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Sample records for atomic structure chemical

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

    E-print Network

    Pennycook, Steve

    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

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

    PubMed

    Kurchii, B A

    1996-01-01

    The chemical structure of descriptors (D) for some plant growth regulators (PGR), herbicides, pesticides and drugs is described. The presence of an active hydrogen atom in molecules is an essential factor determining biological activity of chemicals. The results obtained from the study of dependence existing between the structure of a certain substance and its biological activity may be used in designing of novel compounds which possess in biological activity. PMID:8755094

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

    PubMed Central

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

    2015-01-01

    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

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

    PubMed Central

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondrá?ek, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

    2015-01-01

    Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)–(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule. PMID:26178193

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

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1981-01-01

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

  6. Atomic surface structure of Si(1 0 0) substrates prepared in a chemical vapor environment

    NASA Astrophysics Data System (ADS)

    Döscher, Henning; Kleinschmidt, Peter; Hannappel, Thomas

    2010-11-01

    Subsequent III-V integration by metal-organic vapor phase epitaxy (MOVPE) or chemical vapor deposition (CVD) necessitates elaborate preparation of Si(1 0 0) substrates in chemical vapor environments characterized by the presence of hydrogen used as process gas and of various precursor molecules. The atomic structure of Si(1 0 0) surfaces prepared in a MOVPE reactor was investigated by low energy electron diffraction (LEED) and scanning tunnelling microscopy (STM) available through a dedicated, contamination-free sample transfer to ultra high vacuum (UHV). Since the substrate misorientation has a fundamental impact on the atomic surface structure, we selected a representative set consisting of Si(1 0 0) with 0.1°, 2° and 6° off-cut in [0 1 1] direction for our study. Similar to standard UHV preparation, the LEED and STM results of the CVD-prepared Si(1 0 0) surfaces indicated two-domain (2 × 1)/(1 × 2) reconstructions for lower misorientations implying a predominance of single-layer steps undesirable for subsequent III-V layers. However, double-layer steps developed on 6° misoriented Si(1 0 0) substrates, but STM also showed odd-numbered step heights and LEED confirmed the presence of minority surface reconstruction domains. Strongly depending on misorientation, the STM images revealed complex step structures correlated to the relative dimer orientation on the terraces.

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

    ERIC Educational Resources Information Center

    Schaller, Chris P.; Graham, Kate J.; Johnson, Brian J.; Jakubowski, Henry V.; McKenna, Anna G.; McIntee, Edward J.; Jones, T. Nicholas; Fazal, M. A.; Peterson, Alicia A.

    2015-01-01

    A one-semester, introductory chemistry course is described that develops a primarily qualitative understanding of structure-property relationships. Starting from an atoms-first approach, the course examines the properties and three-dimensional structure of metallic and ionic solids before expanding into a thorough investigation of molecules. In…

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

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios

    1997-01-01

    Provides a critical analysis of the role that atomic theory plays in the science curriculum from elementary through secondary school. Examines structural concepts from the perspective of the theory of meaningful learning, information processing theory, and the alternative conceptions movement. Contains 54 references. (DDR)

  9. The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

    SciTech Connect

    Baggetto, Loic; Bridges, Craig A; Jumas, Dr. Jean-Claude; Mullins, David R; Carroll, Kyler J; Meisner, Roberta; Crumlin, Ethan; Liu, Xiason; Yang, Wanli; Veith, Gabriel M

    2014-01-01

    To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na7Sn3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na9Sn4 (Cmcm) has relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na14.78Sn4 (Pnma), better described as Na16-xSn4, is Na-richer than cubic Na15Sn4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na7Sn3 and Na15Sn4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.

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

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1982-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1981-01-01

    The application of ab initio quantum mechanical approaches in the study of metal atom clusters requires simplifying techniques that do not compromise the reliability of the calculations. Various aspects of the implementation of the effective core potential (ECP) technique for the removal of the metal atom core electrons from the calculation were examined. The ECP molecular integral formulae were modified to bring out the shell characteristics as a first step towards fulfilling the increasing need to speed up the computation of the ECP integrals. Work on the relationships among the derivatives of the molecular integrals that extends some of the techniques pioneered by Komornicki for the calculation of the gradients of the electronic energy was completed and a formulation of the ECP approach that quite naturally unifies the various state-of-the-art "shape- and Hamiltonian-consistent" techniques was discovered.

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

    PubMed

    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

    2014-01-01

    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. PMID:25404060

  13. Atom Interferometric Measurements of Atomic Structure

    NASA Astrophysics Data System (ADS)

    Cronin, Alex

    2014-05-01

    Measurements of atomic polarizability, tune-out wavelengths, and van der Waals potentials made with an atom interferometer all serve as benchmark tests for atomic structure calculations. We used a Pritchard-type atom interferometer with phase shifts caused by electric field gradients in order to measure electric polarizabilities of Na, K, and Rb atoms. We reported ratios of static polarizabilities ?Rb/?Na = 1.959(5) with 0.3 percent uncertainty. We studied atomic phase shifts due to laser light in order to measure a tune-out wavelength (where there is a root in dynamic polarizability) for potassium atoms of ?zero = 768.9712 nm with 1.5 pm uncertainty. Finally, we measured atom-surface interactions with 2 percent precision, which was sufficient to detect the impact of Rb atomic core electrons on van der Waals potentials. These serve as independent benchmarks for atomic structure calculations because polarizability depends on sums of oscillator strengths, tune-out wavelengths depend on ratios of oscillator strengths, and atom-surface van der Waals interactions depend on sums of oscillator strengths weighted by resonance frequencies. Advances in the atom interferometry measurement techniques used for these and next generation measurements will be discussed.

  14. 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

  15. N-linear algebraic maps for chemical structure codification: a suitable generalization for atom-pair approaches?

    PubMed

    Garcia-Jacas, Cesar R; Marrero-Ponce, Yovani; Barigye, Stephen J; Valdes-Martini, Jose R; Rivera-Borroto, Oscar M; Olivero-Verbel, Jesus

    2014-01-01

    The present manuscript introduces, for the first time, a novel 3D-QSAR alignment free method (QuBiLS-MIDAS) based on tensor concepts through the use of the three-linear and four-linear algebraic forms as specific cases of n-linear maps. To this end, the k(th) three-tuple and four-tuple spatial-(dis)similarity matrices are defined, as tensors of order 3 and 4, respectively, to represent 3Dinformation among "three and four" atoms of the molecular structures. Several measures (multi-metrics) to establish (dis)-similarity relations among "three and four" atoms are discussed, as well as, normalization schemes proposed for the n-tuple spatial-(dis)similarity matrices based on the simple-stochastic and mutual probability algebraic transformations. To consider specific interactions among atoms, both for the global and local indices, n-tuple path and length cut-off constraints are introduced. This algebraic scaffold can also be seen as a generalization of the vector-matrix-vector multiplication procedure (which is a matrix representation of the traditional linear, quadratic and bilinear forms) for the calculation of molecular descriptors and is thus a new theoretical approach with a methodological contribution. A variability analysis based on Shannon's entropy reveals that the best distributions are achieved with the ternary and quaternary measures corresponding to the bond and dihedral angles. In addition, the proposed indices have superior entropy behavior than the descriptors calculated by other programs used in chemo-informatics studies, such as, DRAGON, PADEL, Mold2, and so on. A principal component analysis shows that the novel 3D n-tuple indices codify the same information captured by the DRAGON 3D-indices, as well as, information not codified by the latter. A QSAR study to obtain deeper criteria on the contribution of the novel molecular parameters was performed for the binding affinity to the corticosteroid-binding globulin, using Cramer's steroid database. The achieved results reveal superior statistical parameters for the Bond Angle and Dihedral Angle approaches, consistent with the results obtained in variability analysis. Finally, the obtained QuBiLS-MIDAS models yield superior performances than all 3D-QSAR methods reported in the literature using the 31 steroids as training set, and for the popular division of Cramer's database in training (1-21) and test (22-31) sets, comparable to superior results in the prediction of the activity of the steroids are obtained. From the results achieved, it can be suggested that the proposed QuBiLS-MIDAS N-tuples indices are a useful tool to be considered in chemo-informatics studies. PMID:24909423

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

    SciTech Connect

    Oliveira, M. H. Jr.; Viana, G. A.; Marques, F. C.; Lima, M. M. Jr. de; Cros, A.; Cantarero, A.

    2010-12-15

    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.

  17. 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

    Wang, Chia-Yu; Barrow, Lloyd H.

    2013-01-01

    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…

  18. Pure and Hybrid Evolutionary Computing in Global Optimization of Chemical Structures: from Atoms and Molecules to Clusters and Crystals

    E-print Network

    Sarkar, Kanchan

    2015-01-01

    The growth of evolutionary computing (EC) methods in the exploration of complex potential energy landscapes of atomic and molecular clusters, as well as crystals over the last decade or so is reviewed. The trend of growth indicates that pure as well as hybrid evolutionary computing techniques in conjunction of DFT has been emerging as a powerful tool, although work on molecular clusters has been rather limited so far. Some attempts to solve the atomic/molecular Schrodinger Equation (SE) directly by genetic algorithms (GA) are available in literature. At the Born-Oppenheimer level of approximation GA-density methods appear to be a viable tool which could be more extensively explored in the coming years, specially in the context of designing molecules and materials with targeted properties.

  19. Combining structural and chemical information at the nanometer scale by correlative transmission electron microscopy and atom probe tomography.

    PubMed

    Herbig, M; Choi, P; Raabe, D

    2015-06-01

    In many cases, the three-dimensional reconstructions from atom probe tomography (APT) are not sufficiently accurate to resolve crystallographic features such as lattice planes, shear bands, stacking faults, dislocations or grain boundaries. Hence, correlative crystallographic characterization is required in addition to APT at the exact same location of the specimen. Also, for the site-specific preparation of APT tips containing regions of interest (e.g. grain boundaries) correlative electron microscopy is often inevitable. Here we present a versatile experimental setup that enables performing correlative focused ion beam milling, transmission electron microscopy (TEM), and APT under optimized characterization conditions. The setup was designed for high throughput, robustness and practicability. We demonstrate that atom probe tips can be characterized by TEM in the same way as a standard TEM sample. In particular, the use of scanning nanobeam diffraction provides valuable complementary crystallographic information when being performed on atom probe tips. This technique enables the measurement of orientation and phase maps as known from electron backscattering diffraction with a spatial resolution down to one nanometer. PMID:25723104

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

  1. Chemical evolution STRUCTURE OF GALAXIES

    E-print Network

    Kruit, Piet van der

    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

  2. Atomic Structure of Graphene Subnanometer Pores.

    PubMed

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

    2015-12-22

    The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert. PMID:26524121

  3. Development of a TEM to study in situ structural and chemical changes at an atomic level during gas-solid interactions at elevated temperatures.

    PubMed

    Sharma, R; Weiss, K

    1998-08-15

    A Philips (Eindhoven, The Netherlands) 430 (300 keV) high resolution transmission electron microscope has been modified for in situ study of gas-solid interactions at elevated temperatures. This microscope can be best described as a synthesis, processing, and characterization laboratory for nano-size materials. A differentially pumped environmental cell (E-cell), capable of handling up to 20 torr of gas pressure, is fitted in the objective lens pole-piece gap. Single-tilt or double-tilt heating holders can be used to heat the samples up to 1,300 degrees C and 850 degrees C, respectively. The system can handle any non-corrosive gases such as H2, O2, N2, NH3, CO, water vapor. Electron diffraction patterns are used to elucidate the reaction path and to identify stable and/or metastable phases formed. Time, temperature, and pressure resolved electron diffraction patterns can also be used to estimate the thermodynamical conditions for the onset of a reaction and the stability range of different phases observed during the process can also be determined. The high resolution imaging capabilities enable elucidation of the basic structural mechanisms involved at near atomic level. The TV rate camera/video recording system is used to measure the reaction rates (kinetics of the reaction). A post projector energy filter (Gatan Imaging Filter, GIF) is attached at the bottom of the microscope in order to filter the inelastic scattering from the gases/thick samples as well as to obtain energy filtered images (chemical maps). The GIF can also be used as a parallel electron energy loss spectrometer (PEELS) to obtain changes in the sample composition during the reactions. The changes in the near-edge structures of PEELS spectrum is used to monitor changes in bonding and/or chemical environment elements during reaction. The chemical maps obtained can also be used to identify preferred regions of gas reactions, e.g., grain boundaries or surfaces, etc. Various modifications of the microscope are described in detail, with suitable examples showing the performance. PMID:9779832

  4. Surface atomic and chemical structure of relaxor Sr0.63Ba0.37Nb2O6(001)

    NASA Astrophysics Data System (ADS)

    Wang, J. L.; Vilquin, B.; Gautier, B.; Dezanneau, G.; Barrett, N.

    2015-06-01

    The surface atomic and chemical structures of a Sr0.63Ba0.37Nb2O6(001) single crystal are studied using the low-energy electron diffraction (LEED) and X-ray photoelectron spectroscopy. Sharp, well-defined LEED patterns are observed, consisting of the superposition of two surface reconstructions, ( ?{ 5 } × ?{ 5 } )R26.6° and ( 5 ?{ 2 } × ?{ 2 } )R45°, probably due to long-range ordering of the alkaline earth metal vacancies in A1 or A2 sites. The Sr/Ba stoichiometry is determined by high-resolution X-ray photoelectron spectroscopy. The Sr 3d core level has 2 components corresponding to the 12- and 15-fold coordinated A1 and A2 sites. The Ba 3d core level has only one component, consistent with the A2 site occupancy. The long-range order of the cation vacancies implies that it is rather the Sr/Ba occupancy of the A2 sites which is responsible for the local random fields at the origin of the relaxor behavior.

  5. RADIOACTIVE CHEMICAL ELEMENTS IN THE ATOMIC TABLE.

    SciTech Connect

    HOLDEN, N.E.

    2005-08-13

    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.

  6. Engineering spin structures at the atomic scale

    E-print Network

    KuÂ?el, Petr

    Engineering spin structures at the atomic scale Seminá odd. 26 Tenkých vrstev a nanostruktur datum for functional structures with atomic precision of their architecture. But the behavior of the magnetic moments at ultimate length scale is accessible. Artificially engineered Co structures built atom by atom, by means

  7. Atomic Structure in Black Hole

    E-print Network

    Yukinori Nagatani

    2006-11-27

    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.

  8. BOOK REVIEW: Computational Atomic Structure

    NASA Astrophysics Data System (ADS)

    Post, Douglass E.

    1998-02-01

    The primary purpose of `Computational Atomic Structure' is to give a potential user of the Multi-Configuration Hartree-Fock (MCHF) Atomic Structure Package an outline of the physics and computational methods in the package, guidance on how to use the package, and information on how to interpret and use the computational results. The book is successful in all three aspects. In addition, the book provides a good overview and review of the physics of atomic structure that would be useful to the plasma physicist interested in refreshing his knowledge of atomic structure and quantum mechanics. While most of the subjects are covered in greater detail in other sources, the book is reasonably self-contained, and, in most cases, the reader can understand the basic material without recourse to other sources. The MCHF package is the standard package for computing atomic structure and wavefunctions for single or multielectron ions and atoms. It is available from a number of ftp sites. When the code was originally written in FORTRAN 77, it could only be run on large mainframes. With the advances in computer technology, the suite of codes can now be compiled and run on present day workstations and personal computers and is thus available for use by any physicist, even those with extremely modest computing resources. Sample calculations in interactive mode are included in the book to illustrate the input needed for the code, what types of results and information the code can produce, and whether the user has installed the code correctly. The user can also specify the calculational level, from simple Hartree-Fock to multiconfiguration Hartree-Fock. The MCHF method begins by finding approximate wavefunctions for the bound states of an atomic system. This involves minimizing the energy of the bound state using a variational technique. Once the wavefunctions have been determined, other atomic properties, such as the transition rates, can be determined. The book begins with an introduction to atomic structure. It covers single and many electron systems, how to set up a basis set of wavefunctions for a many electron system, LS coupling, single and multi-electron Hamiltonians, the elementary Hartree-Fock approximation and how variational methods are used to determine the ground state energy and wavefunctions. The computational methods used in the codes are outlined and there are exercises at the end of each chapter. For a number of candidate atomic configurations, explicit examples are given that illustrate the physics, the approximations and the computational methods involved, and which provide the reader with the opportunity to check that he is using the suite of codes correctly. Relativistic effects are covered as perturbations with Breit-Pauli Hamiltonians. Isotope and hyperfine level splitting are also covered. A summary chapter covers allowed and forbidden bound-bound transitions. It describes how to set up the matrix elements for transition operators, and the determination of selection rules and computational aspects of the methods for allowed and forbidden lines. The last chapter provides a brief introduction to continuum transitions, including how to compute the necessary wavefunctions to calculate photoionization or photodetachment and autoionization processes. Several appendices provide a summary of angular momentum theory, an introduction to the Dirac and Breit-Pauli theory for relativistic processes, and a description of the input parameters needed to run the programs. In summary, the book is an almost essential guide to anyone planning to use the Multi-Configuration Hartree-Fock suite of codes. With this guide, even someone not thoroughly familiar with the details of the subject or the codes should be able to use them to obtain energy levels, wavefunctions and transition rates for any atomic system of interest. This book serves as a model example for the general computational physics community of how to document an important suite of codes for a wide number of researchers and really make the suite usable to the general physics c

  9. Structural Atomic Representation for Classification.

    PubMed

    Tang, Yuan Yan; Wang, Yulong; Li, Luoqing; Chen, C L Philip

    2015-12-01

    Recently, a large family of representation-based classification methods have been proposed and attracted great interest in pattern recognition and computer vision. This paper presents a general framework, termed as atomic representation-based classifier (ARC), to systematically unify many of them. By defining different atomic sets, most popular representation-based classifiers (RCs) follow ARC as special cases. Despite good performance, most RCs treat test samples separately and fail to consider the correlation between the test samples. In this paper, we develop a structural ARC (SARC) based on Bayesian analysis and generalizing a Markov random field-based multilevel logistic prior. The proposed SARC can utilize the structural information among the test data to further improve the performance of every RC belonging to the ARC framework. The experimental results on both synthetic and real-database demonstrate the effectiveness of the proposed framework. PMID:25622336

  10. Atomic structure of titania nanosheet with vacancies

    PubMed Central

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

    2013-01-01

    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

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

    SciTech Connect

    Censky, M; Spalek, O; Jirasek, V; Kodymova, J; Jakubec, I

    2009-11-30

    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)

  12. Ring structures of atoms and molecules

    NASA Astrophysics Data System (ADS)

    Osmera, Pavel; Werner, Pavel; Osmera, Pavel

    2015-09-01

    Knowledge of structure rules of the atomic nucleus and the properties of vortex electromagnetic field allow us to create relatively precisely the structures of individual atoms and molecules. Properties of atoms are largely described by the structure of their electron shells. However, the standard model of atoms does not allow define this structure exactly. New theory VFRT (vortex-fractal-ring-theory) can solve this lack. Theory VFRT uses fractal ring structure of the electron, the proton and the neutron, and can describe the inner structure of atomic nuclei. Fractal descriptions of Nature are very promising. The atomic nucleus can be built from the ring protons and neutrons. This new theory assumes that the arrangement of electron shells arises from the structure of the atomic nucleus. Electrons are not in orbit around the atomic nucleus, but each electron levitates with the corresponding proton of the nucleus. The levitation bond between the electron and the proton is formed by an electromagnetic vortex structure. Theory VFRT expands understanding of nature through a new perspective on the evolution of lifeless nature using a vortex, fractal and ring substructures with self-organization, from quarks, electrons, protons and neutrons, atoms, molecules, to the structure of complex organic compounds.

  13. Chemical structure and dynamics: Annual report 1993

    SciTech Connect

    Colson, S.D.

    1994-07-01

    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.

  14. Evolution of atomic structure during nanoparticle formation.

    PubMed

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M Ø; Christensen, Mogens; Bøjesen, Espen D; Emerich, Hermann; Vaughan, Gavin; Billinge, Simon J L; Iversen, Bo B

    2014-05-01

    Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structure is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries. PMID:25075335

  15. A Thermo-Chemical Reactor for analytical atomic spectrometry

    NASA Astrophysics Data System (ADS)

    Gilmutdinov, A. Kh.; Nagulin, K. Yu.

    2009-01-01

    A novel atomization/vaporization system for analytical atomic spectrometry is developed. It consists of two electrically and thermally separated parts that can be heated separately. Unlike conventional electrothermal atomizers in which atomization occurs immediately above the vaporization site and at the same instant of time, the proposed system allows analyte atomization via an intermediate stage of fractional condensation as a two stage process: Vaporization ? Condensation ? Atomization. The condensation step is selective since vaporized matrix constituents are mainly non-condensable gases and leave the system by diffusion while analyte species are trapped on the cold surface of a condenser. This kind of sample distillation keeps all the advantages of traditional electrothermal atomization and allows significant reduction of matrix interferences. Integration into one design a vaporizer, condenser and atomizer gives much more flexibility for in situ sample treatment and thus the system is called a Thermo-Chemical Reactor (TCR). Details of the design, temperature measurements, vaporization-condensation-atomization mechanisms of various elements in variety of matrices are investigated in the TCR with spectral, temporal and spatial resolution. The ability of the TCR to significantly reduce interferences and to conduct sample pyrolysis at much higher temperatures as compared to conventional electrothermal atomizers is demonstrated. The analytical potential of the system is shown when atomic absorption determination of Cd and Pb in citrus leaves and milk powder without the use of any chemical modification.

  16. Introduction to Atomic Structure: Demonstrations and Labs.

    ERIC Educational Resources Information Center

    Ciparick, Joseph D.

    1988-01-01

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

  17. Atom structures of relation algebras Ian Hodkinson \\Lambda

    E-print Network

    Hodkinson, Ian

    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

  18. Some Experiments in Atomic Structure

    ERIC Educational Resources Information Center

    Logan, Kent R.

    1974-01-01

    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)

  19. About the atomic structures of icosahedral quasicrystals

    NASA Astrophysics Data System (ADS)

    Quiquandon, Marianne; Gratias, Denis

    2014-01-01

    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….

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

    SciTech Connect

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

    2008-03-29

    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.

  1. New hexagonal structure for silicon atoms

    NASA Astrophysics Data System (ADS)

    Naji, S.; Belhaj, A.; Labrim, H.; Benyoussef, A.; El Kenz, A.

    2012-11-01

    Motivated by recent experimental and theoretical works on silicene and its derived materials and based on the exceptional Lie algebra G2 we propose a new hexagonal symmetry producing the (?3 × ?3)R30° superstructure for silicon atoms. The principal hexagonal unit cell contains twelve atoms instead of the usual structure involving only six ones and it is associated with the G2 root system. In this silicon atom configuration appears two hexagons of unequal side length at angle 30°. This atomic structure can be tessellated to exhibit two superstructures (1 × 1) and (?3 × ?3)R30° on the same atomic sheet. To test this double hexagonal structure, we perform a numerical study using Ab-initio calculations based on FPLO9.00-34 code. We observe that the usual silicon electronic properties and the lattice parameters of planar geometry are modified. In particular, the corresponding material becomes a conductor rather than zero gaped semi-conductor arising in single hexagonal structure. Although the calculation is done for silicon atoms, we expect that this structure could be adapted to all two dimensional materials having a single hexagonal flat geometry.

  2. Atomic Structure Schrdinger equation has approximate solutions for multi-

    E-print Network

    Zakarian, Armen

    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

  3. Local atomic structure in disordered and nanocrystalline catalytic materials.

    SciTech Connect

    Dmowski, W.; Egami, T.; Swider-Lyons, K.; Dai, Sheng; Overbury, Steven {Steve} H

    2007-01-01

    The power of the atomic pair density function method to study the local atomic structure of dispersed materials is discussed for three examples (I) supercapacitor hydrous ruthenia, (II) electroctalyst platinum-iron phosphate and (III) nanoparticle gold catalyst. Hydrous ruthenia appears to be amorphous, but was found to be nanocomposite with RuO{sub 2} nanocrystals supporting electronic and hydrous boundaries protonic conductivity. A platinum-iron phosphate electrocatalyst, that exhibits activity for the oxygen reduction reaction has platinum in a non-metallic state. In catalysts comprised of gold nanoparticles supported on TiO{sub 2}, atomic correlations in the second atomic shell were observed suggesting interaction with the support that could modify gold chemical activity.

  4. Spatially resolved imaging of inhomogeneous charge transfer behavior in polymorphous molybdenum oxide. I. Correlation of localized structural, electronic, and chemical properties using conductive probe atomic force microscopy and Raman microprobe spectroscopy.

    PubMed

    McEvoy, Todd M; Stevenson, Keith J

    2005-04-12

    A detailed study of electrochemically deposited molybdenum oxide thin films has been carried out after they were sintered at 250 degrees C. Conductive probe atomic force microscopy (CP-AFM), Raman microscopy, and X-ray photoelectron spectroscopy (XPS) techniques were employed to assess the complex structural, electronic, and compositional properties of these films. Spatially resolved Raman microprobe spectroscopy studies reveal that sintered molybdenum oxide is polymorphous and phase segregated with three types of domains observed comprising orthorhombic alpha-MoO3, monoclinic beta-MoO3, and intermixed alpha-/beta-MoO3. CP-AFM studies conducted in concert with Raman microprobe spectroscopy allowed for correlation between specific compositional regions and localized electronic properties. Single point tunneling spectroscopy studies of chemically distinct regions show semiconducting current-voltage (I-V) behavior with the beta-MoO3 polymorph exhibiting higher electronic conductivity than intermixed alpha-/beta-MoO3 or microcrystalline alpha-MoO3 domains. XPS valence level spectra of beta-MoO3 films display a small structured band near the Fermi level, indicative of an increased concentration of oxygen vacancies. This accounts for the greatly enhanced electronic conductivity of beta-MoO3 as these positively charged cationic defects (anion vacancies) act to trap excess electrons. Connections between structural features, electronic properties, and chemical composition are established and discussed. Importantly, this work highlights the value of using spatially resolved techniques for correlating structural and compositional features with electrochemical behaviors of disordered, mixed-phase lithium insertion oxides. PMID:15807597

  5. Quantum Structures of the Hydrogen Atom

    E-print Network

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

    2014-05-28

    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?

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

    ERIC Educational Resources Information Center

    Whitman, Mark

    1984-01-01

    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)

  7. Atomic structure of heterophase interfaces

    SciTech Connect

    Merkle, K.L.; Buckett, M.I.; Gao, Y.

    1991-01-01

    High-resolution electron microscopy (HREM) has been used to study internal interfaces between dissimilar materials, notably ceramic/metal interfaces. Structures observed for system with small and large misfits are compared in metal/metal, metal/ceramic, and ceramic/ceramic boundaries. The interfaces were prepared by a variety of techniques, including internal reduction, internal oxidation, and epitaxial growth by MOCVD and special thin-film techniques. While interfaces produced by internal oxidation and reduction in fcc systems typically form boundaries on (111) planes, non-equilibrium boundaries have also been generated using special thin film techniques. All boundaries can be characterized by their tendency to form coherent structures. While it appears that the amount of misfit and the bond strength primarily determine the degree of coherency, kinetic factors and substrate defects also seem to play an important role in determining the local defect structure at the boundary and the type of misfit localization. 24 refs., 9 figs., 1 tab.

  8. Likelihood of atom–atom contacts in crystal structures of halogenated organic compounds

    PubMed Central

    Jelsch, Christian; Soudani, Sarra; Ben Nasr, Cherif

    2015-01-01

    The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a ? interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen?halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C?C interactions in parallel ?-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C—H?Cl and O—H?O are the preferred interactions in compounds containing both O and Cl. PMID:25995842

  9. Atomic vapor spectroscopy in integrated photonic structures

    E-print Network

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

    2015-01-01

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

  10. Electrohydrodynamic atomization (EHDA) assisted wet chemical synthesis of nickel nanoparticles

    SciTech Connect

    Barzegar Vishlaghi, M.; Farzalipour Tabriz, M.; Mohammad Moradi, O.

    2012-07-15

    Highlights: ? Electrohydrodynamic atomization (EHDA) assisted chemical synthesis of nickel nanoparticles is reported. ? Substituting water with non-aqueous media prevents the formation of nickel hydroxide. ? Size of particles decreased from 10 to 20 nm down to 2–4 nm by using multi-jet mode. ? Synthesized nanoparticles have diffraction patterns similar to amorphous materials. -- Abstract: In this study nickel nanoparticles were prepared via chemical reduction of nickel acetate using sodium borohydride using electrohydrodynamic atomization (EHDA) technique. This technique was used to spray a finely dispersed aerosol of nickel precursor solution into the reductive bath. Obtained particles were characterized by means of X-ray diffraction (XRD), UV–Visible spectroscopy, and transmission electron microscopy (TEM). Results confirmed the formation of nickel nanoparticles and showed that applying EHDA technique to chemical reduction method results in producing smaller particles with narrower size distribution in comparison with conventional reductive precipitation method.

  11. Quartet structure in atomic nuclei

    NASA Astrophysics Data System (ADS)

    Fu, G. J.; Zhao, Y. M.; Arima, A.

    2015-05-01

    A quartet is a tightly bound cluster of two protons and two neutrons, similar to the ? particle but occasionally with nonzero spin and/or isospin. If the interaction between two quartets is weak in given states, such states are concluded to be well represented by a quartet structure. In this paper, we study the quartet structure of eight valence nucleons in two cases. The first is a single j shell, demonstrating that the so-called stretch scheme [M. Danos and V. Gillet, Phys. Rev. Lett. 17, 703 (1966), 10.1103/PhysRevLett.17.703] is very good for low-spin states with a quadruple-quadruple interaction, and is reasonably good under realistic interactions. The second case is the ground state of 92Pd in the p1 /2p3 /2f5 /2g9 /2 shell with the JUN45 effective interaction. We show that the quartet correlation is essential in the ground state of 92Pd.

  12. Molecular beam studies of hot atom chemical reactions: Reactive scattering of energetic deuterium atoms

    SciTech Connect

    Continetti, R.E.; Balko, B.A.; Lee, Y.T.

    1989-02-01

    A brief review of the application of the crossed molecular beams technique to the study of hot atom chemical reactions in the last twenty years is given. Specific emphasis is placed on recent advances in the use of photolytically produced energetic deuterium atoms in the study of the fundamental elementary reactions D + H/sub 2/ /minus/> DH + H and the substitution reaction D + C/sub 2/H/sub 2/ /minus/> C/sub 2/HD + H. Recent advances in uv laser and pulsed molecular beam techniques have made the detailed study of hydrogen atom reactions under single collision conditions possible. 18 refs., 9 figs.

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

    E-print Network

    Labushev, Mikhail M

    2012-01-01

    The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

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

    E-print Network

    Mikhail M. Labushev

    2012-06-20

    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.

  15. Atomic structure of Beta-tantalum nanocrystallites.

    PubMed

    Tillmann, Karsten; Thust, Andreas; Gerber, Andreas; Weides, Martin P; Urban, Knut

    2005-12-01

    The structural properties of beta-phase tantalum nanocrystallites prepared by room temperature magnetron sputter deposition on amorphous carbon substrates are investigated at atomic resolution. For these purposes spherical aberration-corrected high-resolution transmission electron microscopy is applied in tandem with the numerical retrieval of the exit-plane wavefunction as obtained from a through-focus series of experimental micrographs. We demonstrate that recent improvements in the resolving power of electron microscopes enable the imaging of the atomic structure of beta-tantalum with column spacings of solely 0.127 nm with directly interpretable contrast features. For the first time ever, we substantiate the existence of grain boundaries of 30 degrees tilt type in beta-Ta whose formation may be well explained by atomic agglomeration processes taking place during sputter deposition. PMID:17481332

  16. Unraveling the Molecular Structures of Asphaltenes by Atomic Force Microscopy.

    PubMed

    Schuler, Bruno; Meyer, Gerhard; Peña, Diego; Mullins, Oliver C; Gross, Leo

    2015-08-12

    Petroleum is one of the most precious and complex molecular mixtures existing. Because of its chemical complexity, the solid component of crude oil, the asphaltenes, poses an exceptional challenge for structure analysis, with tremendous economic relevance. Here, we combine atomic-resolution imaging using atomic force microscopy and molecular orbital imaging using scanning tunnelling microscopy to study more than 100 asphaltene molecules. The complexity and range of asphaltene polycyclic aromatic hydrocarbons are established in detail. Identifying molecular structures provides a foundation to understand all aspects of petroleum science from colloidal structure and interfacial interactions to petroleum thermodynamics, enabling a first-principles approach to optimize resource utilization. Particularly, the findings contribute to a long-standing debate about asphaltene molecular architecture. Our technique constitutes a paradigm shift for the analysis of complex molecular mixtures, with possible applications in molecular electronics, organic light emitting diodes, and photovoltaic devices. PMID:26170086

  17. Pd(0.213)Cd(0.787) and Pd(0.235)Cd(0.765) structures: their long c axis and composite crystals, chemical twinning, and atomic site preferences.

    PubMed

    Schmidt, Joshua Teal; Lee, Stephen; Fredrickson, Daniel C; Conrad, Matthias; Sun, Junliang; Harbrecht, Bernd

    2007-01-01

    We present single-crystal studies of Pd(0.213)Cd(0.787) and Pd(0.235)Cd(0.765), synchrotron powder studies of Pd(1-x)Cd(x), 0.755> or =x> or =0.800, and LDA-DFT and extended Hückel (eH) calculations on these or related phases. The two single-crystal structures have a, b, and c axis lengths of 9.9013(7), 14.0033(10), 37.063(24) and 9.9251(3), 14.0212(7), 60.181(3) A, respectively and they crystallize in the space groups Ccme and F2mm, respectively (solved as (3+1)-dimensional crystals their most convenient superspace group is Xmmm(00gamma)s00). The structures have two different structural components each with their own separate axis parameters. Powder data shows that the ratio of these separate axes (S/L) varies from 1.615 to 1.64, values near the golden mean (1.618). For Pd(0.213)Cd(0.787), different Pd and Cd site occupancies lead to variation in the R factor from 2.6-3.6 %. The site occupancy pattern with the lowest R factor (among the 26 820 variants studied) is the exact site occupancy pattern predicted by LDA-DFT parameterized eH Mulliken charge populations. The phases can be understood through a chemical twinning principle found in gamma-brass, the parent structure for the above phases (a relation with the MgCu(2) Laves phase is also noted). This twinning principle can be used to account for Cd and Pd site preferences. At the same time there is a clean separation among the Cd and Pd atoms for the two separate chain types at height b=0 and 1/2. These results indicate that Cd:Pd stoichiometry plays a role in phase stability. PMID:17091515

  18. Structural materials: understanding atomic scale microstructures

    SciTech Connect

    Marquis, E A; Miller, Michael K; Blavette, D; Ringer, S. P.; Sudbrack, C; Smith, G.D.W.

    2009-01-01

    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.

  19. Atomic Structure Calculations from the Los Alamos Atomic Physics Codes

    DOE Data Explorer

    Cowan, R. D.

    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.

  20. Atomic Resolution Imaging and Quantification of Chemical Functionality of Surfaces

    SciTech Connect

    Schwarz, Udo

    2014-12-10

    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.

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

    E-print Network

    Budker, Dmitry

    "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

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

    E-print Network

    Heyrovska, Raji

    2008-01-01

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

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

    E-print Network

    Raji Heyrovska

    2008-06-21

    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.

  4. Atomic structure of highly ordered pyrolytic graphite doped with boron

    E-print Network

    Kwak, Juhyoun

    Atomic structure of highly ordered pyrolytic graphite doped with boron Eunkyung Kim, Ilwhan Oh substitute for the carbon atom in the graphite structure and promote the graphitization of pyrolytic graphite pyrolytic graphite (HOPG). The eect of the boron doping on the atomic structure of HOPG would be discussed

  5. An Atomic Environment Potential for use in Protein Structure Prediction

    E-print Network

    Summa, Christopher M.

    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

  6. Atoms of multistationarity in chemical reaction networks Badal Joshi and Anne Shiu

    E-print Network

    Rowell, Eric C.

    Atoms of multistationarity in chemical reaction networks Badal Joshi and Anne Shiu 13 July 2012 Abstract Chemical reaction systems are dynamical systems that arise in chemical engineering and systems) multistationary chemical reaction networks, which we propose to call `atoms of multistationarity,' characterize

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

    PubMed

    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

    2013-04-01

    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

  8. The electronic structure and chemical bonding of vitamin B12

    NASA Astrophysics Data System (ADS)

    Kurmaev, E. Z.; Moewes, A.; Ouyang, L.; Randaccio, L.; Rulis, P.; Ching, W. Y.; Bach, M.; Neumann, M.

    2003-05-01

    The electronic structure and chemical bonding of vitamin B12 (cyanocobalamin) and B12-derivative (methylcobalamin) are studied by means of X-ray emission (XES) and photoelectron (XPS) spectroscopy. The obtained results are compared with ab initio electronic structure calculations using the orthogonalized linear combination of the atomic orbital method (OLCAO). We show that the chemical bonding in vitamin B12 is characterized by the strong Co-C bond and relatively weak axial Co-N bond. It is further confirmed that the Co-C bond in cyanocobalamin is stronger than that of methylcobalamin resulting in their different biological activity.

  9. Measurement of atomic indium during metalorganic chemical vapor deposition

    SciTech Connect

    Hebner, G.A.; Killeen, K.P. )

    1990-02-01

    Atomic indium, produced by the pyrolysis of trimethylindium (TMIn) during metalorganic chemical vapor deposition, has been directly observed using resonant fluorescence spectroscopy. The indium fluorescence signal is linear with TMIn flow rate at a susceptor temperature of 500 {degree}C above a small background threshold level. The threshold for the observation of an indium signal is 325 {degree}C. Addition of trimethylantimony (TMSb) at concentrations less than those required for normal InSb epitaxial growth results in quenching of the indium signal.

  10. Style for chemical structures in Nature Chemical Biology CONNECTIVITY

    E-print Network

    Napp, Nils

    Style for chemical structures in Nature Chemical Biology CONNECTIVITY · All bonds should be connected to each other (no gaps between bonds). The primary exception is when a double bond is at the end of a chain. · Discrete bonds should be shown rather than rings. The primary exception

  11. Progress in Visualizing Atomic Size Effects with DFT-Chemical Pressure Analysis: From Isolated Atoms to Trends in AB5 Intermetallics.

    PubMed

    Berns, Veronica M; Engelkemier, Joshua; Guo, Yiming; Kilduff, Brandon J; Fredrickson, Daniel C

    2014-08-12

    The notion of atomic size poses an important challenge to chemical theory: empirical evidence has long established that atoms have spatial requirements, which are summarized in tables of covalent, ionic, metallic, and van der Waals radii. Considerations based on these radii play a central role in the design and interpretation of experiments, but few methods are available to directly support arguments based on atomic size using electronic structure methods. Recently, we described an approach to elucidating atomic size effects using theoretical calculations: the DFT-Chemical Pressure analysis, which visualizes the local pressures arising in crystal structures from the interactions of atomic size and electronic effects. Using this approach, a variety of structural phenomena in intermetallic phases have already been understood in terms that provide guidance to new synthetic experiments. However, the applicability of the DFT-CP method to the broad range of the structures encountered in the solid state is limited by two issues: (1) the difficulty of interpreting the intense pressure features that appear in atomic core regions and (2) the need to divide space among pairs of interacting atoms in a meaningful way. In this article, we describe general solutions to these issues. In addressing the first issue, we explore the CP analysis of a test case in which no core pressures would be expected to arise: isolated atoms in large boxes. Our calculations reveal that intense core pressures do indeed arise in these virtually pressure-less model systems and allow us to trace the issue to the shifts in the voxel positions relative to atomic centers upon expanding and contracting the unit cell. A compensatory grid unwarping procedure is introduced to remedy this artifact. The second issue revolves around the difficulty of interpreting the pressure map in terms of interatomic interactions in a way that respects the size differences of the atoms and avoids artificial geometrical constraints. In approaching this challenge, we have developed a scheme for allocating the grid pressures to contacts inspired by the Hirshfeld charge analysis. Here, each voxel is allocated to the contact between the two atoms whose free atom electron densities show the largest values at that position. In this way, the differing sizes of atoms are naturally included in the division of space without resorting to empirical radii. The use of the improved DFT-CP method is illustrated through analyses of the applicability of radius ratio arguments to Laves phase structures and the structural preferences of AB5 intermetallics between the CaCu5 and AuBe5 structure types. PMID:26588306

  12. Atom structures of cylindric algebras and relation algebras

    E-print Network

    Hodkinson, Ian

    Atom structures of cylindric algebras and relation algebras Ian Hodkinson This is the revised 3 there are two atomic n-dimensional cylindric algebras with the same atom structure, with one cylindric algebra is not always representable, so that the class RCAn of representable n

  13. A PVM Implementation of the MCHF Atomic Structure Package

    E-print Network

    Stathopoulos, Andreas

    A PVM Implementation of the MCHF Atomic Structure Package Andreas Stathopoulos, Anders Ynnerman) is one of the most powerful approaches for atomic structure calculations. The MCHF package consists The MCHF package is a suite of programs that provide the atomic data required by many science

  14. An Atomic Resolution Structure for Human Fibroblast Growth Factor 1

    E-print Network

    Blaber, Michael

    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-Å atomic resolution X

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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.

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

    E-print Network

    Maurice R. Kibler

    2008-01-08

    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.

  17. Electronic Structure of Superheavy Atoms. Revisited

    E-print Network

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

    2012-05-01

    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

  18. Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.

    PubMed

    Knizia, Gerald

    2013-11-12

    Modern quantum chemistry can make quantitative predictions on an immense array of chemical systems. However, the interpretation of those predictions is often complicated by the complex wave function expansions used. Here we show that an exceptionally simple algebraic construction allows for defining atomic core and valence orbitals, polarized by the molecular environment, which can exactly represent self-consistent field wave functions. This construction provides an unbiased and direct connection between quantum chemistry and empirical chemical concepts, and can be used, for example, to calculate the nature of bonding in molecules, in chemical terms, from first principles. In particular, we find consistency with electronegativities (?), C 1s core-level shifts, resonance substituent parameters (?R), Lewis structures, and oxidation states of transition-metal complexes. PMID:26583402

  19. Watching Atoms Work: Nanocluster Structure and Dynamics.

    PubMed

    Pennycook, Stephen J; Zhou, Wu; Pantelides, Sokrates T

    2015-10-27

    In the space of little more than a decade, the resolution of the electron microscope has improved to provide clear views of the atomic world. Not only can atomic arrangements be imaged, but with a little gentle provocation from the electron beam, atoms can be energized and their dynamics can also be revealed. In this issue of ACS Nano, Chen et al. image Si atoms growing under the beam into cubic crystalline arrangements. PMID:26407002

  20. Linear complexions: Confined chemical and structural states at dislocations.

    PubMed

    Kuzmina, M; Herbig, M; Ponge, D; Sandlöbes, S; Raabe, D

    2015-09-01

    For 5000 years, metals have been mankind's most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states. PMID:26339026

  1. Linear complexions: Confined chemical and structural states at dislocations

    NASA Astrophysics Data System (ADS)

    Kuzmina, M.; Herbig, M.; Ponge, D.; Sandlöbes, S.; Raabe, D.

    2015-09-01

    For 5000 years, metals have been mankind’s most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states.

  2. Arithmetic Aspects of Atomic Structures Charles L. Fefferman

    E-print Network

    Seco, Luis A.

    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

  3. Chemical Structure Handling by Computer.

    ERIC Educational Resources Information Center

    Paris, C. Gregory

    1997-01-01

    Organized from the viewpoint of information retrieval theory, this review addresses issues of chemical information representation, comparison and matching, and retrieval strategies. Additional topics include similarity and clustering, visualization, and molecular diversity. Trends in research and application are identified, and gaps in the…

  4. An atomic structure of human ?-secretase

    NASA Astrophysics Data System (ADS)

    Bai, Xiao-Chen; Yan, Chuangye; Yang, Guanghui; Lu, Peilong; Ma, Dan; Sun, Linfeng; Zhou, Rui; Scheres, Sjors H. W.; Shi, Yigong

    2015-09-01

    Dysfunction of the intramembrane protease ?-secretase is thought to cause Alzheimer's disease, with most mutations derived from Alzheimer's disease mapping to the catalytic subunit presenilin 1 (PS1). Here we report an atomic structure of human ?-secretase at 3.4 Å resolution, determined by single-particle cryo-electron microscopy. Mutations derived from Alzheimer's disease affect residues at two hotspots in PS1, each located at the centre of a distinct four transmembrane segment (TM) bundle. TM2 and, to a lesser extent, TM6 exhibit considerable flexibility, yielding a plastic active site and adaptable surrounding elements. The active site of PS1 is accessible from the convex side of the TM horseshoe, suggesting considerable conformational changes in nicastrin extracellular domain after substrate recruitment. Component protein APH-1 serves as a scaffold, anchoring the lone transmembrane helix from nicastrin and supporting the flexible conformation of PS1. Ordered phospholipids stabilize the complex inside the membrane. Our structure serves as a molecular basis for mechanistic understanding of ?-secretase function.

  5. Valence-Bond Theory and Chemical Structure.

    ERIC Educational Resources Information Center

    Klein, Douglas J.; Trinajstic, Nenad

    1990-01-01

    Discussed is the importance of valence bond theory on the quantum-mechanical theory of chemical structure and the nature of the chemical bond. Described briefly are early VB theory, development of VB theory, modern versions, solid-state applications, models, treatment in textbooks, and flaws in criticisms of valence bond theory. (KR)

  6. Atomic Structure of Benzene Which Accounts for Resonance Energy

    E-print Network

    Raji Heyrovska

    2008-07-09

    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.

  7. Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic Representations

    E-print Network

    Brutlag, Doug

    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

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

    NASA Astrophysics Data System (ADS)

    Kim, Duckhoe; Sahin, Ozgur

    2015-03-01

    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.

  9. A Variational Monte Carlo Approach to Atomic Structure

    ERIC Educational Resources Information Center

    Davis, Stephen L.

    2007-01-01

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

  10. The Complete Atomic Structure of the Large Ribosomal Subunit

    E-print Network

    Sereno, Martin

    The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution Nenad Ban,1 * Poul is approximately twice the molecular weight of the smaller (2). The small subunit, which sediments at 30S. Because the structures of several DNA and RNA polymerases have been determined at atomic resolution

  11. Atomic and electronic structures of an extremely fragile liquid

    PubMed Central

    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

    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

  12. Muonic atoms and the nuclear structure

    E-print Network

    Antognini, Aldo

    2015-01-01

    High-precision laser spectroscopy of atomic energy levels enables the measurement of nuclear properties. Sensitivity to these properties is particularly enhanced in muonic atoms which are bound systems of a muon and a nucleus. Exemplary is the measurement of the proton charge radius from muonic hydrogen performed by the CREMA collaboration which resulted in an order of magnitude more precise charge radius as extracted from other methods but at a variance of 7 standard deviations. Here, we summarize the role of muonic atoms for the extraction of nuclear charge radii, we present the status of the so called "proton charge radius puzzle", and we sketch how muonic atoms can be used to infer also the magnetic nuclear radii, demonstrating again an interesting interplay between atomic and particle/nuclear physics.

  13. Structural and Chemical Dynamics of Pyridinic-Nitrogen Defects in Graphene.

    PubMed

    Lin, Yung-Chang; Teng, Po-Yuan; Yeh, Chao-Hui; Koshino, Masanori; Chiu, Po-Wen; Suenaga, Kazu

    2015-11-11

    High density and controllable nitrogen doping in graphene is a critical issue to realize high performance graphene-based devices. In this paper, we demonstrate an efficient method to selectively produce graphitic-N and pyridinic-N defects in graphene by using the mixture plasma of ozone and nitrogen. The atomic structure, electronic structure, and dynamic behavior of these nitrogen defects are systematically studied at the atomic level by using a scanning transmission electron microscopy. The pyridinic-N exhibits higher chemical activity and tends to trap a series of transition metal atoms (Mg, Al, Ca, Ti, Cr, Mn, and Fe) as individual atoms. PMID:26488153

  14. Surface structure, composition, and polarity of indium nitride grown by high-pressure chemical vapor deposition

    E-print Network

    Dietz, Nikolaus

    grown by high-pressure chemical vapor deposition have been studied. Atomic hydrogen cleaning produced and heterostructures--which can be accomplished by low- pressure metalorganic chemical vapor deposition MOCVD --the- rium vapor pressure of nitrogen during growth. This requires different approaches in growing structures

  15. Interlayer Potassium And Its Neighboring Atoms in Micas: Crystal-Chemical Modeling And Xanes Spectroscopy

    SciTech Connect

    Brigatti, M.F.; Malferrari, D.; Poppi, M.; Mottana, A.; Cibin, G.; Marcelli, A.; Cinque, G.

    2009-05-12

    A detailed description of the interlayer site in trioctahedral true micas is presented based on a statistical appraisal of crystal-chemical, structural, and spectroscopic data determined on two sets of trioctahedral micas extensively studied by both X-ray diffraction refinement on single crystals (SC-XRD) and X-ray absorption fine spectroscopy (XAFS) at the potassium K-edge. Spectroscopy was carried out on both random powders and oriented cleavage flakes, the latter setting taking advantage of the polarized character of synchrotron radiation. Such an approach (AXANES) is shown to be complementary to crystal-chemical investigation based on SC-XRD refinement. However, the results are not definitive as they focus on few samples having extreme features only (e.g., end-members, unusual compositions, and samples with extreme and well-identified substitution mechanisms). The experimental absorption K-edge (XANES) for potassium was decomposed by calculation and extrapolated into a full in-plane absorption component ({sigma}{parallel}) and a full out-of-plane absorption component ({sigma}{perpendicular}). These two patterns reflect different structural features: {sigma}{parallel}represents the arrangement of the atoms located in the mica interlayer space and facing tetrahedral sheets; {sigma}{perpendicular} is associated with multiple-scattering interactions entering deep into the mica structure, thus also reflecting interactions with the heavy atoms (essentially Fe) located in the octahedral sheet. The out-of-plane patterns also provide insights into the electronic properties of the octahedral cations, such as their oxidation states (e.g., Fe{sup 2+} and Fe{sup 3+}) and their ordering (e.g., trans- vs. cis-setting). It is also possible to distinguish between F- and OH-rich micas due to peculiar absorption features originating from the F vs. OH occupancy of the O4 octahedral site. Thus, combining crystal-chemical, structural, and spectroscopic information is shown to be a practical method that allows, on one hand, assignment of the observed spectroscopic features to precise structural pathways followed by the photoelectron within the mica structure and, on the other hand, clarification of the amount of electronic interactions and forces acting onto the individual atoms at the various structural sites.

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

    E-print Network

    Heyrovska, Raji

    2008-01-01

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

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

    E-print Network

    Raji Heyrovska; Saraswathi Narayan

    2008-01-28

    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.

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

    SciTech Connect

    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

    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.

  19. Synthesis of multiferroic Er-Fe-O thin films by atomic layer and chemical vapor deposition

    SciTech Connect

    Mantovan, R. Vangelista, S.; Wiemer, C.; Lamperti, A.; Tallarida, G.; Chikoidze, E.; Dumont, Y.; Fanciulli, M.

    2014-05-07

    R-Fe-O (R?=?rare earth) compounds have recently attracted high interest as potential new multiferroic materials. Here, we report a method based on the solid-state reaction between Er{sub 2}O{sub 3} and Fe layers, respectively grown by atomic layer deposition and chemical vapor deposition, to synthesize Er-Fe-O thin films. The reaction is induced by thermal annealing and evolution of the formed phases is followed by in situ grazing incidence X-ray diffraction. Dominant ErFeO{sub 3} and ErFe{sub 2}O{sub 4} phases develop following subsequent thermal annealing processes at 850?°C in air and N{sub 2}. Structural, chemical, and morphological characterization of the layers are conducted through X-ray diffraction and reflectivity, time-of-flight secondary ion-mass spectrometry, and atomic force microscopy. Magnetic properties are evaluated by magnetic force microscopy, conversion electron Mössbauer spectroscopy, and vibrating sample magnetometer, being consistent with the presence of the phases identified by X-ray diffraction. Our results constitute a first step toward the use of cost-effective chemical methods for the synthesis of this class of multiferroic thin films.

  20. Synthesis of multiferroic Er-Fe-O thin films by atomic layer and chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Mantovan, R.; Vangelista, S.; Wiemer, C.; Lamperti, A.; Tallarida, G.; Chikoidze, E.; Dumont, Y.; Fanciulli, M.

    2014-05-01

    R-Fe-O (R = rare earth) compounds have recently attracted high interest as potential new multiferroic materials. Here, we report a method based on the solid-state reaction between Er2O3 and Fe layers, respectively grown by atomic layer deposition and chemical vapor deposition, to synthesize Er-Fe-O thin films. The reaction is induced by thermal annealing and evolution of the formed phases is followed by in situ grazing incidence X-ray diffraction. Dominant ErFeO3 and ErFe2O4 phases develop following subsequent thermal annealing processes at 850 °C in air and N2. Structural, chemical, and morphological characterization of the layers are conducted through X-ray diffraction and reflectivity, time-of-flight secondary ion-mass spectrometry, and atomic force microscopy. Magnetic properties are evaluated by magnetic force microscopy, conversion electron Mössbauer spectroscopy, and vibrating sample magnetometer, being consistent with the presence of the phases identified by X-ray diffraction. Our results constitute a first step toward the use of cost-effective chemical methods for the synthesis of this class of multiferroic thin films.

  1. Chemical structure and dynamics. Annual report 1995

    SciTech Connect

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

    1996-05-01

    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.

  2. Chemical structure and dynamics: Annual report 1996

    SciTech Connect

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

    1997-03-01

    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.

  3. Annual Report 2000. Chemical Structure and Dynamics

    SciTech Connect

    Colson, Steven D.; McDowell, Robin S.

    2001-04-15

    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.

  4. Theory of quasicrystal surfaces: Probing the chemical reactivity by atomic and molecular adsorption

    NASA Astrophysics Data System (ADS)

    Kraj?í, M.; Hafner, J.

    The adsorption of oxygen and carbon atoms and of carbon monoxide molecules on a fivefold surface of icosahedral Al-Pd-Mn quasicrystals has been investigated using ab initio density-functional calculations. The quasicrystalline surface has been modeled by periodically repeated slabs cut from rational approximants to the quasicrystalline structure. Atomic and molecular adsorption have been studied for a large number of possible adsorption sites by performing three-dimensional static relaxations of the adsorbate/substrate complex. Four different scenarios for the dissociative adsorption of the CO molecule have been investigated via nudged-elastic band calculations of the transition states. Al and Mn-metal atoms present at the surface bind C and O atoms rather strongly, while Pd atoms are unstable adsorption sites: during relaxation, the adsorbate drifts to the nearest strong-binding site. The chemical reactivity with respect to a CO molecule varies very strongly across the surface. The adsorption close to Mn sites is promoted by rather strong covalent effects, but CO is only physisorbed at Al sites via weak polarization forces. On the basis of the observed local variations of the adsorption strength, we develop scenarios for dissociation and determine the potential energy barriers for this processes. We find that CO adsorbed close to a transition-metal atom can dissociate via an activated process, but the dissociation rate is expected to be rather low because of a high dissociation barrier and a "late" transition state. CO adsorbed close to Al atoms will desorb before dissociation. Surface vacancies present as a consequence of the irregular coordination of the Mackay cluster in the quasiperiodic structure will act as strongly attractive traps for diffusing molecules. Mn surface atoms are located in the center of truncated Mackay clusters. In scanning tunneling electron microscopy (STM) these truncated clusters are imaged as "white flowers". Surface vacancies are responsible for the "dark stars" in the STM images. Since both are molecular adsorption sites, our study predicts that these characteristic features should be affected by CO adsorption.

  5. ProCS15: a DFT-based chemical shift predictor for backbone and C? atoms in proteins

    PubMed Central

    Larsen, Anders S.; Bratholm, Lars A.; Christensen, Anders S.; Channir, Maher

    2015-01-01

    We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and C? atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. PMID:26623185

  6. Probing Atomic Dynamics and Structures Using Optical Patterns

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2015-05-01

    Pattern formation is a widely studied phenomenon that can provide fundamental insights into nonlinear systems. Emergent patterns in cold atoms are of particular interest in condensed matter physics and quantum information science because one can relate optical patterns to spatial structures in the atoms. In our experimental system, we study multimode optical patterns generated from a sample of cold, thermal atoms. We observe this nonlinear optical phenomenon at record low input powers due to the highly nonlinear nature of the spatial bunching of atoms in an optical lattice. We present a detailed study of the dynamics of these bunched atoms during optical pattern formation. We show how small changes in the atomic density distribution affect the symmetry of the generated patterns as well as the nature of the nonlinearity that describes the light-atom interaction. We gratefully acknowledge the financial support of the National Science Foundation through Grant #PHY-1206040.

  7. Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures

    USGS Publications Warehouse

    Dowty, Eric; Clark, J.R.

    1972-01-01

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

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

    ERIC Educational Resources Information Center

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

    2014-01-01

    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…

  9. The PubChem chemical structure sketcher

    PubMed Central

    2009-01-01

    PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

  10. Fine structure changing collisions between ultra-cold lithium atoms

    SciTech Connect

    Anderson, B.P.; Ritchie, N.W.M.; Xiao, Y.Y.

    1992-12-01

    The authors have designed and assembled an experiment to determine the rate of fine structure changing collisions between ultra-cold ({approximately} 1 mK) laser cooled Li atoms. The atoms are confined by a magneto-optical trap which consists of six polarized orthogonal laser beams tuned slightly below the 2S{sub 1/2}-2P{sub 3/2} resonance frequency of lithium. Measurements show that about 2 x 10{sup 7} atoms are confined to a roughly spherical region of about 1 mm in diameter. Fine structure changing collisions occur when an atom in the 2S{sub 1/2} state and an atom in the 2P{sub 3/2} state collide, and yield an atom in the 2S{sub 1/2} state and an atom in the 2P{sub 1/2} state, with an energy release corresponding to about 10 GHz. This energy adds kinetic energy to the atoms in the trap, and knocks atoms out of the trap. The authors have devised a method to measure the rate of this collisional loss mechanism. The method uses a laser diode and a dye laser to selectively photo-ionize the 2P{sub 1/2} atoms, and a channeltron particle multipiler measures the rate of ion formation. We will report the progress of this experiment.

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

    SciTech Connect

    Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38?n} (0 ? n ? 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atoms are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.

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

    NASA Astrophysics Data System (ADS)

    Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-01

    Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, AunPt38-n (0 ? n ? 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atoms are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold's. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.

  13. Presentation of Atomic Structure in Turkish General Chemistry Textbooks

    ERIC Educational Resources Information Center

    Niaz, Mansoor; Costu, Bayram

    2009-01-01

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

  14. Atomic Structure, Binding Energy, and Magnetic Properties of Iron Atoms Supported on Polyaromatic Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Senapati, L.; Nayak, S. K.; Rao, B. K.; Jena, P.

    2002-03-01

    The atomic structure, energetics, and properties of gas-phase cluster complexes containing coronene (C_12H_12) molecule and up to two iron atoms are studied for the first time using density functional theory and generalized gradient approximation for exchange and correlation. The geometries of the neutral and cationic iron-coronene complexes are optimized without symmetry constraint and by examining the possibility that iron atoms could occupy various sites via individual ? or bridging interactions. In both neutral and cationic complexes a single Fe atom is found to preferentially occupy the on-top site above the outer ring, while two Fe atoms dimerize and bind to outer bridge sites. The binding energy of neutral Fe_2-Coronene defined with respect to dissociation into coronene and Fe2 is larger than that of Fe-coronene while reverse is true for the corresponding cations. The ionization potentials of these complexes are not very sensitive to the number of adsorbed Fe atoms, but are significantly reduced from those of the Fe atom or the coronene molecule. The coupling between the Fe atoms remains ferromagnetic although the magnetic moment/atom is reduced from the free-atom value.

  15. Atomic structure, binding energy, and magnetic properties of iron atoms supported on a polyaromatic hydrocarbon

    NASA Astrophysics Data System (ADS)

    Senapati, L.; Nayak, S. K.; Rao, B. K.; Jena, P.

    2003-05-01

    The atomic structure, energetics, and properties of gas-phase cluster complexes containing coronene (C24H12) molecule and up to two iron atoms are studied for the first time using density functional theory and generalized gradient approximation for exchange and correlation. The geometries of the neutral and cationic iron-coronene complexes are optimized without symmetry constraint and by examining the possibility that iron atoms could occupy various sites via individual ? or bridging interactions. In both neutral and cationic complexes a single Fe atom is found to preferentially occupy the on-top site above the outer ring, while two Fe atoms dimerize and reside on the top of center of the outer rings. The binding energy of neutral Fe2-coronene defined with respect to dissociation into coronene and Fe2 is larger than that of Fe-coronene while reverse is true for the corresponding cations. Although the ionization potentials of these complexes are not very sensitive to the number of adsorbed Fe atoms, they are significantly reduced from those of the Fe atom or the coronene molecule. The photodecomposition of cationic (Fen-coronene)+ complexes proceeds through the ejection of either coronene+ or (Fe-coronene)+ cations while in the case of neutral Fe2-coronene, the ejection of Fe2 is energetically preferred. The coupling between the Fe atoms remains ferromagnetic although the magnetic moment/atom is reduced from the free-atom value. The results compare well with recent mass ion intensity and photofragmentation experiments.

  16. The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer

    PubMed Central

    Zheng, Mingyue; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

    2015-01-01

    Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer. PMID:26047514

  17. Nanoscale structure and transport : from atoms to devices

    E-print Network

    Evans, Matthew Hiram

    2005-01-01

    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 ...

  18. Relating Dynamic Properties to Atomic Structure in Metallic Glasses

    SciTech Connect

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

    2012-07-18

    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.

  19. Atomic structure of highly-charged ions. Final report

    SciTech Connect

    Livingston, A. Eugene

    2002-05-23

    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.

  20. Chemical Structure and Dynamics annual report 1997

    SciTech Connect

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

    1998-03-01

    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.

  1. Quantum chemical studies of protein structure

    PubMed Central

    Oldfield, Eric

    2004-01-01

    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

  2. Atomic Calligraphy: The Direct Writing of Nanoscale Structures using MEMS

    E-print Network

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

    2013-04-04

    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.

  3. First-principles study of the atomic-scale structure of clean silicon tips in dynamic force microscopy

    NASA Astrophysics Data System (ADS)

    Caciuc, V.; Hölscher, H.; Blügel, S.; Fuchs, H.

    2006-10-01

    In the present work we report on our ab initio pseudopotential calculations based on density functional theory to investigate the atomic-scale behavior of clean silicon tips in noncontact atomic force microscopy (AFM). The AFM tip structures are modeled by silicon clusters with [111] and [001] termination. The structural changes induced by their reciprocal interaction are investigated by calculating the short-range chemical forces during a vertical approach and retraction of one silicon tip on top of another tip. For a specific tip geometry with [111] termination, the theoretical force curves exhibit an hysteretic behavior only at the first approach and retraction cycle. The absence of this effect at the second scan is due to sharpening of the initially blunt tip via short-range chemical forces. A specific finger print of the [001]-oriented tip is an energy dissipation induced by a breaking and formation process of a chemical bond between two silicon atoms under its apex atom.

  4. Chemical profiling of silicon nitride structures

    NASA Technical Reports Server (NTRS)

    Vasquez, R. P.

    1989-01-01

    X ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (SE), and scanning electron microscopy (SEM) were used to study structural and chemical inhomogeneities in several electronic materials and device structures of relevance to radiation hard electronics. The systems studied include metal nitride oxide semiconductor (MNOS) structures, silicon oxynitride (SiO(x)N(y)) formed by the thermal nitridation of SiO2, and semiconductor on insulator (SOI) structures. Studies of MNOS structures suggest that the effect of H2 annealing is to make the Si3N4/SiO2 interface less abrupt by causing interdiffusion of silanol and silamine groups with subsequent oxynitride formation. Another effect of the annealing appears to be to relieve the strain at the SiO2/Si interface.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

    A model based on the continuous atomic density function (ADF) approach is applied to predict the atomic structure of grain boundaries (GBs) in iron. Symmetrical [100] and [110] tilt GBs in bcc iron are modeled with the ADF method and relaxed afterwards in molecular dynamics (MD) simulations. The shape of the GB energy curve obtained in the ADF model reproduces well the peculiarities of the angles of 70.53? [?3(112)] and 129.52? [?11(332)] for [110] tilt GBs. The results of MD relaxation with an embedded-atom method potential for iron confirm that the atomic GB configurations obtained in ADF modeling are very close to equilibrium ones. The developed model provides well-localized atomic positions for GBs of various geometries.

  6. Annual Report 1998: Chemical Structure and Dynamics

    SciTech Connect

    SD Colson; RS McDowell

    1999-05-10

    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).

  7. Chemical structure and dynamics. Annual report 1994

    SciTech Connect

    Colson, S.D.

    1995-07-01

    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.

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

    E-print Network

    Grütter, Peter

    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

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

    SciTech Connect

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

    2004-10-12

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

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

    ERIC Educational Resources Information Center

    Izquierdo-Aymerich, Merce; Aduriz-Bravo, Agustin

    2009-01-01

    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…

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

    ERIC Educational Resources Information Center

    Rittenhouse, Robert C.

    2015-01-01

    The "atoms first" philosophy, adopted by a growing number of General Chemistry textbook authors, places greater emphasis on atomic structure as a key to a deeper understanding of the field of chemistry. A pivotal concept needed to understand the behavior of atoms is the restriction of an atom's energy to specific allowed values. However,…

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

    PubMed Central

    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

    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

  13. Structural and chemical heterogeneity of natural crystals and microgeochemical line of research in ontogeny of minerals

    NASA Astrophysics Data System (ADS)

    Alekseev, V. I.; Marin, Yu. B.

    2012-12-01

    A review of the current state of genetic mineralogy in the field of the chemical heterogeneity of mineral individuals is presented. Due to advances in the local analysis of matter, the ontogenetic approach is now being focused on the chemical anatomy of minerals. A new line of research, microgeochemistry, deals with the migration of chemical elements in natural crystals caused by defects in the crystal lattice. It becomes evident that structural and chemical heterogeneity is an intrinsic property of mineral individuals. Phenomenological laws of this heterogeneity and the interaction of atoms with lattice defects are stated.

  14. Sensitivity of chemical reaction networks: a structural approach.

    E-print Network

    Fiedler, Bernold

    Sensitivity of chemical reaction networks: a structural approach. 2. Regular monomolecular systems sensitivity of steady states to perturbations of reaction rates in chemical reaction networks. Strong structure of the metabolic or chemical reaction network, only, we call our approach a structural sensitivity

  15. Isotropic Inelastic Collisions in a Multiterm Atom with Hyperfine Structure

    NASA Astrophysics Data System (ADS)

    Belluzzi, Luca; Landi Degl'Innocenti, Egidio; Trujillo Bueno, Javier

    2015-10-01

    A correct modeling of the scattering polarization profiles observed in some spectral lines of diagnostic interest, the sodium doublet being one of the most important examples, requires taking hyperfine structure (HFS) and quantum interference between different J-levels into account. An atomic model suitable for taking these physical ingredients into account is the so-called multiterm atom with HFS. In this work, we introduce and study the transfer and relaxation rates due to isotropic inelastic collisions with electrons, which enter the statistical equilibrium equations (SEE) for the atomic density matrix of this atomic model. Under the hypothesis that the electron-atom interaction is described by a dipolar operator, we provide useful relations between the rates describing the transfer and relaxation of quantum interference between different levels (whose numerical values are in most cases unknown) and the usual rates for the atomic level populations, for which experimental data and/or approximate theoretical expressions are generally available. For the particular case of a two-term atom with HFS, we present an analytical solution of the SEE for the spherical statistical tensors of the upper term, including both radiative and collisional processes, and we derive the expression of the emission coefficient in the four Stokes parameters. Finally, an illustrative application to the Na i D1 and D2 lines is presented.

  16. Vortex-ring-fractal Structure of Atom and Molecule

    SciTech Connect

    Osmera, Pavel

    2010-06-17

    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.

  17. The Chemical Bond and Quantum Mechanics* The behavior of electrons in molecules and atoms is described by

    E-print Network

    Rioux, Frank

    The Chemical Bond and Quantum Mechanics* The behavior of electrons in molecules and atoms) and delocalization (to reduce kinetic energy). 2/3 1/3 / /E KE PE A V B V= + - A bond will form between two atoms energy than the separate-atom distributions (atomic orbitals). An example is a covalent bond, in which

  18. Effect of Ion-Binding and Chemical Phospholipid Structure on the Nanomechanics of Lipid Bilayers Studied by Force Spectroscopy

    E-print Network

    Fernandez, Julio M.

    Effect of Ion-Binding and Chemical Phospholipid Structure on the Nanomechanics of Lipid Bilayers lipid bilayers has been studied by force spectroscopy with atomic force microscopy. We have needed to puncture a 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer with an atomic force microscope

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

    SciTech Connect

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

    2010-11-05

    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.

  20. Chemical compositions, methods of making the chemical compositions, and structures made from the chemical compositions

    DOEpatents

    Yang, Lei; Cheng, Zhe; Liu, Ze; Liu, Meilin

    2015-01-13

    Embodiments of the present disclosure include chemical compositions, structures, anodes, cathodes, electrolytes for solid oxide fuel cells, solid oxide fuel cells, fuel cells, fuel cell membranes, separation membranes, catalytic membranes, sensors, coatings for electrolytes, electrodes, membranes, and catalysts, and the like, are disclosed.

  1. Atomic Parity Nonconservation: Electroweak Parameters and Nuclear Structure

    E-print Network

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

    1992-11-05

    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.

  2. High carrier mobility in chemically modified graphene on an atomically flat high-resistive substrate

    NASA Astrophysics Data System (ADS)

    Kotin, I. A.; Antonova, I. V.; Komonov, A. I.; Seleznev, V. A.; Soots, R. A.; Prinz, V. Ya

    2013-07-01

    Special high-resistive substrates for graphene sheets are suggested with the aim of providing high conductivity and mobility of charge carriers in graphene. The substrates were created from N-methylpyrrolidone-intercalated few-layer graphene (FLG) using anneals given to FLG samples in the temperature range 100-180 °C. Structures containing a highly conductive single-layer graphene on an atomically flat, high-resistive substrate were produced by recovering the top-layer conductivity. The obtained structures have potential in electronic applications due to a high carrier mobility (up to 16?000-42?000 cm2 V-1 s-1) and strong gate-voltage-induced modulation (by 4-5 orders of magnitude) of the current in the top graphene layer. The strong gate-voltage-induced modulation of the current clearly demonstrated that the top layer was chemically modified graphene. The possibility of governing the surface conductivity in the described structures offers a unique tool for two-dimensional nanodesign.

  3. Solitonic fullerene structures in light atomic nuclei

    E-print Network

    R. A. Battye; P. M. Sutcliffe

    2001-02-16

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

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

  5. Local atomic structure around Ni, Nb, and Zr atoms in Ni-Nb-Zr-H glassy alloys

    NASA Astrophysics Data System (ADS)

    Oji, H.; Handa, K.; Ide, J.; Honma, T.; Umesaki, N.; Yamaura, S.; Fukuhara, M.; Inoue, A.; Emura, S.

    2009-11-01

    In order to elucidate the hydrogen effect on the atomic configuration in the Ni-Nb-Zr glassy alloys, we measured Ni, Nb, and Zr K-edge XAFS spectra of the Ni-Nb-Zr glassy alloy films with two different chemical compositions, i.e., Ni42Nb28Zr30 and Ni36Nb24Zr40, and their hydrogen-charged ones, i.e., (Ni42Nb28Zr30)0.91H0.09 and (Ni36Nb24Zr40)0.89H0.11. The Fourier transforms of the XAFS oscillations of these samples clearly shows that there is a significant difference in the structural response between the Zr30at.% and the Zr40at.% alloys when hydrogen atoms are charged. The curve-fitting analysis indicates that the hydrogenation does not alter the local alignment around the three metal atoms for the Zr30at.% alloy, but for the Zr40at.% alloy; it elongates the inter-atomic distances of Zr-Zr, Zr-Nb and Nb-Ni. On the basis of the curve fitting analysis, we propose the distorted icosahedral Zr5Ni5Nb3 cluster models. The XANES spectra at each (Ni, Zr and Nb) edge of (Ni36Nb24Zr40)0.89H0.11 also present the distinct shape from the other samples. The pre-edge peak (shoulder) vanishes or weakens, suggesting the conversion of the electronic state of the metal ions owing to the hydrogenation. The post-edge energy region shows clear multi-scattering effects from hydrogen atoms by charging these.

  6. Atomic and electronic structure of Ni-Nb metallic glasses

    SciTech Connect

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

    2013-12-07

    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.

  7. Chemical mapping of mammalian cells by atom probe tomography

    PubMed Central

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

    2012-01-01

    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

  8. 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)

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

    2015-01-01

    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.

  9. Atomic structure of Na-adsorbed Si(100) surfaces

    NASA Astrophysics Data System (ADS)

    Ko, Young-Jo; Chang, K. J.; Yi, Jae-Yel

    1995-02-01

    We examine the atomic and electronic structure of Na-adsorbed Si(100)-p(2×2) surfaces for various Na coverages (FTHETA) through first-principles pseudopotential calculations. At FTHETA=1/4, we find that the 4×1 structure with linear Na chains adsorbed on the valley bridge sites is energetically most stable, while substrate Si dimers are rearranged by buckling towards the Na chains. At FTHETA=1/2, the adsorption site of Na is the valley bridge site; however, the 2×2 structure is found to be more stable than the 2×1 structure. From the calculated formation energies, we suggest that the saturation coverage is one monolayer with the Na atoms occupying the pedestal and valley bridge sites, exhibiting a 2×1 reconstruction. The coverage dependences of surface geometry and work function are discussed.

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

    E-print Network

    Golovchenko, Jene A.

    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

  11. 1MSE 2090: Introduction to Materials Science Chapter 2, Bonding Review of Atomic Structure

    E-print Network

    Zhigilei, Leonid V.

    1MSE 2090: Introduction to Materials Science Chapter 2, Bonding · Review of Atomic Structure the individual atoms coalesce into larger structures and take on the characteristics and properties of many Chapter 2, Bonding Atoms = nucleus (protons and neutrons) + electrons Structure of atoms: Brief review

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

    SciTech Connect

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

    1988-12-01

    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.

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

    SciTech Connect

    Not Available

    1981-03-01

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

  14. Atomic structure of dislocation kinks in silicon R. W. Nunes

    E-print Network

    Vanderbilt, David

    Atomic structure of dislocation kinks in silicon R. W. Nunes Complex System Theory Branch, Naval excitations reconstruction defects and kinks of dislocations in silicon, using a linear-scaling density-matrix technique. The two predomi- nant dislocations the 90° and 30° partials are examined, focusing for the 90

  15. Spectroscopic Imaging STM: Atomic-Scale Visualization of Electronic Structure

    E-print Network

    Davis, James C.

    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

  16. On the structure of the interstellar atomic gas

    E-print Network

    P. Hennebelle; E. Audit

    2007-01-24

    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.

  17. The relativistic hydrogen atom: a theoretical laboratory for structure functions

    E-print Network

    X. Artru; K. Benhizia

    2006-01-17

    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

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

    PubMed

    Berns, Veronica M; Fredrickson, Daniel C

    2014-10-01

    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

  19. Ground State Hyperfine Structure of Muonic Helium Atom

    E-print Network

    A. A. Krutov; A. P. Martynenko

    2008-07-21

    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 \

  20. 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

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

    1982-09-02

    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.

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

    E-print Network

    Yukinori Nagatani

    2005-01-04

    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.

  2. Chemical weathering within high mountain depositional structures

    NASA Astrophysics Data System (ADS)

    Emberson, R.; Hovius, N.; Hsieh, M.; Galy, A.

    2013-12-01

    Material eroded from active mountain belts can spend extended periods in depositional structures within the mountain catchments before reaching its final destination. This can be in the form of colluvial fills, debris fans, or alluvial valley fills and terraces. The existence of these landforms is testament to the catastrophic nature of the events that lead to their formation. Sourced by landslides or debris flows, the material that forms them is in many cases either unweathered or incompletely weathered (e.g. Hsieh and Chyi 2010). Due to their porosity and permeability, these deposits likely serve as locations for extensive chemical weathering within bedrock landscapes. Recent studies considering the weathering flux from active mountain belts (e.g. Calmels et al. 2011) have distinguished between shallow and deep groundwater in terms of the contribution to the solute budget from a catchment; in this study we have attempted to more tightly constrain the sources of these groundwater components in the context of the previously mentioned depositional structures. We have collected water samples from a large number of sites within the Chen-you-lan catchment (370 km2) in central west Taiwan to elucidate the location of chemical weathering as well as how the sourcing of weathering products varies depending on the meteorological conditions. Central Taiwan has good attributes for this work considering both the extremely active tectonics and tropical climate, (including extensive cyclonic activity) which stimulate both extensive physical erosion (Dadson et al. 2003) and chemical weathering (Calmels et al. 2011). The Chen-you-lan catchment in particular contains some of the largest alluvial deposits inside the Taiwan mountain belt (Hsieh and Chyi 2010). Our preliminary results suggest that weathering within intramontane deposits may be a significant source of solutes, with the hyporheic systems within mountain rivers of particular import. This input of solutes occurs over relatively short length scales, with moderate increases in dissolved solutes over as little as 1km along the course of a river crossing a debris fan within the catchment. We hypothesise that debris fans and associated hyporheic regimes act as a filter of sorts, with the solute output from these sources being driven by dissolution and reprecipitation depending on the residence time of water within the vadose zone. This is controlled primarily by the prevailing seasonal weather: groundwater reservoirs are rapidly flushed during heavy precipitation associated with typhoons and tropical storms. In view of an expected increase of typhoon activity in the region, we propose that long-term monitoring of hydrological and chemical fluxes from mixed bedrock-alluvial mountain catchments can contribute to understanding of the impact of climate variability and change on Earth's carbon cycle.

  3. Challenges to the Structural Conception of Chemical Bonding

    E-print Network

    Weisberg, Michael

    Challenges to the Structural Conception of Chemical Bonding Michael Weisberg University's viability. Crucial to chemical practice and discourse is the notion of the chemi- cal bond, specifically­H single bonds. While the chemical bond plays a central role in chemical predictions, interventions

  4. Experimental study of atomic structure in strong electromagnetic fields

    SciTech Connect

    Szoke, A.; Landen, O.L.; Perry, M.D. )

    1989-09-01

    We have measured the energy spectrum of photoelectrons emitted in multiphoton ionization of atoms by a short-pulse, tunable laser. The spectrum shows prominent resonances, confirming the observations of Freeman {ital et} {ital al}. (Phys. Rev. Lett. 59, 1092 (1987)). The study of the position and intensity of such resonances, as a function of laser wavelength and intensity, probes the structure of the atom in the presence of the strong electromagnetic field and allows their spectroscopic assignment. A systematic study of the ac Stark shift of one of the resonances, the 7{ital s}(3/2){degree} level of xenon, is presented.

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

    PubMed Central

    2013-01-01

    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

  6. Anomalous decay of an atom in structured band gap reservoirs

    E-print Network

    Filippo Giraldi; Francesco Petruccione

    2011-04-09

    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.

  7. Stable atomic structure of NiTi austenite

    SciTech Connect

    Zarkevich, Nikolai A; Johnson, Duane D

    2014-08-01

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

  8. Quantum Degeneracy in Atomic Point Contacts Revealed by Chemical Force and Conductance

    NASA Astrophysics Data System (ADS)

    Sugimoto, Yoshiaki; Ondrá?ek, Martin; Abe, Masayuki; Pou, Pablo; Morita, Seizo; Perez, Ruben; Flores, Fernando; Jelínek, Pavel

    2013-09-01

    Quantum degeneracy is an important concept in quantum mechanics with large implications to many processes in condensed matter. Here, we show the consequences of electron energy level degeneracy on the conductance and the chemical force between two bodies at the atomic scale. We propose a novel way in which a scanning probe microscope can detect the presence of degenerate states in atomic-sized contacts even at room temperature. The tunneling conductance G and chemical binding force F between two bodies both tend to decay exponentially with distance in a certain distance range, usually maintaining direct proportionality G?F. However, we show that a square relation G?F2 arises as a consequence of quantum degeneracy between the interacting frontier states of the scanning tip and a surface atom. We demonstrate this phenomenon on the Si(111)-(7×7) surface reconstruction where the Si adatom possesses a strongly localized dangling-bond state at the Fermi level.

  9. Collagen structure deciphered CAMBRIDGE, Mass.--For the first time, an MIT researcher's atom-by-atom study of the

    E-print Network

    Buehler, Markus J.

    Collagen structure deciphered CAMBRIDGE, Mass.--For the first time, an MIT researcher's atom-by-atom study of the deformation and fracture of collagen explains Nature's design of its most abundant protein material. It is due to the basis of the collagen structure that leads to its high strength and ability

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

    PubMed Central

    March, Norman H.; Parr, Robert G.

    1980-01-01

    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

  11. Catalytic activity of bimetallic catalysts highly sensitive to the atomic composition and phase structure at the nanoscale

    NASA Astrophysics Data System (ADS)

    Shan, Shiyao; Petkov, Valeri; Prasai, Binay; Wu, Jinfang; Joseph, Pharrah; Skeete, Zakiya; Kim, Eunjoo; Mott, Derrick; Malis, Oana; Luo, Jin; Zhong, Chuan-Jian

    2015-11-01

    The ability to determine the atomic arrangement in nanoalloy catalysts and reveal the detailed structural features responsible for the catalytically active sites is essential for understanding the correlation between the atomic structure and catalytic properties, enabling the preparation of efficient nanoalloy catalysts by design. Herein we describe a study of CO oxidation over PdCu nanoalloy catalysts focusing on gaining insights into the correlation between the atomic structures and catalytic activity of nanoalloys. PdCu nanoalloys of different bimetallic compositions are synthesized as a model system and are activated by a controlled thermochemical treatment for assessing their catalytic activity. The results show that the catalytic synergy of Pd and Cu species evolves with both the bimetallic nanoalloy composition and temperature of the thermochemical treatment reaching a maximum at a Pd : Cu ratio close to 50 : 50. The nanoalloys are characterized structurally by ex situ and in situ synchrotron X-ray diffraction, including atomic pair distribution function analysis. The structural data show that, depending on the bimetallic composition and treatment temperature, PdCu nanoalloys adopt two different structure types. One features a chemically ordered, body centered cubic (B2) type alloy consisting of two interpenetrating simple cubic lattices, each occupied with Pd or Cu species alone, and the other structure type features a chemically disordered, face-centered cubic (fcc) type of alloy wherein Pd and Cu species are intermixed at random. The catalytic activity for CO oxidation is strongly influenced by the structural features. In particular, it is revealed that the prevalence of chemical disorder in nanoalloys with a Pd : Cu ratio close to 50 : 50 makes them superior catalysts for CO oxidation in comparison with the same nanoalloys of other bimetallic compositions. However, the catalytic synergy can be diminished if the Pd50Cu50 nanoalloys undergo phase segregation into distinct chemically-ordered (B2-type) and disordered (fcc-type) domains. This finding is significant since it provides a rational basis for streamlining the design and preparation of Pd-based nanoalloy catalysts in terms of atomic structure and phase state.The ability to determine the atomic arrangement in nanoalloy catalysts and reveal the detailed structural features responsible for the catalytically active sites is essential for understanding the correlation between the atomic structure and catalytic properties, enabling the preparation of efficient nanoalloy catalysts by design. Herein we describe a study of CO oxidation over PdCu nanoalloy catalysts focusing on gaining insights into the correlation between the atomic structures and catalytic activity of nanoalloys. PdCu nanoalloys of different bimetallic compositions are synthesized as a model system and are activated by a controlled thermochemical treatment for assessing their catalytic activity. The results show that the catalytic synergy of Pd and Cu species evolves with both the bimetallic nanoalloy composition and temperature of the thermochemical treatment reaching a maximum at a Pd : Cu ratio close to 50 : 50. The nanoalloys are characterized structurally by ex situ and in situ synchrotron X-ray diffraction, including atomic pair distribution function analysis. The structural data show that, depending on the bimetallic composition and treatment temperature, PdCu nanoalloys adopt two different structure types. One features a chemically ordered, body centered cubic (B2) type alloy consisting of two interpenetrating simple cubic lattices, each occupied with Pd or Cu species alone, and the other structure type features a chemically disordered, face-centered cubic (fcc) type of alloy wherein Pd and Cu species are intermixed at random. The catalytic activity for CO oxidation is strongly influenced by the structural features. In particular, it is revealed that the prevalence of chemical disorder in nanoalloys with a Pd : Cu ratio close to 50 : 50 makes them superior catalysts for CO oxidation in co

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

    PubMed

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

    2015-02-20

    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

  13. 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)

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

    2014-02-01

    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.

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

    SciTech Connect

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

    2012-02-10

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

  15. PROTEIN STRUCTURE REPORT Atomic resolution structure of the

    E-print Network

    determined here also are in good agreement with the auto-cleavage mechanism described for the flagellar° ). These crystallographic studies provide structural insights into the conformational changes induced upon auto region that is highly conserved among YscU orthologs.7 The cytoplasmic domain of YscU undergoes auto

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

    E-print Network

    Li, Yunqi; Roy, Ambrish; Zhang, Yang

    2009-08-20

    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...

  17. Delta-doping of boron atoms by photoexcited chemical vapor deposition

    SciTech Connect

    Akazawa, Housei

    2012-03-15

    Boron delta-doped structures in Si crystals were fabricated by means of photoexcited chemical vapor deposition (CVD). Core electronic excitation with high-energy photons ranging from vacuum ultraviolet to soft x rays decomposes B{sub 2}H{sub 6} molecules into fragments. Combined with in situ monitoring by spectroscopic ellipsometry, limited number of boron hydrides can be delivered onto a Si(100) surface by using the incubation period before the formation of a solid boron film. The boron-covered surface is subsequently embedded in a Si cap layer by Si{sub 2}H{sub 6} photo-excited CVD. The crystallinity of the Si cap layer depended on its thickness and the substrate temperature. The evaluation of the boron depth profile by secondary ion mass spectroscopy revealed that boron atoms were confined within the delta-doped layer at a concentration of 2.5 x 10{sup 20} cm{sup -3} with a full width at half maximum of less than 9 nm, while the epitaxial growth of a 130-nm-thick Si cap layer was sustained at 420 deg. C.

  18. Direct structure determination by atomic-resolution incoherent STEM imaging

    SciTech Connect

    Nellist, P.D.; Xin, Y.; Pennycook, S.J.

    1997-11-01

    Use of a large, annular dark-field (ADF) detector in a scanning transmission electron microscope is shown to give images that can allow direct structure determination, being a convolution between the illuminating probe intensity and an object function localized at the atomic column positions. The ADF image is also shown to resolve crystal spacings more than twice smaller than the phase contrast point resolution limit of the microscope used, with sub-angstrom structural information being retrieved. ADF image of several semiconductor materials are studied.

  19. Atomic-scale recognition of surface structure and intercalation mechanism of Ti3C2X.

    PubMed

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

    2015-02-25

    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

  20. ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

    PubMed

    Fooshee, David; Andronico, Alessio; Baldi, Pierre

    2013-11-25

    Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu . PMID:24160861

  1. On hot atom non-equilibrium processes in laser chemistry and chemical lasers

    NASA Astrophysics Data System (ADS)

    Temkin, A. Ya.

    1986-09-01

    Hot atom reactions in laser chemistry and in the pumping of some kinds of chemical lasers are treated by the method of the non-equilibrium chemical kinetics proposed in previous works of the author. This method is based on the use of the multigroup approximation for the description of hot atom slowing down. The three-group approximation is applied to the kinetics of two hot H atom reactions with N 2O having different activation energies. The hot atoms are supposed to be produced by 248 nm excimer laser photolysis of HI and to have initial kinetic energies of 1.8907 and 0.95400 eV. The kinetics of these reactions and the dependence of the product yields on the rare gas concentration in the system are obtained. It was shown how the same formulae (with a change of symbols) can be applied to the description of the vibrotational level populations of product molecules. Some kinetic experiments are suggested to obtain the data necessary for the determination of the group constants. The hot atom kinetics of the chemical laser pumping made by the light of a flash-lamp (or of a laser) or by the particle beam is studied by use of the two-group approximation. A two-level model of the lasing molecule is employed. Lasing molecules are supposed to be produced by a hot atom reaction with the bulk molecules. The inverse population and its dependence on the rare gas concentration in the system are obtained. The possibility and usefulness of more complicated models (more energy groups and more molecular levels) are discussed.

  2. Atomic structure of antiphase domain boundaries of a thin Al2O3 film on NiAl(110).

    PubMed

    Kulawik, M; Nilius, N; Rust, H-P; Freund, H-J

    2003-12-19

    Line defects of a thin alumina film on NiAl(110) have been studied on the atomic level with scanning tunneling microscopy at 4 K. While boundaries between two reflection domains do not expose a characteristic structure, antiphase domain boundaries are well ordered. The latter boundaries result from the insertion of a row of O atoms, as atomically resolved images of the topmost oxygen layer show. The insertion occurs only in two of the three characteristic directions of the quasihexagonal O lattice. Depending on the direction, either straight or zigzagged boundaries form. An atomic characterization of line defects on the oxide surface is a first step to correlate their topographic structure and chemical activity. PMID:14754127

  3. Chemical and Structural Variations at Augite (100) Twin Boundaries

    NASA Astrophysics Data System (ADS)

    Zhang, S.; Veblen, D. R.

    2006-05-01

    Twins and stacking faults on (100) are far less abundant in calcic pyroxenes like augite than they are in low-Ca compositions, such as pigeonite and orthopyroxene. The paucity of such twinning in augite has been attributed to high energies associated with octahedral skew reversals in pyroxenes where the M2 site is occupied by cations larger than Mg or Fe (e.g., Ca, Na). Deformation-twin boundaries in augite occurring in a pyroxene granulite from Hamnoy, Lofoten, Norway, were examined using high-resolution transmission electron microscopy. HRTEM images are consistent with Ca depletion at (100) twin boundaries, which can be interpreted structurally as a single unit cell of the low-Ca protoenstatite structure, or one-half unit cell of orthopyroxene. The high-resolution images show that the augite (100) twin planes are coherent or semi-coherent and are, in some cases, associated with (100) stacking faults. Although some of the twin planes have only a single, 0.9-nm layer of Ca-depleted pyroxene, most of them have been replaced by several unit cells of low-Ca clinopyroxene (pigeonite or clinoenstatite) that apparently nucleated on the low-Ca twin plane. We predict that future energy-filtered compositional imaging (EFTEM) investigations will confirm that the simple twin boundaries are, in fact, depleted in Ca. These nanometer-scale, Ca-depleted twin planes, and the pigeonite lamellae that nucleate on them, may result from a protracted thermal high during deformation, or from a later, retrograde metamorphic event experienced by these rocks. The atomic structure at the deformation-twin boundaries is topologically identical to that of the (100) herringbone twin planes that are found almost universally in augite from basalts and gabbros. Future investigations of (100) twin planes in augite from basalts and gabbros therefore should indicate whether or not long annealing times are required for Ca depletion at (100) twin planes in high-Ca pyroxenes. These results also suggest that traditional structural models of twin boundaries in complex inorganic solids are oversimplified. In cases such as this, chemical diffusion results in a different chemical composition, and, no doubt, in concomitant structural variations in the vicinity of the twin plane, compared to that of the host structure.

  4. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS REMO: A new protocol to refine full atomic

    E-print Network

    Zhang, Yang

    proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS REMO: A new protocol to refine full atomic protein, an important intermediate step in protein structure predic- tion is to construct appropriate full atomic models, it is an important step to construct full atomic models from the reduced structure decoys. Most of the current full

  5. Author's personal copy Lowest-energy structures of 13-atom binary clusters: Do

    E-print Network

    Author's personal copy Lowest-energy structures of 13-atom binary clusters: Do icosahedral clusters is less clear in liquid alloys. We study the lowest-energy structures of 13-atom AxB13Àx Lennard the strategy taken by Frank [1], and determine the lower-energy structures of isolated 13- atom AxB13Àx Lennard

  6. Reconstructing Polyatomic Structures from Discrete XRays: NPCompleteness Proof for Three Atoms

    E-print Network

    Chrobak, Marek

    Reconstructing Polyatomic Structures from Discrete X­Rays: NP­Completeness Proof for Three Atoms tomography problem that arises in the study of the atomic structure of crystal lattices. A polyatomic molecules and for investigating the atomic structure of crystals. In particular, a technique called

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

    E-print Network

    Zhang, Yang

    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

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

    E-print Network

    Marks, Laurence D.

    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

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

    E-print Network

    Himpsel, Franz J.

    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

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

    E-print Network

    Himpsel, Franz J.

    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

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

    E-print Network

    Pennycook, Steve

    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

  12. Dynamic Load Balancing of Atomic Structure Programs on a PVM Cluster

    E-print Network

    Stathopoulos, Andreas

    Dynamic Load Balancing of Atomic Structure Programs on a PVM Cluster Andreas Stathopoulos \\Lambda structure. The resulting codes have already been used for large, break­through atomic structure calculations of atomic data required by many science and engineering disciplines. As a means of meeting its high compu

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

    E-print Network

    Das, Rhiju

    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

  14. Hyperfine structure of the metastable 3 P2 state of alkaline earth atoms as an accurate

    E-print Network

    Johnson, Walter R.

    Hyperfine structure of the metastable 3 P2 state of alkaline earth atoms as an accurate probe and electric hexadecapole moments. Here, using relativistic many-body methods of atomic structure the hyperfine structure of long-lived 3 P2 states of cold divalent atoms may facilitate extracting the so far

  15. The Meshless Dynamic Relaxation Techniques for Simulating Atomic Structures of Materials

    E-print Network

    Niewczas, Marek

    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

  16. Structural and chemical derivatization of graphene for electronics and sensing

    NASA Astrophysics Data System (ADS)

    Mohanty, Nihar Ranjan

    Graphene - a single atom thick two dimensional sheet of sp 2 bonded carbon atoms arranged in a honeycomb lattice - has shown great promise for both fundamental research & applications because of its unique electrical, optical, thermal, mechanical and chemical properties. Derivatization of graphene unlocks a plethora of novel properties unavailable to their pristine parent "graphene". In this dissertation we have synthesized various structural and chemical derivatives of graphene; characterized them in detail; and leveraged their exotic properties for diverse applications. We have synthesized protein/DNA/ethylenediamine functionalized derivatives of graphene via a HATU catalyzed amide reaction of primary-amine-containing moieties with graphene oxide (GO) -- an oxyfunctional graphene derivative. In contrast to non-specificity of graphene, this functionalization of GO has enabled highly specific interactions with analytes. Devices fabricated from the protein (concanavalin -- A) and DNA functionalized graphene derivatives were demonstrated to enable label-free, specific detection of bacteria and DNA molecules, respectively, with single quanta sensitivity. Room temperature electrical characterization of the sensors showed a generation of ˜ 1400 charge carriers for single bacterium attachment and an increase of 5.6 X 1012 charge carriers / cm2 for attachment of a single complementary strand of DNA. This work has shown for the first time the viability of graphene for bio-electronics and sensing at single quanta level. Taking the bio-interfacing of graphene to the next level, we demonstrate the instantaneous swaddling of a single live bacterium (Bacillus subtilis ) with several hundred sq. micron (˜ 600 mum2) areal protein-functionalized graphene sheets. The atomic impermeability and high yield strength of graphene resulted in hermetic compartmentalization of bacteria. This enabled preservation of the dimensional and topological characteristics of the bacterium against the degrading effects of harsh environments such as the ultrahigh vacuum (˜ 10-5 Torr) and high intensity electron beam (˜ 150 A/cm2) in a transmission electron microscope (TEM) column. While an unwrapped bacterium shrank by ˜ 76% and displayed significant charge buildup in the TEM column; a wrapped bacterium remained uncontracted and undamaged owing to the graphenic wraps. This work has shown for the first time an impermeable graphenic encasement of bacteria and its application in high vacuum TEM imaging without using any lengthy traditional biological TEM sample preparation techniques. In an inch-scale, we fabricated robust free-standing paper composed of TWEEN/Graphene composite which exhibited excellent chemical stability and mechanical strength. This paper displayed excellent biocompatibility towards three mammalian cell lines while inhibiting the non-specific binding of bacteria (Bacillus cereus). We predict this composite and its derivatives to have excellent applications in biomedical engineering for transplant devices, invasive instrument coatings and implants. We also demonstrate a novel, ultra-fast and high yield process for reducing GO to reduced graphene oxide (RGO) using a facile hydride-based chemistry. The RGO sheets thus-produced exhibited high carrier mobilities (˜ 100-600 cm2/V·s) and reinstatement of the ambipolar characteristic of graphene. Raman spectra and UV-Vis spectroscopy on the RGO sheets displayed a high degree of restoration of the crystalline sp2 lattice with relatively low defects. We fabricated graphene nanoribbons (GNRs) -- 1D structural derivatives of graphene -- using a nano-scale cutting process from highly oriented pyrolytic graphite (HOPG) blocks, with widths pre-determinable between 5 nm to 600 nm. The as-produced GNRs had very high aspect ratio in the longitudinal direction (˜ 0.01); exhibited predominantly mono-layered structure (< 10% bilayer); and smooth edges (Raman ID/G ˜ 0.25 -0.28). Low temperature electrical transport measurements on back-gated thin film GNR devices were performed and a ca

  17. Use of radiation effects for a controlled change in the chemical composition and properties of materials by intentional addition or substitution of atoms of a certain kind

    SciTech Connect

    Gurovich, B. A.; Prikhod'ko, K. E. Kuleshova, E. A.; Maslakov, K. I.; Komarov, D. A.

    2013-06-15

    This study is a continuation of works [1-12] dealing with the field developed by the authors, namely, to widen the possibilities of radiation methods for a controlled change in the atomic composition and properties of thin-film materials. The effects under study serve as the basis for the following two methods: selective atom binding and selective atom substitution. Such changes in the atomic composition are induced by irradiation by mixed beams consisting of protons and other ions, the energy of which is sufficient for target atom displacements. The obtained experimental data demonstrate that the changes in the chemical composition of thin-film materials during irradiation by an ion beam of a complex composition take place according to mechanisms that differ radically from the well-known mechanisms controlling the corresponding chemical reactions in these materials. These radical changes are shown to be mainly caused by the accelerated ioninduced atomic displacements in an irradiated material during irradiation; that is, they have a purely radiation nature. The possibilities of the new methods for creating composite structures consisting of regions with a locally changed chemical composition and properties are demonstrated for a wide class of materials.

  18. Atomic-scale structure of nancrystalline CeO{sub 2}-ZrO{sub 2} oxides by total x-ray diffraction and pair distribution function analysis.

    SciTech Connect

    Gateshki, M.; Niederberger, M.; Deshpande, A. S.; Ren, Y.; Petkov, V.; Central Michigan Univ.; Colloid Univ.

    2007-01-01

    Total x-ray diffraction and atomic pair distribution function analysis have been used to determine the atomic ordering in nanocrystalline ({approx}1.5 nm in size) CeO{sub 2}-ZrO{sub 2} prepared by a sol-gel route. Experimental data show that the oxides are a structurally and chemically inhomogeneous mixture of nanoscale domains with cubic-type and monoclinic-type atomic ordering, predominantly occupied by Ce and Zr atomic species, respectively. The study is another demonstration of the great potential of non-traditional crystallography in studying the structure of nanocrystalline materials.

  19. Analysis of weblike network structures of directed graphs for chemical reactions in methane plasmas

    NASA Astrophysics Data System (ADS)

    Sakai, Osamu; Nobuto, Kyosuke; Miyagi, Shigeyuki; Tachibana, Kunihide

    2015-10-01

    Chemical reactions of molecular gases like methane are so complicated that a chart of decomposed and/or synthesized species originating from molecules in plasma resembles a weblike network in which we write down species and reactions among them. Here we consider properties of the network structures of chemical reactions in methane plasmas. In the network, atoms/molecules/radical species are assumed to form nodes and chemical reactions correspond to directed edges in the terminology of graph theory. Investigation of the centrality index reveals importance of CH3 in the global chemical reaction, and difference of an index for each radical species between cases with and without electrons clarifies that the electrons are at an influential position to tighten the network structure.

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

    PubMed

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

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (?)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic ?-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  1. Quantitative metallography of structural materials with the atomic force microscope

    SciTech Connect

    Goeken, M.; Vehoff, H.

    1996-10-15

    The atomic force microscopy (AFM) is now a well-established technique for imaging surface topography with high resolution and can be used to study the microstructure of structural materials in a nanometer range. On multiphase materials a contrast in the topographic AFM images is obtained from small height differences between the different phases. Accordingly investigations of microstructures that are prepared to have small height differences between the phases can be done. The AFM needs no vacuum, large specimen areas compared to the small areas in thinned TEM foils can be analyzed. This reduces the costs of the measurements significantly. In addition it is advantageous that all measurements are stored as data files in the computer and therefore quantitative evaluations of the topographic data can be performed directly. The microstructures of different crystalline alloys were investigated with the atomic force microscope. The examples include superalloys (Waspaloy, CMSX-6), martensitic transformed surfaces (NiAlCo), and steels (microalloyed steel, perlitic carbon steel).

  2. Atomic Clocks and Variations of the FIne Structure Constant

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  3. Images of Atoms.

    ERIC Educational Resources Information Center

    Wright, Tony

    2003-01-01

    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)

  4. Chemical shifts of atomic core levels and structure of K{sub 1-x}Ti{sub 1-x}Sb{sub x}OPO{sub 4}, x=0-0.23, solid solutions

    SciTech Connect

    Atuchin, V.V. . E-mail: atuchin@thermo.isp.nsc.ru; Alekseeva, O.A.; Kesler, V.G.; Pokrovsky, L.D.; Sorokina, N.I.; Voronkova, V.I.

    2006-08-15

    Antimony-doped K{sub 1-x}Ti{sub 1-x}Sb{sub x}OPO{sub 4}, x=0.23, crystals have been prepared by spontaneous nucleation from the flux in the quaternary system K{sub 2}O-TiO{sub 2}-P{sub 2}O{sub 5}-Sb{sub 2}O{sub 5}. Crystal structure observation with TEM method reveals the presence of superstructure ordering. Core level electronic parameters have been studied by X-ray photoelectron spectroscopy. Strong effect of Sb doping has been detected for inner shells of Ti{sup 4+} ions. Prominent decreasing of the binding energy difference {delta}(O 1s-Ti 2p{sub 3/2}) correlates with the shortening of mean oxide bond length L(Ti-O) at x=0.23 that suggests increased ionicity of Ti-O bonds in K{sub 1-x}Ti{sub 1-x}Sb{sub x}OPO{sub 4} solid solutions.

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

    SciTech Connect

    Veremeichik, T. F.

    2006-07-15

    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.

  6. Ordering of carbon atoms in boron carbide structure

    SciTech Connect

    Ponomarev, V. I. Kovalev, I. D.; Konovalikhin, S. V.; Vershinnikov, V. I.

    2013-05-15

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

  7. Atomic-resolution structures of prion AGAAAAGA amyloid fibrils

    E-print Network

    Zhang, Jiapu

    2011-01-01

    To the best of the author's knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, although many experimental studies have shown that this region has amyloid fibril forming properties and plays an important role in prion diseases. In view of this, the present study is devoted to address this problem from computational approaches such as local optimization steepest descent, conjugate gradient, discrete gradient and Newton methods, global optimization simulated annealing and genetic algorithms, canonical dual optimization theory, and structural bioinformatics. The optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils reported in this Chapter have a value to the scientific community in its drive to find treatments for prion diseases or at least be useful for the goals of medicinal chemistry.

  8. Reverse engineering chemical structures from molecular descriptors: how many solutions?

    PubMed

    Faulon, Jean-Loup; Brown, W Michael; Martin, Shawn

    2005-01-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration. PMID:16267694

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

    E-print Network

    Raji Heyrovska

    2007-11-09

    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.

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

    ScienceCinema

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

    2013-04-19

    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

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

    SciTech Connect

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

    2008-01-01

    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.

  12. Atomic structure calculations on the CRAY X-MP

    SciTech Connect

    Fischer, C.F.

    1988-01-01

    Atomic structure calculations require both radial and angular integrations, where the latter are often based on Racah algebra. With relatively minor modifications, good performance is obtained on vector machines for radial integrations. Angular integrations, however, present the bottleneck. Some recent improvements in the algorithms for angular integrations are described, as well as some multitasking experiments on the CRAY X-MP and CRAY 2. These show that the workload can easily be distributed evenly among available processors with dynamic scheduling. 18 refs., 1 fig., 3 tabs.

  13. Simultaneous Stark and Zeeman effects in atoms with hyperfine structure

    NASA Astrophysics Data System (ADS)

    Virgo, Wilton L.

    2013-12-01

    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.

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

    PubMed

    Dostál, Ji?í; Pecina, Adam; Hrušková-Heidingsfeldová, Olga; Mare?ková, Lucie; Pichová, Iva; ?ezá?ová, Pavlina; Lepšík, Martin; Brynda, Ji?í

    2015-12-01

    The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83?Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized. PMID:26627656

  15. Using graphs to interrogate the atomic structure of polymer blends

    NASA Astrophysics Data System (ADS)

    Wodo, Olga; Ganapathysubramanian, Baskar

    2015-03-01

    The nanomorphology of polymer blend thin films critically affects performance especially in electronic devices. However, many aspects of the underlying physics linking morphology to performance are still poorly understood. Furthermore, there is increasing evidence that atomic organization can hold the key to efficient charge transport within organic electronic devices. In this work, we take advantage of recent advances in molecular dynamic simulations and quantify atomic-scale morphological aspects of the thin films. Specifically, we present a graph-based technique that allows quantifying the point-cloud data. In our approach, we first convert the point cloud data from atomistic simulation into a labelled, weighted, undirected graph and then use standard graph-based algorithms to calculate and quantify morphology features. The conversion of the CGMD-data into a graph preserves all the topological and geometric information about the internal structure, and local connectivity between individual atoms/beads (along and across the polymer chains). Our method provides hierarchical information about the charge paths that a hole/electron needs to take to reach the electrode (path length, fraction of intra-molecular hops, path balance). We showcase capabilities of our approach by analyzing coarse grained molecular simulations, and quantifying effect of various thermal treatment as well as electrode materials on the P3HT:PCBM blend.

  16. Electronic structure imperfections and chemical bonding at graphene interfaces

    NASA Astrophysics Data System (ADS)

    Schultz, Brian Joseph

    The manifestation of novel phenomena upon scaling to finite size has inspired a paradigm shift in materials science that takes advantage of the distinctive electrical and physical properties of nanomaterials. Remarkably, the simple honeycomb arrangement of carbon atoms in a single atomic layer has become renowned for exhibiting never-before-seen electronic and physical phenomena. This archetypal 2-dimensional nanomaterial is known as graphene, a single layer of graphite. Early reports in the 1950's eluded to graphene-like nanostructures that were evidenced from exfoliation of oxidized graphite followed by chemical reduction, absorbed carbon on transition metals, and thermal decomposition of SiC. Furthermore, the earliest tight binding approximation calculations in the 1950's held clues that a single-layer of graphite would behave drastically different than bulk graphite. Not until 2004, when Giem and Novoselov first synthesized graphene by mechanical exfoliation from highly-oriented pyrolytic graphite did the field of graphene-based research bloom within the scientific community. Since 2004, the availability and relatively straight forward synthesis of single-layer graphene (SLG) enabled the observation of remarkable phenomena including: massless Dirac fermions, extremely high mobilities of its charge carriers, room temperature half-integer quantum Hall effect, the Rashba effect, and the potential for ballistic conduction over macroscopic distances. These enticing electronic properties produce the drive to study graphene for use in truly nanoscale electrical interconnects, integrated circuits, transparent conducting electrodes, ultra-high frequency transistors, and spintronic devices, just to name a few. Yet, for almost all real world applications graphene will need to be interfaced with other materials, metals, dielectrics, organics, or any combination thereof that in turn are constituted from various inorganic and organic components. Interfacing graphene, a nanomaterial with lateral dimensions in the hundreds of microns if not larger, with a corresponding atomic vertical thickness poses significant difficulties. Graphene's unique structure is dominated by surface area or potentially hybridized interfaces; consequently, the true realization of this remarkable nanomaterial in device constructs relies on engineering graphene interfaces at the surface in order to controllably mold the electronic structure. Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy and the transmission mode analogue scanning transmission X-ray microscopy (STXM) are particularly useful tools to study the unoccupied states of graphene and graphene interfaces. In addition, polarized NEXAFS and STXM studies provide information on surface orientation, bond sterics, and the extent of substrate alignment before and after interfacial hybridization. The work presented in this dissertation is fundamentally informed by NEXAFS and STXM measurements on graphene/metal, graphene/dielectric, and graphene/organic interfaces. We start with a general review of the electronic structure of freestanding graphene and graphene interfaces in Chapter 1. In Chapter 2, we investigate freestanding single-layer graphene via STXM and NEXAFS demonstrating that electronic structure heterogeneities from synthesis and processing are ubiquitous in 2-dimensional graphene. We show the mapping of discrete charge transfer regions as a result of doped impurities that decorate the surfaces of graphene and that transfer processing imparts local electronic corrugations or ripples. In corroboration with density functional theory, definitive assignments to the spectral features, global steric orientations of the localized domains, and quantitative charge transfer schemes are evidenced. In the following chapters, we deliberately (Chapter 3) incorporate substitutional nitrogen into reduced graphene oxide to induce C--N charge redistribution and improve global conductivity, (Chapter 4) fabricate graphene/metal interfaces and metal/graphene/metal sandwich structures evidencing classic

  17. Chemical structure representations and applications in computational toxicity.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2012-01-01

    Efficient storage and retrieval of chemical structures is one of the most important prerequisite for solving any computational-based problem in life sciences. Several resources including research publications, text books, and articles are available on chemical structure representation. Chemical substances that have same molecular formula but several structural formulae, conformations, and skeleton framework/scaffold/functional groups of the molecule convey various characteristics of the molecule. Today with the aid of sophisticated mathematical models and informatics tools, it is possible to design a molecule of interest with specified characteristics based on their applications in pharmaceuticals, agrochemicals, biotechnology, nanomaterials, petrochemicals, and polymers. This chapter discusses both traditional and current state of art representation of chemical structures and their applications in chemical information management, bioactivity- and toxicity-based predictive studies. PMID:23007430

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

    SciTech Connect

    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

    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.

  19. The Atomic Structure Factor in Coordinate and Momentum Space Frank Rioux

    E-print Network

    Rioux, Frank

    The Atomic Structure Factor in Coordinate and Momentum Space Frank Rioux The following expression for the atomic structure factor in the coordinate and momentum representations can be found in a paper calculations using the hydrogen atom ground state eigenfunction in the position and momentum representations

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

    E-print Network

    Zhu, Xiangdong

    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

  1. 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

  2. Atomic-scale structure: From surfaces to nanomaterials

    NASA Astrophysics Data System (ADS)

    Hove, M. A. Van

    2009-06-01

    This brief overview is dedicated to Professor G. Ertl's profound influence on shaping the field of surface science. I sketch recent accomplishments toward the determination and understanding of the atomic-scale structure of nanostructures. I argue that, to properly understand nanoscience and develop nanotechnology, there is a dire need to determine many more than the ˜1,000 detailed surface structures known today. Techniques need to be adapted or invented to make this possible. As will be exhibited here, only two techniques are now essentially ready for this task: scanning tunneling microscopy, if interpreted by theory, and, to a lesser extent, x-ray diffraction. I also describe how low-energy electron diffraction is currently being developed for the same purpose.

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

    PubMed Central

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

    2015-01-01

    Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)—making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperatures. The variation of Mo content was modelled to understand the change in alloy structure and behaviour with fuel burnup (Mo molar content decreases in these alloys as burnup increases). The predicted structures compare extremely well with experimentally ascertained values. Vacancy formation energies and the behaviour of extrinsic defects (including iodine and xenon) in the epsilon phase were also investigated to further understand the impact that the metallic precipitates have on fuel performance. PMID:26064629

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

    PubMed

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

    2015-04-01

    Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)-making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperatures. The variation of Mo content was modelled to understand the change in alloy structure and behaviour with fuel burnup (Mo molar content decreases in these alloys as burnup increases). The predicted structures compare extremely well with experimentally ascertained values. Vacancy formation energies and the behaviour of extrinsic defects (including iodine and xenon) in the epsilon phase were also investigated to further understand the impact that the metallic precipitates have on fuel performance. PMID:26064629

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

    PubMed Central

    2014-01-01

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

  6. Quantum structural phase transition in chains of interacting atoms

    E-print Network

    Efrat Shimshoni; Giovanna Morigi; Shmuel Fishman

    2010-12-20

    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 $\\phi^4$ model. We propose a mapping of the $\\phi^4$ 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.

  7. Quantum structural phase transition in chains of interacting atoms

    SciTech Connect

    Shimshoni, Efrat; Morigi, Giovanna; Fishman, Shmuel

    2011-03-15

    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.

  8. Embedded atom study of dislocation core structure in Fe

    SciTech Connect

    Farkas, D.; Rodriguez, P.L. . Dept. of Materials Science and Engineering Centro Atomico Bariloche )

    1994-04-01

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

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

    E-print Network

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

    2011-11-02

    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.

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

    SciTech Connect

    Bai, Yanwen; Bian, Xiufang Qin, Jingyu; Hu, Lina; Yang, Jianfei; Zhang, Kai; Zhao, Xiaolin; Yang, Chuncheng; Zhang, Shuo; Huang, Yuying

    2014-01-28

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

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

    NASA Astrophysics Data System (ADS)

    Dave, Mudra R.; Sharma, A. C.

    2015-06-01

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

  12. Entanglement dynamics of three interacting two-level atoms within a common structured environment

    SciTech Connect

    An, Nguyen Ba; Kim, Jaewan; Kim, Kisik

    2011-08-15

    We derive exact time evolution of three two-level atoms coupled to a common environment. The environment is structured and is modeled by a leaky cavity with Lorentzian spectral density. The atoms are initially prepared in a generalized W state and later on experience pairwise dipole-dipole interactions and couplings to the cavity. We study tripartite disentangling and entangling dynamics as well as protecting bipartite entanglement with both atom-atom interactions and atom-cavity couplings taken simultaneously into account.

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

    PubMed

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

    2015-12-18

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

  14. Atomistic analysis of short range interaction and local chemical order in LPSO structures of Magnesium alloys

    NASA Astrophysics Data System (ADS)

    Fronzi, Marco; Kimizuka, Hajime; Matsubara, Kazuki; Ogata, Shigenobu

    2013-03-01

    Magnesium alloys have been object of interest as lightweight material with high strength weight ratio. In particular Long Period Stacking Ordered (LPSO) structure phases show to have a strong influence in enhancing mechanical properties of such kind alloys. However the chemical order of the interacting atomic species in the Mg lattice has not been fully understood. We perform first principles Density Functional Theory (DFT) calculation to compute formation energies as well as interaction energies of the doping atoms in both Faced Centered Cubic (FCC) and Hexagonal Close Packed (HCP) Mg lattices. In particular we consider the Mg-Al-Gd and Mg-Zn-Y ternary systems. We also calculate activation energies for vacancy assisted doping atoms diffusion in order to perform a further analysis of the kinetics of the process. In order to describe short range interaction and cluster formation in the Mg matrix, we build an on lattice potential based on first principles DFT interaction energies. By means of these inter-atomic potentials, we perform Monte Carlo simulations to analyze the chemical order occurring in LPSO Mg-Al-Gd structures.

  15. Chemical identification of point defects and adsorbates on a metal oxide surface by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Lauritsen, Jeppe V.; Foster, Adam S.; Olesen, Georg H.; Christensen, Mona C.; Kühnle, Angelika; Helveg, Stig; Rostrup-Nielsen, Jens R.; Clausen, Bjerne S.; Reichling, Michael; Besenbacher, Flemming

    2006-07-01

    Atomic force microscopy in the non-contact mode (nc-AFM) can provide atom-resolved images of the surface of, in principle, any material independent of its conductivity. Due to the complex mechanisms involved in the contrast formation in nc-AFM imaging, it is, however, far from trivial to identify individual surface atoms or adsorbates from AFM images. In this work, we successfully demonstrate how to extract detailed information about defects and the chemical identity of adsorbates on a metal oxide surface from nc-AFM images. We make use of the observation that the apex of the AFM tip can be altered to expose either a positive or negative tip termination. The complementary set of images recorded with the two tip terminations unambiguously define the ionic sub-lattices and reveal the exact positions of oxygen vacancies and hydroxyl (OH) defects on a TiO2 surface. Chemical specificity is extracted by comparing the characteristic contrast patterns of the defects with results from comprehensive AFM simulations. Our methodology of analysis is generally applicable and may be pivotal for uncovering surface defects and adsorbates on other transition metal oxides designed for heterogeneous catalysis, photo-electrolysis or biocompatibility.

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

    PubMed Central

    Hay, Mark E.

    2012-01-01

    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

  17. Bayesian inference of protein structure from chemical shift data

    PubMed Central

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

    2015-01-01

    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. PMID:25825683

  18. Sensitivity of chemical reaction networks: a structural approach.

    E-print Network

    Fiedler, Bernold

    Sensitivity of chemical reaction networks: a structural approach. 2. Regular monomolecular systems to perturbations of reaction rates in chemical reaction networks. Strong motivation for our study comes from recent For the deceptively innocent case of monomolecular reactions, only, we embark on a systematic mathematical analysis

  19. Atomic-Scale Structures Fabricated on a Hydrogen-Terminated SI Surface

    NASA Astrophysics Data System (ADS)

    Hashizume, T.; Heike, S.; Fujimori, M.; Kato, M.; Ishibashi, M.

    2002-10-01

    Atomic-scale structures on a hydrogen-terminated Si(100)-2x1-H surface are investigated by scanning tunneling microscopy/spectroscopy (STM/STS). Relaxation of atomic-scale dangling-bond (DB) structures can be well described by a Jahn-Teller distortion. When Ga atoms were deposited on the surface at 100 K, we observed a characteristic one-dimensional structure (Ga-bar structure). The Ga-bar structure is an STM image of a rapidly-migrating Ga atom confined in a linear potential well.

  20. A Method for the Automatic Classification of Chemical Structures

    ERIC Educational Resources Information Center

    Adamson, George W.; Bush, Judith A.

    1973-01-01

    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)

  1. Consistent blind protein structure generation from NMR chemical shift data

    E-print Network

    Baker, David

    Consistent blind protein structure generation from NMR chemical shift data Yang Shen*, Oliver Lange been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 k

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

    E-print Network

    Sparks, Donald L.

    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

  3. 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...

  4. Formation of atomically smooth epitaxial metal films on a chemically reactive interface: Mg on Si(111)

    NASA Astrophysics Data System (ADS)

    Özer, Mustafa M.; Weitering, Hanno H.

    2013-07-01

    Deposition of Mg on Si(111)7 × 7 produces an epitaxial magnesium silicide layer. Under identical annealing conditions, the thickness of this Mg2Si(111) layer increases with deposition amount, reaching a maximum of 4 monolayer (ML) and decreasing to ˜3 ML at higher Mg coverage. Excess Mg coalesces into atomically flat, crystalline Mg(0001) films. This surprising growth mode can be attributed to the accidental commensurability of the Mg(0001), Si(111), and Mg2Si(111) interlayer spacing and the concurrent minimization of in-plane Si mass transfer and domain-wall energies. The commensurability of the interlayer spacing defines a highly unique solid-phase epitaxial growth process capable of producing trilayer structures with atomically abrupt interfaces and atomically smooth surface morphologies.

  5. We present a unique approach to the design and synthesis of "giant molecules" based on "nano-atoms" for engineering structures across multiple length scales and controlling their macroscopic properties.

    E-print Network

    Pennycook, Steve

    on "nano-atoms" for engineering structures across multiple length scales and controlling their macroscopic properties. Herein, "nano-atoms" refer to shape-persistent molecular nanoparticles (MNPs) with precisely-defined chemical structures and surface functionalities that can serve as elemental building blocks

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

    E-print Network

    Huirong Yan; A. Lazarian

    2006-12-13

    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.

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

    E-print Network

    Jiang, Wen

    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

  8. Structural relaxation in atomic clusters: Master equation dynamics

    NASA Astrophysics Data System (ADS)

    Miller, Mark A.; Doye, Jonathan P. K.; Wales, David J.

    1999-10-01

    The role of the potential energy landscape in determining the relaxation dynamics of model clusters is studied using a master equation. Two types of energy landscape are examined: a single funnel, as exemplified by 13-atom Morse clusters, and the double funnel landscape of the 38-atom Lennard-Jones cluster. Interwell rate constants are calculated using Rice-Ramsperger-Kassel-Marcus theory within the harmonic approximation, but anharmonic model partition functions are also considered. Decreasing the range of the potential in the Morse clusters is shown to hinder relaxation toward the global minimum, and this effect is related to the concomitant changes in the energy landscape. The relaxation modes that emerge from the master equation are interpreted and analyzed to extract interfunnel rate constants for the Lennard-Jones cluster. Since this system is too large for a complete characterization of the energy landscape, the conditions under which the master equation can be applied to a limited database are explored. Connections are made to relaxation processes in proteins and structural glasses.

  9. Defects in p-GaN and their atomic structure

    SciTech Connect

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

    2004-10-08

    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

  10. Sommerfeld Fine-Structure Formula for Two-Body Atoms

    E-print Network

    John H. Connell

    2013-03-20

    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.

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

    E-print Network

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

    2011-02-23

    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.

  12. Atomic-level 2-dimensional chemical mapping and imaging of individual dopants in a phosphor crystal.

    PubMed

    Zhu, Guo-zhen; Lazar, Sorin; Knights, Andrew P; Botton, Gianluigi A

    2013-07-21

    The ability to visualize and identify individual dopants, as well as measure their local physical and chemical environments in a bulk, provides deep insight for designing new functional materials and predicting their properties. However, a full understanding of dopants inside a solid has been limited by currently available characterization techniques. We demonstrate the first atomic-level 2-dimensional elemental maps of Pr dopants using the electron energy-loss spectroscopy (EELS) technique and we image Al dopants located in a lattice. Based on spectroscopic and imaging evidence we provide plausible local defect configurations of implanted Pr(+) and Al(+) ions within SrTiO3 single crystals. Our results demonstrate the detection of single Pr atoms and the formation of Al-rich nanoscale clusters ranging from 1 to 3 nm in size randomly distributed in the implanted lattice. These results provide insight into the mechanism of red light emission in doped SrTiO3. PMID:23744110

  13. Catalytic activity of bimetallic catalysts highly sensitive to the atomic composition and phase structure at the nanoscale.

    PubMed

    Shan, Shiyao; Petkov, Valeri; Prasai, Binay; Wu, Jinfang; Joseph, Pharrah; Skeete, Zakiya; Kim, Eunjoo; Mott, Derrick; Malis, Oana; Luo, Jin; Zhong, Chuan-Jian

    2015-12-01

    The ability to determine the atomic arrangement in nanoalloy catalysts and reveal the detailed structural features responsible for the catalytically active sites is essential for understanding the correlation between the atomic structure and catalytic properties, enabling the preparation of efficient nanoalloy catalysts by design. Herein we describe a study of CO oxidation over PdCu nanoalloy catalysts focusing on gaining insights into the correlation between the atomic structures and catalytic activity of nanoalloys. PdCu nanoalloys of different bimetallic compositions are synthesized as a model system and are activated by a controlled thermochemical treatment for assessing their catalytic activity. The results show that the catalytic synergy of Pd and Cu species evolves with both the bimetallic nanoalloy composition and temperature of the thermochemical treatment reaching a maximum at a Pd?:?Cu ratio close to 50?:?50. The nanoalloys are characterized structurally by ex situ and in situ synchrotron X-ray diffraction, including atomic pair distribution function analysis. The structural data show that, depending on the bimetallic composition and treatment temperature, PdCu nanoalloys adopt two different structure types. One features a chemically ordered, body centered cubic (B2) type alloy consisting of two interpenetrating simple cubic lattices, each occupied with Pd or Cu species alone, and the other structure type features a chemically disordered, face-centered cubic (fcc) type of alloy wherein Pd and Cu species are intermixed at random. The catalytic activity for CO oxidation is strongly influenced by the structural features. In particular, it is revealed that the prevalence of chemical disorder in nanoalloys with a Pd?:?Cu ratio close to 50?:?50 makes them superior catalysts for CO oxidation in comparison with the same nanoalloys of other bimetallic compositions. However, the catalytic synergy can be diminished if the Pd50Cu50 nanoalloys undergo phase segregation into distinct chemically-ordered (B2-type) and disordered (fcc-type) domains. This finding is significant since it provides a rational basis for streamlining the design and preparation of Pd-based nanoalloy catalysts in terms of atomic structure and phase state. PMID:26404795

  14. The Nuclear Physics of Hyperfine Structure in Hydrogenic Atoms

    E-print Network

    J. L. Friar; G. L. Payne

    2005-02-01

    The theory of QED corrections to hyperfine structure in light hydrogenic atoms and ions has recently advanced to the point that the uncertainty of these corrections is much smaller than 1 part per million (ppm), while the experiments are even more accurate. The difference of the experimental results and the corresponding QED theory is due to nuclear effects, which are primarily the result of the finite nuclear charge and magnetization distributions. This difference varies from tens to hundreds of ppm. We have calculated the dominant nuclear component of the 1s hyperfine interval for deuterium, tritium and singly ionized helium, using a unified approach with modern second-generation potentials. The calculated nuclear corrections are within 3% of the experimental values for deuterium and tritium, but are roughly 20% discrepant for helium. The nuclear corrections for the trinucleon systems can be qualitatively understood by invoking SU(4) symmetry.

  15. Atomic and electronic structure of divacancies in carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Berber, Savas; Oshiyama, Atsushi

    2008-04-01

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

  16. The atomic structure of niobium and tantalum containing borophosphate glasses.

    PubMed

    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

    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

  17. First Optical Hyperfine Structure Measurement in an Atomic Anion

    SciTech Connect

    Fischer, A.; Canali, C.; Warring, U.; Kellerbauer, A.; Fritzsche, S.

    2010-02-19

    We have investigated the hyperfine structure of the transition between the 5d{sup 7}6s{sup 2} {sup 4}F{sub 9/2}{sup e} ground state and the 5d{sup 6}6s{sup 2}6p {sup 6}D{sub J}{sup o} excited state in the negative osmium ion by high-resolution collinear laser spectroscopy. This transition is unique because it is the only known electric-dipole transition in atomic anions and might be amenable to laser cooling. From the observed hyperfine structure in {sup 187}Os{sup -} and {sup 189}Os{sup -} the yet unknown total angular momentum of the bound excited state was found to be J=9/2. The hyperfine structure constants of the {sup 4}F{sub 9/2}{sup e} ground state and the {sup 6}D{sub 9/2}{sup o} excited state were determined experimentally and compared to multiconfiguration Dirac-Fock calculations. Using the knowledge of the ground and excited state angular momenta, the full energy level diagram of {sup 192}Os{sup -} in an external magnetic field was calculated, revealing possible laser cooling transitions.

  18. On the atomic structure of cocaine in solution.

    PubMed

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

    2015-12-23

    Cocaine is an amphiphilic drug which has the ability to cross the blood-brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ?5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Å of cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function. PMID:26660073

  19. 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

  20. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    E-print Network

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  1. 221A Lecture Notes Fine and Hyperfine Structures of the Hydrogen Atom

    E-print Network

    Murayama, Hitoshi

    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

  2. Direct observation of electron emission from the grain boundaries of chemical vapour deposition diamond films by tunneling atomic force microscopy

    E-print Network

    Bristol, University of

    observation of the emission sites over a large area of polycrystalline diamond using tunneling atomic forceDirect observation of electron emission from the grain boundaries of chemical vapour deposition for polycrystalline low pressure chemical vapour deposition ZnO:B films J. Appl. Phys. 113, 123104 (2013); 10

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

    SciTech Connect

    Balat-Pichelin, Marianne J.H.; Bedra, L.; Badie, J.-M.; Boubert, P.

    2005-05-16

    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.

  4. Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures

    E-print Network

    Chang, D. E.

    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 ...

  5. Visual Chemistry: Three-Dimensional Perception of Chemical Structures

    NASA Astrophysics Data System (ADS)

    Balaban, Alexandru T.

    1999-12-01

    Chemical structures are being modeled by formulas which in turn may be viewed as graphs. They have to be represented pictorially in two (constitutional formulas) or three dimensions (stereochemical formulas). How to present the latter formulas is the topic of the present paper. First, however, a discussion of isomerism is necessary. Then, for quantitative structure-activity relationships (QSAR) one has to find a correspondence between chemical formulas (or the shape of chemical compounds) and numerical molecular descriptors (also called topological indices). The various types of conventions for translating three-dimensional objects into two-dimensional representations are presented and discussed. It is hoped that stereo-drawings and colored images will facilitate the task of molecular modelers in search for new medicinal drugs. The ultimate goal, the production of holograms for chemical structures, needs the development of specialized software.

  6. The grasp2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

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

    2007-10-01

    This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a "make" facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report. Program summaryProgram title: grasp2K Catalogue identifier: ADZL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 213 524 No. of bytes in distributed program, including test data, etc.: 1 328 588 Distribution format: tar.gz Programming language: Fortran and C Computer: Intel 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

  7. Countable models A structure M is atomic iff tpM

    E-print Network

    Monk, Don

    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

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

    E-print Network

    Walsworth, Ronald L.

    Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures D. E. Chang,1 J. D. Simultaneously, the guided surface plasmon modes of the nanotip allow the atom to be optically manipulated manipulate, and measure indi- vidual cold atoms within $100 nm of a surface. Here, we describe a technique

  9. Atomic Structure. Independent Learning Project for Advanced Chemistry (ILPAC). Unit S2.

    ERIC Educational Resources Information Center

    Inner London Education Authority (England).

    This unit on atomic structure is one of 10 first year units produced by the Independent Learning Project for Advanced Chemistry (ILPAC). The unit consists of two levels. Level one focuses on the atomic nucleus. Level two focuses on the arrangement of extranuclear electrons, approaching atomic orbitals through both electron bombardment and spectra.…

  10. Chemically-selective imaging of brain structures with CARS microscopy

    E-print Network

    Xie, Xiaoliang Sunney

    Chemically-selective imaging of brain structures with CARS microscopy Conor L. Evans1§ , Xiaoyin Xu anti-Stokes Raman scattering (CARS) microscopy to image brain structure and pathology ex vivo. Although. Definitive diagnosis still requires brain biopsy in a significant number of cases. CARS microscopy

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

    PubMed

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

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

  12. Chemical Stability of Titania and Alumina Thin Films Formed by Atomic Layer Deposition.

    PubMed

    Correa, Gabriela C; Bao, Bo; Strandwitz, Nicholas C

    2015-07-15

    Thin films formed by atomic layer deposition (ALD) are being examined for a variety of chemical protection and diffusion barrier applications, yet their stability in various fluid environments is not well characterized. The chemical stability of titania and alumina thin films in air, 18 M? water, 1 M KCl, 1 M HNO3, 1 M H2SO4, 1 M HCl, 1 M KOH, and mercury was studied. Films were deposited at 150 °C using trimethylaluminum-H2O and tetrakis(dimethylamido)titanium-H2O chemistries for alumina and titania, respectively. A subset of samples were heated to 450 and 900 °C in inert atmosphere. Films were examined using spectroscopic ellipsometry, atomic force microscopy, optical microscopy, scanning electron microscopy, and X-ray diffraction. Notably, alumina samples were found to be unstable in pure water, acid, and basic environments in the as-synthesized state and after 450 °C thermal treatment. In pure water, a dissolution-precipitation mechanism is hypothesized to cause surface roughening. The stability of alumina films was greatly enhanced after annealing at 900 °C in acidic and basic solutions. Titania films were found to be stable in acid after annealing at or above 450 °C. All films showed a composition-independent increase in measured thickness when immersed in mercury. These results provide stability-processing relationships that are important for controlled etching and protective barrier layers. PMID:26107803

  13. Single-collision studies of hot atom energy transfer and chemical reaction

    SciTech Connect

    Valentini, J.J. )

    1991-01-01

    This report discusses research in the collision dynamics of translationally hot atoms, with funding with DOE for the project Single-Collision Studies of Hot Atom Energy Transfer and Chemical Reaction,'' Grant Number DE-FG03-85ER13453. The work reported here was done during the period September 9, 1988 through October 31, 1991. During this period this DOE-funded work has been focused on several different efforts: (1) experimental studies of the state-to-state dynamics of the H + RH {yields} H{sub 2} R reactions where RH is CH{sub 4}, C{sub 2}H{sub 6}, or C{sub 3}H{sub 8}, (2) theoretical (quasiclassical trajectory) studies of hot hydrogen atom collision dynamics, (3) the development of photochemical sources of translationally hot molecular free radicals and characterization of the high resolution CARS spectroscopy of molecular free radicals, (4) the implementation of stimulated Raman excitation (SRE) techniques for the preparation of vibrationally state-selected molecular reactants.

  14. Single-collision studies of hot atom energy transfer and chemical reaction. Final report

    SciTech Connect

    Valentini, J.J.

    1991-12-31

    This report discusses research in the collision dynamics of translationally hot atoms, with funding with DOE for the project ``Single-Collision Studies of Hot Atom Energy Transfer and Chemical Reaction,`` Grant Number DE-FG03-85ER13453. The work reported here was done during the period September 9, 1988 through October 31, 1991. During this period this DOE-funded work has been focused on several different efforts: (1) experimental studies of the state-to-state dynamics of the H + RH {yields} H{sub 2} R reactions where RH is CH{sub 4}, C{sub 2}H{sub 6}, or C{sub 3}H{sub 8}, (2) theoretical (quasiclassical trajectory) studies of hot hydrogen atom collision dynamics, (3) the development of photochemical sources of translationally hot molecular free radicals and characterization of the high resolution CARS spectroscopy of molecular free radicals, (4) the implementation of stimulated Raman excitation (SRE) techniques for the preparation of vibrationally state-selected molecular reactants.

  15. Chemical Bonding and Electronic Structure of Buckminsterfullerene As is well-known C60 resembles an American soccerball, containing 12 pentagons and

    E-print Network

    Rioux, Frank

    Chemical Bonding and Electronic Structure of Buckminsterfullerene As is well-known C60 resembles is an indication of weakness in the Lewis' localized electron pair model of chemical bonding, because the existence, but keeping the seams, leaves 60 vertices for the carbon atoms and 90 covalent bonds between them, 60 single

  16. Effect of atomic bond structure on crystallographic orientation dependence of carbon doping in GaAs

    NASA Astrophysics Data System (ADS)

    Park, Young K.; Son, Chang-Sik; Kim, Seong-Il; Kim, Yong; Kim, Eun Kyu; Min, Suk-Ki; Choi, In-Hoon

    1998-03-01

    The effect of atomic bond structure at the deposition surface on the crystallographic orientation dependence of carbon doping in GaAs was studied. Carbon doping into GaAs epilayers was performed by atmospheric pressure metalorganic chemical vapor deposition using extrinsic carbon sources of carbon tetrachloride (CCl4) and carbon tetrabromide (CBr4). Epitaxial growths were done on the exact (100) and four different misoriented GaAs substrates with orientations of (511)A, (311)A, (211)A, and (111)A. The electrical properties were measured by van der Pauw Hall analysis at room temperature. Electrically active concentrations in excess of 1×1019 cm-3 were obtained so that 4 and CBrCCl4 were demonstrated as efficient p-type dopant sources for carbon doping into GaAs. The dependence of hole concentration on the offset angle of CCl4-doped and CBr4-doped GaAs shows the same tendency, whereas the trend of carbon doping from intrinsic carbon doping technique is different from our results. In particular, the hole concentration on the (100) surface is higher than that on the (111)A surface in the cases of CCl4 and CBr4. The result is opposite to that of the intrinsic doping case. A model based on the atomic bond structure of an adsorption site of carbon-containing species is proposed to explain the difference.

  17. Earth's interdependent thermal, structural, and chemical evolution

    NASA Astrophysics Data System (ADS)

    Hofmeister, A.; Criss, R. E.

    2012-12-01

    The popular view that 30-55% of Earth's global power is primordial, with deep layers emanating significant power, rests on misunderstandings and models that omit magmatism and outgassing. These processes link Earth's chemical and thermal evolution, while creating layers, mainly because magmas transport latent heat and radioactive isotopes rapidly upwards. We link chemistry to heat flow, measured and theoretical, to understand the interior layering and workings. Quasi-steady state conditions describe most of Earth's history: (1) Accretion was cold and was not a source of deep heat. (2) Friction during core formation cannot have greatly heated the interior (thermodynamics plus buoyancy). (3) Conduction is the governing microscopic mechanism in the deep Earth. (4) Using well-constrained values of thermal conductivity (k), we find that homogeneously distributed radionuclides provide extremely high internal temperature (T) under radial symmetry. Moreover, for any given global power, sequestering heat producing elements into the upper mantle reduces Earth's central temperature by a factor of 10 from a homogeneous distribution. Hence, (5) core formation was a major cooling event. From modern determinations of k(T) we provide a reference conductive geotherm. Present-day global power of 30 TW from heat flux measurements and sequestering of heat producing elements in the upper mantle and transition zone, produces nearly isothermal T = 5300 K below 670 km, which equals experimentally determined freezing of pure Fe0 at the inner core boundary. Core freezing buffers the interior temperatures, while the Sun constrains the surface temperature, providing steady state conditions: Earth's deep interior is isothermal due to these constraints, low flux and high k. Our geotherms point to a stagnant lower mantle and convection above 670 km. Rotational flattening cracks the brittle lithosphere, providing paths for buoyant magmas to ascend. Release of latent heat augments the conductive gradient, making these oriented cracks equivalent to vertical hot plates, thereby imparting a large lateral component and preferred direction to upper mantle circulation. The latent heat release limits lower mantle flux to 1 TW and its temperature change to 500 K High lower mantle temperatures require a bulk composition more like the Moon than chondrites, which is consistent with proposals that calcuim-aluminum inclusions constitute a presolar reservoir near the nebula center. From oxygen isotopes and chemical composition of meteorites, we provide a new class of meteoritic model, based on mixing and not volatile element depletion, for the types and amounts of Earth's heat producing elements. Our model permits crust preservation at ~ 4 Ga, whereas hypothetical primordial heat would delay this significantly. The lower mantle is chemically distinct from the peridotite (chondritic) upper mantle, being comprised of refractory phases with much higher Ca, Al and Ti contents than previously considered. Huge changes in chemistry and temperature are required across the transition zone and profoundly affect the workings of the Earth. The lower mantle formed during gravitational sorting very early on, as did the core, in the drive towards energy minimization.

  18. Materials by Design—A Perspective From Atoms to Structures

    PubMed Central

    Buehler, Markus J.

    2013-01-01

    Biological materials are effectively synthesized, controlled, and used for a variety of purposes—in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science. PMID:24163499

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

    SciTech Connect

    Flynn, George W

    2015-02-16

    Executive Summary of Final Report for Award DE-FG02-88ER13937 Project Title: Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and its Precursors on Metal Surfaces Applicant/Institution: Columbia University Principal Investigator: George W. Flynn Objectives: The objectives of this project were to reveal the mechanisms and reaction processes that solid carbon materials undergo when combining with gases such as oxygen, water vapor and hydrocarbons. This research was focused on fundamental chemical events taking place on single carbon sheets of graphene, a two-dimensional, polycyclic carbon material that possesses remarkable chemical and electronic properties. Ultimately, this work is related to the role of these materials in mediating the formation of polycyclic aromatic hydrocarbons (PAH’s), their reactions at interfaces, and the growth of soot particles. Our intent has been to contribute to a fundamental understanding of carbon chemistry and the mechanisms that control the formation of PAH’s, which eventually lead to the growth of undesirable particulates. We expect increased understanding of these basic chemical mechanisms to spur development of techniques for more efficient combustion of fossil fuels and to lead to a concomitant reduction in the production of undesirable solid carbon material. Project Description: Our work treated specifically the surface chemistry aspects of carbon reactions by using proximal probe (atomic scale imaging) techniques to study model systems of graphene that have many features in common with soot forming reactions of importance in combustion flames. Scanning tunneling microscopy (STM) is the main probe technique that we used to study the interfacial structure and chemistry of graphene, mainly because of its ability to elucidate surface structure and dynamics with molecular or even atomic resolution. Scanning tunneling spectroscopy (STS), which measures the local density of quantum states over a single atom, provides information about the electronic structure of graphene and is particularly sensitive to the sign and magnitude of the charge transfer between graphene and any surface adsorbed species. Results: (A) Graphene on SiO2 In an effort designed to unravel aspects of the mechanisms for chemistry on graphene surfaces, STM and STS were employed to show that graphene on SiO2 is oxidized at lower temperatures than either graphite or multi-layer graphene. Two independent factors control this charge transfer: (1) the degree of graphene coupling to the substrate, and (2) exposure to oxygen and moisture. (B) Graphene on Copper In the case of graphene grown on copper surfaces, we found that the graphene grows primarily in registry with the underlying copper lattice for both Cu(111) and Cu(100). On Cu(111) the graphene has a hexagonal superstructure with a significant electronic component, whereas it has a linear superstructure on Cu(100). (C) Nitrogen Doped Graphene on Copper Using STM we have also studied the electronic structure and morphology of graphene films grown on a copper foil substrate in which N atoms substitute for carbon in the 2-D graphene lattice. The salient features of the results of this study were: (1) Nitrogen doped graphene on Cu foil exhibits a triangular structure with an “apparent” slight elevation of ~ 0.8 Å at N atom substitution sites; (2) Nitrogen doping results in ~0.4 electrons per N atom donated to the graphene lattice; (3) Typical N doping of graphene on Cu foil shows mostly single site Carbon atom displacement (~ 3N/1000C); (4) Some multi-site C atom displacement is observed (<10% of single site events). (D) Boron Doped Graphene on Copper We also used scanning tunneling microscopy and x-ray spectroscopy to characterize the atomic and electronic structure of boron-doped graphene created by chemical vapor deposition on copper substrates. Microscopic measurements show that boron, like nitrogen, incorporates into the carbon lattice primarily in the graphitic form and contributes ~0.5 free carriers into the graphene sheet per dopa

  20. Energetic and structural analysis of 102-atom Pd-Pt nanoparticles

    NASA Astrophysics Data System (ADS)

    Pacheco-Contreras, Rafael; Arteaga-Guerrero, Alvaro; Borbon-Gonzalez, Dora Julia; Posada-Amarillas, Alvaro; Schoen, J. Christian; Johnston, Roy L.

    2009-03-01

    We present an extensive study of the structural and energetic changes of 102-atom PdmPt102-m nanoparticles as a function of composition m, where the interatomic interactions are modeled with the many-body Gupta potential. The minimum energy structures are obtained through a genetic algorithm. The excess energy is calculated, as well as the pair distribution function g(r). The radial distribution of the atoms is computed for each composition; the result indicates a multi-layer segregation for some compositions, with a shell growth sequence as follows: a core with a small number of Pd atoms is followed by an intermediate shell of Pt atoms and the external shell consists of Pd atoms. A region where Pd and Pt atoms are mixed is observed between the outermost and intermediate shells. Furthermore, the pure Pd102 and Pt102 nanoparticles have the same structure, while a variety of different structures are observed for the bimetallic clusters.

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

    PubMed Central

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

    2014-01-01

    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

  2. Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation.

    PubMed

    Mollica, Luca; Baias, Maria; Lewandowski, Józef R; Wylie, Benjamin J; Sperling, Lindsay J; Rienstra, Chad M; Emsley, Lyndon; Blackledge, Martin

    2012-12-01

    Solid-state NMR can provide atomic-resolution information about protein motions occurring on a vast range of time scales under similar conditions to those of X-ray diffraction studies and therefore offers a highly complementary approach to characterizing the dynamic fluctuations occurring in the crystal. We compare experimentally determined dynamic parameters, spin relaxation, chemical shifts, and dipolar couplings, to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, providing insight into the nature of structural dynamics occurring within the crystalline lattice. This simulation allows us to test the accuracy of commonly applied procedures for the interpretation of experimental solid-state relaxation data in terms of dynamic modes and time scales. We discover that the potential complexity of relaxation-active motion can lead to significant under- or overestimation of dynamic amplitudes if different components are not taken into consideration. PMID:26291002

  3. PACSY, a relational database management system for protein structure and chemical shift analysis

    PubMed Central

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

    2012-01-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

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

    SciTech Connect

    Paesler, M.; Sayers, D.

    1988-12-01

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

  5. Local Structures of High-Entropy Alloys (HEAs) on Atomic Scales: An Overview

    NASA Astrophysics Data System (ADS)

    Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; Egami, Takeshi; Liaw, Peter K.

    2015-08-01

    The high-entropy alloys, containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on the atomic level are essential to understand the mechanical behaviors and related mechanisms. In this article, the local structure and stress on the atomic level are reviewed by the pair-distribution function of neutron-diffraction data, ab-initio molecular dynamics simulations, and the atomic probe microscopy.

  6. Local structures of high-entropy alloys (HEAs) on atomic scales: An overview

    DOE PAGESBeta

    Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; Egami, Takeshi; Liaw, Peter K.

    2015-08-29

    The high-entropy alloys, containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on the atomic level are essential to understand the mechanical behaviors and related mechanisms. This article covers the local structure and stress on the atomic level are reviewed by the pair-distribution function of neutron-diffraction data, ab-initio molecular dynamics simulations, and the atomic probe microscopy.

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

    E-print Network

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

    2015-01-01

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

  8. Chemical stabilization and improved thermal resilience of molecular arrangements: possible formation of a surface network of bonds by multiple pulse atomic layer deposition.

    PubMed

    de Pauli, Muriel; Matos, Matheus J S; Siles, Pablo F; Prado, Mariana C; Neves, Bernardo R A; Ferreira, Sukarno O; Mazzoni, Mário S C; Malachias, Angelo

    2014-08-14

    In this work, we make use of an atomic layer deposition (ALD) surface reaction based on trimethyl-aluminum (TMA) and water to modify O-H terminated self-assembled layers of octadecylphosphonic acid (OPA). The structural modifications were investigated by X-ray reflectivity, X-ray diffraction, and atomic force microscopy. We observed a significant improvement in the thermal stability of ALD-modified molecules, with the existence of a supramolecular packing structure up to 500 °C. Following the experimental observations, density functional theory (DFT) calculations indicate the possibility of formation of a covalent network with aluminum atoms connecting OPA molecules at terrace surfaces. Chemical stability is also achieved on top of such a composite surface, inhibiting further ALD oxide deposition. On the other hand, in the terrace edges, where the covalent array is discontinued, the chemical conditions allow for oxide growth. Analysis of the DFT results on band structure and density of states of modified OPA molecules suggests that besides the observed thermal resilience, the dielectric character of OPA layers is preserved. This new ALD-modified OPA composite is potentially suitable for applications such as dielectric layers in organic devices, where better thermal performance is required. PMID:25055162

  9. Nuclear structure effects in light muonic atoms Krzysztof Pachucki and Albert Wienczek

    E-print Network

    Pachucki, Krzysztof

    Nuclear structure effects in light muonic atoms Krzysztof Pachucki and Albert Wienczek Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland (Dated: April 28, 2015) Nuclear structure corrections to energy levels of light muonic atoms are derived with particu- lar attention to the nuclear mass

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

    E-print Network

    Caflisch, Amedeo

    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

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

    E-print Network

    Himpsel, Franz J.

    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 Â 3 ground state to a 1 Â

  12. Atom Exchange between Aqueous Fe(II) and Structural Fe in Clay Anke Neumann,*,,

    E-print Network

    Johnson, Clark M.

    Atom Exchange between Aqueous Fe(II) and Structural Fe in Clay Minerals Anke Neumann,*,,§ Lingling environments. Recent findings of interfacial electron transfer between aqueous Fe(II) and structural Fe in clay tracer approach to simultaneously trace Fe atom movement from the aqueous phase to the solid (57 Fe

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

    NASA Astrophysics Data System (ADS)

    Lima, P. M.

    1991-07-01

    The solution of many problems concerning the electronic structure of atoms requires the evaluation of the matrix elements of the Hamiltonian operator, including the electrostatic interaction. These matrix elements may be expressed as weighted sums of radial integrals. The program we describe in this paper evaluates the coefficients of the Slater integrals and, if these are given, computes all the matrix elements for a given set of configurations. This program has nearly the same purposes as Hibbert's program (Comput. Phys. Commun. 1 (1969) 359) and is also based on the Racach techniques. The main difference between this algorithm and the cited one is the method used to calculate the recoupling coefficients. While Hibbert's programs use Burke's algorithm (Comput. Phys. Commun. 1 (1970) 241) to calculate these coefficients, in our program they are computed using the graphical techniques developed by Jucys et al. (Mathematical Apparatus of the Theory of Angular Momenta, Israel Program for Scientific Translation, Jerusalem, 1962). According to this method, that we describe in another paper (Comput. Phys. Commun. 66 (1991) 89, this issue) the formulae needed to calculate the recoupling coefficients are previously derived and simplified (as a first step of the program). The use of this method may considerably reduce the running time, specially in the case of large configuration interaction matrices.

  14. Lens capsule structure assessed with atomic force microscopy

    PubMed Central

    Sueiras, Vivian M.; Moy, Vincent T.

    2015-01-01

    Purpose To image the ultrastructure of the anterior lens capsule at the nanoscale level using atomic force microscopy (AFM). Methods Experiments were performed on anterior lens capsules maintained in their in situ location surrounding the lens from six human cadavers (donor age range: 44–88 years), four cynomolgus monkeys (Macaca fascicularis age range: 4.83–8.92 years), and seven pigs (<6 months). Hydration of all samples was maintained using Dulbecco’s Modified Eagle Medium (DMEM). Whole lenses were removed from the eye and placed anterior side up in agarose gel before gel hardening where only the posterior half of the lens was contained within the gel. After the gel hardened, the Petri dish was filled with DMEM until the point where the intact lens was fully submerged. AFM was used to image the anterior lens surface in contact mode. An integrated analysis program was used to calculate the interfibrillar spacing, fiber diameter, and surface roughness of the samples. Results The AFM images depict a highly ordered fibrous structure at the surface of the lens capsule in all three species. The interfibrillar spacing for the porcine, cynomolgus monkey, and human lens capsules was 0.68±0.25, 1.80±0.39, and 1.08±0.25 ?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. PMID:25814829

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

    PubMed

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

    2015-08-01

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics. PMID:26254642

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.

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

    E-print Network

    Savely G. Karshenboim

    2005-09-01

    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.

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

    SciTech Connect

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

    2003-09-11

    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.

  19. Atomic and electronic structures of Si(1 1 1)-[Formula: see text]-Au and (6 × 6)-Au surfaces.

    PubMed

    Patterson, C H

    2015-12-01

    Si(1 1 1)-Au surfaces with around one monolayer of Au exhibit many ordered structures and structures containing disordered domain walls. Hybrid density functional theory (DFT) calculations presented here reveal the origin of these complex structures and tendency to form domain walls. The conjugate honeycomb chain trimer (CHCT) structure of the [Formula: see text]-Au phase contains Si atoms with non-bonding surface states which can bind Au atoms in pairs in interstices of the CHCT structure and make this surface metallic. Si adatoms adsorbed on the [Formula: see text]-Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the [Formula: see text]-Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the [Formula: see text]-Au phase. Extra Au atoms bound in interstitial sites of the [Formula: see text]-Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a [Formula: see text]-Au phase, whose in-plane top atomic layer positions were previously determined by an electron holography technique (Grozea et al 1998 Surf. Sci. 418 32), is calculated using total energy minimization. The Patterson function for this structure is calculated and is in good agreement with data from an in-plane x-ray diffraction study (Dornisch et al 1991 Phys. Rev. B 44 11221). Filled and empty state scanning tunneling microscopy (STM) images are calculated for domain walls and the [Formula: see text]-Au structure. The [Formula: see text]-Au phase is 2D chiral and this is evident in computed and actual STM images. [Formula: see text]-Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si-Au top layers of the [Formula: see text]-Au and [Formula: see text]-Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given. PMID:26459741

  20. Semi-empirical predictions of even atomic energy levels and their hyperfine structure for the scandium atom

    SciTech Connect

    Dembczynski, J. . E-mail: Jerzy.Dembczynski@put.poznan.pl; Elantkowska, M.; Ruczkowski, J.; Stefanska, D.

    2007-01-15

    We report fine and hyperfine structure analysis of the system of even configurations of the Sc atom in a large multi-configuration basis. The complete energy scheme in the energy region up to about 50,000 cm{sup -1} has been established with the predicted values of the hyperfine cture constants A. The effects of the configuration interaction in the fine and hyperfine structure are discussed.

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

    SciTech Connect

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

    1984-01-01

    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.

  2. First-Principles Mobility Calculations and Atomic-Scale Interface Roughness in Nanoscale Structures

    SciTech Connect

    Evans, Matthew H; Zhang, Xiaoguang; Joannopoulos, J. D.; Pantelides, Sokrates T

    2005-01-01

    Calculations of mobilities have so far been carried out using approximate methods that suppress atomic-scale detail. Such approaches break down in nanoscale structures. Here we report the development of a method to calculate mobilities using atomic-scale models of the structures and density functional theory at various levels of sophistication and accuracy. The method is used to calculate the effect of atomic-scale roughness on electron mobilities in ultrathin double-gate silicon-on-insulator structures. The results elucidate the origin of the significant reduction in mobility observed in ultrathin structures at low electron densities.

  3. [18] improving structures using all-atom contacts 385 The methodology of macromolecular crystallography is mature, powerful,

    E-print Network

    Richardson, David

    [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

  4. 1MSE 2090: Introduction to Materials Science Chapter 3, Structure of solids How do atoms arrange themselves to form solids?

    E-print Network

    Zhigilei, Leonid V.

    1MSE 2090: Introduction to Materials Science Chapter 3, Structure of solids How do atoms arrange Why do atoms assemble into ordered structures (crystals)? Energyofinteratomicbond 0 Interatomic structure To discuss crystalline structures it is useful to consider atoms as being hard spheres with well

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

    PubMed

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

    2015-04-28

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by "dynamic heterogeneity" in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ?Ga with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time ?? can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations. PMID:25933773

  6. Chemical Vapor Deposition of High-Quality and Atomically Layered ReS2.

    PubMed

    He, Xuexia; Liu, Fucai; Hu, Peng; Fu, Wei; Wang, Xingli; Zeng, Qingsheng; Zhao, Wu; Liu, Zheng

    2015-10-01

    Recently, anisotropic 2D materials, such as black phosphorus and rhenium disulfides (ReS2 ), have attracted a lot attention because of their unique applications on electronics and optoelectronics. In this work, the direct growth of high-quality ReS2 atomic layers and nanoribbons has been demonstrated by using chemical vapor deposition (CVD) method. A possible growth mechanism is proposed according to the controlled experiments. The CVD ReS2 -based filed-effect transistors (FETs) show n-type semiconducting behavior with a current on/off ratio of ?10(6) and a charge carrier mobility of ?9.3 cm(2) Vs(-1) . These results suggested that the quality of CVD grown ReS2 is comparable to mechanically exfoliated ReS2 , which is also further supported by atomic force microscopy imaging, high-resolution transmission electron microscopy imaging and thickness-dependent Raman spectra. The study here indicates that CVD grown ReS2 may pave the way for the large-scale fabrication of ReS2 -based high-performance optoelectronic devices, such as anisotropic FETs and polarization detection. PMID:26305164

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

    USGS Publications Warehouse

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

    1982-01-01

    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.

  8. Observation of Metastable Structural Excitations and Concerted Atomic Motions on a Crystal Surface

    NASA Astrophysics Data System (ADS)

    Hwang, Ing-Shouh; Golovchenko, Jene

    1992-11-01

    The addition of a small number of lead atoms to a germanium(111) surface reduces the energy barrier for activated processes, and with a tunneling microscope it is possible to observe concerted atomic motions and metastable structures on this surface near room temperature. The formation and annihilation of these metastable structural surface excitations is associated with the shift in position of large numbers of germanium surface atoms along a specific row direction like beads on an abacus. The effect provides a mechanism for understanding the transport of atoms on a semiconductor surface.

  9. Plumes clustering around thermo-chemical structures with steep edges

    NASA Astrophysics Data System (ADS)

    Tan, E.

    2011-12-01

    The two Large Low Shear Velocity Provinces (LLSVPs) at the base of lower mantle are prominent features in all shear wave tomography models. LLSVPs cover about 20% of the core-mantle boundary (CMB) by area and have high elevation, extending at least 500 km above the CMB. Various lines of evidence suggest that the LLSVPs are thermo-chemical and are stable on the order of hundreds of million years. Reconciling the observed high elevation of LLSVPs and the conceived longevity is difficult in dynamic models unless the LLSVPs are made of high bulk modulus material. Hotspots and Large Igneous Province (LIP) eruption sites tend to cluster around the edges of LLSVPs. In iso-chemical models, plume roots commonly locate near the edges of slabs, which have strong lateral temperature gradients at the CMB. However, in thermo-chemical models, plumes are more likely to root on crests of the chemical anomalies. With 3-D global spherical dynamic models, we investigate the relation between the location of plumes and of chemical structures, which are composed of dense, high bulk modulus material. With reasonable values of bulk modulus and density anomalies, we find that the anomalous material forms dome-like structures with steep edges, which can survive for billions of years before being entrained. We find that more plumes occur near the edges, rather than on top, of the chemical domes. Moreover, plumes near the edges of domes have higher temperature than those atop the domes. We adjust the surface temperature to control the strength of the downwellings. When surface temperature is high and downwellings are weak or absent, plumes can originate from everywhere on the CMB. Only when the surface temperature are cold and downwellings are strong enough, the downwellings start pushing plumes toward the edges of the thermo-chemical structures. We conclude that the observed clustering of plumes around LLSVPs indicates that (1) LLSVPs have steep edges and (2) subducted slabs can reach to the CMB.

  10. The Flexible Pocketome Engine for Structural Chemical Genomics

    PubMed Central

    Abagyan, Ruben; Kufareva, Irina

    2010-01-01

    Biological metabolites, substrates, cofactors, chemical probes, and drugs bind to flexible pockets in multiple biological macromolecules to exert their biological effect. The rapid growth of the structural databases, sequence data, including SNPs and disease-related genome modifications, complemented by the new cutting-edge 3D docking, scoring and profiling methods created a unique opportunity to develop a comprehensive structural map of interactions between any small molecule and biopolymers. Here we demonstrated that a comprehensive structural genomics engine can be built using multiple pocket conformations, experimentally determined or generated with a variety of modeling methods, and new efficient ensemble docking algorithms. In contrast to traditional ligand-activity based engines trained on known chemical structures and their activities, the structural pocketome and docking engine will allow to predict poses and activities for new, previously unknown, protein binding sites, and new, previously uncharacterized, chemical scaffolds. This de novo structure-based activity prediction engine may dramatically accelerate the discovery of potent and specific therapeutics with reduced side effects. PMID:19727619

  11. Effect of Chemical Structure on Elastohydrodynamic Traction Coefficient

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The elastohydrodynamic traction properties of a series of biobased and petroleum based oils of varying chemical structures in steel-steel contact were investigated. Traction was measured on a ball-on disk type elastohydrodynamic traction instrument. Elastohydrodynamic traction coefficient (tc) was m...

  12. STRUCTURAL FEATURES ASSOCIATED WITH DEGRADABLE AND PERSISTENT CHEMICALS

    EPA Science Inventory

    A multivariate statistical method and a heuristic method were employed to examine the structural features associated with the persistence of degradation of 287 chemicals tested with the standard biochemical oxygen demand(BOD) procedure. The data base consisted of 196 'degradable'...

  13. Modeling the Atomic-to-molecular Transition and Chemical Distributions of Turbulent Star-forming Clouds

    NASA Astrophysics Data System (ADS)

    Offner, Stella S. R.; Bisbas, Thomas G.; Viti, Serena; Bell, Tom A.

    2013-06-01

    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+, C, H2, 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 H2 abundances are discrepant in the boundary regions (A v <= 5), which is due to the different number of rays used by the two approaches.

  14. From Petascale to Exascale: Prospects for Transforming Atomic, Molecular, and Chemical Dynamics with Leadership Computing

    NASA Astrophysics Data System (ADS)

    Wells, Jack

    2013-05-01

    Modeling and simulation with petascale computing has supercharged the process of innovation and understanding, dramatically accelerating time-to-insight and time-to-discovery. From petascale modeling of combustion for advanced engines, to designing bio-inspired catalysts for renewable energy, to exploring the evolution of complex systems such as our earth's climate, or breakthroughs gained from quantum many-body applications in chemical and nuclear physics, petascale computing is delivering high impact results that are transforming science and engineering. This presentation will provide an overview of the unique computational resources and user programs at the Oak Ridge Leadership Computing Facility (OLCF) at DOE's Oak Ridge National Laboratory, discuss a range of ambitious computational research projects underway in atomic, molecular, and chemical physics, and discuss scientific opportunities and challenges associated with advancing computational capabilities to the exascale. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

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

    SciTech Connect

    Offner, Stella S. R.; Bisbas, Thomas G.; Viti, Serena; Bell, Tom A.

    2013-06-10

    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.

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

    NASA Astrophysics Data System (ADS)

    de Silva, Piotr; Korchowiec, Jacek; Wesolowski, Tomasz A.

    2014-04-01

    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.

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

    DOEpatents

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

    2004-07-13

    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.

  18. New version: GRASP2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

    Jönsson, P.; Gaigalas, G.; Biero?, J.; Fischer, C. Froese; Grant, I. P.

    2013-09-01

    A revised version of GRASP2K [P. Jönsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597] is presented. It supports earlier non-block and block versions of codes as well as a new block version in which the njgraf library module [A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375] has been replaced by the librang angular package developed by Gaigalas based on the theory of [G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747, G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263]. Tests have shown that errors encountered by njgraf do not occur with the new angular package. The three versions are denoted v1, v2, and v3, respectively. In addition, in v3, the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Changes in v2 include minor improvements. For example, the new version of rci2 may be used to compute quantum electrodynamic (QED) corrections only from selected orbitals. In v3, a new program, jj2lsj, reports the percentage composition of the wave function in LSJ and the program rlevels has been modified to report the configuration state function (CSF) with the largest coefficient of an LSJ expansion. The bioscl2 and bioscl3 application programs have been modified to produce a file of transition data with one record for each transition in the same format as in ATSP2K [C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. All versions of the codes have been adapted for 64-bit computer architecture. Program SummaryProgram title: GRASP2K, version 1_1 Catalogue identifier: ADZL_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_1.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.: 730252 No. of bytes in distributed program, including test data, etc.: 14808872 Distribution format: tar.gz Programming language: Fortran. Computer: Intel Xeon, 2.66 GHz. Operating system: Suse, Ubuntu, and Debian Linux 64-bit. RAM: 500 MB or more Classification: 2.1. Catalogue identifier of previous version: ADZL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 597 Does the new version supersede the previous version?: Yes Nature of problem: Prediction of atomic properties — atomic energy levels, oscillator strengths, radiative decay rates, hyperfine structure parameters, Landé gJ-factors, and specific mass shift parameters — using a multiconfiguration Dirac-Hartree-Fock approach. Solution method: The computational method is the same as in the previous GRASP2K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A comprehensive user manual in pdf format for the program package has been added. Restrictions: The packing

  19. Smallest Nanoelectronic with Atomic Devices with Precise Structures

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige

    2000-01-01

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

  20. Atomic and electronic structure of nitrogen- and boron-doped phosphorene

    E-print Network

    Boukhvalov, Danil W

    2015-01-01

    First principle modeling of nitrogen- and boron-doped phosphorene demonstrates the tendency toward formation of highly ordered structures. Nitrogen doping leads to the formation of -N-P-P-P-N- lines. Further transformation to -P-N-P-N- lines across the chains of phosphorene occurs with increasing band gap and increasing nitrogen concentration, which coincides with the decreasing chemical activity of N-doped phosphorene. In contrast to the case of nitrogen, boron atoms prefer to form -B-B- pairs with the further formation of -P-P-B-B-P-P- patterns along the phosphorene chains. The low concentration of boron dopants converts the phosphorene from a semiconductor into a semimetal with the simultaneous enhancement of its chemical activity. Co-doping of phosphorene by both boron and nitrogen starts from the formation of -B-N- pairs, which provide flat bands and the further transformation of these pairs to hexagonal BN lines and ribbons across the phosphorene chains.

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

    NASA Astrophysics Data System (ADS)

    Suewattana, Malliga

    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.

  2. Global Materials Structure Search with Chemically Motivated Coordinates.

    PubMed

    Panosetti, Chiara; Krautgasser, Konstantin; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces. PMID:26444084

  3. Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

    SciTech Connect

    Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

    2005-03-01

    Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

  4. Atomic structure and magnetic properties of Fe1-xCox alloys

    SciTech Connect

    Nguyen, Manh Cuong; Zhao, Xin; Ji, Min; Wang, Cai-Zhuang; Harmon, Bruce; Ho, Kai-Ming

    2012-03-09

    Using genetic algorithm with first-principle calculations, we searched for low-energy crystal structures of Fe1?xCox alloys. We found that Fe1?xCox alloys are highly configurationally degenerate with many additional off-stoichiometric stable structures to the well-known B2 structure. The average magnetic moment of Fe atom increases with concentration of Co in the alloy, while that of Co atom is almost constant, which are consistent with experiments and earlier studies. The magnetic moment of Fe atom is strongly dependent on the number of Co nearest neighbor and it increases with this number.

  5. Direct Determination of Grain Boundary Atomic Structure in SrTiO3.

    PubMed

    McGibbon, M M; Browning, N D; Chisholm, M F; McGibbon, A J; Pennycook, S J; Ravikumar, V; Dravid, V P

    1994-10-01

    An atomic structure model for a 25 degrees [001] symmetric tilt grain boundary in SrTiO(3) has been determined directly from experimental data with the use of high-resolution Z-contrast imaging coupled with electron energy loss spectroscopy. The derived model of the grain boundary was refined by bond-valence sum calculations and reveals candidate sites for dopant atoms in the boundary plane. These results show how the combined techniques can be used to deduce the atomic structure of defects and interfaces without recourse to preconceived structural models or image simulations. PMID:17814005

  6. Structure activity relationships to assess new chemicals under TSCA

    SciTech Connect

    Auletta, A.E.

    1990-12-31

    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.

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

    PubMed Central

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

    2014-01-01

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

  8. Investigation of plasma-doped fin structure and characterization of dopants by atom probe tomography

    SciTech Connect

    Kim, B. H.; Park, S. M.; Park, S. W.; Park, Y. B.; Kim, H. J.; Park, C. G.

    2012-11-19

    As and P dopants in a plasma-doped Si-based fin structure were analyzed using atom probe tomography. The distributions and concentrations of As and P atoms in various regions of the fin structure and the oxidation levels for different dopants were determined. Most dopants were segregated at the fin boundary, and the As and P concentrations exceeded 9 Multiplication-Sign 10{sup 20} atoms/cm{sup 3} and 2 Multiplication-Sign 10{sup 20} atoms/cm{sup 3}, respectively. The atomic oxygen and SiO{sub 2} concentrations depended on the dopant type. The larger and heavier As dopant severely damaged the surface of the fin structure and could cause more severe oxidation.

  9. Towards chemical structure resolution with nanoscale nuclear magnetic resonance spectroscopy

    E-print Network

    Xi Kong; Alexander Stark; Jiangfeng Du; Liam P. McGuinness; Fedor Jelezko

    2015-06-19

    Nuclear magnetic resonance (NMR) spectroscopy has approached the limit of single molecule sensitivity, however the spectral resolution is currently insufficient to obtain detailed information on chemical structure and molecular interactions. Here we demonstrate more than two orders of magnitude improvement in spectral resolution by performing correlation spectroscopy with shallow nitrogen-vacancy (NV) magnetic sensors in diamond. In principle, the resolution is sufficient to observe chemical shifts in $\\sim$1 T magnetic fields, and is currently limited by molecular diffusion at the surface. We measure oil diffusion rates of $D = 0.15 - 0.2$\\,nm$^2/\\mathrm{\\mu}$s within (5 nm)$^3$ volumes at the diamond surface.

  10. Structure of adsorbed monolayers. The surface chemical bond

    SciTech Connect

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

    1984-06-01

    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.

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

    E-print Network

    Bristol, University of

    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

  12. Learning about Atoms, Molecules, and Chemical Bonds: A Case Study of Multiple-Model Use in Grade 11 Chemistry.

    ERIC Educational Resources Information Center

    Harrison, Allan G.; Treagust, David F.

    2000-01-01

    Reports in detail on a year-long case study of multiple-model use at grade 11. Suggests that students who socially negotiated the shared and unshared attributes of common analogical models for atoms, molecules, and chemical bonds used these models more consistently in their explanations. (Author/CCM)

  13. Racing carbon atoms. Atomic motion reaction coordinates and structural effects on Newtonian kinetic isotope effects.

    PubMed

    Andujar-De Sanctis, Ivonne L; Singleton, Daniel A

    2012-10-19

    Intramolecular (13)C kinetic isotope effects were determined for the dimerization of methacrolein. Trajectory studies accurately predict the isotope effects and support an origin in Newton's second law of motion, with no involvement of zero-point energy or transition state recrossing. Atomic motion reaction coordinate diagrams are introduced as a way to qualitatively understand the selectivity. PMID:23025278

  14. Method development for the determination of lead in wine using electrothermal atomic absorption spectrometry comparing platform and filter furnace atomizers and different chemical modifiers.

    PubMed

    Dessuy, Morgana B; Vale, Maria Goreti R; Souza, Anderson S; Ferreira, Sérgio L C; Welz, Bernhard; Katskov, Dmitri A

    2008-02-15

    A method has been developed for the determination of lead in wine by electrothermal atomic absorption spectrometry without any sample preparation and calibration against aqueous standards, using 7.5 microg Pd as a chemical modifier. The results obtained for seven wines using the proposed method and an acid digestion procedure did not show any significant difference using a Student's t-test. Atomization in a transversally heated filter atomizer (THFA) was compared with atomization in a conventional transversally heated platform furnace. The former provided a 2.6-fold higher sensitivity, improving the characteristic mass from 34 to 12 pg and a 1.6-fold better limit of detection (0.3 microg L(-1) compared to 0.5 microg L(-1)) for aqueous solutions using the same injection volume of 20 microL. However, the average precision, expressed as the relative standard deviation for the determination of lead in wine under routine conditions was improved from 4.6% with platform atomization to 0.6% in the THFA. The lead content found in seven arbitrarily chosen white and red wines, five from Brazil, one from Chile and one from Spain, ranged from 6 to 60 microg L(-1) Pb with an average content of 11.4 microg L(-1) Pb for the wines from South America. PMID:18371785

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

    E-print Network

    Raji Heyrovska

    2008-06-21

    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.

  16. Three-Dimensional Structure of Nanocomposites from Atomic Pair Distribution Function Analysis: Study of Polyaniline and

    E-print Network

    Trikalitis, Pantelis N.

    Three-Dimensional Structure of Nanocomposites from Atomic Pair Distribution Function Analysis of an 84-atom orthorhombic unit cell. The nanocomposite (PANI)0.5V2O5,1.0H2O too is locally well ordered polymeric nanocomposites have attracted much attention because of their unique and novel properties

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

    ERIC Educational Resources Information Center

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

    2002-01-01

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

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

    ERIC Educational Resources Information Center

    Park, Eun Jung; Light, Gregory

    2009-01-01

    Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…

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

    E-print Network

    Birkl, Gerhard

    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

  20. Resolving the atomic structure of supported nanometer-size Au clusters Department of Physics, Purdue University, West Lafayette, Indiana 47907

    E-print Network

    Resolving the atomic structure of supported nanometer-size Au clusters D. Lovall Department to resolve the atomic structure and orientation of individual nanometer- size Au clusters supported on sharp Traditionally, the atomic structure of a small metal cluster has been investigated using high

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

    E-print Network

    Zhigilei, Leonid V.

    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

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

    E-print Network

    Zhang, Yang

    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

  3. Ultrafast electron diffraction and direct observation of transient structures in a chemical reaction

    PubMed Central

    Cao, Jianming; Ihee, Hyotcherl; Zewail, Ahmed H.

    1999-01-01

    Ultrafast electron diffraction is a unique method for the studies of structural changes of complex molecular systems. In this contribution, we report direct ultrafast electron diffraction study of the evolution of short-lived intermediates in the course of a chemical change. Specifically, we observe the transient intermediate in the elimination reaction of 1,2-diiodotetrafluoroethane (C2F4I2) to produce the corresponding ethylene derivative by the breakage of two carbon–iodine, C—I, bonds. The evolution of the ground-state intermediate (C2F4I radical) is directly revealed in the population change of a single chemical bond, namely the second C—I bond. The elimination of two iodine atoms was shown to be nonconcerted, with reaction time of the second C—I bond breakage being 17 ± 2 ps. The structure of the short-lived C2F4I radical is more favorable to the classical radical structure than to the bridged radical structure. This leap in our ability to record structural changes on the ps and shorter time scales bodes well for many future applications in complex molecular systems. PMID:9892634

  4. Atomic-Scale Chemical Imaging of Composition and Bonding at Perovskite Oxide Interfaces

    NASA Astrophysics Data System (ADS)

    Fitting Kourkoutis, L.

    2010-03-01

    Scanning transmission electron microscopy (STEM) in combination with electron energy loss spectroscopy (EELS) has proven to be a powerful technique to study buried perovskite oxide heterointerfaces. With the recent addition of 3^rd order and now 5^th order aberration correction, which provides a factor of 100x increase in signal over an uncorrected system, we are now able to record 2D maps of composition and bonding of oxide interfaces at atomic resolution [1]. Here, we present studies of the microscopic structure of oxide/oxide multilayers and heterostructures by STEM in combination with EELS and its effect on the properties of the film. Using atomic-resolution spectroscopic imaging we show that the degradation of the magnetic and transport properties of La0.7Sr0.3MnO3/SrTiO3 multilayers correlates with atomic intermixing at the interfaces and the presence of extended defects in the La0.7Sr0.3MnO3 layers. When these defects are eliminated, metallic ferromagnetism at room temperature can be stabilized in 5 unit cell thick manganite layers, almost 40% thinner than the previously reported critical thickness of 3-5 nm for sustaining metallic ferromagnetism below Tc in La0.7Sr0.3MnO3 thin films grown on SrTiO3.[4pt] [1] D.A. Muller, L. Fitting Kourkoutis, M. Murfitt, J.H. Song, H.Y. Hwang, J. Silcox, N. Dellby, O.L. Krivanek, Science 319, 1073-1076 (2008).

  5. Applications of the Cambridge Structural Database in chemical education1

    PubMed Central

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

    2010-01-01

    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

  6. Atomic and electronic structure of bismuth-bilayer-terminated Bi2Se3 (0001) prepared by atomic hydrogen etching

    NASA Astrophysics Data System (ADS)

    Shokri, Roozbeh; Meyerheim, Holger L.; Roy, Sumalay; Mohseni, Katayoon; Ernst, A.; Otrokov, M. M.; Chulkov, E. V.; Kirschner, J.

    2015-05-01

    A bilayer of bismuth is recognized as a prototype two-dimensional topological insulator. Here we present a simple and well reproducible top-down approach to prepare a flat and well ordered bismuth bilayer with a lateral size of several hundred nanometers on Bi2Se3 (0001). Using scanning tunneling microscopy, surface x-ray diffraction, and Auger electron spectroscopy we show that exposure of Bi2Se3 (0001) to atomic hydrogen completely removes selenium from the top quintuple layer. The band structure of the system, calculated from first principles for the experimentally derived atomic structure, is in excellent agreement with recent photoemission data. Our results open interesting perspectives for the study of topological insulators in general.

  7. Electronic structure, magnetic structure, and metal-atom site preferences in CrMnAs

    NASA Astrophysics Data System (ADS)

    Lutz, Laura Christine

    Density functional theory was used to examine stoichiometric CrMnAs, one of a class of 3d-metal arsenides that exhibit cooperative magnetic ordering. CrMnAs is a tetragonal structure with two inequivalent metal sites: M(I), which is tetrahedral coordinate, and M(II), which is square pyramidal coordinate. CrMnAs thus presents a "coloring problem," the question of how the two types of metal atoms are distributed between the two types of metal sites. Previous diffraction studies have determined that CrMnAs is antiferromagnetic with the M(I) site primarily occupied by Cr. TB-LMTO-ASA local density approximation (LDA) calculations showed indications of instability in the nonmagnetic structure, which could be resolved either by structural distortion or by spin polarization. LDA crystal orbital Hamilton population (COHP) curves were used to predict the nature of particular direct-exchange interactions upon spin polarization. Spin-polarized total energy calculations were performed using VASP with the generalized gradient approximation (GGA). The lowest-energy structure had Mn at the M(I) site and a different antiferromagnetic ordering than previously observed. The structure with the second-lowest calculated total energy also had Mn at M(I). Next lowest were four structures with Cr at M(I), including the experimentally observed structure. Those four had calculated total energies ranging from 154.2 to 167.8 meV/f.u. higher than the lowest-energy case. The number of possible structures with small energy differences suggests that the observed magnetic ordering and coloring may be due to entropy rather than reflecting a true electronic ground state.

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

    E-print Network

    Rohrer, Gregory S.

    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

  9. In situ metal-organic chemical vapor deposition atomic-layer deposition of aluminum oxide on GaAs using trimethyaluminum

    E-print Network

    In situ metal-organic chemical vapor deposition atomic-layer deposition of aluminum oxide on Ga 26 June 2008; published online 21 July 2008 In situ atomic-layer deposition ALD of Al2O3 on p­4 Recently, many ex situ methods such as atomic-layer deposition ALD of high-k on GaAs have achieved success

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

    NASA Astrophysics Data System (ADS)

    Heyrovska, Raji; Narayan, Sara

    2009-04-01

    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.

  11. High-precision relativistic atomic structure calculations and the EBIT

    E-print Network

    Johnson, Walter R.

    interactions, relaxed-core QED corrections, two-loop Lamb shifts, negative-energy state corrections, nuclear of finite nuclear size corrections to the atomic transition energies by Seely et al. As shown in Fig. 1 polarizations and nuclear recoils. PACS Nos.: 31.30.Jv, 32.30.Rj, 31.25.-v, 31.15.Ar 1. Introduction

  12. Atomic and Electronic Structure of Polar Oxide Interfaces

    SciTech Connect

    Gajdardziska-Josifovska, Marija

    2014-01-17

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

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

    PubMed Central

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

    2013-01-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    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.

  15. Directional analysis of 3D tubular structures via isotropic well-localized atoms

    E-print Network

    Labate, Demetrio

    Directional analysis of 3D tubular structures via isotropic well-localized atoms David Jim segmentation of 3D vessel-like structures is a major challenge in medical imaging. In this paper, we introduce a novel approach for the de- tection of 3D tubular structures that is particularly suited to capture

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

    SciTech Connect

    Curtis, L. J.

    2004-05-01

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

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

    SciTech Connect

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

    2013-08-01

    Details of five very high-resolution accurate structures of bovine trypsin are compared in the context of the reproducibility of models obtained from crystals grown under identical conditions. Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C{sup ?} 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.

  18. Quantum Chemical Insight into the LiF Interlayer Effects in Organic Electronics: Reactions between Al Atom and LiF Clusters.

    PubMed

    Wu, Shui-Xing; Kan, Yu-He; Li, Hai-Bin; Zhao, Liang; Wu, Yong; Su, Zhong-Min

    2015-08-01

    It is well known that the aluminum cathode performs dramatically better when a thin lithium fluoride (LiF) layer inserted in organic electronic devices. The doping effect induced by the librated Li atom via the chemical reactions producing AlF3 as byproduct was previously proposed as one of possible mechanisms. However, the underlying mechanism discussion is quite complicated and not fully understood so far, although the LiF interlayer is widely used. In this paper, we perform theoretical calculations to consider the reactions between an aluminum atom and distinct LiF clusters. The reaction pathways of the Al-(LiF)n (n = 2, 4, 16) systems were discovered and the energetics were theoretically evaluated. The release of Li atom and the formation of AlF3 were found in two different chemical reaction routes. The undissociated Al-(LiF)n systems have chances to change to some structures with loosely bound electrons. Our findings about the interacted Al-(LiF)n systems reveal new insights into the LiF interlayer effects in organic electronics applications. PMID:26267187

  19. The chemical structure of the pigments in Ara macao plumage.

    PubMed

    Stradi, R; Pini, E; Celentano, G

    2001-08-01

    Parrots (Psittaciformes) harbor unusually bright, non-carotenoid, feather pigments. We successfully extracted and purified a sufficient quantity of pigment from the red plumage of the Scarlet Macaw (Ara macao) for a partial chemical analysis. The extracts were analyzed by HPLC coupled with UV-VIS and mass spectroscopy before and after total hydrogenation. We found at least four pigment components. We propose a linear polyenal structure comparable with the molecules tetradecahexenal, hexadecaheptenal, octadecaoctenal and eicosanonenal. PMID:11470444

  20. Usnic acid: preparation, structure, properties and chemical transformations

    NASA Astrophysics Data System (ADS)

    Sokolov, D. N.; Luzina, O. A.; Salakhutdinov, Nariman F.

    2012-08-01

    Published data on the chemistry of usnic acid since the time of its isolation in a pure state up to now are integrated and analyzed. The preparation methods, structure and properties of this compound are considered. The data on the chemical transformations of usnic acid comprise reactions that do not affect the carbon skeleton and reactions accompanied by carbon skeleton destruction. The bibliography includes 96 references.

  1. Electronic and chemical structure of metal-silicon interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, P. J.; Grunthaner, F. J.

    1984-01-01

    This paper reviews our current understanding of the near-noble metal silicides and the interfaces formed with Si(100). Using X-ray photoemission spectroscopy, we compare the chemical composition and electronic structure of the room temperature metal-silicon and reacted silicide-silicon interfaces. The relationship between the interfacial chemistry and the Schottky barrier heights for this class of metals on silicon is explored.

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

    PubMed Central

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

    2015-01-01

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry. PMID:26286479

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

    SciTech Connect

    Kim, Min-Geun; Jang, Hong-Lae; Cho, Seonho

    2013-05-01

    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.

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

    PubMed

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

    2015-08-12

    We report an aberration-corrected electron microscopy analysis of the adhesion and atomic structures of gold nanoparticle catalysts supported on ceria nanocubes and nanorods. Under oxidative conditions, the as-prepared gold nanoparticles on the ceria nanocubes have extended atom layers at the metal-support interface. In contrast, regular gold nanoparticles and rafts are present on the ceria nanorod supports. Under the reducing conditions of water-gas shift reaction, the extended gold atom layers and rafts vanish. In addition, the gold particles on the nanocubes change in morphology and increase in size while those on the nanorods are almost unchanged. The size, morphology, and atomic interface structures of gold strongly depend on the surface structures of ceria supports ((100) surface versus (111) surface) and the reaction environment (reductive versus oxidative). These findings provide insights into the deactivation mechanisms and the shape-dependent catalysis of oxide supported metal catalysts. PMID:26222267

  5. Bifunctional sensing characteristics of chemical vapor deposition synthesized atomic-layered MoS2.

    PubMed

    Cho, Byungjin; Kim, Ah Ra; Park, Youngjin; Yoon, Jongwon; Lee, Young-Joo; Lee, Sangchul; Yoo, Tae Jin; Kang, Chang Goo; Lee, Byoung Hun; Ko, Heung Cho; Kim, Dong-Ho; Hahm, Myung Gwan

    2015-02-01

    Two-dimensional (2D) molybdenum disulfide (MoS2) atomic layers have a strong potential to be adopted for 2D electronic components due to extraordinary and novel properties not available in their bulk foams. Unique properties of the MoS2, including quasi-2D crystallinity, ultrahigh surface-to-volume, and a high absorption coefficient, have enabled high-performance sensor applications. However, implementation of only a single-functional sensor presents a limitation for various advanced multifunctional sensor applications within a single device. Here, we demonstrate the charge-transfer-based sensitive (detection of 120 ppb of NO2) and selective gas-sensing capability of the chemical vapor deposition synthesized MoS2 and good photosensing characteristics, including moderate photoresponsivity (?71 mA/W), reliable photoresponse, and rapid photoswitching (<500 ms). A bifunctional sensor within a single MoS2 device to detect photons and gas molecules in sequence is finally demonstrated, paving a way toward a versatile sensing platform for a futuristic multifunctional sensor. PMID:25575096

  6. STM study of the atomic structure of the icosahedral Al-Cu-Fe fivefold surface

    NASA Astrophysics Data System (ADS)

    Cai, T.; Fournée, V.; Lograsso, T.; Ross, A.; Thiel, P. A.

    2002-04-01

    We use scanning tunneling microscopy (STM) to investigate the atomic structure of the icosahedral (i-) Al-Cu-Fe fivefold surface in ultra high vacuum (UHV). Studies show that large, atomically flat terraces feature many ten-petal ``flowers'' with internal structure. The observed flower patterns can be associated with features on Al rich dense atomic planes generated from two-dimensional cuts of bulk models based on x-ray and neutron diffraction experiments. The results confirm that the fivefold surface of i-Al-Cu-Fe corresponds to a bulk-terminated plane.

  7. Quantitative structure-property relationships in boron nitrides: the 15N- and 11B chemical shifts.

    PubMed

    Marian, C M; Gastreich, M

    2001-01-01

    Nuclear Magnetic Resonance (NMR) chemical shifts(delta) for elements in solids may often be approached by ab initio cluster calculations. We employ this technique to investigate the influence of structural alterations on the 15N and 11B chemical shifts in boron nitrides--in both hexagonal and cubic modifications. Within a given class of connectivity, i.e., three- or fourfold coordinated nitrogen, for the first time, an almost linear correlation between the 15N chemical shift and N-B bond lengths could be established. Also, the 11B shifts in hexagonal boron nitride correlate with the B-N bond distance; however, the effect is less pronounced. For the value of the chemical shift (CS), the decisive property is the average bond length at the atom in focus. Variations of CS are predominantly caused by changes in the paramagnetic deshielding. Further, second-nearest neighbor effects on the shieldings at 15N nuclei are quantified by subtraction schemes. The present work is closely related to the verification of models for amorphous high-demand Si/B/N ceramics. PMID:11407601

  8. Atomic structure of the (310) twin in niobium: Experimental determination and comparison with theoretical predictions

    NASA Astrophysics Data System (ADS)

    Campbell, Geoffrey H.; Foiles, Stephen M.; Gumbsch, Peter; Rühle, Manfred; King, Wayne E.

    1993-01-01

    The atomic structure of the (310) twin in Nb was predicted using interatomic potentials derived from the embedded atom method (EAM), Finnis-Sinclair theory (FS), and the model generalized pseudopotential theory (MGPT). The EAM and FS predicted structures with crystal translations which break mirror symmetry. The MGPT predicted one stable structure which possessed mirror symmetry. This defect was experimentally determined to have mirror symmetry. These findings emphasize that the angular dependent interactions modeled by the MGPT are important for determining defect structures in bcc transition metals.

  9. The structural evolution and diffusion during the chemical transformation from cobalt to cobalt phosphide nanoparticles

    SciTech Connect

    Ha, Don-Hyung; Moreau, Liane M.; Bealing, Clive R.; Zhang, Haitao; Hennig, Richard G.; Robinson, Richard D.

    2011-01-01

    We report the structural evolution and the diffusion processes which occur during the phase transformation of nanoparticles (NPs), ?-Co to Co{sub 2}P to CoP, from a reaction with tri-n-octylphosphine (TOP). Extended X-ray absorption fine structure (EXAFS) investigations were used to elucidate the changes in the local structure of cobalt atoms which occur as the chemical transformation progresses. The lack of long-range order, spread in interatomic distances, and overall increase in mean-square disorder compared with bulk structure reveal the decrease in the NP’s structural order compared with bulk structure, which contributes to their deviation from bulk-like behavior. Results from EXAFS show both the Co{sub 2}P and CoP phases contain excess Co. Results from EXAFS, transmission electron microscopy, X-ray diffraction, and density functional theory calculations reveal that the inward diffusion of phosphorus is more favorable at the beginning of the transformation from ?-Co to Co{sub 2}P by forming an amorphous Co-P shell, while retaining a crystalline cobalt core. When the major phase of the sample turns to Co{sub 2}P, the diffusion processes reverse and cobalt atom out-diffusion is favored, leaving a hollow void, characteristic of the nanoscale Kirkendall effect. For the transformation from Co{sub 2}P to CoP theory predicts an outward diffusion of cobalt while the anion lattice remains intact. In real samples, however, the Co-rich nanoparticles continue Kirkendall hollowing. Knowledge about the transformation method and structural properties provides a means to tailor the synthesis and composition of the NPs to facilitate their use in applications.

  10. Electron correlation and relativistic effects in atomic structure calculations of the thorium atom

    NASA Astrophysics Data System (ADS)

    Roy, S. K.; Prasad, Rajendra; Chandra, P.

    2011-06-01

    Relativistic two-component ab initio calculations have been performed for the Th atom. The spin free low lying states have been calculated at state-averaged complete active space self-consistent field (SA-CASSCF) and multi-state complete active space second-order perturbation (MS-CASPT2) level of theories using different sets of active orbitals. The spin-orbit states have been computed using Douglas-Kroll type of atomic mean-field integral approach. The effects of dynamic electron correlation have been studied at the MS-CASPT2 level. The energy levels of spin-orbit states below 30 000 cm-1 obtained by the inclusion of dynamic electron correlation are in very good agreement with the experimental values. The radiative properties such as weighted transition probabilities (gA) and oscillator strengths (gf) among several spin-orbit states have been calculated at the SA-CASSCF and MS-CASPT2 levels and are expected to be very helpful for future experiments.

  11. Chemical and physical structures of proteinoids and related polyamino acids

    NASA Astrophysics Data System (ADS)

    Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

    Studies of polyamino acid formation pathways in the prebiotic condition are important for the study of the origins of life. Several pathways of prebiotic polyamino acid formation have been reported. Heating of monoammonium malate [1] and heating of amino acids in molten urea [2] are important pathways of the prebiotic peptide formation. The former case, globular structure called proteinoid microsphere is formed in aqueous conditions. The later case, polyamino acids are formed from unrestricted amino acid species. Heating of aqueous aspargine is also interesting pathway for the prebiotic polyamino acid formation, because polyamino acid formation proceeds in aqueous condition [3]. In this study, we analyzed the chemical structure of the proteinoids and related polyamino acids formed in the above three pathways using with mass spectrometer. In addition, their physical structures are analyzed by the electron and optical microscopes, in order to determine the self-organization abilities. We discuss the relation between the chemical and the physical structures for the origins of life. References [1] Harada, K., J. Org. Chem., 24, 1662 (1959), Fox, S. W., Harada, K., and Kendrick, J., Science, 129, 1221 (1959). [2] Terasaki, M., Nomoto, S., Mita, H., and Shimoyama, A., Chem. Lett., 480 (2002), Mita, H., Nomoto, S., Terasaki, M., Shimoyama, A., and Yamamoto, Y., Int. J. Astrobiol., 4, 145 (2005). [3] Kovacs, K and Nagy, H., Nature, 190, 531 (1961), Munegumi, T., Tanikawa, N., Mita, H. and Harada, K., Viva Origino, 22, 109 (1994).

  12. Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures

    PubMed Central

    Chen, Xianfeng; Weber, Irene; Harrison, Robert W.

    2009-01-01

    Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability and dynamics, as well as interacting with the bulk water. Water potential functions are often parameterized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution (?1.0 Å) protein crystal structures with a high level of hydration water by calculating the experimental water-protein radial distribution function or surface distribution function (SDF) and water radial distribution function (RDF). Two maxima are observed in SDF: the first maximum at a radius of 2.75 Å reflects first shell and hydrogen bond interactions between protein and water, the second maximum at 3.65 Å reflects second shell and van der Waals interactions between water and non-polar atoms of protein forming clathrate-hydrate-like structures. Thus, the two shells do not overlap. The RDF showed the features of liquid water rather than solid ice. The first and second maxima of RDF at 2.75 and 4.5 Å, respectively, are the same as for bulk water, but the peaks are sharper indicating hydration water is more stable than bulk water. Both distribution functions are inversely correlated with the distribution of B factors (atomic thermal factors) for the waters, suggesting that the maxima reflect stable positions. Therefore, the average water structure near the protein surface has experimentally observable differences from bulk water. This analysis will help improve the accuracy for models of water on the protein surface by providing rigorous data for the effects of the apparent chemical potential of the water near a protein surface. PMID:18754631

  13. Visualization of the atomic structure of solid solutions with the NaCl structure

    NASA Astrophysics Data System (ADS)

    Babanov, Yu. A.; Ponomarev, D. A.; Ustinov, V. V.

    2015-04-01

    It has been shown how an atomic cluster for a solid solution with a rock salt structure can be constructed using the Pauling model. Simulation has been performed for 343000 ions of Ni x Zn1 - x O3 ( x = 0, 0.3, 0.5, 0.7, 1.0) oxide substitutional solid solutions. Coordinates of all cluster ions are obtained and distribution functions of ion pairs (Ni-O, Ni-Ni, Ni-Zn, Zn-Zn, Zn-O, O-O) are constructed as functions of distance. The shape of the normal distribution indicates the existence of bounded chaos in the system of oxide solid solutions. The width of the Gaussian distribution function is determined by the difference of metal ionic radii. The results are in agreement with both X-ray diffraction and EXAFS spectroscopy data.

  14. 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...

  15. 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...

  16. Chemical and structural changes in blood undergoing laser photocoagulation.

    PubMed

    Black, John F; Barton, Jennifer Kehlet

    2004-01-01

    The treatment of cutaneous vascular lesions (port wine stains etc.) using lasers has been guided by theories based on the "cold" or room-temperature optical properties of the hemoglobin target chromophore. We have recently presented evidence showing that under the influence of laser irradiation, the optical properties of blood in vitro are time and temperature dependent. Such complications are not currently subsumed into the in vivo theory. Here, we study the time-domain optical properties of blood undergoing photocoagulation in vitro using two newly developed time-resolved techniques. We also study the asymptotic effect of laser photocoagulation on the chemical and structural properties of the components of the blood matrix. We present evidence showing that the photocoagulation process involves significant changes in the optical absorption and scattering properties of blood, coupled with photothermally induced chemical and structural changes. We demonstrate the first use of a laser to deliberately generate magnetic resonance imaging contrast in vitro. We show that this technique offers significant potential advantages to in vivo intravenous chemical contrast agent injection. PMID:15339203

  17. 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

    Friesner, Richard A.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.

    2003-03-01

    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.

  18. J. Phys. Chem. 1995, 99, 15557-15564 15557 Confined Clusters of Rare Gas Atoms: Structures and Phases

    E-print Network

    Berry, R. Stephen

    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

  19. Atomic structure and dynamic behaviour of truly one-dimensional ionic chains inside carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Senga, Ryosuke; Komsa, Hannu-Pekka; Liu, Zheng; Hirose-Takai, Kaori; Krasheninnikov, Arkady V.; Suenaga, Kazu

    2014-11-01

    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.

  20. Cation-Poor Complex Metallic Alloys in Ba(Eu)-Au-Al(Ga) Systems: Identifying the Keys that Control Structural Arrangements and Atom Distributions at the Atomic Level.

    PubMed

    Smetana, Volodymyr; Steinberg, Simon; Mudryk, Yaroslav; Pecharsky, Vitalij; Miller, Gordon J; Mudring, Anja-Verena

    2015-11-01

    Four complex intermetallic compounds BaAu6±xGa6±y (x = 1, y = 0.9) (I), BaAu6±xAl6±y (x = 0.9, y = 0.6) (II), EuAu6.2Ga5.8 (III), and EuAu6.1Al5.9 (IV) have been synthesized, and their structures and homogeneity ranges have been determined by single crystal and powder X-ray diffraction. Whereas I and II originate from the NaZn13-type structure (cF104-112, Fm3?c), III (tP52, P4/nbm) is derived from the tetragonal Ce2Ni17Si9-type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupation by Au and triel (Tr = Al, Ga) atoms, while a successive decrease of local symmetry from the parental structures of I and II to III and, ultimately, to IV correlates with increasing separation of Au and Tr on individual crystallographic sites. Density functional theory-based calculations were employed to determine the crystallographic site preferences of Au and the respective triel element to elucidate reasons for the atom distribution ("coloring scheme"). Chemical bonding analyses for two different "EuAu6Tr6" models reveal maximization of the number of heteroatomic Au-Tr bonds as the driving force for atom organization. The Fermi levels fall in broad pseudogaps for both models allowing some electronic flexibility. Spin-polarized band structure calculations on the "EuAu6Tr6" models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu6.2Ga5.8 (III) and EuAu6.1Al5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at TC = 6 K and net magnetic moments of 7.35 ?B/f.u. at 2 K. The effective moments of 8.3 ?B/f.u., determined from Curie-Weiss fits, point to divalent oxidation states for europium in both III and IV. PMID:26479308

  1. Atomic structure of silicene nanoribbons on Ag(110)

    NASA Astrophysics Data System (ADS)

    Tchalala, Mohammed Rachid; Enriquez, Hanna; Mayne, Andrew J.; Kara, Abdelkader; Dujardin, Gérald; Ait Ali, Mustapha; Oughaddou, Hamid

    2014-03-01

    The growth of silicene nano-ribbons (NRs) on Ag(110) substrate is re-investigated using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). Deposition of one silicon monolayer at 230°C induces the formation of one-dimensional 1.6 nm wide silicene nanoribbons into a well-ordered compact array with a nanometer-scale pitch of just 2 nm. Based on the STM analysis we derived an atomic model of the silicene nanoribbons (NRs) where they are substantially buckled, and quantum confinement of the electrons in the NRs contribute to electronic density of states.

  2. Electronic structure and anisotropic chemical bonding in TiNF from ab initio study

    SciTech Connect

    Matar, Samir F.

    2012-01-15

    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.

  3. Facile chemical synthesis and structure characterization of copper molybdate nanoparticles

    NASA Astrophysics Data System (ADS)

    Rahimi-Nasrabadi, Mehdi; Pourmortazavi, Seied Mahdi; Khalilian-Shalamzari, Morteza

    2015-03-01

    Experimental parameters of a synthesis route were optimized by Taguchi robust design for the facile and controllable synthesis of copper molybdate nanoparticles. CuMoO4 nanoparticles were synthesized by chemical precipitation followed by hydrothermal process. Effects of different parameters of synthesis procedure, i.e. concentrations of both reagents, copper feeding flow rate and temperature of reactor on the particle size of prepared copper molybdate nanoparticles were investigated. The results of statistical optimization revealed that the size of copper molybdate particles is dependent on the procedure variables involving copper concentrations, flow rate and temperature of the reactor; while, molybdate concentration has a no considerable role in determining the size of CuMoO4 particles. Based on the results obtained by statistical optimization process, the nanoparticles of copper molybdate were prepared and then their structure and chemical composition were characterized by various techniques, i.e. SEM, TEM, XRD, EDX, FT-IR, UV-Vis and photoluminescence spectroscopy.

  4. Predicting physical-chemical properties of compounds from molecular structures by recursive neural networks.

    PubMed

    Bernazzani, Luca; Duce, Celia; Micheli, Alessio; Mollica, Vincenzo; Sperduti, Alessandro; Starita, Antonina; Tiné, Maria Rosaria

    2006-01-01

    In this paper, we report on the potential of a recently developed neural network for structures applied to the prediction of physical chemical properties of compounds. The proposed recursive neural network (RecNN) model is able to directly take as input a structured representation of the molecule and to model a direct and adaptive relationship between the molecular structure and target property. Therefore, it combines in a learning system the flexibility and general advantages of a neural network model with the representational power of a structured domain. As a result, a completely new approach to quantitative structure-activity relationship/quantitative structure-property relationship (QSPR/QSAR) analysis is obtained. An original representation of the molecular structures has been developed accounting for both the occurrence of specific atoms/groups and the topological relationships among them. Gibbs free energy of solvation in water, Delta(solv)G degrees , has been chosen as a benchmark for the model. The different approaches proposed in the literature for the prediction of this property have been reconsidered from a general perspective. The advantages of RecNN as a suitable tool for the automatization of fundamental parts of the QSPR/QSAR analysis have been highlighted. The RecNN model has been applied to the analysis of the Delta(solv)G degrees in water of 138 monofunctional acyclic organic compounds and tested on an external data set of 33 compounds. As a result of the statistical analysis, we obtained, for the predictive accuracy estimated on the test set, correlation coefficient R = 0.9985, standard deviation S = 0.68 kJ mol(-1), and mean absolute error MAE = 0.46 kJ mol(-1). The inherent ability of RecNN to abstract chemical knowledge through the adaptive learning process has been investigated by principal components analysis of the internal representations computed by the network. It has been found that the model recognizes the chemical compounds on the basis of a nontrivial combination of their chemical structure and target property. PMID:16995734

  5. Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.

    PubMed

    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

    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

  6. The prediction of protein structural class using averaged chemical shifts.

    PubMed

    Lin, Hao; Ding, Chen; Song, Qiang; Yang, Ping; Ding, Hui; Deng, Ke-Jun; Chen, Wei

    2012-01-01

    Knowledge of protein structural class can provide important information about its folding patterns. Many approaches have been developed for the prediction of protein structural classes. However, the information used by these approaches is primarily based on amino acid sequences. In this study, a novel method is presented to predict protein structural classes by use of chemical shift (CS) information derived from nuclear magnetic resonance spectra. Firstly, 399 non-homologue (about 15% identity) proteins were constructed to investigate the distribution of averaged CS values of six nuclei ((13)CO, (13)C?, (13)C?, (1)HN, (1)H? and (15)N) in three protein structural classes. Subsequently, support vector machine was proposed to predict three protein structural classes by using averaged CS information of six nuclei. Overall accuracy of jackknife cross-validation achieves 87.0%. Finally, the feature selection technique is applied to exclude redundant information and find out an optimized feature set. Results show that the overall accuracy increased to 88.0% by using the averaged CSs of (13)CO, (1)H? and (15)N. The proposed approach outperformed other state-of-the-art methods in terms of predictive accuracy in particular for low-similarity protein data. We expect that our proposed approach will be an excellent alternative to traditional methods for protein structural class prediction. PMID:22545995

  7. Atomic-scale structure and band-gap bowing in Cu(In,Ga)Se2

    NASA Astrophysics Data System (ADS)

    Schnohr, C. S.; Kämmer, H.; Stephan, C.; Schorr, S.; Steinbach, T.; Rensberg, J.

    2012-06-01

    Mixed systems such as the Cu(In,Ga)Se2 chalcopyrite semiconductor consist of different local atomic arrangements, that is, of different combinations of first-nearest-neighbor cations surrounding the Se anions. The anion position of Cu-III-VI2 compounds is predicted to strongly influence the material band gap. We therefore used extended x-ray absorption fine structure spectroscopy to study the atomic-scale structure of Cu(In,Ga)Se2 as a function of composition. Based on these results, the anion position was modeled for all first-nearest-neighbor configurations using a valence force-field approach. We show that the atomic-scale structure strongly depends on the kind of first-nearest-neighbor atoms. Structural relaxation of the anion occurs with respect to both (i) Cu and group III atoms and (ii) In and Ga atoms. In both cases, the average anion displacement exhibits a nonlinear behavior with changing composition and thus results in two separate but significant contributions to the band gap bowing observed in Cu(In,Ga)Se2.

  8. Virtual reality based approach to protein heavy-atom structure reconstruction

    E-print Network

    Xubiao Peng; Alireza Chenani; Shuangwei Hu; Yifan Zhou; Antti J. Niemi

    2014-12-26

    A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C-alpha coordinates. Each heavy atom can be visualised on the surfaces of the different two-spheres, that are centered at the other heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters which display strong dependence on the underlying backbone secondary structure. Our method easily detects those atoms in a crystallographic protein structure which have been been likely misplaced. Our approach forms a basis for the development of a new generation, visualisation based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy over existing methods.

  9. Atomic Force Microscopy of Physical and Chemical Processes at the Solid-Liquid Interface

    NASA Astrophysics Data System (ADS)

    Manne, Srinivas

    This thesis describes research using atomic force microscopy (AFM) to study dynamics of solid surfaces in contact with liquids. Specifically, three applications are described: electrochemistry (Chapters 1-3), crystal growth (Chapters 4 and 5), and biomineralization (Chapter 6). Chapter 1 shows the feasibility of using AFM to image metal atoms in liquid, which sets the stage for high -resolution electrochemistry. Chapter 2 describes methods to convert the standard AFM liquid cell into an electrochemical cell and shows images of a gold electrode during oxidation/reduction cycling. Chapter 3 follows an electroplating cycle, wherein copper is deposited from electrolyte onto a gold electrode and then stripped off. The surface lattice is shown to change from that of bulk gold to bulk copper during plating, and back to bulk gold after stripping. Moreover, the first monolayer of copper--which deposits at an "underpotential", before the bulk deposition--is shown to have a lattice which differs from the bulk and is electrolyte dependent. Like electrochemistry, the study of crystal growth is also perfectly suited to a surface technique such as AFM. AFM makes it possible to image "elemental steps" (i.e., steps one unit cell thick) on a single crystal and quantify their motion during growth and dissolution. This is illustrated for the inorganic crystal calcite (Chapter 4) and the more fragile organic crystal L-leucine (Chapter 5). In both cases it is shown that step speed is independent of spacing between steps, indicating that motion occurs by direct interaction of the step-site molecules with the solvent. Chapter 5 also describes techniques for growing and imaging organic crystals. Living organisms also use crystal growth, modified by inorganic and organic additives, to grow mineralized structures such as bones, teeth and seashells. In Chapter 6, AFM reveals the three-dimensional structure of the nacreous or pearly layer of mollusc shells by slowly etching away successive mineral layers (in weak acid) while imaging. Etch figures on the mineral (aragonite) are correlated with crystallographic directions, revealing overall crystalline order on large scans. In bivalves, this order is observed both laterally across the layer and vertically between layers, whereas gastropod nacre is observed to be ordered only vertically.

  10. Nuclear Corrections to Hyperfine Structure in Light Hydrogenic Atoms

    E-print Network

    J. L. Friar; G. L. Payne

    2005-04-04

    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.

  11. Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling

    NASA Astrophysics Data System (ADS)

    Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro

    2012-10-01

    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.

  12. Predicting Physical-Chemical Properties of Compounds from Molecular Structures by Recursive Neural Networks

    E-print Network

    Sperduti, Alessandro

    Predicting Physical-Chemical Properties of Compounds from Molecular Structures by Recursive Neural of a recently developed neural network for structures applied to the prediction of physical chemical properties. INTRODUCTION To predict the physical-chemical properties of com- pounds, starting from the molecular structure

  13. Chemical Vapor Deposition Synthesized Atomically Thin Molybdenum Disulfide with Optoelectronic-Grade Crystalline Quality.

    PubMed

    Bilgin, Ismail; Liu, Fangze; Vargas, Anthony; Winchester, Andrew; Man, Michael K L; Upmanyu, Moneesh; Dani, Keshav M; Gupta, Gautam; Talapatra, Saikat; Mohite, Aditya D; Kar, Swastik

    2015-09-22

    The ability to synthesize high-quality samples over large areas and at low cost is one of the biggest challenges during the developmental stage of any novel material. While chemical vapor deposition (CVD) methods provide a promising low-cost route for CMOS compatible, large-scale growth of materials, it often falls short of the high-quality demands in nanoelectronics and optoelectronics. We present large-scale CVD synthesis of single- and few-layered MoS2 using direct vapor-phase sulfurization of MoO2, which enables us to obtain extremely high-quality single-crystal monolayer MoS2 samples with field-effect mobility exceeding 30 cm(2)/(V s) in monolayers. These samples can be readily synthesized on a variety of substrates, and demonstrate a high-degree of optoelectronic uniformity in Raman and photoluminescence mapping over entire crystals with areas exceeding hundreds of square micrometers. Because of their high crystalline quality, Raman spectroscopy on these samples reveal a range of multiphonon processes through peaks with equal or better clarity compared to past reports on mechanically exfoliated samples. This enables us to investigate the layer thickness and substrate dependence of the extremely weak phonon processes at 285 and 487 cm(-1) in 2D-MoS2. The ultrahigh, optoelectronic-grade crystalline quality of these samples could be further established through photocurrent spectroscopy, which clearly reveal excitonic states at room temperature, a feat that has been previously demonstrated only on samples which were fabricated by micro-mechanical exfoliation and then artificially suspended across trenches. Our method reflects a big step in the development of atomically thin, 2D-MoS2 for scalable, high-quality optoelectronics. PMID:26256639

  14. Electrostatic Chemical Strain: An Approach to Electronic Structure Engineering in Layered Oxides

    NASA Astrophysics Data System (ADS)

    Rondinelli, James

    2015-03-01

    Traditional approaches to create and control functional electronic materials have focused on new phases in previously unknown bulk minerals. More recently, interlayer physics has spawned interest in known materials in unexplored atomic scale geometries, especially in complex transition metal oxides (TMO), where heterostructures and superlattices with abrupt interfaces can be created on demand. The interfaces between TMO overs a handle to direct the electrostatic field exerted on the transition metal centers via the coordinating oxygen ligands, which alter the M cation's d-orbital occupancies and spin state, thereby imparting desirable electronic functionality. In this talk, I describe an atomistic engineering approach that makes use of long-range electrostatic interactions between atomic metal-monoxide planes (AO and A'O) in naturally occurring superlattices, e.g., Ruddlesden-Popper (RP), phases, to tune interlayer atomic structure, orbital degeneracies, and magnetic properties. Using first-principles electronic structure calculations, I show how this electrostatic chemical strain (ECS) effect can be used to tune both crystal field energies and the frontier orbital structure in correlated (La, A)NiO4 RP phases at fixed stoichiometry. I describe how to enhance the Ni eg orbital polarization, resulting in NiO6 units that exhibit a single d (x2 -y2) band at the Fermi level--electronic features similar to the layered superconducting cuprates. This approach is generic in construction, making it applicable to any layered topology supporting heterovalent cation substitutions. I conclude by showing it is a realistic strategy to tailor the electronic properties of known materials, and discover yet-to-be realized novel functional oxides without resorting to complex assembly of multi-component heterostructures. Funding for this work is provided by the Defense Advanced Research Projects Agency (DARPA), Grant No. N66001-12-4224 and performed in collaboration with P. Balachandran and A. Cammarata.

  15. Quantum chemical and solution phase evaluation of metallocenes as reducing agents for the prospective atomic layer deposition of copper.

    PubMed

    Dey, Gangotri; Wrench, Jacqueline S; Hagen, Dirk J; Keeney, Lynette; Elliott, Simon D

    2015-06-14

    We propose and evaluate the use of metallocene compounds as reducing agents for the chemical vapour deposition (and specifically atomic layer deposition, ALD) of the transition metal Cu from metalorganic precursors. Ten different transition metal cyclopentadienyl compounds are screened for their utility in the reduction of Cu from five different Cu precursors by evaluating model reaction energies with density functional theory (DFT) and solution phase chemistry. PMID:25914999

  16. Atomic structure of PdNiP bulk metallic glass from ab initio simulations

    NASA Astrophysics Data System (ADS)

    Kumar, Vijay; Fujita, T.; Chen, M. W.; Inoue, A.; Kawazoe, Y.

    2009-03-01

    The atomic structure of Pd40Ni40P20 bulk metallic glass (BMG) has been simulated using ab initio molecular dynamics plane wave method and PAW pseudopotentials. We use generalized gradient approximation to calculate the exchange-correlation energy and a cubic simulation box whose size and shape have been optimized after the BMG has been formed in simulations. The resulting radial distribution function and density agree remarkably well with the experimental data. The structure is analysed in terms of local clusters centered around Pd, Ni and P atoms and their electronic structures have been used to understand the bonding, stability, and the formation of the PdNiP BMG.

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

    SciTech Connect

    Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.

    2013-12-12

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

  18. Si-H bending modes as a probe of local chemical structure: Thermal and chemical routes to decomposition of H2O on Si(100)-(2×1)

    NASA Astrophysics Data System (ADS)

    Weldon, M. K.; Queeney, K. T.; Gurevich, A. B.; Stefanov, B. B.; Chabal, Y. J.; Raghavachari, Krishnan

    2000-08-01

    Surface infrared spectroscopy and density functional cluster calculations are used to study the thermal and atomic hydrogen-induced decomposition of water molecules on the clean Si(100)-(2×1) surface. We report the first observation of the Si-H bending modes associated with the initial insertion of oxygen into the dimer and backbonds of a silicon dimer. We find that, while one and two oxygen-containing dimers are formed almost simultaneously during the thermal decomposition of water on this surface, atomic H can be used to drive the preferential formation of the singly oxidized dimer. This work highlights the sensitivity of Si-H bending modes to the details of local chemical structure in an inhomogeneous system, suggesting that the combined experimental and theoretical approach demonstrated herein may be extremely useful in studying even more complex systems such as the hydrogenation of defects in SiO2 films.

  19. Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation

    E-print Network

    Langmead, Christopher James

    Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP, we show that the entropy compo- nent of our free energy estimates can be useful in distinguishing

  20. Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation

    E-print Network

    Xing, Eric P.

    Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP, we show that the entropy component of our free energy estimates can useful in distinguishing native

  1. Free Energy Estimates of All-atom Protein Structures Using Generalized Belief

    E-print Network

    Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation H Detection, Free Energy, Probabilistic Graphical Models #12;Abstract We present a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP). The accuracy and utility

  2. Atomic Resolution Structures of Rieske Iron-Sulfur Protein: Role of Hydrogen Bonds in Tuning

    E-print Network

    Crofts, Antony R.

    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

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

    SciTech Connect

    Borisova, Svetlana D. E-mail: rusina@ispms.tsc.ru Rusina, Galina G. E-mail: rusina@ispms.tsc.ru

    2014-11-14

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

  4. Atomic structure of the 310 twin in niobium: Theoretical predictions and comparison with experimental observation

    NASA Astrophysics Data System (ADS)

    Campbell, G. H.; King, W. E.; Foiles, S. M.; Ruehle, M.

    1992-11-01

    High-resolution transmission electron microscopy (HREM) has been used to characterize the atomic structure of the symmetric 36.9(degrees) tilt grain boundary with zone (001) tilt axes forming a twin about (310) in Nb. The projected structure was imaged along two different directions in the plane of the boundary and was compared to model structures through high-resolution image simulation. The atomic structure of this (Sigma)-5 boundary was predicted with atomistic simulations using interatomic potentials derived from the Embedded Atom Method (EAM), Finnis-Sinclair (FS), and the Model Generalized Pseudopotential Theory (MGPT). The EAM and FS predicted structures with translations of the adjacent crystals which break mirror symmetry. The MGPT predicted one stable structure with mirror symmetry. The atomic structure of the (310) twin in Nb was found by HREM to be mirror symmetric. These findings indicate that the angular dependent interactions modeled in the MGPT are important for determining the grain boundary structures of bcc transition metals.

  5. 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)

    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

    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.

  6. Structural and chemical trends in doped silicon nanocrystals: First-principles calculations

    NASA Astrophysics Data System (ADS)

    Zhou, Zhiyong; Steigerwald, Michael L.; Friesner, Richard A.; Brus, Louis; Hybertsen, Mark S.

    2005-06-01

    Electronic and structural properties of substitutional group-V donors (N, P, As, Sb) and group-III acceptors (B, Al, Ga, In) in silicon nanocrystals with hydrogen passivation are explored using first-principles calculations based on hybrid density functional theory with complete geometrical optimization. The bonding near the impurity is similar to that found for the impurity in bulk crystalline silicon, with some quantitative differences. The N case shows large local distortions, as it does in the bulk, characteristic of a deep trap. For the other impurities, no evidence is found for a transition to atomic scale localization induced by the small size of the nanocrystal. The chemical trends of the donor and acceptor binding energies and the donor excited state energies in doped nanocrystals are similar to those in the bulk; however, the absolute magnitudes are substantially larger. The increase in the magnitude of the binding energy is mainly due to the quantum confinement effect combined with the reduced screening of the impurity potential in small nanocrystals. The screening of the impurity potential is carefully examined using the self-consistent electrostatic potential from the full calculations. Strong chemical and local-field effects are seen within the radius of the first neighbor bonds to the impurity atom. This explains the large increase in the donor excited state energy level splittings and the relative importance of the central cell contributions to the binding energies. The acceptor and donor orbitals have different atomic character on the impurity site, leading to substantially different acceptor and donor energy level splittings.

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

    NASA Astrophysics Data System (ADS)

    Kim, Min-Geun; Jang, Hong-Lae; Cho, Seonho

    2013-05-01

    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.

  8. Electrical, structural, and chemical characterization of silicon sheet materials

    NASA Technical Reports Server (NTRS)

    Ast, D. G.; Hyland, S. L.

    1985-01-01

    Progress on the electrical, structural, and chemical characterization of silicon sheet material is reported. In the study on high temperature deformation of dendritic web ribbon, experimental creep tests were performed in four point bending under constant load conditions, and unusual behavior was observed. Also, measurements of oxygen content in web ribbon were made. Two conclusions reached are creep behavior of web which is very different from any seen for single crystal silicon and oxygen level in web silicon which is near the saturation level at the melting point of silicon.

  9. Designing allosteric control into enzymes by chemical rescue of structure

    E-print Network

    Deckert, Katelyn Noel

    2012-12-31

    stream_size 45659 stream_content_type text/plain stream_name Deckert_ku_0099M_12538_DATA_1.pdf.txt stream_source_info Deckert_ku_0099M_12538_DATA_1.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8... Designing allosteric control into enzymes by chemical rescue of structure By Katelyn Deckert Submitted to the graduate degree program in Molecular Biosciences and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements...

  10. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary.

    PubMed

    Yilmaz, Emel Maden; Güntert, Peter

    2015-09-01

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary. PMID:26123317

  11. Atomic structure and chemistry of human serum albumin

    NASA Technical Reports Server (NTRS)

    He, Xiao M.; Carter, Daniel C.

    1992-01-01

    The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

  12. Detailed Atomic Structure of Neutral and Near-Neutral Systems

    SciTech Connect

    Oliver, Paul; Hibbert, Alan

    2011-05-11

    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.

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

    NASA Technical Reports Server (NTRS)

    Zink, Lyndon R.; Evenson, Kenneth M.; Matsushima, Fusakazu; Nelis, Thomas; Robinson, Ruth L.

    1991-01-01

    Fine-structure splittings of atomic oxygen (O-16) in the ground state have been accurately measured using a tunable far-infrared spectrometer. The 3P0-3pl splitting is 2,060,069.09 (10) MHz, and the 3Pl-3P2 splitting is 4,744,777.49 (16) MHz. These frequencies are important for measuring atomic oxygen concentration in earth's atmosphere and the interstellar medium.

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  15. Virtual reality based approach to protein heavy-atom structure reconstruction

    E-print Network

    Peng, Xubiao; Hu, Shuangwei; Zhou, Yifan; Niemi, Antti J

    2014-01-01

    A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C-alpha coordinates. Each heavy atom can be visualised on the surfaces of the different two-spheres, that are centered at the other heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters which display strong dependence on the underlying backbone secondary structure. Our method easily detects those atoms in a crystallographic protein structure which have been been likely misplaced. Our approach forms a basis for the development of a new generation, visualisation based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondar...

  16. THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS

    EPA Science Inventory

    Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

  17. Student perception and conceptual development as represented by student mental models of atomic structure

    NASA Astrophysics Data System (ADS)

    Park, Eun Jung

    The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

  18. The Mystery of Matter, World of the Atom Series.

    ERIC Educational Resources Information Center

    Pollard, William G.

    This booklet is one in the "World of the Atome Series" for junior high school students and their teachers. It describes the fascinating story of the search for the key to the structure of matter. These topics are reviewed: the chemical atom of the 19th century, the planetary atom, the wave atom, inside the elementary particles, and the mystery of…

  19. Local electronic structure and photoelectrochemical activity of partial chemically etched Ti-doped hematite

    NASA Astrophysics Data System (ADS)

    Rioult, Maxime; Belkhou, Rachid; Magnan, Hélène; Stanescu, Dana; Stanescu, Stefan; Maccherozzi, Francesco; Rountree, Cindy; Barbier, Antoine

    2015-11-01

    The direct conversion of solar light into chemical energy or fuel through photoelectrochemical water splitting is promising as a clean hydrogen production solution. Ti-doped hematite (Ti:?-Fe2O3) is a potential key photoanode material, which despite its optimal band gap, excellent chemical stability, abundance, non-toxicity and low cost, still has to be improved. Here we give evidence of a drastic improvement of the water splitting performances of Ti-doped hematite photoanodes upon a HCl wet-etching. In addition to the topography investigation by atomic force microscopy, a detailed determination of the local electronic structure has been carried out in order to understand the phenomenon and to provide new insights in the understanding of solar water splitting. Using synchrotron radiation based spectromicroscopy (X-PEEM), we investigated the X-ray absorption spectral features at the L3 Fe edge of the as grown surface and of the wet-etched surface on the very same sample thanks to patterning. We show that HCl wet etching leads to substantial surface modifications of the oxide layer including increased roughness and chemical reduction (presence of Fe2 +) without changing the band gap. We demonstrate that these changes are profitable and correlated to the drastic changes of the photocatalytic activity.

  20. Why Isn't the Ground State Electronic Structure of the Lithium Atom 1s3? The purpose of this tutorial is to point out that if all that mattered in the determination of atomic structure was

    E-print Network

    Rioux, Frank

    Why Isn't the Ground State Electronic Structure of the Lithium Atom 1s3? The purpose of this tutorial is to point out that if all that mattered in the determination of atomic structure was energy minimization, the electronic structure of lithium would be 1s3, rather than 1s22s1. To deal with this issue we

  1. Comprehensive DFT study on molecular structures of Lewisites in support of the Chemical Weapons Convention

    NASA Astrophysics Data System (ADS)

    Saeidian, Hamid; Sahandi, Morteza

    2015-11-01

    The structure of all of Lewisite's stereoisomers has been examined by B3LYP/6-311++G(3df,3pd) calculations. The geometry analysis for trans Lewisite L1-1 shows that the calculated bond angles, bond distances and dipole moment have a satisfactory relation compared with experimental values. HOMO-LUMO analysis of Lewisites reveals that L1-2 and L3-7 have the maximum and minimum electrophilicity index, respectively. The calculated chemical shifts were compared with experimental data, showing a very good agreement both for 1H and 13C. The vibrational and Raman frequencies of Lewisites have been precisely assigned and theoretical data were compared with the experimental vibrations. The bonding trends and Mulliken and atomic polar tensor charge distribution in Lewisites can be explained by the Bent's rule and the donor-acceptor interaction, respectively.

  2. Atomically thick Pt-Cu nanosheets: self-assembled sandwich and nanoring-like structures.

    PubMed

    Saleem, Faisal; Xu, Biao; Ni, Bing; Liu, Huiling; Nosheen, Farhat; Li, Haoyi; Wang, Xun

    2015-03-25

    Atomically thick and flexible Pt-Cu alloy nanosheets are prepared and loaded with either Pd or Pt to produce sandwich structures or nanoring-like nanosheet structures, respectively. Core-shell alloy nanoparticles containing Rh, Ir, and Ru are also prepared. All of these structures exhibit superior specific and mass activities for the oxidation of formic acid for fuel cells for portable electronic devices as compared to commercial Pd/C catalyst. PMID:25677842

  3. Tiny-Scale Atomic Structure and the Cold Neutral Medium--Review and Recap

    E-print Network

    Carl Heiles

    2007-01-22

    Almost a decade ago I wrote an article with the same title as this. It focused on the physical properties of the Tiny-Scale Atomic Structure (TSAS) as discrete structures of the Cold Neutral Medium (CNM). To be observable, tiny discrete structures that don't grossly violate pressure equilibrium need two attributes: low temperatures and geometrical anisotropy. Here I update that article. I discuss thermal and pressure equilibrium, ionization, optical lines, H_2 abundance, and evaporation.

  4. Functional Nano-Structures Using Atomic Layer Deposition

    E-print Network

    Salgård Cunha, Pedro

    2014-05-27

    % and 170 % respectively since 1990, compared to 20 % and 7 % for the USA and the European Union over the same time period. The world’s energy usage is expected to continue to rise at an increasing rate to a predicted usage of 327 000 TW h by 2050. A... on the formation of gyroid-structured core- shell Cu/Cu2O/CuO solar cells via the post-deposition thermal oxidation of electro- deposited copper. Chapter 6 deals with the replication of gyroid-structured polystyrene templates using metal oxides deposited via ALD...

  5. Atomic structure of interface states in silicon heterojunction solar cells.

    PubMed

    George, B M; Behrends, J; Schnegg, A; Schulze, T F; Fehr, M; Korte, L; Rech, B; Lips, K; Rohrmüller, M; Rauls, E; Schmidt, W G; Gerstmann, U

    2013-03-29

    Combining orientation dependent electrically detected magnetic resonance and g tensor calculations based on density functional theory we assign microscopic structures to paramagnetic states involved in spin-dependent recombination at the interface of hydrogenated amorphous silicon crystalline silicon (a-Si:H/c-Si) heterojunction solar cells. We find that (i) the interface exhibits microscopic roughness, (ii) the electronic structure of the interface defects is mainly determined by c-Si, (iii) we identify the microscopic origin of the conduction band tail state in the a-Si:H layer, and (iv) present a detailed recombination mechanism. PMID:23581355

  6. Atomic layer structure of manganese atoms on wurtzite gallium nitride Abhijit Chinchore, Kangkang Wang, Wenzhi Lin, Jeongihm Pak, and Arthur R. Smitha

    E-print Network

    Atomic layer structure of manganese atoms on wurtzite gallium nitride ,,0001¯... Abhijit Chinchore of Physics. DOI: 10.1063/1.3006434 Mn-doped gallium nitride GaN was proposed as a pos- sible dilute magnetic evident in Figs. 1 a and 1 b are 3 and higher- order streaks indicating gallium adatom reconstructions

  7. Regularities and symmetries in atomic structure and spectra

    E-print Network

    Pain, Jean-Christophe

    2013-01-01

    The use of statistical methods for the description of complex quantum systems was primarily motivated by the failure of a line-by-line interpretation of atomic spectra. Such methods reveal regularities and trends in the distributions of levels and lines. In the past, much attention was paid to the distribution of energy levels (Wigner surmise, random-matrix model...). However, information about the distribution of the lines (energy and strength) is lacking. Thirty years ago, Learner found empirically an unexpected law: the logarithm of the number of lines whose intensities lie between 2^kI_0 and 2^{k+1}I_0, I_0 being a reference intensity and k an integer, is a decreasing linear function of k. In the present work, the fractal nature of such an intriguing regularity is outlined and a calculation of its fractal dimension is proposed. Other peculiarities are also presented, such as the fact that the distribution of line strengths follows Benford's law of anomalous numbers, the existence of additional selection r...

  8. Regularities and symmetries in atomic structure and spectra

    NASA Astrophysics Data System (ADS)

    Pain, Jean-Christophe

    2013-09-01

    The use of statistical methods for the description of complex quantum systems was primarily motivated by the failure of a line-by-line interpretation of atomic spectra. Such methods reveal regularities and trends in the distributions of levels and lines. In the past, much attention was paid to the distribution of energy levels (Wigner surmise, random-matrix model…). However, information about the distribution of the lines (energy and strength) is lacking. Thirty years ago, Learner found empirically an unexpected law: the logarithm of the number of lines whose intensities lie between 2kI0 and 2k+1I0, I0 being a reference intensity and k an integer, is a decreasing linear function of k. In the present work, the fractal nature of such an intriguing regularity is outlined and a calculation of its fractal dimension is proposed. Other peculiarities are also presented, such as the fact that the distribution of line strengths follows Benford's law of anomalous numbers, the existence of additional selection rules (PH coupling), the symmetry with respect to a quarter of the subshell in the spin-adapted space (LL coupling) and the odd-even staggering in the distribution of quantum numbers, pointed out by Bauche and Cossé.

  9. Structure, chemical bonding and electrochemical behavior of heteroatom-substituted carbons prepared by arc discharge and chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Nakajima, Tsuyoshi; Koh, Meiten; Katsube, Toshiyuki

    1998-01-01

    The structural characteristics, chemical bonding and electrochemical properties of the heteroatom-substituted carbons synthesized by arc discharge and chemical vapor deposition have been investigated. C xN was prepared only as a soot by arc discharge in nitrogen atmosphere; BC x and B xC yN z were obtained both as soot and cathode deposits by arc discharge of graphite rods having B 4C and boron nitride (BN) in argon and nitrogen atmospheres, respectively. Transmission electron microscopic study showed that C xN, BC x and B xC yN z soots were composed of nanoparticles with diameters of 20-100 nm, while cathode deposits contained nanotubes with diameters of ca. 20 nm or less and nanoparticles with diameters less than 100 nm. It was found from XPS study that C xN contained a large amount of pyridine type nitrogen atoms at the edge of graphene layer; the B?BC 2 structure was dominant in BC x; and B 3N, B 2NC and BNC 2 structures might exist in B xC yN z. Carbon- and C xN-coated graphite were prepared by deposition of carbon and C xN onto natural graphite powder, respectively. The concentrations of coated C xN layers were between C 21N and C 62N. Charge-discharge profiles of C xN, BC x and B xC yN z soots prepared by arc discharge were similar to each other, giving linearly increasing potential with lithium ion deintercalation. C xN soot heat-treated at 3000°C showed a similar profile for charge-discharge curves to that of graphite with a charge capacity of 334 mAh g -1. On the other hand, C xN-coated graphite exhibited as high as 397 mAh g -1 larger than ˜365 mAh g -1 for carbon-coated graphite and that of heat-treated C xN soot.

  10. Atomic Structure and Phase Transformations in Pu Alloys

    SciTech Connect

    Schwartz, A J; Cynn, H; Blobaum, K M; Wall, M A; Moore, K T; Evans, W J; Farber, D L; Jeffries, J R; Massalski, T B

    2008-04-28

    Plutonium and plutonium-based alloys containing Al or Ga exhibit numerous phases with crystal structures ranging from simple monoclinic to face-centered cubic. Only recently, however, has there been increased convergence in the actinides community on the details of the equilibrium form of the phase diagrams. Practically speaking, while the phase diagrams that represent the stability of the fcc {delta}-phase field at room temperature are generally applicable, it is also recognized that Pu and its alloys are never truly in thermodynamic equilibrium because of self-irradiation effects, primarily from the alpha decay of Pu isotopes. This article covers past and current research on several properties of Pu and Pu-(Al or Ga) alloys and their connections to the crystal structure and the microstructure. We review the consequences of radioactive decay, the recent advances in understanding the electronic structure, the current research on phase transformations and their relations to phase diagrams and phase stability, the nature of the isothermal martensitic {delta} {yields} {alpha}{prime} transformation, and the pressure-induced transformations in the {delta}-phase alloys. New data are also presented on the structures and phase transformations observed in these materials following the application of pressure, including the formation of transition phases.

  11. Structure, chemical ordering and thermal stability of Pt-Ni alloy nanoclusters

    NASA Astrophysics Data System (ADS)

    Cheng, Daojian; Yuan, Shuai; Ferrando, Riccardo

    2013-09-01

    Equilibrium structures, chemical ordering and thermal properties of Pt-Ni nanoalloys are investigated by using basin hopping-based global optimization, Monte Carlo (MC) and molecular dynamics (MD) methods, based on the second-moment approximation of the tight-binding potentials (TB-SMA). The TB-SMA potential parameters for Pt-Ni nanoalloys are fitted to reproduce the results of density functional theory calculations for small clusters. The chemical ordering in cuboctahedral (CO) Pt-Ni nanoalloys with 561 and 923 atoms is obtained from the so called semi-grand-canonical ensemble MC simulation at 100 K. Two ordered phases of L12 (PtNi3) and L10 (PtNi) are found for the CO561 and CO923 Pt-Ni nanoalloys, which is in good agreement with the experimental phase diagram of the Pt-Ni bulk alloy. In addition, the order-disorder transition and thermal properties of these nanoalloys are studied by using MC and MD methods, respectively. It is shown that the typical perfect L10 PtNi structure is relatively stable, showing high order-disorder transition temperature and melting point among these CO561 and CO923 Pt-Ni nanoalloys.

  12. Atomic Substitutions in Yba2cu3o7 - Modification of the Electronic-Structure 

    E-print Network

    RICHERT, BA; Allen, Roland E.

    1988-01-01

    (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. Here ~e report studies... 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 transition tempera- ture, 7 s indicating that this site...

  13. Crossed-beam reaction of carbon atoms with hydrocarbon molecules. V. Chemical dynamics of n-C4H3 formation from reaction of C,,3

    E-print Network

    Kaiser, Ralf I.

    data indicate that the carbon atom attacks the -orbitals of the allenic carbon­carbon double bond chemical processes in hydro- carbon-rich planetary atmospheres,2 and outflow of dying carbon stars as well

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

    DOE PAGESBeta

    Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

    2012-01-01

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

  15. Observations of Small Scale ISM Structure in Dense Atomic Gas

    E-print Network

    J. T. Lauroesch; David M. Meyer

    1999-05-14

    We present high resolution (R~170,000) Kitt Peak National Observatory Co'ude Feed telescope observations of the interstellar KI 7698 angstrom line towards 5 multiple star systems with saturated NaI components. We compare the KI absorption line profiles in each of the two (or three) lines of sight in these systems, and find significant differences between the sight-lines in 3 out of the 5 cases. We infer that the small scale structure traced by previous NaI observations is also present in at least some of the components with saturated NaI absorption lines, and thus the small scale structures traced by the neutral species are occurring at some level in clouds of all column densities. We discuss the implications of that conclusion and a potential explanation by density inhomogeneities.

  16. Atomic structures and mechanical properties of single-crystal GaN nanotubes

    SciTech Connect

    Xu, B.; Lu, A.J.; Pan, B.C.; Yu, Q.X.

    2005-03-15

    An approach is proposed to theoretically construct a realistic single-crystal GaN nanotube at atomic scale. The generated atomic structures of the single-crystal GaN nanotubes match the structural aspects from experiment very well. Our energetic calculations show that a single-crystal GaN nanotube with [100]-oriented lateral facets is more stable than that with [110]-oriented lateral facets, when they have around the same wall thickness. For a specified orientation of the lateral facets on the single-crystal GaN nanotubes, the energetic stabilities of the tubes obey a P rule, in which P is the ratio of the number of four-coordinated atoms to the number of three-coordinated atoms. Furthermore, the Young's modulus of the considered GaN nanotubes decrease with increasing the ratio of the number of bulk atoms to the number of surface atoms in each type of tube. Our calculations and analysis demonstrate that the surface effect of a single-crystal nanotube enhances its Young's modulus significantly.

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

    NASA Astrophysics Data System (ADS)

    Edwards, Trenton Gerard

    This dissertation details the characterization of the atomic structure, relaxation processes and phase transformation mechanisms in a variety of chalcogenide (selenides and tellurides) and other non-oxide (Ga-Sb alloys) glasses which are highly relevant to optoelectronic and phase change memory applications. One of the principal goals of these studies is to develop a fundamental, atomistic understanding of the structure-property relationships in these materials. Variable temperature Raman spectroscopy is used to the study the structure and its temperature dependent relaxation in GexSe100-x glasses and supercooled liquids with x ? 33.33 %. It is shown that the compositional dependence of the relative fractions of the edge- and corner-shared GeSe4 tetrahedra is fully consistent with a structural model based on random connectivity between the tetrahedral and chain elements. Temperature-dependent structural changes involve a progressive conversion of edge-shared to corner shared GeSe4 tetrahedra with decreasing equilibration temperature. The time scale of this structural conversion agrees with both enthalpy and shear relaxation near the glass transition. The temperature dependent change in the edge- vs. corner- sharing tetrahedral speciation is shown to be related to the production of configurational entropy, indicating a connection between structural relaxation, configurational entropy, and viscous flow. A combination of Raman and 77Se nuclear magnetic resonance (NMR) spectroscopy is applied to study the structure of a series of Se-deficient GexSe100-x glasses, with 42 ? x ? 33.33. Considerable violation of chemical order in the nearest-neighbor coordination environments of the constituent atoms is observed in the stoichiometric GeSe2 glass. On the other hand, the presence of a random distribution of Ge-Ge bonds can be inferred in the Se-deficient glasses. Furthermore, the results of this study conclusively indicate that the structure of these glasses is intermediate between a randomly connected and a fully clustered network of GeSe4 tetrahedra and Se chains. Additionally, a new two-dimensional NMR spectroscopic technique is developed and applied to Ge-Se glasses that allowed the separation of isotropic and anisotropic chemical shifts. Through the analysis of the anisotropic sideband pattern in the second dimension it is possible to detect up to four distinct types of Se environments in the glass structure on the basis of their characteristic chemical shift anisotropies. 125Te NMR chemical shift systematics is established for coordination environments of Te atoms in a wide range of crystalline and glassy tellurides in the Ga-As-Sb-Te system. 125Te NMR spectroscopy is then used to investigate the short-range structure of amorphous and crystalline Ge1Sb2 Te4 and Ge2Sb2Te5 phase change alloys. Both alloys are found to consist of only heteropolar Ge/Sb-Te bonds in the amorphous and crystalline state and strong vacancy clustering in the nanocrystalline state that may facilitate a rapid displacive transformation between the amorphous and crystalline states without the need of significant atomic rearrangement or diffusion. Based on these 125Te NMR results a Te-centric model of the phase change mechanism in GST alloys is proposed. Structure and phase changes in amorphous Ga-Sb alloys are studied using synchrotron x-ray diffraction and 71Ga and 121Sb NMR spectroscopy. Pressure induced phase transformations in amorphous GaSb is shown to be consistent with the existence of an underlying polyamorphic phase transition between a low and a high-density amorphous phase. NMR results for amorphous Ga46Sb54 indicate that both Ga and Sb atoms are fourfold coordinated with 40% of these atoms participating in homopolar bonding in the as-deposited film. Subsequent crystallization into the zinc blend structure therefore requires extensive bond switching and elimination of homopolar bonds. For amorphous Ga14Sb86 both Ga and Sb atoms are found to be threefold coordinated allowing for a fast phase change kinetics although crystallization of thi

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  20. Surface structure of MX-chains studied by atomic force microscopy

    SciTech Connect

    Bar, G.; Scott, B.; Johnson, S.R.; Kanner, G.S.; Swanson, B.I.

    1995-03-01

    The surfaces of mixed-valence halogen-bridged transition metal linear chain compounds [[Pt(en){sub 2}][Pt(en)]{sub 2}(X{sub 1-y}X{prime}{sub y}){sub 2}](ClO{sub 4}){sub 4} (X, X{prime} = Cl, Br, or I; en = C{sub 2}H{sub 8}N{sub 2}; y = 0.0 - 1.0) were examined by atomic force microscopy (AFM). The AFM images are consistent with the surfaces expected from the bulk crystal structure. The surface unit cell parameters of the images correspond to the lattice constants of the bulk crystals. The patterns of the atomic-scale AFM images are dominated by the most protruded H atoms of the en ligands and the most protruded O atoms of the ClO{sub 4}{sup -} anions.

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

    ERIC Educational Resources Information Center

    Tsai, Chin-Chung

    1998-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Schnohr, C. S.

    2015-09-01

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

  3. Identification of structure-activity relationships from screening a structurally compact DNA-encoded chemical library.

    PubMed

    Franzini, Raphael M; Ekblad, Torun; Zhong, Nan; Wichert, Moreno; Decurtins, Willy; Nauer, Angela; Zimmermann, Mauro; Samain, Florent; Scheuermann, Jörg; Brown, Peter J; Hall, Jonathan; Gräslund, Susanne; Schüler, Herwig; Neri, Dario

    2015-03-23

    Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA-encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL-100K, a DNA-encoded chemical library containing 103?200 structurally compact compounds. Affinity screening experiments and DNA-sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate-specific membrane antigen and tankyrase?1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small-molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding. PMID:25650139

  4. Atomic structures and electronic properties of 2H-NbSe{sub 2}: The impact of Ti doping

    SciTech Connect

    Li, Hongping E-mail: zcwang@wpi-aimr.tohoku.ac.jp; Chen, Lin; Zhang, Kun; Liang, Jiaqing; Tang, Hua; Li, Changsheng; Liu, Xiaojuan; Meng, Jian; Wang, Zhongchang E-mail: zcwang@wpi-aimr.tohoku.ac.jp

    2014-09-14

    Layered transition metal dichalcogenides have aroused renewed interest as electronic materials, yet their electronic performances could be modified by chemical doping. Here, we perform a systematic first-principles calculation to investigate the effect of Ti doping on atomic structure and electronic properties of the 2H-NbSe{sub 2}. We consider a total of three possible Ti-doping models and find that both the substitution and intercalated models are chemically preferred with the intercalation model being more favorable than the substitution one. Structural analyses reveal a slight lattice distortion triggered by Ti doping, but the original structure of 2H-NbSe{sub 2} is maintained. We also observe an expansion of c axis in the substituted model, which is attributed to the reduced van der Waals interaction arising from the increased Se-Se bond length. Our calculations also predict that the electron transport properties can be enhanced by the Ti doping, especially for the Ti-intercalated 2H-NbSe{sub 2}, which should be beneficial for the realization of superconductivity. Furthermore, the covalence element is found in the Ti-Se bonds, which is ascribed to the hybridization of Ti 3d and Se 4p orbitals. The findings indicate that doping of transition metals can be regarded as a useful way to tailor electronic states so as to improve electron transport properties of 2H-NbSe{sub 2}.

  5. New horizons in chemical propulsion. [processes using free radicals, atomic hydrogen, excited species, etc

    NASA Technical Reports Server (NTRS)

    Cohen, W.

    1973-01-01

    After a review of the work of the late-Fifties on free radicals for propulsion, it is concluded that atomic hydrogen would provide a potentially large increase in specific impulse. Work conducted to find an approach for isolating atomic hydrogen is considered. Other possibilities for obtaining propellants of greatly increased capability might be connected with the technology for the generation of activated states of gases, metallic hydrogen, fuels obtained from other planets, and laser transfer of energy.

  6. Atomic structure, alloying behavior, and magnetism in small Fe-Pt clusters

    NASA Astrophysics Data System (ADS)

    Chittari, Bheema Lingam; Kumar, Vijay

    2015-09-01

    We report results of the atomic structure, alloying behavior, and magnetism in F emP tn(m +n =2 -10 ) clusters using projector augmented wave (PAW) pseudopotential method and spin-polarized generalized gradient approximation (GGA) for the exchange-correlation energy. These results are compared with those obtained by using HCTH exchange-correlation functional and LANL2DZ basis set in the Gaussian program and the overall trends are found to be similar. As in bulk Fe-Pt alloys, clusters with equal composition of Fe and Pt have the largest binding energy and the largest heat of nanoalloy formation for a given number of atoms in the cluster. There are some deviations due to the different symmetries in clusters and in cases where the total number of atoms is odd. The lowest energy isomers tend to maximize bonds between unlike atoms with Fe (Pt) atoms occupying high (low) coordination sites in the core (surface) of the cluster. The binding energy, heat of formation, and the second order difference of the total energy show F e2P t2 , F e4P t4 , and F e4P t6 clusters to be the most stable ones among the different clusters we have studied. The magnetic moments on Fe atoms are high in Pt-rich clusters as well as in small Fe-rich clusters and decrease as the aggregation of Fe atoms and the cluster size increases. The maximum value of the magnetic moments on Fe atoms is ˜3.8 ?B , whereas for Pt atoms it is 1 ?B. These are quite high compared with the values for bulk Fe as well as bulk FePt and F e3Pt phases while bulk Pt is nonmagnetic. There is significant charge transfer from those Fe atoms that interact directly with Pt atoms. We discuss the hybridization between the electronic states of Pt and Fe atoms as well as the variation in the magnetic moments on Fe and Pt atoms. Our results provide insight into the understanding of the nanoalloy behavior of Fe-Pt and we hope that this would help to design Fe based nanoalloys and their assemblies with high magnetic moments for strong magnets without rare earths as well as Pt alloy catalysts.

  7. Atomic Assembly of Magnetoresistive Multilayers

    E-print Network

    Wadley, Haydn

    chemical and structural complexity. The nature of the interfaces between the dissimilar materials used and simulation tools to the reactive, ion-assisted vapor deposition of multilay- ered structures. It is motivated's nanoscopically structured devices are made by controlling the condensation of an atomic or molecular vapor

  8. Hydrogen Atom and Time Variation of Fine-Structure Constant

    E-print Network

    Mu-Lin Yan

    2009-11-21

    In this paper, we have solved the de Sitter special relativistic ($\\mathcal{SR}_{cR}$-) Dirac equation of hydrogen in the earth-QSO(quasar) framework reference by means of the adiabatic approach. The aspects of geometry effects of de Sitter space-time described by Beltrami metric are explored and taken into account. It is found that the $\\mathcal{SR}_{cR}$-Dirac equation of hydrogen is a time dependent quantum Hamiltonian system. We provide an explicit calculation to justify the adiabatic approach in dealing with this time-dependent system. Since the radius of de Sitter sphere $R$ is cosmologically large, the evolution of the system is very slow so that the adiabatic approximation legitimately works with high accuracy. We conclude that the electromagnetic fine-structure constant, the electron mass and the Planck constant are time variations. This prediction of fine-structure constant is consistent with the presently available observation data. For confirming it further, experiments/observations are required.

  9. Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

    PubMed Central

    Lee, H. V.; Hamid, S. B. A.; Zain, S. K.

    2014-01-01

    Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate's application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein. PMID:25247208

  10. Conversion of lignocellulosic biomass to nanocellulose: structure and chemical process.

    PubMed

    Lee, H V; Hamid, S B A; Zain, S K

    2014-01-01

    Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate's application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein. PMID:25247208

  11. On the physical and chemical details of alumina atomic layer deposition: A combined experimental and numerical approach

    SciTech Connect

    Pan, Dongqing; Ma, Lulu; Xie, Yuanyuan; Yuan, Chris; Jen, Tien Chien

    2015-03-15

    Alumina thin film is typically studied as a model atomic layer deposition (ALD) process due to its high dielectric constant, high thermal stability, and good adhesion on various wafer surfaces. Despite extensive applications of alumina ALD in microelectronics industries, details on the physical and chemical processes are not yet well understood. ALD experiments are not able to shed adequate light on the detailed information regarding the transient ALD process. Most of current numerical approaches lack detailed surface reaction mechanisms, and their results are not well correlated with experimental observations. In this paper, the authors present a combined experimental and numerical study on the details of flow and surface reactions in alumina ALD using trimethylaluminum and water as precursors. Results obtained from experiments and simulations are compared and correlated. By experiments, growth rate on five samples under different deposition conditions is characterized. The deposition rate from numerical simulation agrees well with the experimental results. Details of precursor distributions in a full cycle of ALD are studied numerically to bridge between experimental observations and simulations. The 3D transient numerical model adopts surface reaction kinetics and mechanisms based on atomic-level studies to investigate the surface deposition process. Surface deposition is shown as a strictly self-limited process in our numerical studies. ALD is a complex strong-coupled fluid, thermal and chemical process, which is not only heavily dependent on the chemical kinetics and surface conditions but also on the flow and material distributions.

  12. 3rd annual symposium of chemical and pharmaceutical structure analysis.

    PubMed

    Weng, Naidong; Zheng, Jenny; Lee, Mike

    2012-08-01

    The 3rd Annual Symposium on Chemical and Pharmaceutical Structure Analysis was once again held in Shanghai, where a rich history of 'East meets West' continued. This meeting is dedicated to bringing together scientists from pharmaceutical companies, academic institutes, CROs and instrument vendors to discuss current challenges and opportunities on the forefront of pharmaceutical research and development. The diversified symposia and roundtables are highly interactive events where scientists share their experiences and visions in a collegial setting. The symposium highlighted speakers and sessions that provided first-hand experiences as well as the latest guidance and industrial/regulatory thinking, which was reflected by the theme of this year's meeting 'From Bench to Decision Making - from Basics to Application.' In addition to the highly successful Young Scientist Excellence Award, new events were featured at this year's meeting, such as the Executive Roundtable and the inaugural Innovator Award. PMID:22943615

  13. Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging

    E-print Network

    V. M. Giordano; B. Ruta

    2015-11-23

    Understanding and controlling physical aging, i.e. the spontaneous temporal evolution of out-of-equilibrium systems, represents one of the greatest tasks in material science. Recent studies have revealed the existence of a complex atomic motion in metallic glasses, with different aging regimes in contrast with the typical continuous aging observed in macroscopic quantities. By combining dynamical and structural synchrotron techniques, for the first time we directly connect previously identified microscopic structural mechanisms with the peculiar atomic motion, providing a broader unique view of their complexity. We show that the atomic scale is dominated by the interplay between two processes: rearrangements releasing residual stresses related to a cascade mechanism of relaxation, and medium range ordering processes, which do not affect the local density, likely due to localized relaxations of liquid-like regions. As temperature increases, a surprising additional secondary relaxation process sets in, together with a faster medium range ordering, likely precursors of crystallization.

  14. Strong-field spatial intensity-intensity correlations of light scattered from regular structures of atoms

    E-print Network

    M. Macovei; J. Evers; C. H. Keitel

    2007-02-14

    Photon correlations and cross-correlations of light scattered by a regular structure of strongly driven atoms are investigated. At strong driving, the scattered light separates into distinct spectral bands, such that each band can be treated as independent, thus extending the set of observables. We focus on second-order intensity-intensity correlation functions in two- and multi-atom systems. We demonstrate that for a single two-photon detector as, e.g., in lithography, increasing the driving field intensity leads to an increased spatial resolution of the second-order two-atom interference pattern. We show that the cross-correlations between photons emitted in the spectral sidebands violate Cauchy-Schwartz inequalities, and that their emission ordering cannot be predicted. Finally, the results are generalized for multi-particle structures, where we find results different from those in a Dicke-type sample.

  15. Synthesis of diosgenin p-nitrobenzoate by Steglich method, its crystal structure and quantum chemical studies

    NASA Astrophysics Data System (ADS)

    Sethi, Arun; Bhatia, Akriti; Shukla, Dolly; Kumar, Abhinav; Sonker, Ravi; Prakash, Rohit; Bhatia, Gitika

    2012-11-01

    In the present study, a novel one pot synthetic route for the synthesis of diosgenin p-nitrobenzoate (2) is described from cheap, commercially available naturally occurring sapogenin-diosgenin. The molecular geometry, IR frequencies, Gauge-including atomic orbital (GIAO), 1H and 13C NMR chemical shifts of compound 2 has been calculated in the ground state by using the Hartree-Fock (HF) and density functional method (DFT/B3LYP) using 6-31G(d,p) basis set. The structure of diosgenin p-nitrobenzoate (2) has been confirmed by single crystal X-ray diffraction. The compound crystallizes in monoclinic form having space group P21 with cell parameters a = 7.719(2) Å, b = 8.425(2) Å and c = 22.578(6) Å, ? = 90.00, ? = 98.46 and ? = 90.00. The oxygen atoms O5 and O4 of the nitro and carbonyl ester, respectively display weak intermolecular N1sbnd O5⋯H7' and C1'dbnd O4⋯H4' interactions having dimensions of 2.61 and 2.59 Å, respectively to form intricate 1D network. The study of the electronic properties such as HOMO and LUMO energy were performed using time dependent DFT (TD-DFT) calculations. The calculated HOMO and LUMO energy values indicate that charge transfer takes place within the molecule. The compound was screened for cytotoxicity and anti-adipogenic activity.

  16. Structural-chemical features and morphology of glauconites in sedimentary iron ore of Bakchar prospect (Western Siberia)

    NASA Astrophysics Data System (ADS)

    Rudmin, M.; Reva, I.; Gunko, A.; Mazurov, A.; Abramova, R.

    2015-11-01

    The research embraces the investigation results of glauconites in Bakchar iron ore occurrences to evaluate the potential diversified commercial application of this mineral. The following lab methods were used to analyze the morphology, chemical composition and structure of glauconites: granulometric analysis, optical microscopy, electron microscopy, X-ray fluorescence analysis, atomic arc-emission analysis and infrared spectroscopy. Glauconite was classified according to morphology and grain color and chemical composition and some specific characteristics were also determined (relative content of absorbed water, random distribution of smectite flakes within the grain structures). The research results showed that pistacho-green glauconite grains are less subjected to alteration than greenish-yellow grains due to the content of potassium, iron, absorbed water and organic impurities.

  17. A SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  18. SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES.

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    SciTech Connect

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

    2014-04-01

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

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

    E-print Network

    Jacob D. Bekenstein

    2003-01-29

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

  2. Structure in multilayer films of zinc sulfide and copper sulfide via atomic layer deposition

    SciTech Connect

    Short, Andrew; Jewell, Leila; Bielecki, Anthony; Keiber, Trevor; Bridges, Frank; Carter, Sue; Alers, Glenn

    2014-01-15

    Multilayer film stacks of ZnS and Cu{sub x}S (x???2) were made via atomic layer deposition. The precursors were bis(2,2,6,6-tetramethyl-3,5-heptanedionato)zinc, bis(2,2,6,6-tetramethyl-3,5-heptanedionato)copper, and H{sub 2}S generated in situ for sulfur. Samples were deposited at 200?°C, in layers ranging from approximately 2 to 20 nm thick, based on binary growth rates. The properties of the film stacks were studied with atomic force microscopy, ultraviolet–visible spectroscopy, and extended x-ray absorption fine structure. The results demonstrate that the structure of films with the thinnest layers is dominated by Cu{sub x}S, whereas in the thicker films, the structure is determined by whichever material is first deposited. This can be attributed to the crystal structure mismatch of ZnS and Cu{sub x}S.

  3. Designing Allosteric Control into Enzymes by Chemical Rescue of Structure

    SciTech Connect

    Deckert, Katelyn; Budiardjo, S. Jimmy; Brunner, Luke C.; Lovell, Scott; Karanicolas, John

    2012-08-07

    Ligand-dependent activity has been engineered into enzymes for purposes ranging from controlling cell morphology to reprogramming cellular signaling pathways. Where these successes have typically fused a naturally allosteric domain to the enzyme of interest, here we instead demonstrate an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. We present two examples, W33G in a {beta}-glycosidase enzyme ({beta}-gly) and W492G in a {beta}-glucuronidase enzyme ({beta}-gluc), in which we engineer indole-dependent activity into enzymes by removing a buried tryptophan side chain that serves as a buttress for the active site architecture. In both cases, we observe a loss of function, and in both cases we find that the subsequent addition of indole can be used to restore activity. Through a detailed analysis of {beta}-gly W33G kinetics, we demonstrate that this rescued enzyme is fully functionally equivalent to the corresponding wild-type enzyme. We then present the apo and indole-bound crystal structures of {beta}-gly W33G, which together establish the structural basis for enzyme inactivation and rescue. Finally, we use this designed switch to modulate {beta}-glycosidase activity in living cells using indole. Disruption and recovery of protein structure may represent a general technique for introducing allosteric control into enzymes, and thus may serve as a starting point for building a variety of bioswitches and sensors.

  4. Tuning the electronic structure and transport properties of graphene by noncovalent functionalization: effects of organic donor, acceptor and metal atoms

    NASA Astrophysics Data System (ADS)

    Zhang, Yong-Hui; Zhou, Kai-Ge; Xie, Ke-Feng; Zeng, Jing; Zhang, Hao-Li; Peng, Yong

    2010-02-01

    Using density functional theory and nonequilibrium Green's function (NEGF) formalism, we have theoretically investigated the binding of organic donor, acceptor and metal atoms on graphene sheets, and revealed the effects of the different noncovalent functionalizations on the electronic structure and transport properties of graphene. The adsorptions of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and tetrathiafulvalene (TTF) induce hybridization between the molecular levels and the graphene valence bands, and transform the zero-gap semiconducting graphene into a metallic graphene. However, the current versus voltage (I-V) simulation indicates that the noncovalent modifications by organic molecules are not sufficient to significantly alter the transport property of the graphene for sensing applications. We found that the molecule/graphene interaction could be dramatically enhanced by introducing metal atoms to construct molecule/metal/graphene sandwich structures. A chemical sensor based on iron modified graphene shows a sensitivity two orders of magnitude higher than that of pristine graphene. The results of this work could help to design novel graphene-based sensing or switching devices.

  5. Imaging the atomic surface structures of CeO2 nanoparticles

    SciTech Connect

    Lin, Yuyuan; Wu, Zili; Wen, Jianguo; Poeppelmeier, Kenneth R; Marks, Laurence D

    2014-01-01

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

  6. Atomic lattice structure and continuum plate theories for the vibrational characteristics of graphenes

    NASA Astrophysics Data System (ADS)

    Arghavan, S.; Singh, A. V.

    2011-10-01

    This paper is concerned with the equivalent extensional and flexural rigidities of a single layer graphene sheet by treating it as a plane lattice structure made of tightly packed carbon atoms into an array of honeycomb-shaped cells. Each carbon atom is modeled as a node with concentrated atomic mass and prescribed six degrees of freedom. The covalent bond between adjacent carbon atoms provides axial, bending, and torsional stiffness. Using the Poisson's ratio of 0.16 and thickness of 3.4 Å, the equivalent Young's moduli are found to be approximately 0.112 TPa for bending and in the range of 1.03-1.04 TPa for in-plane modes. Subsequently, the graphene structure is simulated by a classical plate with prescribed geometric and mechanical properties. The in-plane and out-of-plane free vibration analyses of the rectangular plate provide the natural frequencies and associated mode shapes. Results are compared with eigen analyses of the lattice structure model for different sizes of graphene. Examples are considered to show close agreement in the results from these two methods. Mode shapes reveal that the lattice structure model shows symmetry about the horizontal and vertical axes and also about the diagonals.

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

    ERIC Educational Resources Information Center

    Sunyono; Yuanita, L.; Ibrahim, M.

    2015-01-01

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

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

    ERIC Educational Resources Information Center

    Tuvi, Inbal; Nachmias, Rafi

    2001-01-01

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

  9. Sparse Matrix Multiplications for Linear Scaling Electronic Structure Calculations in an Atom-Centered

    E-print Network

    Baer, Roi

    Sparse Matrix Multiplications for Linear Scaling Electronic Structure Calculations in an Atom October 2002 Abstract: A sparse matrix multiplication scheme with multiatom blocks is reported, a tool to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use

  10. Magnetic domain structure of Fe55 at.%Pd alloy at different stages of atomic ordering

    E-print Network

    Laughlin, David E.

    Magnetic domain structure of Fe­55 at.%Pd alloy at different stages of atomic ordering Lisha Wanga, The Ohio State University, 2041 College Road, Columbus, Ohio 43210 Armen G. Khachaturyan Department of Ceramic and Materials Engineering, Rutgers University, 607 Taylor Road, Piscataway, New Jersey 08854

  11. Contact atomic structure and electron transport through molecules San-Huang Ke

    E-print Network

    Baranger, Harold U.

    Contact atomic structure and electron transport through molecules San-Huang Ke Department American Institute of Physics. DOI: 10.1063/1.1851496 I. INTRODUCTION Understanding electron transport of future molecular electronics technology.1­5 One of the critical issues in this regard is to construct

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

    ERIC Educational Resources Information Center

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

    2013-01-01

    Research in science education has recognized the importance of teaching atomic structure within a history and philosophy of science perspective. The objective of this study is to evaluate general physics textbooks published in Korea based on the eight criteria developed in previous research. The result of this study shows that Korean general…

  13. Pseudospin, supersymmetry and the shell structure of atomic nuclei

    E-print Network

    S. Typel

    2008-04-21

    The evolution of single-particle energies with varying isospin asymmetry in the shell model is an important issue when predicting changes in the shell structure for exotic nuclei. In many cases pseudospin partner levels, that are almost degenerate in energy for stable nuclei, are relevant in extracting the size of the shell gaps. A breaking of the pseudospin symmetry can affect the size of these gaps and change the magic numbers accordingly. The strength of the pseudospin splitting is expected to depend in particular on isovector-dependent and tensor contributions to the effective nuclear interaction. A description employing supersymmetric quantum mechanics allows to derive a pseudospin symmetry breaking potential that is regular in contrast to the pseudospin-orbit potential in the conventional relativistic treatment. The derived perturbation potential provides a measure to quantify the symmetry breaking and it can be employed to improve mean-field calculations in order to better reproduce the experimentally observed shell evolution. General potentials with exact pseudospin symmetry are obtained that can be used in relativistic mean-field Hamiltonians.

  14. Breit–Pauli atomic structure calculations for Fe XI

    SciTech Connect

    Aggarwal, Sunny Singh, Jagjit; Mohan, Man

    2013-11-15

    Energy levels, oscillator strengths, and transition probabilities are calculated for the lowest-lying 165 energy levels of Fe XI using configuration-interaction wavefunctions. The calculations include all the major correlation effects. Relativistic effects are included in the Breit–Pauli approximation by adding mass-correction, Darwin, and spin–orbit interaction terms to the non-relativistic Hamiltonian. For comparison with the calculated ab initio energy levels, we have also calculated the energy levels by using the fully relativistic multiconfiguration Dirac–Fock method. The calculated results are in close agreement with the National Institute of Standards and Technology compilation and other available results. New results are predicted for many of the levels belonging to the 3s3p{sup 4}3d and 3s3p{sup 3}3d{sup 2} configurations, which are very important in astrophysics, relevant, for example, to the recent observations by the Hinode spacecraft. We expect that our extensive calculations will be useful to experimentalists in identifying the fine structure levels in their future work.

  15. Atomic-scale dynamical structures of fatty acid bilayers observed by ultrafast electron crystallography

    PubMed Central

    Chen, Songye; Seidel, Marco T.; Zewail, Ahmed H.

    2005-01-01

    The structure and dynamics of a biological model bilayer are reported with atomic-scale resolution by using ultrafast electron crystallography. The bilayer was deposited as a Langmuir-Blodgett structure of arachidic (eicosanoic) fatty acids with the two chains containing 40 carbon atoms (?50 Å), on a hydrophobic substrate, the hydrogen terminated silicon(111) surface. We determined the structure of the 2D assembly, establishing the orientation of the chains and the subunit cell of the CH2 distances: a0 = 4.7 Å, b0 = 8.0 Å, and c0 = 2.54 Å. For structural dynamics, the diffraction frames were taken every 1 picosecond after a femtosecond temperature jump. The observed motions, with sub-Å resolution and monolayer sensitivity, clearly indicate the coherent anisotropic expansion of the bilayer solely along the aliphatic chains, followed by nonequilibrium contraction and restructuring at longer times. This motion is indicative of a nonlinear behavior among the anharmonically coupled bonds on the ultrashort time scale and energy redistribution and diffusion on the longer time scale. The ability to observe such atomic motions of complex structures and at interfaces is a significant leap forward for the determination of macromolecular dynamical structures by using ultrafast electron crystallography. PMID:15956181

  16. Structural analysis of photosystem I polypeptides using chemical crosslinking

    NASA Technical Reports Server (NTRS)

    Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1994-01-01

    Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

  17. Molecular structure, vibrational, electronic and thermal properties of 4-vinylcyclohexene by quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Nagabalasubramanian, P. B.; Periandy, S.; Karabacak, Mehmet; Govindarajan, M.

    2015-06-01

    The solid phase FT-IR and FT-Raman spectra of 4-vinylcyclohexene (abbreviated as 4-VCH) have been recorded in the region 4000-100 cm-1. The optimized molecular geometry and vibrational frequencies of the fundamental modes of 4-VCH have been precisely assigned and analyzed with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method at 6-311++G(d,p) level basis set. The theoretical frequencies were properly scaled and compared with experimentally obtained FT-IR and FT-Raman spectra. Also, the effect due the substitution of vinyl group on the ring vibrational frequencies was analyzed and a detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated total energy distribution (TED). The time dependent DFT (TD-DFT) method was employed to predict its electronic properties, such as electronic transitions by UV-Visible analysis, HOMO and LUMO energies, molecular electrostatic potential (MEP) and various global reactivity and selectivity descriptors (chemical hardness, chemical potential, softness, electrophilicity index). Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Atomic charges obtained by Mulliken population analysis and NBO analysis are compared. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are also calculated.

  18. Synthesis, crystal structure, atomic Hirshfeld surfaces, and physical properties of hexagonal CeMnNi4.

    PubMed

    Skovsen, Iben; Christensen, Mogens; Clausen, Henrik Fanø; Overgaard, Jacob; Stiewe, Christian; Desgupta, Titas; Mueller, Eckhard; Spackman, Mark A; Iversen, Bo B

    2010-10-18

    The hexagonal polymorph of CeMnNi(4) has been synthesized using cold crucible, high-frequency induction melting with subsequent Czochralski crystal pulling. Single-crystal X-ray diffraction, multitemperature synchrotron powder X-ray diffraction (90 to 600 K), and neutron powder diffraction data have been measured to establish the detailed crystal structure and in particular the location of the Mn atoms. The neutron diffraction data provide sufficient scattering contrast between Mn and Ni to establish that the 2c site has an occupancy of 13% Mn atoms, while the 3g site has an occupancy of 25% Mn atoms. Thus, the crystal structure is complex with considerable disorder. Rietveld refinement of the multitemperature synchrotron data establishes a near linear thermal expansion coefficient of 13.9(3) × 10(-6) K(-1) and 14.9(3) × 10(-6) K(-1) for the a and c axes, respectively. Atomic Hirshfeld surfaces are introduced as a new tool to investigate the atomic coordination and interactions in intermetallic compounds. The atomic displacement parameters (ADPs) are observed to be much larger for the heavy Ce atom than for the lighter Mn and Ni atoms, and this correlates with the large atomic Hirshfeld volume of Ce relative to Mn and Ni. The fit of a Debye model to the ADPs gives ?(D) = 312(3) K. Magnetic susceptibility data measured between 2 and 350 K indicate ferromagnetic ordering at 122(2) K (Weiss constant) based on a linear fit of the inverse magnetic susceptibility in the paramagnetic region. Transport properties were measured on a polycrystalline sample containing CeO(2) (2.8%) and Ni (7.7%) impurities. The electrical conductivity is observed to be metallic with a distinct kink in the data around 120 K coinciding with the observed Curie temperature. The lattice thermal conductivity (?(L)) increases from 0.5 W/Km at 2 K to 8 W/Km at 50 K, and the relatively moderate value of ?(L) probably reflects the significant structural disorder. PMID:20845926

  19. Using effective operators in calculating the hyperfine structure of atoms V. A. Dzuba and V. V. Flambaum

    E-print Network

    Titov, Anatoly

    Using effective operators in calculating the hyperfine structure of atoms V. A. Dzuba and V. V´ksp. Teor. Fiz. 114, 1636­1645 November 1998 We propose a method for calculating the hyperfine structure hfs of multielectron atoms based on a combination of configuration superposition and many-body perturbation theory

  20. Understanding the Properties and Structure of Metallic Glasses at the Atomic Level

    SciTech Connect

    Egami, T.

    2010-01-01

    Liquids and glasses have been well known to human kind for millennia. And yet major mysteries remain in the behavior of glasses and liquids at the atomic level, and identifying the microscopic mechanisms that control the properties of glasses is one of the most challenging unsolved problems in physical sciences. For this reason, applying simplistic approaches to explain the behavior of metallic glasses can lead to serious errors. On the other hand because metallic glasses are atomic glasses with relatively simple structure, they may offer better opportunities to advance our fundamental understanding on the nature of the glass. The difficulties inherent to the problem and some recent advances are reviewed here.

  1. Atomic, electronic and magnetic structure of graphene/iron and nickel interfaces: theory and experiment

    E-print Network

    Boukhvalov, D W; Uimin, M A; Korolev, A V; Yermakov, A Ye

    2014-01-01

    First-principles calculations of the effect of carbon coverage on the atomic, electronic and magnetic structure of nickel and iron substrates demonstrate insignificant changes in the interatomic distances and magnetic moments on the atoms of the metallic substrates. The coverage of the iron surface by mono- and few-layer graphene induces significant changes in the orbital occupancies and exchange interactions between the layers in contrast to the case of a nickel substrate for which changes in the orbital ordering and exchange interactions are much smaller. Experimental measurements demonstrate the presence of ferromagnetic fcc-iron in Fe@C nanoparticles and the superparamagnetic behavior of Ni@C nanoparticles.

  2. Structure of the InAlAs/InP interface by atomically resolved energy dispersive spectroscopy

    SciTech Connect

    Klenov, Dmitri O.; Zide, Joshua M. O.

    2011-10-03

    The structure of epitaxially grown InAlAs/InP interfaces was studied using atomically resolved x-ray energy dispersive spectroscopy in scanning transmission electron microscopy. As and P sublattices show sharp termination on the interface. The In sublattice is continuous across the interface. The study has shown the depletion of the Al concentration at the interface; at the last atomic columns of the InAlAs, In occupancy is close to 100%, while Al occupancy is almost zero. A monolayer of InAs at the interface is consistent with substitution of As for P at the surface preceding growth.

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

    E-print Network

    Juan Israel Rivas; Abel Camacho; Ertan Goeklue

    2011-05-31

    We consider the consequences of the presence of metric fluctuations upon the properties of a hydrogen atom. Particularly, we introduce these metric fluctuations in the corresponding effective Schroedinger equation and deduce the modifications that they entail upon the hyperfine structure related to a hydrogen atom. We will find the change that these effects imply for the ground state energy of the system and obtain a bound for its size comparing our theoretical predictions against the experimental uncertainty reported in the literature. In addition, we analyze the corresponding Lamb shift effect emerging from these fluctuations of spacetime. Once again, we will set a bound to these oscillations resorting to the current experimental outcomes

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

    DOEpatents

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

    2008-07-15

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

  5. On the chemical and structural evolution of the galactic disk

    SciTech Connect

    Toyouchi, Daisuke; Chiba, Masashi

    2014-06-10

    We study the detailed properties of the radial metallicity gradient in the stellar disk of our Galaxy to constrain its chemical and structural evolution. For this purpose we select and analyze ?18,500 disk stars taken from two data sets, the Sloan Digital Sky Survey (SDSS) and the High-Accuracy Radial velocity Planetary Searcher (HARPS). On these surveys we examine the metallicity gradient, ?[Fe/H]/?R {sub g}, along the guiding center radii, R {sub g}, of stars and its dependence on the [?/Fe] ratios to infer the original metallicity distribution of the gas disk from which those stars formed and its time evolution. In both sample sources, the thick-disk candidate stars characterized by high [?/Fe] ratios ([?/Fe] > 0.3 in SDSS, [?/Fe] > 0.2 in HARPS) are found to show a positive ?[Fe/H]/?R {sub g}, whereas the thin-disk candidate stars characterized by lower [?/Fe] ratios show a negative one. Furthermore, we find that the relatively young thin-disk population characterized by much lower [?/Fe] ratios ([?/Fe] < 0.2 in SDSS, [?/Fe] < 0.1 in HARPS) notably shows a flattening ?[Fe/H]/?R {sub g} with decreasing [?/Fe], in contrast to the old one with higher [?/Fe] ratios ([?/Fe] ? 0.2 in SDSS, [?/Fe] ? 0.1 in HARPS). The possible implication for early disk evolution is discussed in the context of galaxy formation accompanying the rapid infall of primordial gas on the inner disk region, which can generate a positive metallicity gradient, and the subsequent chemical evolution of the disk, which results in a flattening effect of a metallicity gradient at later epochs.

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

    DOE PAGESBeta

    Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

    2015-09-03

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

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

    SciTech Connect

    Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

    2015-09-03

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

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

    NASA Astrophysics Data System (ADS)

    Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel

    2015-09-01

    Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.

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

    E-print Network

    Bristol, University of

    (CVD) of diamond. Macroscopic study and intuition have already gone far to make the growth of diamond-PACVD) or in the arc jet of a plasma torch. The resulting H atoms begin a series of abstraction reactions in the gas

  10. An x ray scatter approach for non-destructive chemical analysis of low atomic numbered elements

    NASA Technical Reports Server (NTRS)

    Ross, H. Richard

    1993-01-01

    A non-destructive x-ray scatter (XRS) approach has been developed, along with a rapid atomic scatter algorithm for the detection and analysis of low atomic-numbered elements in solids, powders, and liquids. The present method of energy dispersive x-ray fluorescence spectroscopy (EDXRF) makes the analysis of light elements (i.e., less than sodium; less than 11) extremely difficult. Detection and measurement become progressively worse as atomic numbers become smaller, due to a competing process called 'Auger Emission', which reduces fluorescent intensity, coupled with the high mass absorption coefficients exhibited by low energy x-rays, the detection and determination of low atomic-numbered elements by x-ray spectrometry is limited. However, an indirect approach based on the intensity ratio of Compton and Rayleigh scattered has been used to define light element components in alloys, plastics and other materials. This XRS technique provides qualitative and quantitative information about the overall constituents of a variety of samples.

  11. Modern Chemical Technology, Volume 2.

    ERIC Educational Resources Information Center

    Pecsok, Robert L.; Chapman, Kenneth

    This volume contains chapters 8 to 13 of the ACS "Modern Chemical Technology" (ChemTeC) curriculum material which is intended to prepare chemical technologists. The content is centered around the background needed to understand the structure of the atom, covalence, electrovalence, elements and compounds, liquids and solutions, and chemical

  12. Atomic Chain Electronics

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige; Saini, Subhash (Technical Monitor)

    1998-01-01

    Adatom chains, precise structures artificially created on an atomically regulated surface, are the smallest possible candidates for future nanoelectronics. Since all the devices are created by combining adatom chains precisely prepared with atomic precision, device characteristics are predictable, and free from deviations due to accidental structural defects. In this atomic dimension, however, an analogy to the current semiconductor devices may not work. For example, Si structures are not always semiconducting. Adatom states do not always localize at the substrate surface when adatoms form chemical bonds to the substrate atoms. Transport properties are often determined for the entire system of the chain and electrodes, and not for chains only. These fundamental issues are discussed, which will be useful for future device considerations.

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

    SciTech Connect

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

    2013-08-16

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

  14. Surface structures and electronic states of silicon nanotubes stabilized by oxygen atoms

    NASA Astrophysics Data System (ADS)

    Zhao, Mingwen; Zhang, R. Q.; Xia, Yueyuan

    2007-07-01

    The geometric and electronic structures of silicon nanotubes stabilized by incorporating oxygen atoms were studied using first-principles calculations within density functional theory. The predicted tubes present one-dimensional characters stacked with n-side silicon polygons connected by oxygen atoms. The stable configurations considered in this work include the tubes with varied facet number of the silicon polygons (n) from n =4 to 28 and of different surface structures. The configurations with n =5, 12, 15, 18, and 21 were found energetically extremely favorable. All the tubes are narrow-band-gap semiconductors with the band gap varying between 0.17 and 0.84eV, dependent on the surface structure of the tubes. This study provides an interesting route to stabilize silicon nanotubes and tune their electronic properties.

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

    SciTech Connect

    Merkle, K.L.; Buckett, M.I.; Gao, Y.; Rozeveld, S.J.; Vuchic, B.L.; Wolf, D.

    1994-01-01

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

  16. High {Tc} trilayer tunneling and Josephson junction structures made using atomic layer by layer growth

    SciTech Connect

    Eckstein, J.N.; Bozovic, I.; Virshup, G.F.

    1994-12-31

    Very precise artificial structuring of high {Tc} heterostructures is possible using atomic layer-by-layer molecular beam epitaxy (ALL-MBE). Cuprates are combined with other oxides, such as titanates, to make atomically precise heterostructures for studying transport and interfacial effects. Titanate slabs as thin as one unit cell thick can be grown without pinholes and provide tunneling barriers for c-axis transport. Single doped unit cells of BSCCO-2212 can also be used as barriers. These give SNS Josephson junctions at temperatures as high as 65 K. Since the crystallographic structure of the barrier is identical to the structure of the 2212 electrode material, it is easily possible to stack more than junction in close proximity. This results in phase-locked operation of two junctions together.

  17. Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR

    PubMed Central

    Franks, W. Trent; Wylie, Benjamin J.; Schmidt, Heather L. Frericks; Nieuwkoop, Andrew J.; Mayrhofer, Rebecca-Maria; Shah, Gautam J.; Graesser, Daniel T.; Rienstra, Chad M.

    2008-01-01

    Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of ?1 ?, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 ± 0.13 ? (1.52 ± 0.12 ? for all heavy atoms), which improved to 0.49 ± 0.05 ? (1.19 ± 0.07 ?) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 ± 0.06 ? bbRMSD (1.06 ± 0.07 ?); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 ± 0.09 ?; 1.29 ± 0.07 ?) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography. PMID:18344321

  18. QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP MODELS FOR PREDICTION OF ESTROGEN RECEPTOR BINDING AFFINITY OF STRUCTURALLY DIVERSE CHEMICALS

    EPA Science Inventory

    The demonstrated ability of a variety of structurally diverse chemicals to bind to the estrogen receptor has raised the concern that chemicals in the environment may be causing adverse effects through interference with nuclear receptor pathways. Many structure-activity relationsh...

  19. Novel chemical route for atomic layer deposition of MoS2 thin film on SiO2/Si substrate

    NASA Astrophysics Data System (ADS)

    JinThese Authors Equally Contributed To This Work., Zhenyu; Shin, Seokhee; Kwon, Do Hyun; Han, Seung-Joo; Min, Yo-Sep

    2014-11-01

    Recently MoS2 with a two-dimensional layered structure has attracted great attention as an emerging material for electronics and catalysis applications. Although atomic layer deposition (ALD) is well-known as a special modification of chemical vapor deposition in order to grow a thin film in a manner of layer-by-layer, there is little literature on ALD of MoS2 due to a lack of suitable chemistry. Here we report MoS2 growth by ALD using molybdenum hexacarbonyl and dimethyldisulfide as Mo and S precursors, respectively. MoS2 can be directly grown on a SiO2/Si substrate at 100 °C via the novel chemical route. Although the as-grown films are shown to be amorphous in X-ray diffraction analysis, they clearly show characteristic Raman modes (E12g and A1g) of 2H-MoS2 with a trigonal prismatic arrangement of S-Mo-S units. After annealing at 900 °C for 5 min under Ar atmosphere, the film is crystallized for MoS2 layers to be aligned with its basal plane parallel to the substrate.Recently MoS2 with a two-dimensional layered structure has attracted great attention as an emerging material for electronics and catalysis applications. Although atomic layer deposition (ALD) is well-known as a special modification of chemical vapor deposition in order to grow a thin film in a manner of layer-by-layer, there is little literature on ALD of MoS2 due to a lack of suitable chemistry. Here we report MoS2 growth by ALD using molybdenum hexacarbonyl and dimethyldisulfide as Mo and S precursors, respectively. MoS2 can be directly grown on a SiO2/Si substrate at 100 °C via the novel chemical route. Although the as-grown films are shown to be amorphous in X-ray diffraction analysis, they clearly show characteristic Raman modes (E12g and A1g) of 2H-MoS2 with a trigonal prismatic arrangement of S-Mo-S units. After annealing at 900 °C for 5 min under Ar atmosphere, the film is crystallized for MoS2 layers to be aligned with its basal plane parallel to the substrate. Electronic supplementary information (ESI) available: XPS depth profiles for the as-grown and the annealed MoS2 films. See DOI: 10.1039/c4nr04816d

  20. Undergraduate Chemical Physics

    E-print Network

    Bristol, University of

    a final-year research project or scientific dissertation. #12;bristol.ac.uk/study You will benefit fromUndergraduate Chemical Physics Faculty of Science #12;bristol.ac.uk/study Chemical physics covers nanotechnology, surface science, laser spectroscopy, atomic and molecular structure, materials, and all those