysics Data System (ADS)

The reduction of native oxides on an InAs surface using various wet and dry chemical treatments, including hydrochloric acid (HCl) treatment, sulfide treatment, and in situ trimethyl aluminum (TMA) treatment before the atomic layer deposition (ALD) of Al2O3 on InAs is studied. X-ray photoelectron spectrum (XPS) results show that the effect of surface cleaning by TMA was apparent almost after the first pulse but that TMA cleaning is not as effective as wet chemical surface cleaning. The combination of wet chemical treatment and TMA pretreatment is the most effective method for InAs surface cleaning, as indicated by the XPS analysis. Capacitance-voltage (C-V) and current density-voltage (J-V) characteristics on metal-oxide-semiconductor capacitance (MOSCAP) structures were also investigated to evaluate the Al2O3/n-InAs interface quality after different surface treatments, and the results are consistent with the XPS analysis.

Trinh, Hai-Dang; Chang, Edward Yi; Wong, Yuen-Yee; Yu, Chih-Chieh; Chang, Chia-Yuan; Lin, Yueh-Chin; Nguyen, Hong-Quan; Tran, Binh-Tinh

2010-11-01

343

Measuring the Effect of Fuel Chemical Structure on Particulate and Gaseous Emissions using Isotope Tracing  

SciTech Connect

Using accelerator mass spectrometry (AMS), a technique initially developed for radiocarbon dating and recently applied to internal combustion engines, carbon atoms within specific fuel molecules can be labeled and followed in particulate or gaseous emissions. In addition to examining the effect of fuel chemical structure on emissions, the specific source of carbon for PM can be identified if an isotope label exists in the appropriate fuel source. Existing work has focused on diesel engines, but the samples (soot collected on quartz filters or combustion gases captured in bombs or bags) are readily collected from large industrial combustors as well.

Buchholz, B A; Mueller, C J; Martin, G C; Upatnicks, A; Dibble, R W; Cheng, S

2003-09-11

344

Molecular structure and chemical bonding in K3C60 and K6C60  

NASA Astrophysics Data System (ADS)

We present the results of local-density-approximation-based Car-Parrinello calculations of orientationally ordered phases of K3C60 and K6C60. Our investigation focuses on the following points: the effects of alkali-mental intercalation on the structural and electronic properties of C60, the chemical bonding, the inhomogeneity of the electron distribution, and the degree of freedom of the potassium atoms in the interstitial region. The results are discussed in view of experimental data, such as x-ray and neutron-diffraction data as well as nuclear magnetic resonance spectroscopy.

Andreoni, Wanda; Giannozzi, Paolo; Parrinello, Michele

1995-01-01

345

Temporal evolution of the chemical structure during the pattern transfer by ion-beam sputtering  

NASA Astrophysics Data System (ADS)

Ru films patterned by ion-beam sputtering (IBS) serve as sacrificial masks for the transfer of the patterns to Si(1 0 0) and metallic glass substrates by continued IBS. Under the same sputter condition, however, both bare substrates remain featureless. Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution reveal that the pattern transfer, despite its apparent success, suffers from premature degradation before the mask is fully removed by IBS. Moreover, the residue of the mask or Ru atoms stubbornly remains near the surface, resulting in unintended doping or alloying of both patterned substrates.

Ha, N.-B.; Jeong, S.; Yu, S.; Ihm, H.-I.; Kim, J.-S.

2015-01-01

346

Quantum Chemical 13Ca Chemical Shift Calculations for Protein NMR Structure Determination, Refinement, and Validation  

SciTech Connect

A recently determined set of 20 NMR-derived conformations of a 48-residue all-?-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13C? chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13C? chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13C? chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13C? chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-A resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13C? chemical shifts in solution than the 3BHP crystal structure. In addition, the 13C?-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.

Vila, J.; Aramini, J; Rossi, P; Kuzin, A; Su, M; Seetharaman, J; Xiao, R; Tong, L; Montelione, G; Scheraga, H

2008-01-01

347

Improved atomic force microscope infrared spectroscopy for rapid nanometer-scale chemical identification.  

PubMed

Atomic force microscope infrared spectroscopy (AFM-IR) can perform IR spectroscopic chemical identification with sub-100 nm spatial resolution, but is relatively slow due to its low signal-to-noise ratio (SNR). In AFM-IR, tunable IR laser light is incident upon a sample, which results in a rise in temperature and thermomechanical expansion of the sample. An AFM tip in contact with the sample senses this nanometer-scale photothermal expansion. The tip motion induces cantilever vibrations, which are measured either in terms of the peak-to-peak amplitude of time-domain data or the integrated magnitude of frequency-domain data. Using a continuous Morlet wavelet transform to the cantilever dynamic response, we show that the cantilever dynamics during AFM-IR vary as a function of both time and frequency. Based on the observed cantilever response, we tailor a time-frequency-domain filter to identify the region of highest vibrational energy. This approach can increase the SNR of the AFM cantilever signal, such that the throughput is increased 32-fold compared to state-of-the art procedures. We further demonstrate significant increases in AFM-IR imaging speed and chemical identification of nanometer-scale domains in polymer films. PMID:24113150

Cho, Hanna; Felts, Jonathan R; Yu, Min-Feng; Bergman, Lawrence A; Vakakis, Alexander F; King, William P

2013-11-01

348

MODELING THE ATOMIC-TO-MOLECULAR TRANSITION AND CHEMICAL DISTRIBUTIONS OF TURBULENT STAR-FORMING CLOUDS  

SciTech Connect

We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C{sup +}, C, H{sub 2}, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H{sub 2} abundances are discrepant in the boundary regions (A{sub v} {<=} 5), which is due to the different number of rays used by the two approaches.

Offner, Stella S. R. [Department of Astronomy, Yale University, New Haven, CT 06511 (United States); Bisbas, Thomas G.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6B (United Kingdom); Bell, Tom A., E-mail: stella.offner@yale.edu [Centro de Astrobiologia (CSIC-INTA), Carretera de Ajalvir, km 4, E-28850 Madrid (Spain)

2013-06-10

349

Merging structural biology with chemical biology: Structural Chemistry at Eskitis  

Microsoft Academic Search

This review introduces the Structural Chemistry Program at Griffith University’s Eskitis Institute, and provides a brief overview\\u000a over its current and future research portfolio. Capitalising on the co-location with the Queensland Compound Library (QCL),\\u000a Australia’s only small molecule repository, our laboratory investigates the structure and function of proteins with the aim\\u000a of learning about their molecular mechanisms. Consequently, these studies

Andreas HofmannConan; Conan K. Wang; Asiah Osman; David Camp

2010-01-01

350

Atomic-Resolution X-ray Energy-Dispersive Spectroscopy Chemical Mapping of Substitutional Dy Atoms in a High-Coercivity Neodymium Magnet  

NASA Astrophysics Data System (ADS)

We have investigated local element distributions in a Dy-doped Nd2Fe14B hot-deformed magnet by atomic-column resolution chemical mapping using an X-ray energy-dispersive spectrometer (XEDS) attached to an aberration-corrected scanning transmission electron microscope (Cs-corrected STEM). The positions of the Nd and Dy atomic columns were visualized in the XEDS maps. The substitution of Dy was limited to a surface layer 2-3 unit cells thick in the Nd2Fe14B grains, and the Dy atoms preferentially occupied the 4f-Nd sites of Nd2Fe14B. These results provide further insights into the principal mechanism governing the coercivity enhancement due to Dy doping.

Itakura, Masaru; Watanabe, Natsuki; Nishida, Minoru; Daio, Takeshi; Matsumura, Syo

2013-05-01

351

Chemical probing of RNA with the hydroxyl radical at single-atom resolution.  

PubMed

While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5'-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5'-aldehyde. We conclude that hydroxyl radical abstracts a 5'-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5' deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2'-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple. PMID:25313156

Ingle, Shakti; Azad, Robert N; Jain, Swapan S; Tullius, Thomas D

2014-11-10

352

Chemical probing of RNA with the hydroxyl radical at single-atom resolution  

PubMed Central

While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5?-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5?-aldehyde. We conclude that hydroxyl radical abstracts a 5?-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5? deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2?-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple. PMID:25313156

Ingle, Shakti; Azad, Robert N.; Jain, Swapan S.; Tullius, Thomas D.

2014-01-01

353

Atomic structure of Au-nanoparticles on silica support by X-ray PDF study  

SciTech Connect

We investigated the atomic structure of gold nanoparticles with an average size of 5 nm in diameter, supported by silica. We used high-energy X-ray diffraction and the atomic pair distribution function (PDF) to probe the local atomic structure. Measurements were performed from 25 to 950 C. The structure is approximately fcc in average but exhibits small distortions. The structural distortion increases with the temperature and could be related to the catalytic activity of gold nanoparticles. Above 425 C, rapid particle growth and coalescence were observed.

Dmowski, W. [University of Tennessee, Knoxville (UTK); Yin, Hongfeng [ORNL; Dai, Sheng [ORNL; Overbury, Steven {Steve} H [ORNL; Egami, T. [University of Tennessee, Knoxville (UTK)

2010-01-01

354

Atomic Structure of Au Nanoparticles on a Silica Support by an X-ray PDF Study  

SciTech Connect

We investigated the atomic structure of gold nanoparticles with an average size of {approx}5 nm in diameter, supported by silica. We used high-energy X-ray diffraction and the atomic pair distribution function (PDF) to probe the local atomic structure. Measurements were performed from 25 to 950 C. The structure is approximately fcc in average but exhibits small distortions. The structural distortion increases with the temperature and could be related to the catalytic activity of gold nanoparticles. Above 425 C, rapid particle growth and coalescence were observed.

Dmowski, Wojtek; Yin, Hongfeng; Dai, Sheng; Overbury, Steven H.; Egami, Takeshi (Tennessee-K); (ORNL)

2010-05-04

355

[18] improving structures using all-atom contacts 385 The methodology of macromolecular crystallography is mature, powerful,  

E-print Network

[18] improving structures using all-atom contacts 385 The methodology of macromolecular of protein and nucleic acid crystal structures. [18] New Tools and Data for Improving Structures, Using All-atom criteria for protein structure validation: (1) development of the all-atom contact method, which can

Richardson, David

356

Data quality in predictive toxicology: identification of chemical structures and calculation of chemical properties.  

PubMed Central

Every technique for toxicity prediction and for the detection of structure-activity relationships relies on the accurate estimation and representation of chemical and toxicologic properties. In this paper we discuss the potential sources of errors associated with the identification of compounds, the representation of their structures, and the calculation of chemical descriptors. It is based on a case study where machine learning techniques were applied to data from noncongeneric compounds and a complex toxicologic end point (carcinogenicity). We propose methods applicable to the routine quality control of large chemical datasets, but our main intention is to raise awareness about this topic and to open a discussion about quality assurance in predictive toxicology. The accuracy and reproducibility of toxicity data will be reported in another paper. PMID:11102292

Helma, C; Kramer, S; Pfahringer, B; Gottmann, E

2000-01-01

357

Quasilattice-Conserved Optimization of the Atomic Structure of Decagonal Ael-Co-Ni Quasicrystals  

NASA Astrophysics Data System (ADS)

The detailed atomic structure of quasicrystals has been an open question for decades. Here, we present a quasilattice-conserved optimization method (quasiOPT), with particular quasiperiodic boundary conditions. As the atomic coordinates described by basic cells and quasilattices, we are able to maintain the self-similarity characteristics of qusicrystals with the atomic structure of the boundary region updated timely following the relaxing region. Exemplified with the study of decagonal Al-Co-Ni (d-Al-Co-Ni), we propose a more stable atomic structure model based on Penrose quasilattice and our quasiOPT simulations. In particular, "rectangle-triangle" rules are suggested for the local atomic structures of d-Al-Co-Ni quasicrystals.

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

2015-03-01

358

CHEMICAL COMPOUND CLASSIFICATION WITH AUTOMATICALLY MINED STRUCTURE PATTERNS.  

PubMed

In this paper we propose new methods of chemical structure classification based on the integration of graph database mining from data mining and graph kernel functions from machine learning. In our method, we first identify a set of general graph patterns in chemical structure data. These patterns are then used to augment a graph kernel function that calculates the pairwise similarity between molecules. The obtained similarity matrix is used as input to classify chemical compounds via a kernel machines such as the support vector machine (SVM). Our results indicate that the use of a pattern-based approach to graph similarity yields performance profiles comparable to, and sometimes exceeding that of the existing state-of-the-art approaches. In addition, the identification of highly discriminative patterns for activity classification provides evidence that our methods can make generalizations about a compound's function given its chemical structure. While we evaluated our methods on molecular structures, these methods are designed to operate on general graph data and hence could easily be applied to other domains in bioinformatics. PMID:20448828

Smalter, A M; Huan, J; Lushington, G H

2008-01-01

359

Atomic Structure and Fundamental Symmetry Measurements in a Thallium Atomic Beam  

NASA Astrophysics Data System (ADS)

We have completed construction and testing of a new high-flux thallium atomic beam apparatus. Using a multiple slit oven source we achieve a favorable combination of throughput and modest Doppler narrowing. An in-vacuum chopper wheel provides ? 100 Hz modulation of the atomic beam and allows lock-in detection in the case of weak atomic beam absorption. Electric field plates allow precise application of ± 30 kV/cm fields in the interaction region. We will describe ongoing atomic beam spectroscopy of the 378 nm E1 transition, and a planned measurement of the Stark-induced amplitudes within the thallium 6P_1/2 - 6P_3/2 1283 nm M1 transition. We will also present the details of a new experimental proposal to search for time reversal-violating (T-odd, P-even) forces in thallium. In this new scheme, the 1283 nm M1 laser, tuned near the F=0arrowF'=1 transition, would be directed into high-finesse cavity which incorporates the atomic beam. In the presence of a longitudinal static electric field, E, a `TOPE' signature is revealed here by a cavity phase shift proportional to (hatk\\cdotE). We would search for a differential phase shift of counterpropagating (± hatk) laser beams correlated to electric field reversal. The cavity finesse both amplifies any TOPE effect and increases the precision with which it can be detected, while the differencing technique greatly reduces sensitivity to laser frequency or mechanical fluctuations.

Majumder, P. K.; Nicholas, P. C.

1998-05-01

360

Atomic shell structure from the Single-Exponential Decay Detector  

SciTech Connect

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

Silva, Piotr de, E-mail: piotr.desilva@unige.ch [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland); Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland); Korchowiec, Jacek [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland)] [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland); Wesolowski, Tomasz A. [Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland)] [Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland)

2014-04-28

361

Resonance enhanced multiphoton ionization probing of H atoms and CH3 radicals in a hot lament chemical vapour deposition reactor  

E-print Network

reactor used for diamond chemical vapour deposition (CVD). Parameters varied include the hydrocarbon (CH4 to reinforce the consensus view that H atom production during diamond CVD in a hot ®lament reactor arises as a result of dissociative adsorption on the hot ®lament surface, whereas CH3 radical formation is dominated

Bristol, University of

362

Smallest Nanoelectronic with Atomic Devices with Precise Structures  

NASA Technical Reports Server (NTRS)

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

Yamada, Toshishige

2000-01-01

363

Method for large-scale fabrication of atomic-scale structures on material surfaces using surface vacancies  

DOEpatents

A method for forming atomic-scale structures on a surface of a substrate on a large-scale includes creating a predetermined amount of surface vacancies on the surface of the substrate by removing an amount of atoms on the surface of the material corresponding to the predetermined amount of the surface vacancies. Once the surface vacancies have been created, atoms of a desired structure material are deposited on the surface of the substrate to enable the surface vacancies and the atoms of the structure material to interact. The interaction causes the atoms of the structure material to form the atomic-scale structures.

Lim, Chong Wee (Urbana, IL); Ohmori, Kenji (Urbana, IL); Petrov, Ivan Georgiev (Champaign, IL); Greene, Joseph E. (Champaign, IL)

2004-07-13

364

Monte Carlo simulations of ferroelectric crystal growth and molecular electronic structure of atoms and molecules  

NASA Astrophysics Data System (ADS)

In this thesis, we explore two stochastic techniques to study properties of materials in realistic systems. Specifically, the kinetic Monte Carlo (KMC) method is utilized to study the crystal growth process of ferroelectric materials and the quantum Monte Carlo (QMC) approach is used to investigate the ground state properties of atoms and molecules. In the growth simulations, we study the growth rates and chemical ordering of ferroelectric alloys using an electrostatic model with long-range Coulomb interactions. Crystal growth is characterized by thermodynamic processes involving adsorption and evaporation, with solid-on-solid restrictions and excluding diffusion. A KMC algorithm is formulated to simulate this model efficiently in the presence of long-range interactions. The growth process is simulated as a function of temperature, chemical composition, and substrate orientation. We carried out the simulations on two heterovalent binaries, those of the NaCl and the Ba(Mg1/3Nb2/3))O3(BMN) structures. Compared to the simple rocksalt ordered structures, ordered BMN grows only at very low temperatures and only under finely tuned conditions. For materials with tetravalent compositions, such as (1-x)Ba(Mg 1/3Nb2/3))O3 + x BaZrO3 (BMN-BZ), the model does not incorporate tetravalent ions at low-temperature, exhibiting a phase-separated ground state instead. At higher temperatures, tetravalent ions can be incorporated, but the resulting crystals show no chemical ordering in the absence of diffusive mechanisms. In the second part of the thesis, we present results from an auxiliary field quantum Monte Carlo (AFQMC) study of ground state properties, in particular dissociation and ionization energy, of second-row atoms and molecules. The method projects the many-body ground state from a trial wavefunction by random walks in the space of Slater determinants. The Hubbard-Stratonovich transformation is employed to decouple the Coulomb interaction between electrons. A trial wave function is used in the approximation to control the "phase problem". We also carry out Hartree-Fock (HF) and Density Functional Theory (DFT) calculations for comparison to AFQMC results and to serve as starting wavefunctions for our AFQMC calculations. Results of dissociation energy are in excellent agreement with experimental values. Ionization energy errors are somewhat larger than those of other methods. We conclude with a discussion of several possible sources of error as well as a direction for the improvement.

Suewattana, Malliga

365

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

PubMed Central

Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C? and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5?Å and more than one third were conserved within 0.1?Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments. PMID:23897468

Liebschner, Dorothee; Dauter, Miroslawa; Brzuszkiewicz, Anna; Dauter, Zbigniew

2013-01-01

366

Weighted voting-based consensus clustering for chemical structure databases.  

PubMed

The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures. PMID:24830925

Saeed, Faisal; Ahmed, Ali; Shamsir, Mohd Shahir; Salim, Naomie

2014-06-01

367

Semiflexible polymer rings on topographically and chemically structured surfaces  

E-print Network

We investigate morphologies of semiflexible polymer rings, such as circular DNA, which are adsorbed onto topographically or chemically structured substrate surfaces. We classify all equilibrium morphologies for two striped surface structures, (i) topographical surface grooves and (ii) chemically structured surface domains. For both types of stripes, we find four equilibrium shapes: a round toroidal and a confined elongated shape as well as two shapes containing bulges. We determine the complete bifurcation diagram of these morphologies as a function of their contour length and the ratio of adhesive strength to bending rigidity. For more complex geometries consisting of several stripes we find a cascade of transitions between elongated shapes. Finally, we compare our findings to ring condensation by attractive interactions.

Petra Gutjahr; Reinhard Lipowsky; Jan Kierfeld

2014-05-25

368

[Physico-chemical properties of microbial and plant polysaccharides structurants].  

PubMed

The comparative investigation of physico-chemical properties of plant (guar gum, konjac-mannan) and microbial (xanthan gum) origin structurants have been carried out. Among them, xanthan sigma (1544 mPa) and konjac-mannan (5000 mPa) have the best initial viscosity. It has been shown that due to molecular-mass characteristics xanthan (74.3%) gum, ksampan (39%) and konjac-mannan (42.1%) have the highest percentage of high-weight fractions. It has been established that mannose, glucose and galactose as well as unidentified substances are presented in different concentrations in the structure of structurants. PMID:22686017

Votselko, S K; Dankevytch, L A; Lytvynchuk, O O

2012-01-01

369

A bond-topological approach to theoretical mineralogy: crystal structure, chemical composition and chemical reactions  

NASA Astrophysics Data System (ADS)

Here, I describe a theoretical approach to the structure and chemical composition of minerals based on their bond topology. This approach allows consideration of many aspects of minerals and mineral behaviour that cannot be addressed by current theoretical methods. It consists of combining the bond topology of the structure with aspects of graph theory and bond-valence theory (both long range and short range), and using the moments approach to the electronic energy density-of-states to interpret topological aspects of crystal structures. The structure hierarchy hypothesis states that higher bond-valence polyhedra polymerize to form the (usually anionic) structural unit, the excess charge of which is balanced by the interstitial complex (usually consisting of large low-valence cations and (H2O) groups). This hypothesis may be justified within the framework of bond topology and bond-valence theory, and may be used to hierarchically classify oxysalt minerals. It is the weak interaction between the structural unit and the interstitial complex that controls the stability of the structural arrangement. The principle of correspondence of Lewis acidity-basicity states that stable structures will form when the Lewis-acid strength of the interstitial complex closely matches the Lewis-base strength of the structural unit, and allows us to examine the factors that control the chemical composition and aspects of the structural arrangements of minerals. It also provides a connection between a structure, the speciation of its constituents in aqueous solution and its mechanism of crystallization. The moments approach to the electronic energy density-of-states provides a link between the bond topology of a structure and its thermodynamic properties, as indicated by correlations between average anion coordination number and reduced enthalpy of formation from the oxides for [6]Mg{/m [4]}Si n O( m+2 n) and MgSO4(H2O) n .

Hawthorne, Frank C.

2012-11-01

370

Structure activity relationships to assess new chemicals under TSCA  

SciTech Connect

Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

1990-12-31

371

Structure of adsorbed monolayers. The surface chemical bond  

SciTech Connect

This paper attempts to provide a summary of what has been learned about the structure of adsorbed monolayers and about the surface chemical bond from molecular surface science. While the surface chemical bond is less well understood than bonding of molecules in the gas phase or in the solid state, our knowledge of its properties is rapidly accumulating. The information obtained also has great impact on many surface science based technologies, including heterogeneous catalysis and electronic devices. It is hoped that much of the information obtained from studies at solid-gas interfaces can be correlated with molecular behavior at solid-liquid interfaces. 31 references, 42 figures, 1 table.

Somorjai, G.A.; Bent, B.E.

1984-06-01

372

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

PubMed

We describe the realization of a high moment state in fcc Fe nanoparticles through a controlled change in their atomic structure. Embedding Fe nanoparticles in a Cu(1-x)Au(x) matrix causes their atomic structure to switch from bcc to fcc. Extended x-ray absorption fine structure (EXAFS) measurements show that the structure in both the matrix and the Fe nanoparticles expands as the amount of Au in the matrix is increased, with the data indicating a tetragonal stretch in the Fe nanoparticles. The samples were prepared directly from the gas phase by co-deposition, using a gas aggregation source and MBE-type sources respectively for the nanoparticle and matrix materials. The structure change in the Fe nanoparticles is accompanied by a sharp increase in atomic magnetic moment, ultimately to values of ~2.5 ± 0.3 ?(B)/atom . PMID:22469915

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

2012-05-01

373

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

PubMed Central

A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs. PMID:24469299

Tan, J.; Wang, G.; Liu, Z. Y.; Bednar?ík, J.; Gao, Y. L.; Zhai, Q. J.; Mattern, N.; Eckert, J.

2014-01-01

374

Structure and interactions of ultracold Yb ions and Rb atoms  

E-print Network

In order to study ultracold charge-transfer processes in hybrid atom-ion traps, we have mapped out the potential energy curves and molecular parameters for several low lying states of the Rb, Yb$^+$ system. We employ both a multi-reference configuration interaction (MRCI) and a full configuration interaction (FCI) approach. Turning points, crossing points, potential minima and spectroscopic molecular constants are obtained for the lowest five molecular states. Long-range parameters, including the dispersion coefficients are estimated from our {\\it ab initio} data. The separated-atom ionization potentials and atomic polarizability of the ytterbium atom ($\\alpha_d=128.4$ atomic units) are in good agreement with experiment and previous calculations. We present some dynamical calculations for (adiabatic) scattering lengths for the two lowest (Yb,Rb$^+$) channels that were carried out in our work. However, we find that the pseudo potential approximation is rather limited in validity, and only applies to nK temperatures. The adiabatic scattering lengths for both the triplet and singlet channels indicate that both are large and negative in the FCI approximation.

H. D. L. Lamb; J. F. McCann; B. M. McLaughlin; J. Goold; N. Wells; I. Lane

2012-07-23

375

Characterization of chemically and enzymatically treated hemp fibres using atomic force microscopy and spectroscopy  

NASA Astrophysics Data System (ADS)

The mechanical and moisture resistance properties of natural fibre reinforced composites are dependent on the adhesion between the matrix of choice and the fibre. The main goal of this study was to investigate the effect of NaOH swelling of hemp fibres prior to enzymatic treatment and a novel chemical sulfonic acid method on the physical properties of hemp fibres. The colloidal properties of treated hemp fibres were studied exclusively using an atomic force microscope. AFM imaging in tapping mode revealed that each treatment rendered the surface topography of the hemp fibres clean and exposed the individual fibre bundles. Hemp fibres treated with laccase had no effect on the surface adhesion forces measured. Interestingly, mercerization prior to xylanase + cellulase and laccase treatments resulted in greater enzyme access evident in the increased adhesion force measurements. Hemp fibres treated with sulfonic acid showed an increase in surface de-fibrillation and smoothness. A decrease in adhesion forces for 4-aminotoulene-3-sulfonic acid (AT3S) treated fibres suggested a reduction in surface polarity. This work demonstrated that AFM can be used as a tool to estimate the surface forces and roughness for modified fibres and that enzymatic coupled with chemical methods can be used to improve the surface properties of natural fibres for composite applications. Further, this work is one of the first that offers some insight into the effect of mercerization prior to enzymes and the effect on the surface topography. AFM will be used to selectively screen treated fibres for composite applications based on the adhesion forces associated with the colloidal interface between the AFM tip and the fibre surfaces.

George, Michael; Mussone, Paolo G.; Abboud, Zeinab; Bressler, David C.

2014-09-01

376

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

E-print Network

Recently, the bond lengths of the molecular components of nucleic acids and of caffeine and related molecules were shown to be sums of the appropriate covalent radii of the adjacent atoms. Thus, each atom was shown to have its specific contribution to the bond length. This enabled establishing their atomic structures for the first time. In this work, the known bond lengths for amino acids and the peptide bond are similarly shown to be sums of the atomic covalent radii. Based on this result, the atomic structures of all the twenty essential amino acids and a tripeptide have been presented.

Raji Heyrovska

2008-06-21

377

HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic Calculations  

Microsoft Academic Search

The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily shaped particles, by means of bead models, we have constructed a computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure. From the atomic coordinates file used

J Garc??a de la Torre; M. L. Huertas; B. Carrasco

2000-01-01

378

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

ERIC Educational Resources Information Center

Reports on a study aimed at facilitating freshman general chemistry students' understanding of atomic structure based on the work of Thomson, Rutherford, and Bohr. Hypothesizes that classroom discussions based on arguments/counterarguments of the heuristic principles on which these scientists based their atomic models can facilitate students'…

Niaz, Mansoor; Aguilera, Damarys; Maza, Arelys; Liendo, Gustavo

2002-01-01

379

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

ERIC Educational Resources Information Center

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…

Park, Eun Jung; Light, Gregory

2009-01-01

380

Formation of Graphene-on-Diamond Structure by Graphitization of Atomically Flat Diamond (111) Surface  

NASA Astrophysics Data System (ADS)

We succeeded in the formation of a graphene-on-diamond (GOD) structure by the graphitization of a diamond (111) surface. Before the graphitization, atomically flat diamond (111) surfaces were formed by homoepitaxial lateral growth. The graphene layers, which were formed on the atomically flat diamond (111) surfaces horizontally, were observed by cross-sectional high-resolution transmission electron microscopy.

Tokuda, Norio; Fukui, Makoto; Makino, Toshiharu; Takeuchi, Daisuke; Yamsaki, Satoshi; Inokuma, Takao

2013-11-01

381

Optical properties and band structure of atomically thin MoS2  

Microsoft Academic Search

Atomically thin layers of materials can be expected to exhibit distinct electronic structure and novel properties compared to their bulk counterparts. Layered compounds, for which stable atomically thin samples can be produced, are ideal candidates for such studies. Graphene, a monolayer slice of the graphite crystal, is an illustrative example of both the stability and of the interest and importance

Jie Shan; Kin Fai Mak; Changgu Lee; James Hone; Tony Heinz

2010-01-01

382

Phase space structure of the hydrogen atom in a circularly polarized microwave field  

E-print Network

Phase space structure of the hydrogen atom in a circularly polarized microwave field Esther Barrab the problem of the hydrogen atom interacting with a circularly polarized microwave field, modeled an enormous number of advances in physics and mathematics, including the discovery of classical chaos [11

Politècnica de Catalunya, Universitat

383

Insertion of Zn atoms into Cu3N lattice: Structural distortion and modification of electronic properties  

E-print Network

Insertion of Zn atoms into Cu3N lattice: Structural distortion and modification of electronic Article history: Received 16 November 2010 Received in revised form 27 January 2011 Accepted 16 February enlarged lattice constant suggests insertion of zinc atoms to the center of cells of primitive Cu3N lattice

Zexian, Cao

384

Applications of the Cambridge Structural Database in chemical education1  

PubMed Central

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

2010-01-01

385

Interferometer-Type Structures for Guided Atoms R. Dumke, T. Muther, M. Volk, W. Ertmer, and G. Birkl*  

E-print Network

Interferometer-Type Structures for Guided Atoms R. Dumke, T. Mu¨ther, M. Volk, W. Ertmer, and G structures for neutral atoms based on dipole potentials created by microfabricated optical systems atom optical setups based on microfabricated guiding structures. Using mi- crofabricated current

Birkl, Gerhard

386

Time-resolved diffraction profiles and atomic dynamics in short-pulse laser-induced structural transformations: Molecular dynamics study  

E-print Network

Time-resolved diffraction profiles and atomic dynamics in short-pulse laser-induced structural on the atomic-level structural rearrangements available from the simulations to the diffraction spectra measured of the irradiated surface and provides limited direct information on atomic structural rearrangements. Recent

Zhigilei, Leonid V.

387

Atomic Ordering in Self-assembled Epitaxial and Endotaxial Compound and Element Semiconductor Quantum Dot Structures: The First Review  

E-print Network

superior long term structural stability. Such atomically ordered quantum dots should, therefore-12]. In these systems it appears that it is atomically ordered or phase separated QDs that are structurally stable, i]. The general observation is that only parts of epitaxial layers transform into atomically ordered structures

Moeck, Peter

388

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization  

E-print Network

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-step, atomic-level energy minimization. The main-chain structures are first constructed from initial Ca traces physics- and knowledge-based force field. We tested the method by performing an atomic structure

Zhang, Yang

389

Real-space imaging of molecular structure and chemical bonding by single-molecule inelastic tunneling probe.  

PubMed

The arrangement of atoms and bonds in a molecule influences its physical and chemical properties. The scanning tunneling microscope can provide electronic and vibrational signatures of single molecules. However, these signatures do not relate simply to the molecular structure and bonding. We constructed an inelastic tunneling probe based on the scanning tunneling microscope to sense the local potential energy landscape of an adsorbed molecule with a carbon monoxide (CO)-terminated tip. The skeletal structure and bonding of the molecule are revealed from imaging the spatial variations of a CO vibration as the CO-terminated tip probes the core of the interactions between adjacent atoms. An application of the inelastic tunneling probe reveals the sharing of hydrogen atoms among multiple centers in intramolecular and extramolecular bonding. PMID:24855265

Chiang, Chi-lun; Xu, Chen; Han, Zhumin; Ho, W

2014-05-23

390

Atomic Structures of Molecules Based on Additivity of Atomic and/or Ionic Radii (abstract)  

NASA Astrophysics Data System (ADS)

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

Heyrovska, Raji; Narayan, Sara

2009-04-01

391

Chemical and structural properties of polymorphous silicon thin films grown from dichlorosilane  

NASA Astrophysics Data System (ADS)

We have examined the effects of hydrogen dilution (RH) and deposition pressure on the morphological, structural and chemical properties of polymorphous silicon thin films (pm-Si:H), using dichlorosilane as silicon precursor in the plasma enhanced chemical vapor deposition (PECVD) process. The use of silicon chlorinated precursors enhances the crystallization process in as grown pm-Si:H samples, obtaining crystalline fractions from Raman spectra in the range of 65-95%. Atomic Force Microscopy results show the morphological differences obtained when the chlorine chemistry dominates the growth process and when the plasma-surface interactions become more prominent. Augmenting RH causes a considerable reduction in both roughness and topography, demonstrating an enhancement of ion bombardment and attack of the growing surface. X-ray Photoelectron Spectroscopy results show that, after ambient exposure, there is low concentration of oxygen inside the films grown at low RH, present in the form of SiO, which can be considered as structural defects. Instead, oxidation increases with deposition pressure and dilution, along with film porosity, generating a secondary SiOx phase. For higher pressure and dilution, the amount of chlorine incorporated to the film decreases congruently with HCl chlorine extraction processes involving atomic hydrogen interactions with the surface. In all cases, weak silicon hydride (SiH) bonds were not detected by infrared spectroscopy, while bonding configurations associated to the silicon nanocrystal surface were clearly observed. Since these films are generally used in photovoltaic devices, analyzing their chemical and structural properties such as oxygen incorporation to the films, along with chlorine and hydrogen, is fundamental in order to understand and optimize their electrical and optical properties.

Álvarez-Macías, C.; Monroy, B. M.; Huerta, L.; Canseco-Martínez, M. A.; Picquart, M.; Santoyo-Salazar, J.; Sánchez, M. F. García; Santana, G.

2013-11-01

392

Chemical composition, crystallographic structure and impedance spectroscopy of titanium oxynitride TiN xO y thin films  

Microsoft Academic Search

Titanium oxynitride TiNxOy thin films have been deposited by DC-pulsed magnetron sputtering from Ti target in the Ar+N2+O2 reactive atmosphere controlled by plasma emission spectroscopy. Correlation between chemical composition and crystallographic structure of thin films has been determined and presented in the form of the pseudo-equilibrium ternary phase diagram. The atomic N\\/Ti and O\\/Ti ratios have been derived from Rutherford

M. Radecka; E. Pamula; A. Trenczek-Zajac; K. Zakrzewska; A. Brudnik; E. Kusior; N.-T. H. Kim-Ngan; A. G. Balogh

2011-01-01

393

Atomic Structures of Silicene Layers Grown on Ag(111): Scanning Tunneling Microscopy and Noncontact Atomic Force Microscopy Observations  

PubMed Central

Silicene, the considered equivalent of graphene for silicon, has been recently synthesized on Ag(111) surfaces. Following the tremendous success of graphene, silicene might further widen the horizon of two-dimensional materials with new allotropes artificially created. Due to stronger spin-orbit coupling, lower group symmetry and different chemistry compared to graphene, silicene presents many new interesting features. Here, we focus on very important aspects of silicene layers on Ag(111): First, we present scanning tunneling microscopy (STM) and non-contact Atomic Force Microscopy (nc-AFM) observations of the major structures of single layer and bi-layer silicene in epitaxy with Ag(111). For the (3 × 3) reconstructed first silicene layer nc-AFM represents the same lateral arrangement of silicene atoms as STM and therefore provides a timely experimental confirmation of the current picture of the atomic silicene structure. Furthermore, both nc-AFM and STM give a unifying interpretation of the second layer (?3 × ?3)R ± 30° structure. Finally, we give support to the conjectured possible existence of less stable, ~2% stressed, (?7 × ?7)R ± 19.1° rotated silicene domains in the first layer. PMID:23928998

Resta, Andrea; Leoni, Thomas; Barth, Clemens; Ranguis, Alain; Becker, Conrad; Bruhn, Thomas; Vogt, Patrick; Le Lay, Guy

2013-01-01

394

Materials by design—A perspective from atoms to structures  

E-print Network

Biological materials are effectively synthesized, controlled, and used for a variety of purposes in Nature—in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition ...

Buehler, Markus J.

395

Atomic and Electronic Structure of Polar Oxide Interfaces  

SciTech Connect

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.

Gajdardziska-Josifovska, Marija [University of Wisconsin Milwaukee] [University of Wisconsin Milwaukee

2014-01-17

396

Atomic spectral methods for molecular electronic structure calculations  

SciTech Connect

Theoretical methods are reported for ab initio calculations of the adiabatic (Born-Oppenheimer) electronic wave functions and potential energy surfaces of molecules and other atomic aggregates. An outer product of complete sets of atomic eigenstates familiar from perturbation-theoretical treatments of long-range interactions is employed as a representational basis without prior enforcement of aggregate wave function antisymmetry. The nature and attributes of this atomic spectral-product basis are indicated, completeness proofs for representation of antisymmetric states provided, convergence of Schroedinger eigenstates in the basis established, and strategies for computational implemention of the theory described. A diabaticlike Hamiltonian matrix representative is obtained, which is additive in atomic-energy and pairwise-atomic interaction-energy matrices, providing a basis for molecular calculations in terms of the (Coulombic) interactions of the atomic constituents. The spectral-product basis is shown to contain the totally antisymmetric irreducible representation of the symmetric group of aggregate electron coordinate permutations once and only once, but to also span other (non-Pauli) symmetric group representations known to contain unphysical discrete states and associated continua in which the physically significant Schroedinger eigenstates are generally embedded. These unphysical representations are avoided by isolating the physical block of the Hamiltonian matrix with a unitary transformation obtained from the metric matrix of the explicitly antisymmetrized spectral-product basis. A formal proof of convergence is given in the limit of spectral closure to wave functions and energy surfaces obtained employing conventional prior antisymmetrization, but determined without repeated calculations of Hamiltonian matrix elements as integrals over explicitly antisymmetric aggregate basis states. Computational implementations of the theory employ efficient recursive methods which avoid explicit construction the metric matrix and do not require storage of the full Hamiltonian matrix to isolate the antisymmetric subspace of the spectral-product representation. Calculations of the lowest-lying singlet and triplet electronic states of the covalent electron pair bond (H{sub 2}) illustrate the various theorems devised and demonstrate the degree of convergence achieved to values obtained employing conventional prior antisymmetrization. Concluding remarks place the atomic spectral-product development in the context of currently employed approaches for ab initio construction of adiabatic electronic eigenfunctions and potential energy surfaces, provide comparisons with earlier related approaches, and indicate prospects for more general applications of the method.

Langhoff, P.W.; Boatz, J.A.; Hinde, R.J.; Sheehy, J.A. [San Diego Supercomputer Center, University of California, La Jolla, California 92093-0505 (United States); Propulsion Sciences Division, Air Force Research Laboratory (AFRL/PRS), Edwards Air Force Base, California 93524-7680 (United States); Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996-1600 (United States); Propulsion Research Center (TD-40), NASA Marshall Space Flight Center, Huntsville, Alabama 35812-0001 (United States)

2004-11-15

397

IMAGING THE ATOMIC-SCALE STRUCTURE OF MOLYBDENUM AND VANADIUM OXIDES BY SCANNING TUNNELING MICROSCOPY  

E-print Network

IMAGING THE ATOMIC-SCALE STRUCTURE OF MOLYBDENUM AND VANADIUM OXIDES BY SCANNING TUNNELING, the contrast on inhomogenous or defective oxide surfaces can be identified. The vanadium and molybdenum oxides

Rohrer, Gregory S.

398

Local Electronic Structure at Oxide-Oxide Interfaces Probed by Atomic Resolution Electron Energy Loss Spectroscopy  

NASA Astrophysics Data System (ADS)

We report an atomic resolution study of the electronic structure of 12 x 4 LaMnO3-SrMnO3 and 2 x 2 LaMnO3-SrTiO3 superlattices and their interfaces grown on SrTiO3 by EELS. We correlated the interfacial electronic structure with the interfacial atomic structure using atomic resolution Z-contrast STEM using an electron probes of <0.1 nm. The oxide superlattices were synthesized using molecular beam epitaxy. We measured the site-specific unoccupied states of oxygen atoms and transition metals. In the LMO-SMO system we found extra states (holes) near the Fermi level and their dependence on abruptness of interface. In LMO-STO, we will present evidence of site-dependent electronic structure of oxygen and the Mn valence based on the L-edge ratios.

Shah, Amish; Ramasse, Q. M.; May, S. J.; Wen, J. G.; Eckstein, J. N.; Bhattacharya, A.; Zuo, J. M.

2009-03-01

399

Correlating chemical structure and physical properties of vegetable oil esters  

Microsoft Academic Search

The influence of FA ester chemical structures on the rheology and crystallization temperature of those compounds was evaluated\\u000a using methyl, n-butyl, n-octyl, and 2-ethyl-1-hexyl FA esters with different chain lengths and different degrees of unsaturation. The rheological\\u000a properties were analyzed in a high-precision rheometer at various temperatures, and the crystallization temperatures were\\u000a determined by DSC. Esters produced from the esterification

Jorge de A. Rodrigues; Fabianne de P. Cardoso; Elizabeth R. Lachter; Luciana R. M. Estevão; Edson Lima; Regina S. V. Nascimento

2006-01-01

400

Synthesis and structure of chemically vapour-deposited boron nitride  

Microsoft Academic Search

Chemically vapour-deposited boron nitride (CVD-BN) plates have been synthesized on a graphite substrate by the reaction of the BCl3-NH3-H2 gas system in a deposition temperature (Tdep) range from 1200 to 2000° C, with a total gas pressure (Ptot) which was varied from 5 to 60 torr. The effects ofPtot andTdep on the crystal structure and the microstructure of the CVD-BN

Toshitsugu Matsuda; Naoki Uno; Hiroyuki Nakae; Toshio Hirai

1986-01-01

401

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

E-print Network

The Dependence of All-Atom Statistical Potentials on Structural Training Database Chi Zhang, Song An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high

Zhou, Yaoqi

402

MOLView: A program for analyzing and displaying atomic structures on the Macintosh personal computer  

Microsoft Academic Search

A program is described that allows the user to analyze and display atomic structures on any Macintosh personal computer. The program reads ASCII format structure files including PDB, plot files from the graphics programs O and FRODO, and Cartesian coordinates from ChemDraw 3D. The program has a graphical interface that features floating button palettes for objects and tools. The structures

Thomas James Smith

1995-01-01

403

Atomic PDF study of size and structure of CdSe nanoparticles  

Microsoft Academic Search

The atomic pair distribution function (PDF) is used to address the size and structure of series of CdSe nanoparticles prepared by the method of distribution focusing [1]. Due to their limiting structure coherence conventional crystallographic methods, such as Rietveld can't be used to assess quantitative size or structural information. Total scattering techniques, such PDF have been successfully applied recently on

A. S. Masadeh; G. Paglia; E. S. Bozin; S. J. L. Billinge; A. Karkamkar; M. G. Kanatzidis

2006-01-01

404

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

Microsoft Academic Search

In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming

X. Wu; W. Sha

2008-01-01

405

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

SciTech Connect

This project has developed a comprehensive and reliable base of accurate atomic structure data for complex many-electron systems. This has been achieved through the use of sensitive data-based parametric systematizations, precise experimental measurements, and supporting theoretical computations. The atomic properties studies involved primary data (wavelengths, frequency intervals, lifetimes, relative intensities, production rates, etc.) and derived structural parameters (energy levels, ionization potentials, line strengths, electric polarizabilities, branching fractions, excitation functions, etc).

Curtis, L. J.

2004-05-01

406

Atomic Substitutions in Yba2cu3o7 - Modification of the Electronic-Structure  

E-print Network

, College Station, Texas 77843 (Received 1 February 1988) %e have performed semiempirical tight-binding calculations of the electronic structure of YBapCu307, wreath d and s orbitals included for all the metal atoms and p and s orbitals for the oxygen... effect on T?3 s indicating a remarkable insensitivity of the relevant electronic and structural properties to the species on this site. In particu- lar, the magnetic moment of the substituted atom does not appear to affect the superconducting...

RICHERT, BA; Allen, Roland E.

1988-01-01

407

Atomic structure of a symmetric 27{degrees}[001] tilt grain boundary in MgO  

SciTech Connect

The atomic structure of a symmetric 27 degree[001] tilt grain boundary in magnesium oxide has been determined by high-resolution Z-contrast imaging using a 300kV VG HB603U scanning transmission electron microscope with a 1.3 A probe. The atomic configuration in the grain boundary core is found to be considerably less open than the structures proposed for similar materials.

Yan, Yanfa; Chisholm, M.F.; Pennycook, S.J.

1997-04-01

408

Isotope shift and hyperfine structure studies of the krypton ion and the thallium atom  

E-print Network

ISOTOPE SHIFT AND HYPERFINE STRUCTURE STUDIES OF THE KRYPTON ION AND THE THALLIUM ATOM A Thesis by YINGFENG LI Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree... of MASTER OF SCIENCE August 1991 Major Subject: Physics ISOTPE SHIFT AND HYPERFINE STRUCTURE STUDIES OF THE KRYPTON ION AND THE THALLIUM ATOM A Thesis by YINGFENG LI Approved as to style and content by: Hans A. Schuessler (Chair of Committee...

Li, Yingfeng

1991-01-01

409

Surface structure of alanine on Cu(110) via grazing scattering of fast atoms and molecules  

NASA Astrophysics Data System (ADS)

We have studied structures of the chiral amino acid alanine adsorbed on Cu(110) via low-energy electron diffraction (LEED) as well as scattering of fast light atoms and molecules. The adsorption process was controlled in situ by the intensity of specularly reflected 2-keV He atoms. For projectile energies less than 1 keV, we applied the method of fast atom diffraction for studies on the structure of adsorbed alanine molecules on an atomically flat Cu(110) surface with focus on a p(3×2) adsorbate phase. The results are consistent with LEED and explain distortions in LEED patterns via an elongated surface unit cell with incommensurate c(3.16×2) symmetry of parts of the adsorbate. From triangulation using fast atoms via the azimuthal rotation of the target surface, the positions of protruding methyl groups are derived.

Seifert, J.; Busch, M.; Meyer, E.; Winter, H.

2014-02-01

410

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

SciTech Connect

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

Kim, Min-Geun; Jang, Hong-Lae [National Creative Research Initiatives Center for Isogeometric Optimal Design and Department of Naval Architecture and Ocean Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744 (Korea, Republic of)] [National Creative Research Initiatives Center for Isogeometric Optimal Design and Department of Naval Architecture and Ocean Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744 (Korea, Republic of); Cho, Seonho, E-mail: secho@snu.ac.kr [National Creative Research Initiatives Center for Isogeometric Optimal Design and Department of Naval Architecture and Ocean Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744 (Korea, Republic of)] [National Creative Research Initiatives Center for Isogeometric Optimal Design and Department of Naval Architecture and Ocean Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744 (Korea, Republic of)

2013-05-01

411

Structures of quasi-freestanding ultra-thin silicon films deposited on chemically inert surfaces  

NASA Astrophysics Data System (ADS)

Silicon thin films were deposited on a sapphire and a highly oriented pyrolytic graphite (HOPG), which have atomically flat and chemically inert surfaces. The electronic and geometrical structures of the films were analyzed by X-ray photoelectron spectroscopy (XPS) and polarization-dependent X-ray absorption fine structure (XAFS). It was found that the silicon K-edge XAFS spectra for ultra-thin silicon films thinner than 0.2 monolayer exhibited two distinct resonance peaks which were not observed for bulk silicon. The peaks were assigned to the resonance excitations from the Si 1s into the valence unoccupied orbitals with ?? and ?? characters. The average tilted angle of the ?? orbitals was determined by the polarization dependencies of the peak intensities. It was demonstrated that direction of a part of the ?? orbitals in silicon film is perpendicular to the surface. These results support the existence of quasi-freestanding single-layered silicon films with sp2 configuration.

Baba, Y.; Shimoyama, I.; Hirao, N.; Sekiguchi, T.

2014-11-01

412

Atomic structure of highly strained BiFeO3 thin films.  

PubMed

We determine the atomic structure of the pseudotetragonal T phase and the pseudorhombohedral R phase in highly strained multiferroic BiFeO(3) thin films by using a combination of atomic-resolution scanning transmission electron microscopy and electron energy-loss spectroscopy. The coordination of the Fe atoms and their displacement relative to the O and Bi positions are assessed by direct imaging. These observations allow us to interpret the electronic structure data derived from electron energy-loss spectroscopy and provide evidence for the giant spontaneous polarization in strained BiFeO(3) thin films. PMID:22400888

Rossell, M D; Erni, R; Prange, M P; Idrobo, J-C; Luo, W; Zeches, R J; Pantelides, S T; Ramesh, R

2012-01-27

413

Atomic structure evolution of Zr-Ni during severe deformation by HA pair analysis  

NASA Astrophysics Data System (ADS)

The gradual vitrification evolution of atom mixing and local atomic pairing structure of the binary Zr-Ni alloy during severe deformation at room temperature is traced numerically by molecular dynamic simulation. It is found that the icosahedra clusters will gradually develop with the increasing of disorder environment of alloys. Other compoundlike transition structures were also observed in transient in the Zr-Ni couple during the solid-state amorphization process under severe plastic deformation. Since the time scale of the molecular dynamic simulation is several orders of magnitude shorter than reality, the simulated atomic evolution can be viewed as that would occur at ultrahigh strain rates.

Lo, Y. C.; Huang, J. C.; Ju, S. P.; Du, X. H.

2007-07-01

414

Atomic structures of amyloid cross-? spines reveal varied steric zippers  

Microsoft Academic Search

Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-? spine. The atomic architecture of a spine, from the fibril-forming segment GNNQQNY of the yeast prion protein Sup35, was recently revealed by X-ray microcrystallography. It is a pair of ?-sheets, with the facing side chains of the two sheets interdigitated in a dry ‘steric

Michael R. Sawaya; Shilpa Sambashivan; Rebecca Nelson; Magdalena I. Ivanova; Stuart A. Sievers; Marcin I. Apostol; Michael J. Thompson; Melinda Balbirnie; Jed J. W. Wiltzius; Heather T. McFarlane; Anders Ø. Madsen; Christian Riekel; David Eisenberg

2007-01-01

415

How Iron-Containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description Via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations.  

SciTech Connect

Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

Friesner, Richard A.(Columbia University) [Columbia University; Baik, Mu-Hyun (Columbia University) [Columbia University; Gherman, Benjamin F.(Columbia University) [Columbia University; Guallar, Victor (Washington University) [Washington University; Wirstam, Maria E.(1836) [1836; Murphy, Robert B.(Schrodinger Inc) [Schrodinger Inc; Lippard, Stephen J.(Massachusetts Institute of Technology) [Massachusetts Institute of Technology

2003-03-01

416

Atomic structure calculations for F-like tungsten  

NASA Astrophysics Data System (ADS)

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

Sunny, Aggarwal

2014-09-01

417

The role of radial nodes of atomic orbitals for chemical bonding and the periodic table.  

PubMed

The role of radial nodes, or of their absence, in valence orbitals for chemical bonding and periodic trends is discussed from a unified viewpoint. In particular, we emphasize the special role of the absence of a radial node whenever a shell with angular quantum number l is occupied for the first time (lack of "primogenic repulsion"), as with the 1s, 2p, 3d, and 4f shells. Although the consequences of the very compact 2p shell (e.g. good isovalent hybridization, multiple bonding, high electronegativity, lone-pair repulsion, octet rule) are relatively well known, it seems that some of the aspects of the very compact 3d shell in transition-metal chemistry are less well appreciated, e.g., the often weakened and stretched bonds at equilibrium structure, the frequently colored complexes, and the importance of nondynamical electron-correlation effects in bonding. PMID:17143872

Kaupp, Martin

2007-01-15

418

Influences of halogen atoms on indole-3-acetonitrile (IAN): Crystal structure and Hirshfeld surfaces analysis  

NASA Astrophysics Data System (ADS)

Crystal structural investigations and Hirshfeld surface analysis of three halogen atoms (4-Cl, 6-Cl and 4-Br) substituted indole-3-acetonitrile (IAN) were reported in this work. The structures of the present three compounds were characterized by Infrared spectra, Elemental analyses, NMR spectra, differential scanning calorimetry (DSC), thermogravimetric analyses (TGA) and hot stage microscopy (HSM). The Hirshfeld surfaces analysis in terms of crystal structure, intermolecular interactions and ?⋯? stacking motifs were performed. We found that the different kinds of halogen atoms and the different substituted positions have a significant effect on the crystal structures, molecular ?⋯? stacking motifs, melting points, and the nature of intermolecular interactions for IANs.

Luo, Yang-Hui; Yang, Li-Jing; Han, Guangjun; Liu, Qing-Ling; Wang, Wei; Ling, Yang; Sun, Bai-Wang

2014-11-01

419

Advances in Chemical and Structural Characterization of Concretion with Implications for Modeling Marine Corrosion  

NASA Astrophysics Data System (ADS)

The Weins number model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selected-area EDS data collection at precise locations is presented in terms of atomic percent. The mechanism of formation and distribution of the iron-bearing mineral species at specific locations will be presented. Based on water retention measurements, porosity in terms of void volume varies from 15 v/o to 30 v/o (vol.%). The void path displayed by scanning electron microscopy imaging illustrates the tortuous path by which oxygen migrates in the water phase within the concretion from seaside to metalside.

Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Carr, James D.; Conlin, David L.

2014-05-01

420

Chemical vapor deposition and atomic layer deposition of metal oxide and nitride thin films  

NASA Astrophysics Data System (ADS)

Processes for depositing thin films with various electronic, optical, mechanical, and chemical properties are indispensable in many industries today. Of the many deposition methods available, chemical vapor deposition (CVD) has proved over time to be one of the most flexible, efficient, and cost-effective. Atomic layer deposition (ALD) is a newer process that is gaining favor as a method for depositing films with excellent properties and unparalleled precision. This work describes the development of novel CVD and ALD processes to deposit a variety of materials. Hafnium oxide and zirconium oxide show promise as replacements for SiO 2 as gate dielectrics in future-generation transistors. These high-k materials would provide sufficient capacitance with layers thick enough to avoid leakage from tunneling. An ALD method is presented here for depositing conformal hafnium oxide from tetrakis-(diethylamido)hafnium and oxygen gas. A CVD method for depositing zirconium oxide from tetrakis-(dialkylamido)zirconium and either oxygen gas or water vapor is also described. The use of copper for interconnects in integrated circuits requires improved diffusion barrier materials, given its high diffusivity compared to the previously-used aluminum and tungsten. Tungsten nitride has a low resistivity among barrier materials, and can be deposited in amorphous films that are effective diffusion barriers in layers as thin as a few nanometers. Here we demonstrate CVD and plasma-enhanced CVD methods to deposit tungsten nitride films from bis-(dialkylamido)bis-( tert-butylimido)tungsten precursors and ammonia gas. Recent findings had shown uniform copper growth on tantalum silicate films, without the dewetting that usually occurs on oxide surfaces. Tantalum and tungsten silicates were deposited by a CVD reaction from the reaction of either tris-(diethylamido)ethylimido tantalum or bis-(ethylmethylamido)-bis-( tert-butylimido)tungsten with tris-(tert-butoxy)silanol. The ability of evaporated copper layers to wet these surfaces was also investigated. Electrochromic materials are being developed for use in energy-conserving "smart windows" that can control light transmission by varying the voltage across the layer Electrochromic tungsten oxide was deposited from the reaction of tungsten pentacarbonyl alkylisonitriles with oxygen gas. Fluorine-doped tin oxide is a well known transparent conducting oxide (TCO), and zinc stannate has shown promise as a useful TCO with potentially high carrier mobility. A method for depositing fluorine-doped tin oxide from a single-source precursor, dimethyltin-bis-(1,1,1-trifluoro-2,4-hexanedionate), and oxygen gas is presented. Zinc stannate was also deposited by CVD, using zinc acetylacetonate and dibutyltin-bis-(acetylacetonate) and oxygen gas.

Barton, Jeffrey Thomas

421

Comparison of structures of gas atomized and of emulsified highly undercooled Ni-Sn alloy droplets  

NASA Technical Reports Server (NTRS)

A comparison is made of microstructures of droplets of Ni-Sn alloys rapidly solidified by gas atomization and in a glass emulsifying medium. Cooling rate of the gas atomized particles ranged from 10 to the 3rd to 10 to the 6th K/s depending on droplet diameter (20-230 microns). In the hypoeutectic alloy studied, /Ni-(25 wt pct Sn)/, most particles showed a dendritic structure. These same particles, melted and resolidified in a glass medium using DTA (Differential Thermal Analysis), showed undercoolings up to 280 K: the structures were dendritic at low undercoolings and nondendritic at undercoolings above 220 K. It is concluded that the gas atomized particles exhibited little or no undercooling before nucleation; the solidification time of the undercooled emulsified droplets is substantially less than that of gas atomized droplets, and the undercooling required to achieve nondendritic structure depends on sample size.

Yamamoto, M.; Wu, Y.; Shiohara, Y.; Flemings, M. C.

1986-01-01

422

Chemical modifiers in arsenic determination in biological materials by tungsten coil electrothermal atomic absorption spectrometry.  

PubMed

Palladium, iridium, and rhodium are evaluated as possible chemical modifiers in the determination of As in digest solutions of biological materials (human hair and clam) by tungsten coil electrothermal atomic absorption spectrophotometry (TCA-AAS). The modifier in solution was applied onto the coil and thermally pre-reduced; the pre-reduction conditions, the amount of modifier, and the thermal program were optimized. Palladium was not satisfactory, whereas Ir and Rh were effective modifiers and rendered better relative sensitivity for As by a factor of 1.4 and 1.9, respectively compared to the case without modifier. Upon optimization of thermal conditions for As in pre-reduced Ir (2.0 microg) and Rh (2.0 microg) modifiers and in the digest solutions of the study matrices, Rh (2.0 microg) was more effective modifier and was selected as such. The mean within-day repeatability was 2.8% in consecutive measurements (25-100 microg L(-1)) (3 cycles, each of n=6) and confirmed good short-term stability of the absorbance measurements. The mean reproducibility was 4.4% (n=20 in a 3-day period) and the detection limit (3 sigmablank/slope) was 29 pg (n=15). The useful coil lifetime in Rh modifier was extended to 300-400 firings. Validation was by determination of As in the certified reference material (CRM) of "Oyster tissue" solution with a percentage relative error (Erel%) of 2% and percentage relative standard deviation (RSD%) of 3% (n=4), and by analytical recovery of As spiked in CRM of human hair [94 +/- 8% (n=4)]. The methodology is simple, fast (sample readout frequency 21 h(-1)), reliable, of low cost, and was applied to the determination of As in hair samples of exposed and unexposed workers. PMID:14598009

Bruhn, C G; Huerta, V N; Neira, J Y

2004-01-01

423

Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution  

NASA Astrophysics Data System (ADS)

Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of ?-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the ?-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of ?-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in ?-oryzanol loaded systems were found at rather higher field than those in ?-oryzanol free systems, suggesting incorporation of ?-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of ?-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of ?-oryzanol and lipids (solid and liquid) inside the lipid nanoparticle systems are proposed.

Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

2010-03-01

424

Hyperspectral Imaging of Structure and Composition in Atomically Thin Heterostructures  

E-print Network

V, depending on its twist angle ().19-22 However, previous studies could not distinguish these optical microscope that provides imaging and spectroscopy at energies of up to 6.2 eV, allowing comprehensive, all-optical mapping of chemical composition in graphene/h-BN lateral heterojunctions and interlayer rotations

McEuen, Paul L.

425

PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)  

EPA Science Inventory

Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

426

STRUCTURE-ACTIVITY RELATIONSHIP STUIDES AND THEIR ROLE IN PREDICTING AND INVESTIGATING CHEMICAL TOXICITY  

EPA Science Inventory

Structure-Activity Relationship Studies and their Role in Predicting and Investigating Chemical Toxicity Structure-activity relationships (SAR) represent attempts to generalize chemical information relative to biological activity for the twin purposes of generating insigh...

427

Atomic structure and dynamic behaviour of truly one-dimensional ionic chains inside carbon nanotubes  

NASA Astrophysics Data System (ADS)

Materials with reduced dimensionality have attracted much interest in various fields of fundamental and applied science. True one-dimensional (1D) crystals with single-atom thickness have been realized only for few elemental metals (Au, Ag) or carbon, all of which showed very short lifetimes under ambient conditions. We demonstrate here a successful synthesis of stable 1D ionic crystals in which two chemical elements, one being a cation and the other an anion, align alternately inside carbon nanotubes. Unusual dynamical behaviours for different atoms in the 1D lattice are experimentally corroborated and suggest substantial interactions of the atoms with the nanotube sheath. Our theoretical studies indicate that the 1D ionic crystals have optical properties distinct from those of their bulk counterparts and that the properties can be engineered by introducing atomic defects into the chains.

Senga, Ryosuke; Komsa, Hannu-Pekka; Liu, Zheng; Hirose-Takai, Kaori; Krasheninnikov, Arkady V.; Suenaga, Kazu

2014-11-01

428

A theoretical study of the structures and chemical bonds of neptunium (III) molecules by a density functional method  

NASA Astrophysics Data System (ADS)

In this paper, equilibrium structures and chemical bond characteristics of neptunium trihalide molecules NpX3 (X = F, Cl, Br and I) have been investigated by using density functional theory (DFT). The influences of the size of the relativistic effective core potential (RECP) have been examined on the molecular structures. The chemical bond characteristics have also been systematically studied by calculating the density of states (DOS), bond length differences and electronic charge distributions. We have determined that the chemical bonds are mainly ionic in those molecules, and the covalency is enhancing while ionicity decreases from NpF3 to NpI3. The calculated bond energies show that the interaction strength in NpX3 molecules becomes weaker as the halogen atoms becoming heavier.

Yin, Yao-Peng; Dong, Chen-Zhong; Du, Lei-Qiang; Wu, Fang-Xian; Ding, Xiao-Bin

2014-10-01

429

Chemical alteration of poly(vinyl fluoride) Tedlar by hyperthermal atomic oxygen  

Microsoft Academic Search

In this study the erosion of poly(vinyl fluoride) Tedlar by hyperthermal atomic oxygen (AO) has been examined using X-ray photoelectron spectroscopy (XPS). Initially the Tedlar film had F\\/C and O\\/C atom ratios of 0.45 and 0.11, which decrease to 0.018 and 0.04, respectively, after a 2-h exposure to a flux of 2 × 1015atoms\\/cm2s AO with an average kinetic energy

Gar B. Hoflund; Michael L. Everett

2005-01-01

430

What a difference a bond makes: the structural, chemical, and physical properties of methyl-terminated Si(111) surfaces.  

PubMed

The chemical, electronic, and structural properties of surfaces are affected by the chemical termination of the surface. Two-step halogenation/alkylation of silicon provides a scalable, wet-chemical method for grafting molecules onto the silicon surface. Unlike other commonly studied wet-chemical methods of surface modification, such as self-assembly of monolayers on metals or hydrosilylation on silicon, the two-step method enables attachment of small alkyl chains, even methyl groups, to a silicon surface with high surface coverage and homogeneity. The methyl-terminated Si(111) surface, by comparison to hydrogen-terminated Si(111), offers a unique opportunity to study the effects of the first surface bond connecting the overlayer to the surface. This Account describes studies of methyl-terminated Si(111), which have shown that the H-Si(111) and CH3-Si(111) surfaces are structurally nearly identical, yet impart significantly different chemical and electronic properties to the resulting Si surface. The structure of methyl-terminated Si(111) formed by a two-step halogenation/methylation process has been studied by a variety of spectroscopic methods. A covalent Si-C bond is oriented normal to the surface, with the methyl group situated directly atop a surface Si atom. Multiple spectroscopic methods have shown that methyl groups achieve essentially complete coverage of the surface atoms while maintaining the atomically flat, terraced structure of the original H-Si(111) surface. Thus, the H-Si(111) and CH3-Si(111) surface share essentially identical structures aside from the replacement of a Si-H bond with a Si-C bond. Despite their structural similarity, hydrogen and methyl termination exhibit markedly different chemical passivation. Specifically, CH3-Si(111) exhibits significantly greater oxidation resistance than H-Si(111) in air and in aqueous electrolyte under photoanodic current flow. Both surfaces exhibit similar thermal stability in vacuum, and the Si-H and Si-C bond strengths are expected to be very similar, so the results suggest that methyl termination presents a greater kinetic barrier to oxidation of the underlying Si surface. Hydrogen termination of Si(111) provides nearly perfect electronic passivation of surface states (i.e., less than 1 electronic defect per 40 million surface atoms), but this electronic passivation is rapidly degraded by oxidation in air or under electrochemical conditions. In contrast, methyl termination provides excellent electronic passivation that resists degradation due to oxidation. Moreover, alkylation modifies the surface electronic structure by creating a surface dipole that effectively changes the electron affinity of the Si surface, facilitating modification of the charge-transfer kinetics across Si/metal or Si/electrolyte junctions. This Account also briefly describes recent studies of mixed monolayers formed by the halogenation/alkylation of silicon. Mixed monolayers allow attachment of bulkier groups that enable secondary chemistry at the surface (e.g., attachment of molecular catalysts or seeding of atomic layer deposition) to be combined with methyl termination of remaining unreacted surface sites. Thus, secondary chemistry can be enabled while maintaining the chemical and electronic passivation provided by complete termination of surface atoms with Si-C bonds. Such studies of mixed monolayers demonstrate the potential use of a wet-chemical surface modification scheme that combines both chemical and electronic passivation. PMID:25192516

Wong, Keith T; Lewis, Nathan S

2014-10-21

431

J. Phys. Chem. 1995, 99, 15557-15564 15557 Confined Clusters of Rare Gas Atoms: Structures and Phases  

E-print Network

J. Phys. Chem. 1995, 99, 15557-15564 15557 Confined Clusters of Rare Gas Atoms: Structures and the rare gas atoms. The main interests are the differencesin structures and dynamics of rare gas clusters Classical-mechanicalisoenergetic molecular dynamics simulations model Xe atoms and XeN clusters trapped

Berry, R. Stephen

432

Electronic packing frustration in complex intermetallic structures: the role of chemical pressure in Ca2Ag7.  

PubMed

The assignment of distinct roles to electronics and sterics has a long history in our rationalization of chemical phenomena. Exploratory synthesis in the field of intermetallic compounds challenges this dichotomy with a growing list of phases whose structural chemistry points to an interplay between atomic size effects and orbital interactions. In this paper, we begin with a simple model for how this interdependence may arise in the dense atomic packing of intermetallics: correlations between interatomic distances lead to the inability of a phase to optimize bonds without simultaneously shortening electronically under-supported contacts, a conflict we term electronic packing frustration (EPF). An anticipated consequence of this frustration is the emergence of chemical pressures (CPs) acting on the affected atoms. We develop a theoretical method based on DFT-calibrated ?(2)-Hückel calculations for probing these CP effects. Applying this method to the Ca(2)Ag(7) structure, a variant of the CaCu(5) type with defect planes, reveals its formation is EPF-driven. The defect planes resolve severe CPs surrounding the Ca atoms in a hypothetical CaCu(5)-type CaAg(5) phase. CP analysis also points to a rationale for these results in terms of a CP analogue of the pressure-distance paradox and predicts that the impetus for defect plane insertion is tunable via variations in the electron count. PMID:21619054

Fredrickson, Daniel C

2011-07-01

433

Electronic structure and anisotropic chemical bonding in TiNF from ab initio study  

SciTech Connect

Accounting for disorder in anatase titanium nitride fluoride TiNF is done through atoms re-distributions based on geometry optimizations using ultra soft pseudo potentials within density functional theory DFT. The fully geometry relaxed structures are found to keep the body centering of anatase (I4{sub 1}/amd No. 141). The new structural setups are identified with space groups I-4m2 No. 119 and Imm2 No. 44 which obey the 'group to subgroup' relationships with respect to anatase. In the ground state Imm2 structure identified from energy differences, TiNF is found semi-conducting with similar density of states features to anatase TiO{sub 2} and a chemical bonding differentiated between covalent like Ti-N versus ionic like Ti-F. Inter-anion N-F bonding is also identified. - Graphical Abstract: The geometry optimized ground state anatase derived TiNF structure with arrangement of open faceted TiN3F3 distorted octahedra. The insert shows the arrangement of octahedra in anatase TiO{sub 2}. Highlights: Black-Right-Pointing-Pointer Original approach of TiNF structure for addressing the electronic band structure. Black-Right-Pointing-Pointer Based on anatase, two different ordering scheme models with geometry optimization. Black-Right-Pointing-Pointer New structures obeying the group{yields}subgroup relationships with Imm2 ground state from energy. Black-Right-Pointing-Pointer In the ground state TiNF is found semi-conducting with similar density of states to anatase TiO{sub 2}. Black-Right-Pointing-Pointer Chemical bonding differentiated between covalent like Ti-N and ionic Ti-F.

Matar, Samir F., E-mail: matar@icmcb-bordeaux.cnrs.fr [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Dr Albert Schweitzer. 33600 Pessac (France)

2012-01-15

434

Nuclear Corrections to Hyperfine Structure in Light Hydrogenic Atoms  

E-print Network

Hyperfine intervals in light hydrogenic atoms and ions are among the most accurately measured quantities in physics. The theory of QED corrections has recently advanced to the point that uncalculated terms for hydrogenic atoms and ions are probably smaller than 0.1 parts per million (ppm), and the experiments are even more accurate. The difference of the experiments and QED theory is interpreted as the effect on the hyperfine interaction of the (finite) nuclear charge and magnetization distributions, and this difference varies from tens to hundreds of ppm. We have calculated the dominant component of the 1s hyperfine interval for deuterium, tritium and singly ionized helium, using modern second-generation potentials to compute the nuclear component of the hyperfine splitting for the deuteron and the trinucleon systems. The calculated nuclear corrections are within 3% of the experimental values for deuterium and tritium, but are about 20% discrepant for singly ionized helium. The nuclear corrections for the trinucleon systems can be qualitatively understood by invoking SU(4) symmetry.

J. L. Friar; G. L. Payne

2005-04-04

435

Impact of Atomic Layer Deposition to NanoPhotonic Structures and Devices: A Review  

NASA Astrophysics Data System (ADS)

We review the significance of optical thin films by Atomic Layer Deposition (ALD) method to fabricate nanophotonic devices and structures. ALD is a versatile technique to deposit functional coatings on reactive surfaces with conformal growth of compound materials, precise thickness control capable of angstrom resolution and coverage of high aspect ratio nanostructures using wide range of materials. ALD has explored great potential in the emerging fields of photonics, plasmonics, nano-biotechnology, and microelectronics. ALD technique uses sequential reactive chemical reactions to saturate a surface with a monolayer by pulsing of a first precursor (metal alkoxides or covalent halides), followed by reaction with second precursor molecules such as water to form the desired compound coatings. The targeted thickness of the desired compound material is controlled by the number of ALD cycles of precursor molecules that ensures the self limiting nature of reactions. The conformal growth and filling of TiO2 and Al2O3 optical material on nanostructures and their resulting optical properties have been described. The low temperature ALD-growth on various replicated sub-wavelength polymeric gratings is discussed.

Saleem, Muhammad Rizwan; Ali, Rizwan; Khan, Mohammad Bilal; Turunen, Jari; Honkanen, Seppo

2014-10-01

436

Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.  

PubMed

The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory. PMID:22999222

Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

2012-10-24

437

Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases  

PubMed Central

The human cytosolic sulfotransfases (hSULTs) comprise a family of 12 phase II enzymes involved in the metabolism of drugs and hormones, the bioactivation of carcinogens, and the detoxification of xenobiotics. Knowledge of the structural and mechanistic basis of substrate specificity and activity is crucial for understanding steroid and hormone metabolism, drug sensitivity, pharmacogenomics, and response to environmental toxins. We have determined the crystal structures of five hSULTs for which structural information was lacking, and screened nine of the 12 hSULTs for binding and activity toward a panel of potential substrates and inhibitors, revealing unique “chemical fingerprints” for each protein. The family-wide analysis of the screening and structural data provides a comprehensive, high-level view of the determinants of substrate binding, the mechanisms of inhibition by substrates and environmental toxins, and the functions of the orphan family members SULT1C3 and SULT4A1. Evidence is provided for structural “priming” of the enzyme active site by cofactor binding, which influences the spectrum of small molecules that can bind to each enzyme. The data help explain substrate promiscuity in this family and, at the same time, reveal new similarities between hSULT family members that were previously unrecognized by sequence or structure comparison alone. PMID:17425406

Allali-Hassani, Abdellah; Pan, Patricia W; Dombrovski, Ludmila; Najmanovich, Rafael; Tempel, Wolfram; Dong, Aiping; Loppnau, Peter; Martin, Fernando; Thonton, Janet; Edwards, Aled M; Bochkarev, Alexey; Plotnikov, Alexander N; Vedadi, Masoud; Arrowsmith, Cheryl H

2007-01-01

438

Mapping chemical disorder and ferroelectric distortions in the double perovskite compound Sr 2-x Gd x MnTiO6 by atomic resolution electron microscopy and spectroscopy.  

PubMed

In this work we report a study of the chemical and structural order of the double perovskite compound Sr 2-x Gd x MnTiO6 for compositions x=0, 0.25, 0.5, 0.75, and 1. A noticeable disorder at the B-site in the Mn and Ti sublattice is detected at the atomic scale by electron energy-loss spectroscopy for all x values, resulting in Mn-rich and Ti-rich regions. For x ? 0.75, the cubic unit cell doubles and lowers its symmetry because of structural rearrangements associated with a giant ferroelectric displacement of the perovskite B-site cation. We discuss this finding in the light of the large electroresistance observed in Sr 2-x Gd x MnTiO6, x ? 0.75. PMID:24690379

Biškup, Neven; Álvarez-Serrano, Inmaculada; Veiga, Maria; Rivera-Calzada, Alberto; Garcia-Hernandez, Mar; Pennycook, Stephen J; Varela, Maria

2014-06-01

439

Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling  

NASA Astrophysics Data System (ADS)

Grain boundaries influence many physical and chemical properties of crystalline materials. Here, we perform molecular dynamics simulations to study the structure of a series of [100] symmetric tilt grain boundaries in Mg2SiO4 forsterite. The present results show that grain boundary energies depend significantly on misorientation angle. For small misorientation angles (up to 22°), grain boundary structures consist of an array of partial edge dislocations with Burgers vector 1/2[001] associated with stacking faults and their energies can be readily fit with a model which adds the Peach-Koehler equation to the Read-Shockley dislocation model for grain boundaries. The core radius of partial dislocations and the spacing between the partials derived from grain boundary energies show that the transition from low- to high-angle grain boundaries occurs for a misorientation angle between 22° and 32°. For high misorientation angles (32.1° and 60.8°), the cores of dislocations overlap and form repeated structural units. Finally, we use a low energy atomic configuration obtained by molecular dynamics for the misorientation of 12.18° as input to simulate a high-resolution transmission electron microscopy (HRTEM) image. The simulated image is in good agreement with an observed HRTEM image, which indicates the power of the present approach to predict realistic atomic structures of grain boundaries in complex silicates.

Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro

2012-10-01

440

Privileged structures: efficient chemical "navigators" toward unexplored biologically relevant chemical spaces.  

PubMed

In the search for new therapeutic agents for currently incurable diseases, attention has turned to traditionally "undruggable" targets, and collections of drug-like small molecules with high diversity and quality have become a prerequisite for new breakthroughs. To generate such collections, the diversity-oriented synthesis (DOS) strategy was developed, which aims to populate new chemical space with drug-like compounds containing a high degree of molecular diversity. The resulting DOS-derived libraries have been of great value for the discovery of various bioactive small molecules and therapeutic agents, and thus DOS has emerged as an essential tool in chemical biology and drug discovery. However, the key challenge has become how to design and synthesize drug-like small-molecule libraries with improved biological relevancy as well as maximum molecular diversity. This Perspective presents the development of privileged substructure-based DOS (pDOS), an efficient strategy for the construction of polyheterocyclic compound libraries with high biological relevancy. We envisioned the specific interaction of drug-like small molecules with certain biopolymers via the incorporation of privileged substructures into polyheterocyclic core skeletons. The importance of privileged substructures such as benzopyran, pyrimidine, and oxopiperazine in rigid skeletons was clearly demonstrated through the discovery of bioactive small molecules and the subsequent identification of appropriate target biomolecule using a method called "fluorescence difference in two-dimensional gel electrophoresis". Focusing on examples of pDOS-derived bioactive compounds with exceptional specificity, we discuss the capability of privileged structures to serve as chemical "navigators" toward biologically relevant chemical spaces. We also provide an outlook on chemical biology research and drug discovery using biologically relevant compound libraries constructed by pDOS, biology-oriented synthesis, or natural product-inspired DOS. PMID:25310802

Kim, Jonghoon; Kim, Heejun; Park, Seung Bum

2014-10-22

441

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

NASA Astrophysics Data System (ADS)

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

Zhang, Min; Shi, Jun-Jie

2014-01-01

442

Chemical Vapor Generation with Slurry Sampling: A Review of Atomic Absorption Applications  

Microsoft Academic Search

This review summarizes and discusses the analytical methods and techniques described in the literature for hydride generation as a mode of slurry sample introduction into atomization cells. A brief comparison of detection limits for analytical atomic absorption methods and practical applications to analytical samples that utilize slurry hydride generation is discussed. The current state-of-the-art, including advantages and limitations of this

Henryk Matusiewicz

2003-01-01

443

Interplay between bulk atomic clusters and surface structure in complex intermetallic compounds: The case study of the Al5Co2 (001 ) surface  

NASA Astrophysics Data System (ADS)

The Al5Co2 crystal is a complex intermetallic compound, whose structure can be described by a stacking of chemically bonded atomic motifs. It is a potentially new catalytic material for heterogeneous hydrogenation. A single crystal of this phase has been grown by the Czochralski technique in order to study the influence of the three-dimensional bulk substructure on the two-dimensional surface using both experimental ultrahigh vacuum surface techniques and ab initio methods based on the density functional theory. Some bulk properties are first presented, focusing on chemical bond strengths, the determination of the Al and Co chemical potentials in Al5Co2 , the vibrational properties, and the specific heat. Then, the combination of experimental and computational approaches allows the identification of the surface structure, which was found to depend on the surface preparation conditions. In all cases, the surface terminates at specific bulk layers (Al-rich puckered layers) where various fractions of specific sets of Al atoms are missing, identified as Al3 atoms left at the surface resulting from cluster truncation. Finally, electron density of states calculations and spectroscopic measurements were compared and indicate a strong s p -d hybridization of the topmost pure Al layer with subsurface Co atoms. This could influence the surface reactivity and the catalytic performances of this material.

Meier, M.; Ledieu, J.; De Weerd, M.-C.; Huang, Ying-Tzu; Abreu, G. J. P.; Pussi, K.; Diehl, R. D.; Mazet, T.; Fournée, V.; Gaudry, É.

2015-02-01

444

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

SciTech Connect

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.

Debela, T. T. [Zhejiang University; Wang, X. D. [Zhejiang University; Cao, Q. P. [Zhejiang University; Zhang, D. X. [Zhejiang University; Wang, S. Y. [Fudan University; Wang, Cai-Zhuang [Ames Laboratory; Jiang, J. Z. [Zhejiang University

2013-12-12

445

Flow injection-chemical vapor generation atomic fluorescence spectrometry hyphenated system for organic mercury determination: A step forward  

NASA Astrophysics Data System (ADS)

Monomethylmercury and ethylmercury were determined on line using flow injection-chemical vapor generation atomic fluorescence spectrometry without neither requiring a pre-treatment with chemical oxidants, nor UV/MW additional post column interface, nor organic solvents, nor complexing agents, such as cysteine. Inorganic mercury, monomethylmercury and ethylmercury were detected by atomic fluorescence spectrometry in an Ar/H 2 miniaturized flame after sodium borohydride reduction to Hg 0, monomethylmercury hydride and ethylmercury hydride, respectively. The effect of mercury complexing agent such as cysteine, ethylendiaminotetracetic acid and HCl with respect to water and Ar/H 2 microflame was investigated. The behavior of inorganic mercury, monomethylmercury and ethylmercury and their cysteine-complexes was also studied by continuous flow-chemical vapor generation atomic fluorescence spectrometry in order to characterize the reduction reaction with tetrahydroborate. When complexed with cysteine, inorganic mercury, monomethylmercury and ethylmercury cannot be separately quantified varying tetrahydroborate concentration due to a lack of selectivity, and their speciation requires a pre-separation stage (e.g. a chromatographic separation). If not complexed with cysteine, monomethylmercury and ethylmercury cannot be separated, as well, but their sum can be quantified separately with respect to inorganic mercury choosing a suitable concentration of tetrahydroborate (e.g. 10 - 5 mol L - 1 ), thus allowing the organic/inorganic mercury speciation. The detection limits of the flow injection-chemical vapor generation atomic fluorescence spectrometry method were about 45 nmol L - 1 (as mercury) for all the species considered, a relative standard deviation ranging between 1.8 and 2.9% and a linear dynamic range between 0.1 and 5 ?mol L - 1 were obtained. Recoveries of monomethylmercury and ethylmercury with respect to inorganic mercury were never less than 91%. Flow injection-chemical vapor generation atomic fluorescence spectrometry method was validated by analyzing the TORT-1 certificate reference material, which contains only monomethylmercury, and obtaining 83 ± 5% of monomethylmercury recovered, respectively. This method was also applied to the determination of monomethylmercury in saliva samples.

Angeli, Valeria; Biagi, Simona; Ghimenti, Silvia; Onor, Massimo; D'Ulivo, Alessandro; Bramanti, Emilia

2011-11-01

446

What do we really know about the atomic-scale structures of nanophase materials?  

Microsoft Academic Search

Robert W. Balluffi has spent a rich research lifetime critically investigating and elucidating the atomic scale defect structures of materials. Now, a new class of ultrafine-grained materials has been created in which such defects exercise a dominant role. The structures of these new nanophase materials, both metals and ceramics, have been investigated over the past several years by a wide

R. Siegel

1994-01-01

447

Quantitative structure determination of nanostructured materials using the atomic pair distribution function analysis  

Microsoft Academic Search

The employed experimental method in this Ph.D. dissertation research is the atomic pair distribution function (PDF) technique specializing in high real space resolution local structure determination. The PDF is obtained via Fourier transform from powder total scattering data including the important local structural information in the diffuse scattering intensities underneath, and in-between, the Bragg peaks. Having long been used to

Ahmad Salah Masadeh

2008-01-01

448

Atomic Resolution Structures of Rieske Iron-Sulfur Protein: Role of Hydrogen Bonds in Tuning  

E-print Network

Structure Article Atomic Resolution Structures of Rieske Iron-Sulfur Protein: Role of Hydrogen Bonds in Tuning the Redox Potential of Iron-Sulfur Clusters Derrick J. Kolling,1 Joseph S. Brunzelle,3.11.012 SUMMARY The Rieske [2Fe-2S] iron-sulfur protein of cyto- chrome bc1 functions as the initial electron ac

Crofts, Antony R.

449

Chemical bonding, interface strength, and oxygen K electron-energy-loss near-edge structure of the Cu\\/Al2O3 interface  

Microsoft Academic Search

Chemical bondings and oxygen K electron-energy-loss near-edge structures (ELNES) of oxygen terminated Cu\\/Al2O3 heterointerfaces with hollow and on-top configurations were theoretically investigated by using a first principles orthogonalized linear combination of atomic orbitals method. From the chemical bonding analysis, it was found that the hollow configuration has stronger ionic and covalent bondings as compared with the on-top configuration, and the

Teruyasu Mizoguchi; Takeo Sasaki; Shingo Tanaka; Katsuyuki Matsunaga; Takahisa Yamamoto; Masanori Kohyama; Yuichi Ikuhara

2006-01-01

450

Chemical bonding, interface strength, and oxygen K electron-energy-loss near-edge structure of the Cu\\/AlâOâ interface  

Microsoft Academic Search

Chemical bondings and oxygen K electron-energy-loss near-edge structures (ELNES) of oxygen terminated Cu\\/AlâOâ heterointerfaces with hollow and on-top configurations were theoretically investigated by using a first principles orthogonalized linear combination of atomic orbitals method. From the chemical bonding analysis, it was found that the hollow configuration has stronger ionic and covalent bondings as compared with the on-top configuration, and the

Teruyasu Mizoguchi; Takeo Sasaki; Katsuyuki Matsunaga; Yuichi Ikuhara; Shingo Tanaka; Masanori Kohyama; Takahisa Yamamoto

2006-01-01

451

Atomic structure and chemistry of human serum albumin  

NASA Technical Reports Server (NTRS)

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

He, Xiao M.; Carter, Daniel C.

1992-01-01

452

Detailed Atomic Structure of Neutral and Near-Neutral Systems  

SciTech Connect

This paper highlights the issues which need to be addressed in undertaking accurate calculations of multi-electron atoms and ions, particularly at or near the neutral end of an isoelectronic sequence. We illustrate the processes through two calculations--of transitions in Cl I and Sn II--and discuss the convergence of our results as well as updating previous work. In particular, in the case of Cl I, we propose new identifications of the levels involved in certain transitions which are important in determining the abundance of chlorine in the inter-stellar medium (ISM), while in singly ionised tin, our calculations suggest a re-evaluation of the the abundance of tin in the ISM. We also confirm recent identification of Sn II lines seen in tokamak plasmas.

Oliver, Paul; Hibbert, Alan [School of Mathematics and Physics, Queen's University, Belfast BT7 1NN, Northern Ireland (United Kingdom)

2011-05-11

453

Atomic Models of Strong Solids Interfaces Viewed as Composite Structures  

NASA Astrophysics Data System (ADS)

This paper looks back through the 1960s to the invention of carbon fibres and the theories of Strong Solids. In particular it focuses on the fracture mechanics paradox of strong composites containing weak interfaces. From Griffith theory, it is clear that three parameters must be considered in producing a high strength composite:- minimising defects; maximising the elastic modulus; and raising the fracture energy along the crack path. The interface then introduces two further factors:- elastic modulus mismatch causing crack stopping; and debonding along a brittle interface due to low interface fracture energy. Consequently, an understanding of the fracture en