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Sample records for atomic resolution crystal

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

    Science.gov (United States)

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

    2018-01-01

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

  2. Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal

    Directory of Open Access Journals (Sweden)

    Sam Horrell

    2016-07-01

    Full Text Available Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07–1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a `catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

  3. Tomographic diffractive imaging of monolayer crystals at atomic resolution with onedimensional compact support

    Science.gov (United States)

    Weierstall, U.; Spence, J.; Hembree, G.

    2003-09-01

    A solution to the phase problem for diffraction by two-dimensional crystalline slabs is described, based on the application of a compact support normal to the slab. Specifically we apply the iterative Gerchberg-Saxton-Fienup algorithm to simulated three-dimensional transmission electron diffraction data from monolayer organic crystals. We find that oversampling normal to the monolayer alone does not solve the phase problem in this geometry in general. However, based on simulations for a crystalline monolayer (tetracyanoethylene), we find that convergence is obtained if phases are supplied from a few high-resolution electron microscope images recorded at small tilts to the beam direction. Since current cryomicroscopy methods required a large number of images to phase tomographic diffraction data, this method should greatly reduce the labor involved in data acquisition and analysis in cryo-electron microscopy of organic thin crystals by avoiding the need to record images at high tilt angles. We discuss also the use of laser tweezers as a method of supporting nanoparticles in TEM for diffractive imaging

  4. Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata

    Directory of Open Access Journals (Sweden)

    Sanchari Banerjee

    2016-07-01

    Full Text Available Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.

  5. Quantifying B Site Disorder in Polycrystalline and Single Crystal Yb2Ti2O7 Pyrochlore by Quantitative Scanning Transmission Electron Microscopy at Atomic Resolution

    Science.gov (United States)

    Shafieizadeh, Zahra; Xin, Yan; Zhou, Haidong

    The cubic pyrochlore oxides, A2B2O7, have attracted much attention over the past 20 years. A and B ions reside on two distinct interpenetrating lattices of corner-sharing tetrahedral. It has been noticed that the magnetic ground states of Yb2Ti2O7 are sample dependent. It could have long-range ordered collinear ferromagnetic state, or non-collinear ferromagnetic fluctuations, or short ranged fluctuations. In particular, the specific heat shows sharp peaks at 265 mK for polycrystalline samples, but a broad peak at 214 mK to 250 mK for optical floating zone (OFZ) single crystals. Neutron scattering study shows that OFZ single crystals are lightly stuffed pyrochlore with 2.3% Yb on to Ti sites. We have studied this disorder by quantitative scanning electron microscopy at atomic resolution for both polycrystals and single crystals. We have carried out atomic resolution imaging of Yb2Ti2O7 along [110] and by comparing image simulations, we have quantified the Yb atoms on the Ti atomic columns, and compared the disorders for both crystals. We also related the degree of the disorder to their magnetic ground states.

  6. Real-time atomic-resolution imaging of crystal growth process in water by phase modulation atomic force microscopy at one frame per second

    OpenAIRE

    Miyata, Kazuki; Asakawa, Hitoshi; Fukuma, Takeshi

    2013-01-01

    Recent advancement in dynamic-mode atomic force microscopy (AFM) has enabled its operation in liquid with atomic-scale resolution. However, its imaging speed has often been too slow to visualize atomic-scale dynamic processes. Here, we propose a method for making a significant improvement in the operation speed of dynamic-mode AFM. In this method, we use a wideband and low-latency phase detector with an improved algorithm for the signal complexification. We demonstrate atomic-scale imaging of...

  7. Crystal structure of the molybdenum cofactor biosynthesis protein MobA from Escherichia coli at near-atomic resolution.

    Science.gov (United States)

    Stevenson, C E; Sargent, F; Buchanan, G; Palmer, T; Lawson, D M

    2000-11-15

    All mononuclear molybdoenzymes bind molybdenum in a complex with an organic cofactor termed molybdopterin (MPT). In many bacteria, including Escherichia coli, molybdopterin can be further modified by attachment of a GMP group to the terminal phosphate of molybdopterin to form molybdopterin guanine dinucleotide (MGD). This modification reaction is required for the functioning of many bacterial molybdoenzymes, including the nitrate reductases, dimethylsulfoxide (DMSO) and trimethylamine-N-oxide (TMAO) reductases, and formate dehydrogenases. The GMP attachment step is catalyzed by the cellular enzyme MobA. The crystal structure of the 21.6 kDa E. coli MobA has been determined by MAD phasing with selenomethionine-substituted protein and subsequently refined at 1. 35 A resolution against native data. The structure consists of a central, predominantly parallel beta sheet sandwiched between two layers of alpha helices and resembles the dinucleotide binding Rossmann fold. One face of the molecule bears a wide depression that is lined by a number of strictly conserved residues, and this feature suggests that this is where substrate binding and catalysis take place. Through comparisons with a number of structural homologs, we have assigned plausible functions to several of the residues that line the substrate binding pocket. The enzymatic mechanism probably proceeds via a nucleophilic attack by MPT on the GMP donor, most likely GTP, to produce MGD and pyrophosphate. By analogy with related enzymes, this process is likely to require magnesium ions.

  8. Sub-Angstrom Atomic-Resolution Imaging of Heavy Atoms to Light Atoms

    Energy Technology Data Exchange (ETDEWEB)

    O' Keefe, Michael A.; Shao-Horn, Yang

    2003-05-23

    Three decades ago John Cowley and his group at ASU achieved high-resolution electron microscope images showing the crystal unit cell contents at better than 4Angstrom resolution. Over the years, this achievement has inspired improvements in resolution that have enabled researchers to pinpoint the positions of heavy atom columns within the cell. More recently, this ability has been extended to light atoms as resolution has improved. Sub-Angstrom resolution has enabled researchers to image the columns of light atoms (carbon, oxygen and nitrogen) that are present in many complex structures. By using sub-Angstrom focal-series reconstruction of the specimen exit surface wave to image columns of cobalt, oxygen, and lithium atoms in a transition metal oxide structure commonly used as positive electrodes in lithium rechargeable batteries, we show that the range of detectable light atoms extends to lithium. HRTEM at sub-Angstrom resolution will provide the essential role of experimental verification for the emergent nanotech revolution. Our results foreshadow those to be expected from next-generation TEMs with Cs-corrected lenses and monochromated electron beams.

  9. Atomic Force Microscopy and Real Atomic Resolution. Simple Computer Simulations

    NARCIS (Netherlands)

    Koutsos, V.; Manias, E.; Brinke, G. ten; Hadziioannou, G.

    1994-01-01

    Using a simple computer simulation for AFM imaging in the contact mode, pictures with true and false atomic resolution are demonstrated. The surface probed consists of two f.c.c. (111) planes and an atomic vacancy is introduced in the upper layer. Changing the size of the effective tip and its

  10. HRTEM Imaging of Atoms at Sub-Angstrom Resolution

    Energy Technology Data Exchange (ETDEWEB)

    O' Keefe, Michael A.; Allard, Lawrence F.; Blom, Douglas A.

    2005-04-06

    John Cowley and his group at Arizona State University pioneered the use of transmission electron microscopy (TEM) for high-resolution imaging. Images were achieved three decades ago showing the crystal unit cell content at better than 4 Angstrom resolution. This achievement enabled researchers to pinpoint the positions of heavy atom columns within the unit cell. Lighter atoms appear as resolution is improved to sub-Angstrom levels. Currently, advanced microscopes can image the columns of the light atoms (carbon, oxygen, nitrogen) that are present in many complex structures, and even the lithium atoms present in some battery materials. Sub-Angstrom imaging, initially achieved by focal-series reconstruction of the specimen exit surface wave, will become common place for next-generation electron microscopes with CS-corrected lenses and monochromated electron beams. Resolution can be quantified in terms of peak separation and inter-peak minimum, but the limits imposed on the attainable resolution by the properties of the micro-scope specimen need to be considered. At extreme resolution the ''size'' of atoms can mean that they will not be resolved even when spaced farther apart than the resolution of the microscope.

  11. Imaging enzyme kinetics at atomic resolution

    OpenAIRE

    Spence, John; Lattman, Eaton

    2016-01-01

    Serial crystallography at a synchrotron has been used to obtain time-resolved atomic resolution density maps of enzyme catalysis in copper nitrite reductase. Similar XFEL studies, intended to out-run radiation damage, will also soon appear.

  12. Atomic resolution images of graphite in air

    Energy Technology Data Exchange (ETDEWEB)

    Grigg, D.A.; Shedd, G.M.; Griffis, D.; Russell, P.E.

    1988-12-01

    One sample used for proof of operation for atomic resolution in STM is highly oriented pyrolytic graphite (HOPG). This sample has been imaged with many different STM`s obtaining similar results. Atomic resolution images of HOPG have now been obtained using an STM designed and built at the Precision Engineering Center. This paper discusses the theoretical predictions and experimental results obtained in imaging of HOPG.

  13. Imaging Lithium Atoms at Sub-Angstrom Resolution

    Energy Technology Data Exchange (ETDEWEB)

    O' Keefe, Michael A.; Shao-Horn, Yang

    2005-01-03

    John Cowley and his group at ASU were pioneers in the use of transmission electron microscopy (TEM) for high-resolution imaging. Three decades ago they achieved images showing the crystal unit cell content at better than 4A resolution. Over the years, this achievement has inspired improvements in resolution that have enabled researchers to pinpoint the positions of heavy atom columns within the cell. More recently, this ability has been extended to light atoms as resolution has improved. Sub-Angstrom resolution has enabled researchers to image the columns of light atoms (carbon, oxygen and nitrogen) that are present in many complex structures. By using sub-Angstrom focal-series reconstruction of the specimen exit surface wave to image columns of cobalt, oxygen, and lithium atoms in a transition metal oxide structure commonly used as positive electrodes in lithium rechargeable batteries, we show that the range of detectable light atoms extends to lithium. HRTEM at sub-Angstrom resolution will provide the essential role of experimental verification for the emergent nanotech revolution. Our results foreshadow those to be expected from next-generation TEMs with CS-corrected lenses and monochromated electron beams.

  14. Atomic Resolution Microscopy of Nitrides in Steel

    DEFF Research Database (Denmark)

    Danielsen, Hilmar Kjartansson

    2014-01-01

    MN and CrMN type nitride precipitates in 12%Cr steels have been investigated using atomic resolution microscopy. The MN type nitrides were observed to transform into CrMN both by composition and crystallography as Cr diffuses from the matrix into the MN precipitates. Thus a change from one...

  15. Atomic resolution non-contact atomic force microscopy of clean metal oxide surfaces.

    Science.gov (United States)

    Lauritsen, J V; Reichling, M

    2010-07-07

    In the last two decades the atomic force microscope (AFM) has become the premier tool for topographical analysis of surface structures at the nanometre scale. In its ultimately sensitive implementation, namely dynamic scanning force microscopy (SFM) operated in the so-called non-contact mode (NC-AFM), this technique yields genuine atomic resolution and offers a unique tool for real space atomic-scale studies of surfaces, nanoparticles as well as thin films, single atoms and molecules on surfaces irrespective of the substrate being electrically conducting or non-conducting. Recent advances in NC-AFM have paved the way for groundbreaking atomic level insight into insulator surfaces, specifically in the most important field of metal oxides. NC-AFM imaging now strongly contributes to our understanding of the surface structure, chemical composition, defects, polarity and reactivity of metal oxide surfaces and related physical and chemical surface processes. Here we review the latest advancements in the field of NC-AFM applied to the fundamental atomic resolution studies of clean single crystal metal oxide surfaces with special focus on the representative materials Al(2)O(3)(0001), TiO(2)(110), ZnO(1000) and CeO(2)(111). © 2010 IOP Publishing Ltd

  16. Atomic lattice excitons: from condensates to crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kantian, A [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); Daley, A J [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); Toermae, P [Nanoscience Center, Department of Physics, University of Jyvaeskylae, PO Box 35, FIN-40014 (Finland); Zoller, P [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria)

    2007-11-15

    We discuss atomic lattice excitons (ALEs), bound particle-hole pairs formed by fermionic atoms in two bands of an optical lattice. Such a system provides a clean set-up, with tunable masses and interactions, to study fundamental properties of excitons including exciton condensation. We also find that for a large effective mass ratio between particles and holes, effective long-range interactions can mediate the formation of an exciton crystal, for which superfluidity is suppressed. Using a combination of mean-field treatments, bosonized theory based on a Born-Oppenheimer approximation, and one-dimensional (1D) numerical computation, we discuss the properties of ALEs under varying conditions, and discuss in particular their preparation and measurement.

  17. Development of the Atomic-Resolution Environmental Transmission Electron Microscope

    DEFF Research Database (Denmark)

    Gai, Pratibha L.; Boyes, Edward D.; Yoshida, Kenta

    2016-01-01

    The development of the novel atomic-resolution environmental transmission electron microscope (atomic-resolution ETEM) for directly probing dynamic gas–solid reactions in situ at the atomic level under controlled reaction conditions consisting of gas environment and elevated temperatures...... is used to study steels, graphene, nanowires, etc. In this chapter, the experimental setup of the microscope column and its peripherals are described....

  18. A high resolution X-ray crystal spectrometer to study electron and ...

    Indian Academy of Sciences (India)

    We have studied fast ion–atom and electron–atom collision processes using a reconditioned high resolution X-ray spectrometer. The X-rays, generated by the collisions, are dispersed by a curved ADP crystal (Johansson geometry) and detected by a gas proportional counter. A self-written LabVIEW based program has ...

  19. Spiroborate Ions for Crystallization and Resolution

    Science.gov (United States)

    Wong, Lawrence Wan Yin

    Spiroborate anions are boron compounds with two oxygen based chelating ligands which offer useful prospects for crystallization and chiral resolution. In particular the application and the rationale of using chiral spiroborates with either B-based or ligand-based chirality as a simple, cheap and effective auxiliaries for resolution are studied. In Chapter 2 the scope and limitations of spiroborate formation and crystallization are explored through different classes by investigating their structures and properties. Structures of five different classes are described including spiroborates derived from various diols, catechols, a-hydroxy acids, hydroxybenzoic acids and hydroxyl oximes. The crystallizing abilities are demonstrated with successful isolation of stable product using differing cations. Both limitations and difficulties in each system are also discussed. In chapter 3 chiral spiroborate anions bora-bis-mandelate [B(Man) 2] anions are introduced as highly effective auxiliary for resolution of various racemic chiral cations. The scope of their application is well exemplified by, though not limited to, three disparate examples; the pharmaceutically important natural alkaloid tetrahydropalmatine (THP) which forms a mono-cation, the small 1,2-diaminopropane (1,2-dap) which forms a dication and the metal-organic complex [Co(phen)3]3+. The resulting salts with [B(Man)2] are 1:1, 1:2 and 1:3 stoichiometry. The resolutions may be either by a facile one-pot solvothermal procedure or via counter-ion exchange in metathesis crystallizations using a pre-prepared salt such as Na[B(Man) 2]. High ee of > 90 % have been achieved in all three systems and confirmed by chiral chromatography and/or Circular Dichroism spectroscopy. In Chapter 4 the investigation of spiroborate diastereomeric ion pairs using chiral [B(Man)2] anions and chiral aminoalcohols were undertaken to better understand the structural issues of chiral resolution and predict the resolution result. Three other

  20. Low Resolution Refinement of Atomic Models Against Crystallographic Data.

    Science.gov (United States)

    Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

    2017-01-01

    This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, Pro

  1. Intermolecular atom-atom bonds in crystals - a chemical perspective.

    Science.gov (United States)

    Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R

    2015-03-01

    Short atom-atom distances between molecules are almost always indicative of specific intermolecular bonding. These distances may be used to assess the significance of all hydrogen bonds, including the C-H⋯O and even weaker C-H⋯F varieties.

  2. Quantitative High-Resolution Transmission Electron Microscopy of Single Atoms

    OpenAIRE

    Gamm, B.; Popescu, R.; Blank, H.; Schneider, R; Beyer, A.; Gölzhäuser, A.; Gerthsen, D.

    2010-01-01

    Single atoms can be considered as basic objects for electron microscopy to test the microscope performance and basic concepts for modeling of image contrast. In this work high-resolution transmission electron microscopy was applied to image single platinum atoms in an aberration-corrected transmission electron microscope. The atoms are deposited on a self-assembled monolayer substrate which induces only negligible contrast. Single-atom contrast simulations were performed on the basis of Weick...

  3. Direct detection of antihydrogen atoms using a BGO crystal

    Energy Technology Data Exchange (ETDEWEB)

    Nagata, Y. [Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, 184-8588 Tokyo (Japan); Atomic Physics Research Unit, RIKEN, 2-1 Hirosawa, Wako-shi, 351-0198 Saitama (Japan); Kuroda, N., E-mail: kuroda@phys.c.u-tokyo.ac.jp [Institute of Physics, University of Tokyo, 3-8-1 Komaba, Meguro-ku, 153-8902 Tokyo (Japan); Atomic Physics Research Unit, RIKEN, 2-1 Hirosawa, Wako-shi, 351-0198 Saitama (Japan); Ohtsuka, M. [Institute of Physics, University of Tokyo, 3-8-1 Komaba, Meguro-ku, 153-8902 Tokyo (Japan); Leali, M.; Lodi-Rizzini, E.; Mascagna, V. [Dipartimento di Ingegneria dell' Informazione, Universitá di Brescia, Brescia 25133 (Italy); Istituto Nazionale di Fisica Nucleare, Gruppo Collegato di Brescia, Brescia 25133 (Italy); Tajima, M.; Torii, H.A. [Institute of Physics, University of Tokyo, 3-8-1 Komaba, Meguro-ku, 153-8902 Tokyo (Japan); Atomic Physics Research Unit, RIKEN, 2-1 Hirosawa, Wako-shi, 351-0198 Saitama (Japan); Zurlo, N. [Dipartimento di Ingegneria dell' Informazione, Universitá di Brescia, Brescia 25133 (Italy); Istituto Nazionale di Fisica Nucleare, Gruppo Collegato di Brescia, Brescia 25133 (Italy); Matsuda, Y. [Institute of Physics, University of Tokyo, 3-8-1 Komaba, Meguro-ku, 153-8902 Tokyo (Japan); Atomic Physics Research Unit, RIKEN, 2-1 Hirosawa, Wako-shi, 351-0198 Saitama (Japan); Venturelli, L. [Dipartimento di Ingegneria dell' Informazione, Universitá di Brescia, Brescia 25133 (Italy); Istituto Nazionale di Fisica Nucleare, Gruppo Collegato di Brescia, Brescia 25133 (Italy); Yamazaki, Y. [Atomic Physics Research Unit, RIKEN, 2-1 Hirosawa, Wako-shi, 351-0198 Saitama (Japan)

    2016-12-21

    The ASACUSA collaboration has developed a detector consisting of a large size BGO crystal to detect an atomic antihydrogen beam, and performed the direct detection of antihydrogen atoms. Energy spectra from antihydrogen annihilation on the BGO crystal are discussed in comparison to simulation results from the GEANT4 toolkit. Background mainly originating from cosmic rays were strongly suppressed by analyzing the energy deposited in the BGO and requiring a multiplicity of charged pions. Thus antihydrogen events were identified.

  4. Radiation damage free ghost diffraction with atomic resolution

    Science.gov (United States)

    Li, Zheng; Medvedev, Nikita; Chapman, Henry N.; Shih, Yanhua

    2018-01-01

    The x-ray free electron lasers can enable diffractive structural determination of protein nanocrystals and single molecules that are too small and radiation-sensitive for conventional x-ray diffraction. However the electronic form factor may be modified during the ultrashort x-ray pulse due to photoionization and electron cascade caused by the intense x-ray pulse. For general x-ray imaging techniques, the minimization of the effects of radiation damage is of major concern to ensure reliable reconstruction of molecular structure. Here we show that radiation damage free diffraction can be achieved with atomic spatial resolution by using x-ray parametric down-conversion and ghost diffraction with entangled photons of x-ray and optical frequencies. We show that the formation of the diffraction patterns satisfies a condition analogous to the Bragg equation, with a resolution that can be as fine as the crystal lattice length scale of several Ångstrom. Since the samples are illuminated by low energy optical photons, they can be free of radiation damage.

  5. Visualization of arrangements of carbon atoms in graphene layers by Raman mapping and atomic-resolution TEM

    KAUST Repository

    Cong, Chunxiao

    2013-02-01

    In-plane and out-of-plane arrangements of carbon atoms in graphene layers play critical roles in the fundamental physics and practical applications of these novel two-dimensional materials. Here, we report initial results on the edge/crystal orientations and stacking orders of bi-and tri-layer graphene (BLG and TLG) from Raman spectroscopy and transmission electron microscopy (TEM) experiments performed on the same sample. We introduce a new method of transferring graphene flakes onto a normal TEM grid. Using this novel method, we probed the BLG and TLG flakes that had been previously investigated by Raman scattering with high-resolution (atomic) TEM.

  6. Visualization of arrangements of carbon atoms in graphene layers by Raman mapping and atomic-resolution TEM

    Science.gov (United States)

    Cong, Chunxiao; Li, Kun; Zhang, Xi Xiang; Yu, Ting

    2013-01-01

    In-plane and out-of-plane arrangements of carbon atoms in graphene layers play critical roles in the fundamental physics and practical applications of these novel two-dimensional materials. Here, we report initial results on the edge/crystal orientations and stacking orders of bi- and tri-layer graphene (BLG and TLG) from Raman spectroscopy and transmission electron microscopy (TEM) experiments performed on the same sample. We introduce a new method of transferring graphene flakes onto a normal TEM grid. Using this novel method, we probed the BLG and TLG flakes that had been previously investigated by Raman scattering with high-resolution (atomic) TEM. PMID:23378926

  7. Prospects of linear reconstruction in atomic resolution electron holographic tomography

    Energy Technology Data Exchange (ETDEWEB)

    Krehl, Jonas, E-mail: Jonas.Krehl@triebenberg.de; Lubk, Axel

    2015-03-15

    Tomography commonly requires a linear relation between the measured signal and the underlying specimen property; for Electron Holographic Tomography this is given by the Phase Grating Approximation (PGA). While largely valid at medium resolution, discrepancies arise at high resolution imaging conditions. We set out to investigate the artefacts that are produced if the reconstruction still assumes the PGA even with an atomic resolution tilt series. To forego experimental difficulties the holographic tilt series was simulated. The reconstructed electric potential clearly shows peaks at the positions of the atoms. These peaks have characterisitic deformations, which can be traced back to the defocus a particular atom has in the holograms of the tilt series. Exchanging an atom for one of a different atomic number results in a significant change in the reconstructed potential that is well contained within the atom's peak. - Highlights: • We simulate a holographic tilt series of a nanocrystal with atomic resolution. • Using PGA-based Holographic Tomography we reconstruct the atomic structure. • The reconstruction shows characteristic artefacts, chiefly caused by defocus. • Changing one atom's Z produces a well localised in the reconstruction.

  8. Atomic-Resolution Spectrum Imaging of Semiconductor Nanowires.

    Science.gov (United States)

    Zamani, Reza R; Hage, Fredrik S; Lehmann, Sebastian; Ramasse, Quentin M; Dick, Kimberly A

    2017-11-13

    Over the past decade, III-V heterostructure nanowires have attracted a surge of attention for their application in novel semiconductor devices such as tunneling field-effect transistors (TFETs). The functionality of such devices critically depends on the specific atomic arrangement at the semiconductor heterointerfaces. However, most of the currently available characterization techniques lack sufficient spatial resolution to provide local information on the atomic structure and composition of these interfaces. Atomic-resolution spectrum imaging by means of electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) is a powerful technique with the potential to resolve structure and chemical composition with sub-angstrom spatial resolution and to provide localized information about the physical properties of the material at the atomic scale. Here, we demonstrate the use of atomic-resolution EELS to understand the interface atomic arrangement in three-dimensional heterostructures in semiconductor nanowires. We observed that the radial interfaces of GaSb-InAs heterostructure nanowires are atomically abrupt, while the axial interface in contrast consists of an interfacial region where intermixing of the two compounds occurs over an extended spatial region. The local atomic configuration affects the band alignment at the interface and, hence, the charge transport properties of devices such as GaSb-InAs nanowire TFETs. STEM-EELS thus represents a very promising technique for understanding nanowire physical properties, such as differing electrical behavior across the radial and axial heterointerfaces of GaSb-InAs nanowires for TFET applications.

  9. Ambient atomic resolution atomic force microscopy with qPlus sensors: Part 1.

    Science.gov (United States)

    Wastl, Daniel S

    2017-01-01

    Atomic force microscopy (AFM) is an enormous tool to observe nature in highest resolution and understand fundamental processes like friction and tribology on the nanoscale. Atomic resolution in highest quality was possible only in well-controlled environments like ultrahigh vacuum (UHV) or controlled buffer environments (liquid conditions) and more specified for long-term high-resolution analysis at low temperatures (∼4 K) in UHV where drift is nearly completely absent. Atomic resolution in these environments is possible and is widely used. However, in uncontrolled environments like air, with all its pollutants and aerosols, unspecified thin liquid films as thin as a single molecular water-layer of 200 pm or thicker condensation films with thicknesses up to hundred nanometer, have been a problem for highest resolution since the invention of the AFM. The goal of true atomic resolution on hydrophilic as well as hydrophobic samples was reached recently. In this manuscript we want to review the concept of ambient AFM with atomic resolution. The reader will be introduced to the phenomenology in ambient conditions and the problems will be explained and analyzed while a method for scan parameter optimization will be explained. Recently developed concepts and techniques how to reach atomic resolution in air and ultra-thin liquid films will be shown and explained in detail, using several examples. Microsc. Res. Tech. 80:50-65, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. Atom-atom interactions around the band edge of a photonic crystal waveguide.

    Science.gov (United States)

    Hood, Jonathan D; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E; Kimble, H J

    2016-09-20

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields [Formula: see text] outside the bandgap to localized fields [Formula: see text] within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the [Formula: see text] line of atomic cesium for [Formula: see text] atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

  11. High resolution adaptive imaging of a single atom

    CERN Document Server

    Wong-Campos, J D; Neyenhuis, B; Mizrahi, J; Monroe, C

    2015-01-01

    We report the optical imaging of a single atom with nanometer resolution using an adaptive optical alignment technique that is applicable to general optical microscopy. By decomposing the image of a single laser-cooled atom, we identify and correct optical aberrations in the system and realize an atomic position sensitivity of $\\approx$ 0.5 nm/$\\sqrt{\\text{Hz}}$ with a minimum uncertainty of 1.7 nm, allowing the direct imaging of atomic motion. This is the highest position sensitivity ever measured for an isolated atom, and opens up the possibility of performing out-of-focus 3D particle tracking, imaging of atoms in 3D optical lattices or sensing forces at the yoctonewton (10$^{-24}$ N) scale.

  12. A high resolution ion microscope for cold atoms

    Science.gov (United States)

    Stecker, Markus; Schefzyk, Hannah; Fortágh, József; Günther, Andreas

    2017-04-01

    We report on an ion-optical system that serves as a microscope for ultracold ground state and Rydberg atoms. The system is designed to achieve a magnification of up to 1000 and a spatial resolution in the 100 nm range, thereby surpassing many standard imaging techniques for cold atoms. The microscope consists of four electrostatic lenses and a microchannel plate in conjunction with a delay line detector in order to achieve single particle sensitivity with high temporal and spatial resolution. We describe the design process of the microscope including ion-optical simulations of the imaging system and characterize aberrations and the resolution limit. Furthermore, we present the experimental realization of the microscope in a cold atom setup and investigate its performance by patterned ionization with a structure size down to 2.7 μm. The microscope meets the requirements for studying various many-body effects, ranging from correlations in cold quantum gases up to Rydberg molecule formation.

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

    Science.gov (United States)

    Ho, Phuong T; Reddy, Vijay S

    2017-10-27

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

  14. Crystal structures and atomic model of NADPH oxidase

    NARCIS (Netherlands)

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

    2017-01-01

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

  15. Atomic-resolution transmission electron microscopy of electron beam–sensitive crystalline materials

    KAUST Repository

    Zhang, Daliang

    2018-01-18

    High-resolution imaging of electron beam-sensitive materials is one of the most difficult applications of transmission electron microscopy (TEM). The challenges are manifold, including the acquisition of images with extremely low beam doses, the time-constrained search for crystal zone axes, the precise image alignment, and the accurate determination of the defocus value. We develop a suite of methods to fulfill these requirements and acquire atomic-resolution TEM images of several metal organic frameworks that are generally recognized as highly sensitive to electron beams. The high image resolution allows us to identify individual metal atomic columns, various types of surface termination, and benzene rings in the organic linkers. We also apply our methods to other electron beam–sensitive materials, including the organic-inorganic hybrid perovskite CH3NH3PbBr3.

  16. Determining the Molecular Packing Arrangements on Protein Crystal Faces by Atomic Force Microscopy

    Science.gov (United States)

    Li, Huayu; Perozzo, Mary A.; Konnert, John H.; Nadarajan, Arunan; Pusey, Marc L.

    1998-01-01

    Periodic Bond Chain (PBC) analysis of the packing of tetragonal lysozyme crystals have revealed that there are two possible molecular packing arrangements for the crystal faces. The analysis also predicted that only one of these, involving the formation of helices about the 4(sub 3) axes, would prevail during crystal growth. In this study high resolution atomic force microscopy (AFM) was employed to verify these predictions for the (110) crystal face. A computer program was developed which constructs the expected AFM image for a given tip shape for each possible molecular packing arrangement. By comparing the actual AFM image with the predicted images the correct packing arrangement was determined. The prediction of an arrangement involving 4(sub 3) helices was confirmed in this manner,"while the alternate arrangement was not observed. The investigation also showed the protein molecules were packed slightly closer about the 4(sub 3) axes than in the crystallographic arrangement of the crystal interior. This study demonstrates a new approach for determining the molecular packing arrangements on protein crystal faces. It also shows the power of combining a theoretical PBC analysis with experimental high resolution AFM techniques in probing protein crystal growth processes at the molecular level.

  17. Ultrafast terahertz scanning tunneling microscopy with atomic resolution

    DEFF Research Database (Denmark)

    Jelic, Vedran; Iwaszczuk, Krzysztof; Nguyen, Peter H.

    2016-01-01

    We demonstrate that ultrafast terahertz scanning tunneling microscopy (THz-STM) can probe single atoms on a silicon surface with simultaneous sub-nanometer and sub-picosecond spatio-temporal resolution. THz-STM is established as a new technique for exploring high-field non-equilibrium tunneling...

  18. Solid sampling determination of magnesium in lithium niobate crystals by graphite furnace atomic absorption spectrometry

    Science.gov (United States)

    Dravecz, Gabriella; Laczai, Nikoletta; Hajdara, Ivett; Bencs, László

    2016-12-01

    The vaporization/atomization processes of Mg in high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS-GFAAS) were investigated by evaporating solid (powder) samples of lithium niobate (LiNbO3) optical single crystals doped with various amounts of Mg in a transversally heated graphite atomizer (THGA). Optimal analytical conditions were attained by using the Mg I 215.4353 nm secondary spectral line. An optimal pyrolysis temperature of 1500 °C was found for Mg, while the compromise atomization temperature in THGAs (2400 °C) was applied for analyte vaporization. The calibration was performed against solid (powered) lithium niobate crystal standards. The standards were prepared with exactly known Mg content via solid state fusion of the oxide components of the matrix and analyte. The correlation coefficient (R value) of the linear calibration was not worse than 0.9992. The calibration curves were linear in the dopant concentration range of interest (0.74-7.25 mg/g Mg), when dosing 3-10 mg of the powder samples into the graphite sample insertion boats. The Mg content of the studied 19 samples was in the range of 1.69-4.13 mg/g. The precision of the method was better than 6.3%. The accuracy of the results was verified by means of flame atomic absorption spectrometry with solution sample introduction after digestion of several crystal samples.

  19. Quantitative high-resolution transmission electron microscopy of single atoms.

    Science.gov (United States)

    Gamm, Björn; Blank, Holger; Popescu, Radian; Schneider, Reinhard; Beyer, André; Gölzhäuser, Armin; Gerthsen, Dagmar

    2012-02-01

    Single atoms can be considered as the most basic objects for electron microscopy to test the microscope performance and basic concepts for modeling image contrast. In this work high-resolution transmission electron microscopy was applied to image single platinum, molybdenum, and titanium atoms in an aberration-corrected transmission electron microscope. The atoms are deposited on a self-assembled monolayer substrate that induces only negligible contrast. Single-atom contrast simulations were performed on the basis of Weickenmeier-Kohl and Doyle-Turner form factors. Experimental and simulated image intensities are in quantitative agreement on an absolute intensity scale, which is provided by the vacuum image intensity. This demonstrates that direct testing of basic properties such as form factors becomes feasible.

  20. Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

    Energy Technology Data Exchange (ETDEWEB)

    Nath, Seema; Banerjee, Ramanuj; Sen, Udayaditya, E-mail: udayaditya.sen@saha.ac.in

    2014-07-18

    Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.

  1. Atomic Resolution Imaging with a sub-50 pm Electron Probe

    Energy Technology Data Exchange (ETDEWEB)

    Erni, Rolf P.; Rossell, Marta D.; Kisielowski, Christian; Dahmen, Ulrich

    2009-03-02

    Using a highly coherent focused electron probe in a 5th order aberration-corrected transmission electron microscope, we report on resolving a crystal spacing less than 50 pm. Based on the geometrical source size and residual coherent and incoherent axial lens aberrations, an electron probe is calculated, which is theoretically capable of resolving an ideal 47 pm spacing with 29percent contrast. Our experimental data show the 47 pm spacing of a Ge 114 crystal imaged with 11-18percent contrast at a 60-95percent confidence level, providing the first direct evidence for sub 50-pm resolution in ADF STEM imaging.

  2. Atomic resolution imaging and spectroscopy of barium atoms and functional groups on graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Boothroyd, C.B., E-mail: ChrisBoothroyd@cantab.net [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Moreno, M.S. [Centro Atómico Bariloche, 8400 – San Carlos de Bariloche (Argentina); Duchamp, M.; Kovács, A. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Monge, N.; Morales, G.M.; Barbero, C.A. [Department of Chemistry, Universidad Nacional de Río Cuarto, X5804BYA Río Cuarto (Argentina); Dunin-Borkowski, R.E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany)

    2014-10-15

    We present an atomic resolution transmission electron microscopy (TEM) and scanning TEM (STEM) study of the local structure and composition of graphene oxide modified with Ba{sup 2+}. In our experiments, which are carried out at 80 kV, the acquisition of contamination-free high-resolution STEM images is only possible while heating the sample above 400 °C using a highly stable heating holder. Ba atoms are identified spectroscopically in electron energy-loss spectrum images taken at 800 °C and are associated with bright contrast in high-angle annular dark-field STEM images. The spectrum images also show that Ca and O occur together and that Ba is not associated with a significant concentration of O. The electron dose used for spectrum imaging results in beam damage to the specimen, even at elevated temperature. It is also possible to identify Ba atoms in high-resolution TEM images acquired using shorter exposure times at room temperature, thereby allowing the structure of graphene oxide to be studied using complementary TEM and STEM techniques over a wide range of temperatures. - Highlights: • Graphene oxide modified with Ba{sup 2+} was imaged using TEM and STEM at 80 kV. • High-resolution images and spectra were obtained only by heating above 400 °C. • Elemental maps show the distribution of C, Ba, O and Ca on the graphene oxide. • Single Ba atoms were identified in STEM HAADF and HRTEM images.

  3. Sub-nanometer resolution XPS depth profiling: Sensing of atoms

    Energy Technology Data Exchange (ETDEWEB)

    Szklarczyk, Marek, E-mail: szklarcz@chem.uw.edu.pl [Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw (Poland); Shim-Pol, ul. Lubomirskiego 5, 05-080 Izabelin (Poland); Macak, Karol; Roberts, Adam J. [Kratos Analytical Ltd, Wharfside, Trafford Wharf Road, Manchester, M17 1GP (United Kingdom); Takahashi, Kazuhiro [Kratos XPS Section, Shimadzu Corp., 380-1 Horiyamashita, Hadano, Kanagawa 259-1304 (Japan); Hutton, Simon [Kratos Analytical Ltd, Wharfside, Trafford Wharf Road, Manchester, M17 1GP (United Kingdom); Głaszczka, Rafał [Shim-Pol, ul. Lubomirskiego 5, 05-080 Izabelin (Poland); Blomfield, Christopher [Kratos Analytical Ltd, Wharfside, Trafford Wharf Road, Manchester, M17 1GP (United Kingdom)

    2017-07-31

    Highlights: • Angle resolved photoelectron depth profiling of nano thin films. • Sensing atomic position in SAM films. • Detection of direction position of adsorbed molecules. - Abstract: The development of a method capable of distinguishing a single atom in a single molecule is important in many fields. The results reported herein demonstrate sub-nanometer resolution for angularly resolved X-ray photoelectron spectroscopy (ARXPS). This is made possible by the incorporation of a Maximum Entropy Method (MEM) model, which utilize density corrected electronic emission factors to the X-ray photoelectron spectroscopy (XPS) experimental results. In this paper we report on the comparison between experimental ARXPS results and reconstructed for both inorganic and organic thin film samples. Unexpected deviations between experimental data and calculated points are explained by the inaccuracy of the constants and standards used for the calculation, e.g. emission factors, scattering intensity and atomic density through the studied thickness. The positions of iron, nitrogen and fluorine atoms were determined in the molecules of the studied self-assembled monolayers. It has been shown that reconstruction of real spectroscopic data with 0.2 nm resolution is possible.

  4. Electron Cryomicroscopy of Viruses at Near-Atomic Resolutions.

    Science.gov (United States)

    Kaelber, Jason T; Hryc, Corey F; Chiu, Wah

    2017-09-29

    Recently, dozens of virus structures have been solved to resolutions between 2.5 and 5.0 Å by means of electron cryomicroscopy. With these structures we are now firmly within the "atomic age" of electron cryomicroscopy, as these studies can reveal atomic details of protein and nucleic acid topology and interactions between specific residues. This improvement in resolution has been the result of direct electron detectors and image processing advances. Although enforcing symmetry facilitates reaching near-atomic resolution with fewer particle images, it unfortunately obscures some biologically interesting components of a virus. New approaches on relaxing symmetry and exploring structure dynamics and heterogeneity of viral assemblies have revealed important insights into genome packaging, virion assembly, cell entry, and other stages of the viral life cycle. In the future, novel methods will be required to reveal yet-unknown structural conformations of viruses, relevant to their biological activities. Ultimately, these results hold the promise of answering many unresolved questions linking structural diversity of viruses to their biological functions.

  5. Modeling Protein Structure at Near Atomic Resolutions With Gorgon

    Science.gov (United States)

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

    2011-01-01

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

  6. Distinctive features of a crystal, crystal-like properties of a liquid and atomic quantum effects

    Energy Technology Data Exchange (ETDEWEB)

    Pavlov, V V [Ural State Mining University. Kuibyshev str. 30, Ekaterinburg, 620144 (Russian Federation)], E-mail: gmf.chm@ursmu.ru

    2008-02-15

    It is believed that 'a crystal is similar to the crowd which is tightly compressed within enclosed space' and its structure in the simplest case is similar to the closest ball packing. Based on this assumption the strength of a crystal, long range ordering, the granular structure, capability for polymorphic transformation etc. were deduced. In a liquid such properties are impossible even in feebly marked form. However some of crystal-like features of melts are revealed in experiments and they frequently remain unacknowledged with a theory. From the other hand, computer model of crystal does not give even listed distinctive features of a crystal state. In the classical model the solidification more than to sunflower oil consistence was not obtained. It is possible to reach the real solidification if quantum 'freezing' of a part of atomic degrees of freedom would taken into account and any movement would stopped at zero energy level. There are some reasons to believe that another crystal properties and corresponding crystal-like features of liquids also can be got basing on these atomic quantum effects. In this case the reasons of many discussions on 'heredity', 'memory' of liquid and its microheterogeneity disappear.

  7. High-resolution electron microscope and computed images of human tooth enamel crystals.

    Science.gov (United States)

    Brés, E F; Barry, J C; Hutchison, J L

    1985-03-01

    The structure of human enamel crystallites has been studied at a near atomic level by high-resolution electron microscopy. Electron micrographs have been obtained from crystallites present in human enamel with a structure resolution of 0.2 nm in the [0001], [1210], [1213], [1100] and [4510] zone axes directions. In most cases it was possible to match the experimental images with images calculated using the atomic positions of mineral hydroxyapatite. However, in some cases a discrepancy between calculated and experimental image detail was observed in the c direction of the [1210] and the [1100] images. This shows: (i) a structural heterogeneity of the crystals, and (ii) a loss of hexagonal symmetry of the structure. The resolution required to distinguish individual atomic sites in the different zones has been determined, and this will provide a useful basis for future work. As the determination of the "real structure" of biological crystals is of prime importance for the study of calcification mechanisms (crystal growth), biological properties and destructive phenomena of calcified tissues (i.e., dental caries and bone resorption).

  8. Atom interaction propensities of oxygenated chemical functions in crystal packings

    Science.gov (United States)

    Jelsch, Christian; Bibila Mayaya Bisseyou, Yvon

    2017-01-01

    The crystal contacts of several families of hydrocarbon compounds substituted with one or several types of oxygenated chemical groups were analyzed statistically using the Hirshfeld surface methodology. The propensity of contacts to occur between two chemical types is described with the contact enrichment descriptor. The systematic large enrichment ratios of some interactions like the O—H⋯O hydrogen bonds suggests that these contacts are a driving force in the crystal packing formation. The same statement holds for the weaker C—H⋯O hydrogen bonds in ethers, esters and ketones, in the absence of polar H atoms. The over-represented contacts in crystals of oxygenated hydrocarbons are generally of two types: electrostatic attractions (hydrogen bonds) and hydrophobic interactions. While Cl⋯O interactions are generally avoided, in a minority of chloro-oxygenated hydrocarbons, significant halogen bonding does occur. General tendencies can often be derived for many contact types, but outlier compounds are instructive as they display peculiar or rare features. The methodology also allows the detection of outliers which can be structures with errors. For instance, a significant number of hydroxylated molecules displaying over-represented non-favorable oxygen–oxygen contacts turned out to have wrongly oriented hydroxyl groups. Beyond crystal packings with a single molecule in the asymmetric unit, the behavior of water in monohydrate compounds and of crystals with Z′ = 2 (dimers) are also investigated. It was found in several cases that, in the presence of several oxygenated chemical groups, cross-interactions between different chemical groups (e.g. water/alcohols; alcohols/phenols) are often favored in the crystal packings. While some trends in accordance with common chemical principles are retrieved, some unexpected results can however appear. For example, in crystals of alcohol–phenol compounds, the strong O—H⋯O hydrogen bonds between two phenol groups

  9. Atom interaction propensities of oxygenated chemical functions in crystal packings

    Directory of Open Access Journals (Sweden)

    Christian Jelsch

    2017-03-01

    Full Text Available The crystal contacts of several families of hydrocarbon compounds substituted with one or several types of oxygenated chemical groups were analyzed statistically using the Hirshfeld surface methodology. The propensity of contacts to occur between two chemical types is described with the contact enrichment descriptor. The systematic large enrichment ratios of some interactions like the O—H...O hydrogen bonds suggests that these contacts are a driving force in the crystal packing formation. The same statement holds for the weaker C—H...O hydrogen bonds in ethers, esters and ketones, in the absence of polar H atoms. The over-represented contacts in crystals of oxygenated hydrocarbons are generally of two types: electrostatic attractions (hydrogen bonds and hydrophobic interactions. While Cl...O interactions are generally avoided, in a minority of chloro-oxygenated hydrocarbons, significant halogen bonding does occur. General tendencies can often be derived for many contact types, but outlier compounds are instructive as they display peculiar or rare features. The methodology also allows the detection of outliers which can be structures with errors. For instance, a significant number of hydroxylated molecules displaying over-represented non-favorable oxygen–oxygen contacts turned out to have wrongly oriented hydroxyl groups. Beyond crystal packings with a single molecule in the asymmetric unit, the behavior of water in monohydrate compounds and of crystals with Z′ = 2 (dimers are also investigated. It was found in several cases that, in the presence of several oxygenated chemical groups, cross-interactions between different chemical groups (e.g. water/alcohols; alcohols/phenols are often favored in the crystal packings. While some trends in accordance with common chemical principles are retrieved, some unexpected results can however appear. For example, in crystals of alcohol–phenol compounds, the strong O—H...O hydrogen bonds between

  10. Atomic-Scale Time and Space Resolution of Terahertz Frequency Acoustic Waves

    Science.gov (United States)

    Reed, Evan J.; Armstrong, Michael R.; Kim, Ki-Yong; Glownia, James H.

    2008-07-01

    Using molecular dynamics simulations and analytics, we find that strain waves of terahertz frequencies can coherently generate radiation when they propagate past an interface between materials with different piezoelectric coefficients. By considering AlN/GaN heterostructures, we show that the radiation is of detectable amplitude and contains sufficient information to determine the time dependence of the strain wave with potentially subpicosecond, nearly atomic time and space resolution. We demonstrate this phenomenon within the context of high amplitude terahertz frequency strain waves that spontaneously form at the front of shock waves in GaN crystals.

  11. Sub-nanometer resolution XPS depth profiling: Sensing of atoms

    Science.gov (United States)

    Szklarczyk, Marek; Macak, Karol; Roberts, Adam J.; Takahashi, Kazuhiro; Hutton, Simon; Głaszczka, Rafał; Blomfield, Christopher

    2017-07-01

    The development of a method capable of distinguishing a single atom in a single molecule is important in many fields. The results reported herein demonstrate sub-nanometer resolution for angularly resolved X-ray photoelectron spectroscopy (ARXPS). This is made possible by the incorporation of a Maximum Entropy Method (MEM) model, which utilize density corrected electronic emission factors to the X-ray photoelectron spectroscopy (XPS) experimental results. In this paper we report on the comparison between experimental ARXPS results and reconstructed for both inorganic and organic thin film samples. Unexpected deviations between experimental data and calculated points are explained by the inaccuracy of the constants and standards used for the calculation, e.g. emission factors, scattering intensity and atomic density through the studied thickness. The positions of iron, nitrogen and fluorine atoms were determined in the molecules of the studied self-assembled monolayers. It has been shown that reconstruction of real spectroscopic data with 0.2 nm resolution is possible.

  12. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

    Directory of Open Access Journals (Sweden)

    Matthew P. Blakeley

    2015-07-01

    Full Text Available The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden and Sirius (Brazil under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å, for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59% were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+ remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place

  13. Simulation and understanding of atomic and molecular quantum crystals

    Science.gov (United States)

    Cazorla, Claudio; Boronat, Jordi

    2017-07-01

    Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

  14. High resolution X-ray spectroscopy in light antiprotonic atoms

    CERN Document Server

    Borchert, G L; Augsburger, M A; Castelli, C M; Chatellard, D; Egger, J P; El-Khoury, P; Elble, M; Gorke, H; Gotta, D; Hauser, P R; Indelicato, P J; Kirch, K; Lenz, S; Nelms, N; Rashid, K; Schult, O W B; Siems, T; Simons, L M

    2000-01-01

    At the LEAR facility, CERN, antiprotonic L alpha transitions in light elements have been investigated with a focussing crystal spectrometer. The high resolution of the experiment allowed for the first time to resolve in pH/pH the 2/sup 3/P/sub 0/ state from the close-lying states 2/sup 3/P/sub 2/, 2/sup 1/P/sub 1/, and 2/sup 3/P /sub 1/. In pD the corresponding transitions were found to be more than an order of magnitude broader. To a large extent the results for pH support the meson exchange model. (15 refs).

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-01

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

  16. Atomic-resolution structures of prion AGAAAAGA amyloid fibrils

    CERN Document Server

    Zhang, Jiapu

    2011-01-01

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

  17. Resolution of VISION, a crystal-analyzer spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Seeger, Philip A. [239 Loma del Escolar, Los Alamos, NM 87544 (United States)], E-mail: PASeeger@losalamos.com; Daemen, Luke L. [LANSCE, Los Alamos National Laboratory, Los Alamos, NM (United States); Larese, John Z. [Department of Chemistry, University of Tennessee, Knoxville, TN (United States)

    2009-06-11

    We present both analytic and Monte Carlo calculations of the resolution of VISION, which is a crystal-analyzer spectrometer based on the TOSCA design. The analyzer crystal in VISION is configured to focus in time, radial, and transverse directions ('triple focused'). Previously published analytical results have two serious flaws in the handling of the statistics, which gave misleading results. First, Gaussian distributions were assumed for all resolution components, so that full-width-half-maximum could be used. Not only is this a very poor approximation for most terms, it is also completely unnecessary because standard deviations can be combined in quadrature for any shape distribution (except Lorentzian). The second flaw was the choice of variables that are not independent, so that significant correlations were ignored. An example of the effect of including correlations is that the mosaic spread of the analyzer crystals does not contribute to the resolution in first order. Monte Carlo simulation is not limited to first order, and we find a mild optimum value for mosaic spread. A complete set of six independent variables is: neutron emission time, incident flight-path variation (due to moderator tilt), sample thickness, mean path in the analyzer (due to multiple reflections), sample-to-detector radial distance, and detector thickness. We treat separately the resolution contributions from histogramming and rebinning during data acquisition and reduction, and describe a scheme for VISION that minimizes the effect on resolution. We compare the contributions of the six variables to the total resolution, both analytically and by Monte Carlo simulations of a complete VISION model using the Neutron Instrument Simulation Package (NISP)

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

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo D. [Yale Univ., New Haven, CT (United States). Dept. of Mechanical Engineering and Materials Science; Altman, Eric I. [Yale Univ., New Haven, CT (United States). Dept. of Chemical and Environmental Engineering

    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 (3DAFM), 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.

  19. Lamb-Dicke spectroscopy of atoms in a hollow-core photonic crystal fibre

    Science.gov (United States)

    Okaba, Shoichi; Takano, Tetsushi; Benabid, Fetah; Bradley, Tom; Vincetti, Luca; Maizelis, Zakhar; Yampol'skii, Valery; Nori, Franco; Katori, Hidetoshi

    2014-01-01

    Unlike photons, which are conveniently handled by mirrors and optical fibres without loss of coherence, atoms lose their coherence via atom–atom and atom–wall interactions. This decoherence of atoms deteriorates the performance of atomic clocks and magnetometers, and also hinders their miniaturization. Here we report a novel platform for precision spectroscopy. Ultracold strontium atoms inside a kagome-lattice hollow-core photonic crystal fibre are transversely confined by an optical lattice to prevent atoms from interacting with the fibre wall. By confining at most one atom in each lattice site, to avoid atom–atom interactions and Doppler effect, a 7.8-kHz-wide spectrum is observed for the 1S0−3P1(m=0) transition. Atoms singly trapped in a magic lattice in hollow-core photonic crystal fibres improve the optical depth while preserving atomic coherence time. PMID:24934478

  20. Emergence of quasiparticle Bloch states in artificial crystals crafted atom-by-atom

    Directory of Open Access Journals (Sweden)

    Jan Girovsky, Jose L. Lado, Floris E. Kalff, Eleonora Fahrenfort, Lucas J. J. M. Peters, Joaquín Fernández-Rossier, Alexander F. Otte

    2017-06-01

    Full Text Available The interaction of electrons with a periodic potential of atoms in crystalline solids gives rise to band structure. The band structure of existing materials can be measured by photoemission spectroscopy and accurately understood in terms of the tight-binding model, however not many experimental approaches exist that allow to tailor artificial crystal lattices using a bottom-up approach. The ability to engineer and study atomically crafted designer materials by scanning tunnelling microscopy and spectroscopy (STM/STS helps to understand the emergence of material properties. Here, we use atom manipulation of individual vacancies in a chlorine monolayer on Cu(100 to construct one- and two-dimensional structures of various densities and sizes. Local STS measurements reveal the emergence of quasiparticle bands, evidenced by standing Bloch waves, with tuneable dispersion. The experimental data are understood in terms of a tight-binding model combined with an additional broadening term that allows an estimation of the coupling to the underlying substrate.

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

    Science.gov (United States)

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

    2016-02-01

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

  2. Atomic resolution observation of conversion-type anode RuO₂ during the first electrochemical lithiation.

    Science.gov (United States)

    Mao, Minmin; Nie, Anmin; Liu, Jiabin; Wang, Hongtao; Mao, Scott X; Wang, Qingxiao; Li, Kun; Zhang, Xi-Xiang

    2015-03-27

    Transition metal oxides have attracted great interest as alternative anode materials for rechargeable lithium-ion batteries. Among them, ruthenium dioxide is considered to be a prototype material that reacts with the Li ions in the conversion type. In situ transmission electron microscopy reveals a two-step process during the initial lithiation of the RuO2 nanowire anode at atomic resolution. The first step is characterized by the formation of the intermediate phase LixRuO2 due to the Li-ion intercalation. The following step is manifested by the solid-state amorphization reaction driven by advancing the reaction front. The crystalline/amorphous interface is consisted of {011} atomic terraces, revealing the orientation-dependent mobility. In the crystalline matrix, lattice disturbance and dislocation are identified to be two major stress-induced distortions. The latter can be effective diffusion channels, facilitating transportation of the Li ions inside the bulk RuO2 crystal and further resulting in non-uniform Li-ion distribution. It is expected that the local enrichment of the Li ions may account for the homogeneous nucleation of dislocations in the bulk RuO2 crystal and the special island-like structures. These results elucidate the structural evolution and the phase transformation during electrochemical cycling, which sheds light on engineering RuO2 anode materials.

  3. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Dahms, Sven O., E-mail: sdahms@fli-leibniz.de; Kuester, Miriam [Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745 Jena (Germany); Streb, Carsten [Friedrich-Alexander-University Erlangen-Nürnberg, Egerlandstrasse 1, D-91058 Erlangen (Germany); Roth, Christian; Sträter, Norbert [Universität Leipzig, D-04103 Leipzig (Germany); Than, Manuel E., E-mail: sdahms@fli-leibniz.de [Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745 Jena (Germany)

    2013-02-01

    A new approach is presented that allows the efficient localization and orientation of heavy-atom cluster compounds used in experimental phasing by a molecular replacement procedure. This permits the calculation of meaningful phases up to the highest resolution of the diffraction data. Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome.

  4. Atomically Phase-Matched Second-Harmonic Generation in a 2D Crystal

    Science.gov (United States)

    2016-08-26

    OPEN ORIGINAL ARTICLE Atomically phase-matched second-harmonic generation in a 2D crystal Mervin Zhao1,2,*, Ziliang Ye1,2,*, Ryuji Suzuki3,4,*, Yu...arising from a single atomic layer, where the SH light elucidated important information such as the grain boundaries and electronic structure in these ultra...intensity on layer number as a result of atomically phase-matched nonlinear dipoles in layers of the 3R crystal that constructively interfere. By

  5. The effect of experimental resolution on crystal reflectivity and secondary extinction in neutron diffraction

    DEFF Research Database (Denmark)

    Dietrich, O.W.; Als-Nielsen, Jens Aage

    1965-01-01

    The reflectivity for neutrons of a plane slab crystal is calculated in the transmission case when the crystal is placed between two Seller collimators. The calculations indicate that the crystal reflectivity, as well as the secondary extinction coefficient, depends signicantly on the angular...... resolution of the collimators. Curves are given for the extinction of the crystal with different crystal and collimator parameters....

  6. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.

    Science.gov (United States)

    Dahms, Sven O; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E

    2013-02-01

    Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome.

  7. Single crystal to single crystal transformation and hydrogen-atom transfer upon oxidation of a cerium coordination compound.

    Science.gov (United States)

    Williams, Ursula J; Mahoney, Brian D; Lewis, Andrew J; DeGregorio, Patrick T; Carroll, Patrick J; Schelter, Eric J

    2013-04-15

    Trivalent and tetravalent cerium compounds of the octamethyltetraazaannulene (H2omtaa) ligand have been synthesized. Electrochemical analysis shows a strong thermodynamic preference for the formal cerium(IV) oxidation state. Oxidation of the cerium(III) congener Ce(Homtaa)(omtaa) occurs by hydrogen-atom transfer that includes a single crystal to single crystal transformation upon exposure to an ambient atmosphere.

  8. How Photonic Crystals Can Improve the Timing Resolution of Scintillators

    CERN Document Server

    Lecoq, P; Knapitsch, A

    2013-01-01

    Photonic crystals (PhCs) and quantum optics phenomena open interesting perspectives to enhance the light extraction from scintillating me dia with high refractive indices as demonstrated by our previous work. By doing so, they also in fl uence the timing resolution of scintillators by improving the photostatistics. The present cont ribution will demonstrate that they are actually doing much more. Indeed, photonic crystals, if properly designed, allow the extr action of fast light propagation modes in the crystal with higher efficiency, therefore contributing to increasing the density of photons in the early phase of the light pulse. This is of particular interest to tag events at future high-energy physics colliders, such as CLIC, with a bunch-crossing rate of 2 GHz, as well as for a new generation of time-of-flight positron emission tomographs (TOFPET) aiming at a coincidence timing resolution of 100 ps FWHM. At this level of precision, good control of the light propagation modes is crucial if we consid...

  9. The gating cycle of a K+ channel at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Cuello, Luis G. [Center for Membrane Protein Research, Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, United States; Cortes, D. Marien [Center for Membrane Protein Research, Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, United States; Perozo, Eduardo [Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States

    2017-11-22

    C-type inactivation in potassium channels helps fine-tune long-term channel activity through conformational changes at the selectivity filter. Here, through the use of cross-linked constitutively open constructs, we determined the structures of KcsA’s mutants that stabilize the selectivity filter in its conductive (E71A, at 2.25 Å) and deep C-type inactivated (Y82A at 2.4 Å) conformations. These structural snapshots represent KcsA’s transient open-conductive (O/O) and the stable open deep C-type inactivated states (O/I), respectively. The present structures provide an unprecedented view of the selectivity filter backbone in its collapsed deep C-type inactivated conformation, highlighting the close interactions with structural waters and the local allosteric interactions that couple activation and inactivation gating. Together with the structures associated with the closed-inactivated state (C/I) and in the well-known closed conductive state (C/O), this work recapitulates, at atomic resolution, the key conformational changes of a potassium channel pore domain as it progresses along its gating cycle.

  10. Advanced double-biprism holography with atomic resolution.

    Science.gov (United States)

    Genz, Florian; Niermann, Tore; Buijsse, Bart; Freitag, Bert; Lehmann, Michael

    2014-12-01

    The optimum biprism position as suggested by Lichte (Ultramicroscopy 64 (1996) 79 [10]) was implemented into a state-of-the-art transmission electron microscope. For a setup optimized for atomic resolution holograms with a width of 30nm and a fringe spacing of 30pm, we investigated the practical improvements on hologram quality. The setup is additionally supplemented by a second biprism as suggested by Harada et al. (Applied Physics Letters 84 (2004) 3229 [12]). In order to estimate the possibilities and limitations of the double biprism setup, geometric optics arguments lead to calculation of the exploitable shadow width, necessary for strong reduction of biprism-induced artefacts. Additionally, we used the double biprism setup to estimate the biprism vibration, yielding the most stable imaging conditions with lowest overall fringe contrast damping. Electron holograms of GaN demonstrate the good match between experiment and simulation, also as a consequence of the improved stability. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Advanced double-biprism holography with atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Genz, Florian, E-mail: florian.genz@physik.tu-berlin.de [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany); Niermann, Tore [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany); Buijsse, Bart; Freitag, Bert [FEI Company, Achtseweg Noord 5, 5651 GG Eindhoven (Netherlands); Lehmann, Michael [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany)

    2014-12-15

    The optimum biprism position as suggested by Lichte (Ultramicroscopy 64 (1996) 79 [10]) was implemented into a state-of-the-art transmission electron microscope. For a setup optimized for atomic resolution holograms with a width of 30 nm and a fringe spacing of 30 pm, we investigated the practical improvements on hologram quality. The setup is additionally supplemented by a second biprism as suggested by Harada et al. (Applied Physics Letters 84 (2004) 3229 [12]). In order to estimate the possibilities and limitations of the double biprism setup, geometric optics arguments lead to calculation of the exploitable shadow width, necessary for strong reduction of biprism-induced artefacts. Additionally, we used the double biprism setup to estimate the biprism vibration, yielding the most stable imaging conditions with lowest overall fringe contrast damping. Electron holograms of GaN demonstrate the good match between experiment and simulation, also as a consequence of the improved stability. - Highlights: • Investigation of optimum biprism position implementation into state-of-the-art TEM. • Reduction of artefacts, especially vignetting in double-biprism electron holography. • Biprism vibration and most stable imaging conditions in double-biprism holography. • Demonstration of the optimized double-biprism setup using a thin GaN-foil.

  12. Proton–silicon interaction potential extracted from high-resolution measurements of crystal rainbows

    Energy Technology Data Exchange (ETDEWEB)

    Petrović, S., E-mail: petrovs@vinca.rs [Laboratory of Physics, Vinča Institute of Nuclear Sciences, University of Belgrade, P. O. Box 522, 11001 Belgrade (Serbia); Nešković, N.; Ćosić, M. [Laboratory of Physics, Vinča Institute of Nuclear Sciences, University of Belgrade, P. O. Box 522, 11001 Belgrade (Serbia); Motapothula, M. [Center for Ion Beam Applications, Physics Department, National University of Singapore, Lower Kent Ridge Road, Singapore 117542 (Singapore); Breese, M.B.H. [Center for Ion Beam Applications, Physics Department, National University of Singapore, Lower Kent Ridge Road, Singapore 117542 (Singapore); Singapore Synchrotron Light Source (SSLS), National University of Singapore, 5 Research Link, Singapore 117603 (Singapore)

    2015-10-01

    This study provides a way to produce very accurate ion–atom interaction potentials. We present the high-resolution measurements of angular distributions of protons of energies between 2.0 and 0.7 MeV channeled in a 55 nm thick (0 0 1) silicon membrane. Analysis is performed using the theory of crystal rainbows in which the Molière’s interaction potential is modified to make it accurate both close to the channel axis and close to the atomic strings defining the channel. This modification is based on adjusting the shapes of the rainbow lines appearing in the transmission angle plane, with the resulting theoretical angular distributions of transmitted protons being in excellent agreement with the corresponding experimental distributions.

  13. Determining the Molecular Growth Mechanisms of Protein Crystal Faces by Atomic Force Microscopy

    Science.gov (United States)

    Nadarajah, Arunan; Li, Huayu; Pusey, Marc L.

    1999-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height. Theoretical analyses of the packing also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces as they were being incorporated into the lattice. Images of individual growth events on the (110) face of tetragonal lysozyme crystals were observed, shown by jump discontinuities in the growth step in the linescan images as shown in the figure. The growth unit dimension in the scanned direction was obtained from these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme growth unit sizes were obtained. A variety of unit sizes corresponding to 43 helices, were shown to participate in the growth process, with the 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  14. Investigating the fundamentals of drug crystal growth using Atomic Force Microscopy

    OpenAIRE

    Thompson, Claire

    2003-01-01

    The importance of crystals to the pharmaceutical industry is evident - over 90% of pharmaceutical products contain a drug in crystalline form. However, the crystallization phenomena of drug compounds are poorly understood. An increased understanding of these processes may allow a greater degree of control over the crystallization outcomes, such as morphology, purity, or stability. In these studies, we have applied Atomic Force Microscopy (AFM) to the in situ investigations of drug crystal gro...

  15. High-resolution XES and RIXS studies with a von Hamos Bragg crystal spectrometer

    CERN Document Server

    Hoszowska, J; 10.1016/j.elspec.2004.02.005

    2004-01-01

    The high-resolution von Hamos Bragg crystal spectrometer was constructed for the study of K X-ray emission from low-Z elements and L and M X-ray spectra of medium to high Z elements. Recently, this instrument was applied to high-resolution XES and RIXS studies using X-ray synchrotron radiation at the ID21 and BM5 beamlines at the ESRF. An outline of the spectrometer design and performance characteristics will be given. The studies deal with the energy dependent KL double photoexcitation of argon, the L3 and M1 atomic- level widths of elements 54

  16. Optimising multi-frame ADF-STEM for high-precision atomic-resolution strain mapping.

    Science.gov (United States)

    Jones, Lewys; Wenner, Sigurd; Nord, Magnus; Ninive, Per Harald; Løvvik, Ole Martin; Holmestad, Randi; Nellist, Peter D

    2017-08-01

    Annular dark-field scanning transmission electron microscopy is a powerful tool to study crystal defects at the atomic scale but historically single slow-scanned frames have been plagued by low-frequency scanning-distortions prohibiting accurate strain mapping at atomic resolution. Recently, multi-frame acquisition approaches combined with post-processing have demonstrated significant improvements in strain precision, but the optimum number of frames to record has not been explored. Here we use a non-rigid image registration procedure before applying established strain mapping methods. We determine how, for a fixed total electron-budget, the available dose should be fractionated for maximum strain mapping precision. We find that reductions in scanning-artefacts of more than 70% are achievable with image series of 20-30 frames in length. For our setup, series longer than 30 frames showed little further improvement. As an application, the strain field around an aluminium alloy precipitate was studied, from which our optimised approach yields data whos strain accuracy is verified using density functional theory. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Simulation studies of atomic resolution X-ray holography

    Indian Academy of Sciences (India)

    Unknown

    rage atomic arrangement of the atoms. It may be noted that in X-ray holography methods, the concept of unit cell is not required. We know from the optical reciprocity principle that if we exchange the detector with the source, then we obtain the same experiment. We now have a source in the far field producing a plane wave ...

  18. Trapping a single atom with a fraction of a photon using a photonic crystal nanocavity

    NARCIS (Netherlands)

    van Oosten, D.|info:eu-repo/dai/nl/269286470; Kuipers, L.

    2011-01-01

    We consider the interaction between a single rubidium atom and a photonic crystal nanocavity. Because of the ultrasmall mode volume of the nanocavity, an extremely strong coupling regime can be achieved in which the atom can shift the cavity resonance by many cavity linewidths. We show that this

  19. Membrane's Eleven: heavy-atom derivatives of membrane-protein crystals

    DEFF Research Database (Denmark)

    Morth, Jens Preben; Sørensen, Thomas Lykke-Møller; Nissen, Poul

    2006-01-01

    A database has been assembled of heavy-atom derivatives used in the structure determination of membrane proteins. The database can serve as a guide to the design of experiments in the search for heavy-atom derivatives of new membrane-protein crystals. The database pinpoints organomercurials, plat...

  20. Simultaneous current-, force- and work function measurement with atomic resolution

    OpenAIRE

    Herz, Markus; Schiller, Christian H.; Giessibl, Franz J.; Mannhart, Jochen

    2005-01-01

    The local work function of a surface determines the spatial decay of the charge density at the Fermi level normal to the surface. Here, we present a method that enables simultaneous measurements of local work function and tip-sample forces. A combined dynamic scanning tunneling microscope and atomic force microscope is used to measure the tunneling current between an oscillating tip and the sample in real time as a function of the cantilever's deflection. Atomically resolved work function mea...

  1. Atomic Resolution of Calcium and Oxygen Sublattices of Calcite in Ambient Conditions by Atomic Force Microscopy Using qPlus Sensors with Sapphire Tips.

    Science.gov (United States)

    Wastl, Daniel S; Judmann, Michael; Weymouth, Alfred J; Giessibl, Franz J

    2015-01-01

    Characterization and imaging at the atomic scale with atomic force microscopy in biocompatible environments is an ongoing challenge. We demonstrate atomically resolved imaging of the calcite (101̅4) surface plane using stiff quartz cantilevers ("qPlus sensors", stiffness k = 1280 N/m) equipped with sapphire tips in ambient conditions without any surface preparation. With 10 atoms in one surface unit cell, calcite has a highly complex surface structure comprising three different chemical elements (Ca, C, and O). We obtain true atomic resolution of calcite in air at relative humidity ranging from 20% to 40%, imaging atomic steps and single atomic defects. We observe a great durability of sapphire tips with their Mohs hardness of 9, only one step below diamond. Depending on the state of the sapphire tip, we resolve either the calcium or the oxygen sublattice. We determine the tip termination by comparing the experimental images with simulations and discuss the possibility of chemical tip identification in air. The main challenges for imaging arise from the presence of water layers, which form on almost all surfaces and have the potential to dissolve the crystal surface. Frequency shift versus distance spectra show the presence of at least three ordered hydration layers. The measured height of the first hydration layer corresponds well to X-ray diffraction data and molecular dynamic simulations, namely, ∼220 pm. For the following hydration layers we measure ∼380 pm for the second and third layer, ending up in a total hydration layer thickness of at least 1 nm. Understanding the influence of water layers and their structure is important for surface segregation, surface reactions including reconstructions, healing of defects, and corrosion.

  2. The construction of a high resolution crystal backscattering spectrometer HERMES I

    Energy Technology Data Exchange (ETDEWEB)

    Larese, J.Z.

    1998-11-01

    There is a need in the United States for a state-of-the-art, cold-neutron, crystal backscattering spectrometer (CBS) designed to investigate the structure and dynamics of condensed matter systems by the simultaneous utilization of long wavelength elastic diffraction and high-energy-resolution inelastic scattering. Cold neutron spectroscopy with CBS-type instruments has already made many important contributions to the study of atomic and molecular diffusion in biomaterials, polymers, semiconductors, liquid crystals, superionic conductors and the like. Such instruments have also been invaluable for ultra high resolution investigations of the low-lying quantum tunneling processes that provide direct insight into the dynamical response of solids at the lowest energies. Until relatively recently, however, all such instruments were located at steady-state reactors. This proposal describes HERMES I (High Energy Resolution Machines I) a CBS intended for installation at the LANSCE pulsed neutron facility of Los Alamos National Laboratory. As explained in detail in the main text, the authors propose to construct an updated, high-performance CBS which incorporates neutron techniques developed during the decade since IRIS was built, i.e., improved supermirror technology, a larger area crystal analyzer and high efficiency wire gas detectors. The instrument is designed in such a way as to be readily adaptable to future upgrades. HERMES I, they believe, will substantially expand the range and flexibility of neutron investigations in the United States and open new and potentially fruitful directions for condensed matter exploration. This document describes a implementation plan with a direct cost range between $4.5 to 5.6 M and scheduled duration of 39--45 months for identified alternatives.

  3. Crystallized and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates

    Science.gov (United States)

    Liu, Chao-Fei; Fan, Heng; Gou, Shih-Chuan; Liu, Wu-Ming

    2014-02-01

    Vortex is a topological defect with a quantized winding number of the phase in superfluids and superconductors. Here, we investigate the crystallized (triangular, square, honeycomb) and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates (BECs) by using the damped projected Gross-Pitaevskii equation. The amorphous vortices are the result of the considerable deviation induced by the interaction of atomic-molecular vortices. By changing the atom-molecule interaction from attractive to repulsive, the configuration of vortices can change from an overlapped atomic-molecular vortices to carbon-dioxide-type ones, then to atomic vortices with interstitial molecular vortices, and finally into independent separated ones. The Raman detuning can tune the ratio of the atomic vortex to the molecular vortex. We provide a phase diagram of vortices in rotating atomic-molecular BECs as a function of Raman detuning and the strength of atom-molecule interaction.

  4. Heavy-atom derivatives in lipidic cubic phases: results on hen egg-white lysozyme tetragonal derivative crystals with Gd-HPDO3A complex.

    Science.gov (United States)

    Girard, Eric; Pebay-Peyroula, Eva; Vicat, Jean; Kahn, Richard

    2004-08-01

    Gd-HPDO3A, a neutral gadolinium complex, is a good candidate for obtaining heavy-atom-derivative crystals by the lipidic cubic phase crystallization method known to be effective for membrane proteins. Gadolinium-derivative crystals of hen egg-white lysozyme were obtained by co-crystallizing the protein with 100 mM Gd-HPDO3A in a monoolein cubic phase. Diffraction data were collected to a resolution of 1.7 A using Cu Kalpha radiation from a rotating-anode generator. Two binding sites of the gadolinium complex were located from the strong gadolinium anomalous signal. The Gd-atom positions and their refined occupancies were found to be identical to those found in derivative crystals of hen egg-white lysozyme obtained by co-crystallizing the protein with 100 mM Gd-HPDO3A using the hanging-drop technique. Moreover, the refined structures are isomorphous. The lipidic cubic phase is not disturbed by the high concentration of Gd-HPDO3A. This experiment demonstrates that a gadolinium complex, Gd-HPDO3A, can be used to obtain derivative crystals by the lipidic cubic phase crystallization method. Further studies with membrane proteins that are known to crystallize in lipidic cubic phases will be undertaken with Gd-HPDO3A and other Gd complexes to test whether derivative crystals with high Gd-site occupancies can be obtained.

  5. Aberration-corrected STEM for atomic-resolution imaging and analysis.

    Science.gov (United States)

    Krivanek, O L; Lovejoy, T C; Dellby, N

    2015-09-01

    Aberration-corrected scanning transmission electron microscopes are able to form electron beams smaller than 100 pm, which is about half the size of an average atom. Probing materials with such beams leads to atomic-resolution images, electron energy loss and energy-dispersive X-ray spectra obtained from single atomic columns and even single atoms, and atomic-resolution elemental maps. We review briefly how such electron beams came about, and show examples of applications. We also summarize recent developments that are propelling aberration-corrected scanning transmission electron microscopes in new directions, such as complete control of geometric aberration up to fifth order, and ultra-high-energy resolution EELS that is allowing vibrational spectroscopy to be carried out in the electron microscope. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  6. Revisit of alpha-chitin crystal structure using high resolution X-ray diffraction data.

    Science.gov (United States)

    Sikorski, Pawel; Hori, Ritsuko; Wada, Masahisa

    2009-05-11

    High resolution synchrotron X-ray fiber diffraction data recorded from crab tendon chitin have been used to describe the crystal structure of alpha-chitin. Crystal structures at 100 and 300 K have been solved using restrained crystallographic refinement against diffraction intensities measured from the fiber diffraction patterns. The unit cell contains two polymer chains in a 2(1) helix conformation and in the antiparallel orientation. The best agreement between predicated and observed X-ray diffraction intensities is obtained for a model that includes two distinctive conformations of C6-O6 hydroxymethl group. Those conformations are different from what is proposed in the generally accepted alpha-chitin crystal structure (J. Mol. Biol. 1978, 120, 167-181). Based on refined positions of the O6 atoms, a network of hydrogen bonds involving O6 is proposed. This network of hydrogen bonds can explain the main features of the polarized FTIR spectra of alpha-chitin and sheds some light on the origin of splitting of the amide I band observed on alpha-chitin IR spectra.

  7. Angle-resolved x-ray imaging using a resolution-tunable double-crystal analyser

    CERN Document Server

    Hirano, K

    2003-01-01

    A resolution-tunable double-crystal analyser was successfully applied, for the first time, to angle-resolved x-ray imaging. Tuning the resolution between 0.5'' and 2.3'' was done with small loss of peak intensity using a Si(220) double-crystal analyser. The angle-resolved images of a housefly were recorded on nuclear emulsion plates at various angular resolutions. Several methods to improve the angular resolution of the analyser are also proposed.

  8. Stacking it up: Exploring the limits of ultra-high resolution atomic force microscopy

    NARCIS (Netherlands)

    van der Heijden, N.J.|info:eu-repo/dai/nl/369392205

    2017-01-01

    Atomic force microscopy (AFM) is a technique wherein an atomically sharp needle raster scans across a surface, detecting forces between it and the sample. In state-of-the-art AFM experiments the measured forces are typically on the order of pico-Newtons, and the lateral resolution is on the order of

  9. Laser-cooled atoms inside a hollow-core photonic-crystal fiber

    DEFF Research Database (Denmark)

    Bajcsy, Michal; Hofferberth, S.; Peyronel, Thibault

    2011-01-01

    We describe the loading of laser-cooled rubidium atoms into a single-mode hollow-core photonic-crystal fiber. Inside the fiber, the atoms are confined by a far-detuned optical trap and probed by a weak resonant beam. We describe different loading methods and compare their trade-offs in terms...... of implementation complexity and atom-loading efficiency. The most efficient procedure results in loading of ∼30,000 rubidium atoms, which creates a medium with an optical depth of ∼180 inside the fiber. Compared to our earlier study this represents a sixfold increase in the maximum achieved optical depth...

  10. Trapped Atoms in One-Dimensional Photonic Crystals

    Science.gov (United States)

    2013-08-09

    point, where kxa = π ), so the lattice constant a is constrained by a < λ/2, where λ is the smaller of the (vacuum) wavelengths for trapping and...surrounded by NA ‘mirror’ atoms along a 1D- lattice [16], the ratio of the coherent coupling rate g1 = √ NAγ1D/2 to the effective dissipative rate γ ′ would...exceed unity even for NA = 1 atom. For conventional cavity QED, we estimate a 1-photon Rabi frequency ∼2π × 2GHz for figure 5(b) with N = 81. 11 For

  11. Atomic resolution description of the interaction between the nucleoprotein and phosphoprotein of Hendra virus.

    Directory of Open Access Journals (Sweden)

    Guillaume Communie

    Full Text Available Hendra virus (HeV is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, N(TAIL, of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P. Here, we provide an atomic resolution description of the intrinsically disordered N(TAIL domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between N(TAIL and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by α-helical folding of the molecular recognition element of N(TAIL upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to N(TAIL without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae.

  12. Atomic resolution description of the interaction between the nucleoprotein and phosphoprotein of Hendra virus.

    Science.gov (United States)

    Communie, Guillaume; Habchi, Johnny; Yabukarski, Filip; Blocquel, David; Schneider, Robert; Tarbouriech, Nicolas; Papageorgiou, Nicolas; Ruigrok, Rob W H; Jamin, Marc; Jensen, Malene Ringkjøbing; Longhi, Sonia; Blackledge, Martin

    2013-01-01

    Hendra virus (HeV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, N(TAIL), of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P). Here, we provide an atomic resolution description of the intrinsically disordered N(TAIL) domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR) spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between N(TAIL) and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by α-helical folding of the molecular recognition element of N(TAIL) upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to N(TAIL) without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae.

  13. Water polygons in high-resolution protein crystal structures

    Science.gov (United States)

    Lee, Jonas; Kim, Sung-Hou

    2009-01-01

    We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 Å resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of “stable” water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state. PMID:19551896

  14. Averaging scheme for atomic resolution off-axis electron holograms.

    Science.gov (United States)

    Niermann, T; Lehmann, M

    2014-08-01

    All micrographs are limited by shot-noise, which is intrinsic to the detection process of electrons. For beam insensitive specimen this limitation can in principle easily be circumvented by prolonged exposure times. However, in the high-resolution regime several instrumental instabilities limit the applicable exposure time. Particularly in the case of off-axis holography the holograms are highly sensitive to the position and voltage of the electron-optical biprism. We present a novel reconstruction algorithm to average series of off-axis holograms while compensating for specimen drift, biprism drift, drift of biprism voltage, and drift of defocus, which all might cause problematic changes from exposure to exposure. We show an application of the algorithm utilizing also the possibilities of double biprism holography, which results in a high quality exit-wave reconstruction with 75 pm resolution at a very high signal-to-noise ratio. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Atomic layer deposition of TiO{sub 2} photonic crystal waveguide biosensors

    Energy Technology Data Exchange (ETDEWEB)

    Jardinier, E; French, P J [Electronic Instrumentation Laboratory, Delft University of Technology, 4 Mekelweg, 2628 CD Delft (Netherlands); Pandraud, G; Pham, M H; Sarro, P M [Electronic Components, Technology and Materials, Delft University of Technology, 17 Feldmannweg, 2628 CT Delft (Netherlands)], E-mail: g.pandraud@tudelft.nl

    2009-09-01

    A photonic crystal waveguide biosensor in the visible is presented for biosensing. The sensor is applied to Refractive Index (RI) measurements. The sensitivity at different wavelength is presented for both air holes and air core configurations of photonic crystal waveguide (PCW) made of TiO{sub 2}. It is shown that by using Atomic Layer Deposition (ALD) the expected sensitivity of the air core configuration outperforms the previously reported results.

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

    OpenAIRE

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

    1992-01-01

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

  17. Fast interaction of atoms with crystal surfaces: coherent lighting

    Science.gov (United States)

    Gravielle, M. S.

    2017-11-01

    Quantum coherence of incident waves results essential for the observation of interference patterns in grazing incidence fast atom diffraction (FAD). In this work we investigate the influence of the impact energy and projectile mass on the transversal length of the surface area that is coherently illuminated by the atomic beam, after passing through a collimating aperture. Such a transversal coherence length controls the general features of the interference structures, being here derived by means of the Van Cittert-Zernike theorem. The coherence length is then used to build the initial coherent wave packet within the Surface Initial Value Representation (SIVR) approximation. The SIVR approach is applied to fast He and Ne atoms impinging grazingly on a LiF(001) surface along a low-indexed crystallographic direction. We found that with the same collimating setup, by varying the impact energy we would be able to control the interference mechanism that prevails in FAD patterns, switching between inter-cell and unit-cell interferences. These findings are relevant to use FAD spectra adequately as a surface analysis tool, as well as to choose the appropriate collimating scheme for the observation of interference effects in a given collision system.

  18. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

    OpenAIRE

    Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Str?ter, Norbert; Than, Manuel E

    2013-01-01

    Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated tha...

  19. Mapping atomic motions with ultrabright electrons: towards fundamental limits in space-time resolution.

    Science.gov (United States)

    Manz, Stephanie; Casandruc, Albert; Zhang, Dongfang; Zhong, Yinpeng; Loch, Rolf A; Marx, Alexander; Hasegawa, Taisuke; Liu, Lai Chung; Bayesteh, Shima; Delsim-Hashemi, Hossein; Hoffmann, Matthias; Felber, Matthias; Hachmann, Max; Mayet, Frank; Hirscht, Julian; Keskin, Sercan; Hada, Masaki; Epp, Sascha W; Flöttmann, Klaus; Miller, R J Dwayne

    2015-01-01

    The long held objective of directly observing atomic motions during the defining moments of chemistry has been achieved based on ultrabright electron sources that have given rise to a new field of atomically resolved structural dynamics. This class of experiments requires not only simultaneous sub-atomic spatial resolution with temporal resolution on the 100 femtosecond time scale but also has brightness requirements approaching single shot atomic resolution conditions. The brightness condition is in recognition that chemistry leads generally to irreversible changes in structure during the experimental conditions and that the nanoscale thin samples needed for electron structural probes pose upper limits to the available sample or "film" for atomic movies. Even in the case of reversible systems, the degree of excitation and thermal effects require the brightest sources possible for a given space-time resolution to observe the structural changes above background. Further progress in the field, particularly to the study of biological systems and solution reaction chemistry, requires increased brightness and spatial coherence, as well as an ability to tune the electron scattering cross-section to meet sample constraints. The electron bunch density or intensity depends directly on the magnitude of the extraction field for photoemitted electron sources and electron energy distribution in the transverse and longitudinal planes of electron propagation. This work examines the fundamental limits to optimizing these parameters based on relativistic electron sources using re-bunching cavity concepts that are now capable of achieving 10 femtosecond time scale resolution to capture the fastest nuclear motions. This analysis is given for both diffraction and real space imaging of structural dynamics in which there are several orders of magnitude higher space-time resolution with diffraction methods. The first experimental results from the Relativistic Electron Gun for Atomic

  20. Inorganic WS{sub 2} nanotubes revealed atom by atom using ultra-high-resolution transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Bar Sadan, Maya; Heidelmann, Markus; Houben, Lothar [Forschungszentrum Juelich GmbH, Institute of Solid State Research and Ernst Ruska Centre for Microscopy and Spectroscopy with Electrons, Juelich (Germany); Tenne, Reshef [Weizmann Institute of Science, Materials and Interfaces Department, Rehovot (Israel)

    2009-08-15

    The characterization of nanostructures to the atomic dimensions becomes more important, as devices based on a single particle are being produced. In particular, inorganic nanotubes were shown to host interesting properties making them excellent candidates for various devices. The WS{sub 2} nanotubes outperform the bulk in their mechanical properties offering numerous applications especially as part of high strength nanocomposites. In contrast, their electrical properties are less remarkable. The structure-function relationship can be investigated by aberration-corrected high-resolution transmission electron microscopy (HRTEM), which enables the insight into their atomic structure as well as performing spectroscopic measurements down to the atomic scale. In the present work, the deciphering of atomic structure and the chiral angle of the different shells in a multiwall WS{sub 2} nanotube is demonstrated. In certain cases, the helicity of the structure can also be deduced. Finally, first electron energy loss spectra (EELS) of a single tube are presented, acquired by a new acquisition technique that allows for high spatial resolution (denoted StripeSTEM). The measured band gap values correspond with the values found in literature for thin films, obtained by spectroscopic techniques, and are higher than the values resulting from STM measurements. (orig.)

  1. Metal-graphene interaction studied via atomic resolution scanning transmission electron microscopy.

    Science.gov (United States)

    Zan, Recep; Bangert, Ursel; Ramasse, Quentin; Novoselov, Konstantin S

    2011-03-09

    Distributions and atomic sites of transition metals and gold on suspended graphene were investigated via high-resolution scanning transmission electron microscopy, especially using atomic resolution high angle dark field imaging. All metals, albeit as singular atoms or atom aggregates, reside in the omni-present hydrocarbon surface contamination; they do not form continuous films, but clusters or nanocrystals. No interaction was found between Au atoms and clean single-layer graphene surfaces, i.e., no Au atoms are retained on such surfaces. Au and also Fe atoms do, however, bond to clean few-layer graphene surfaces, where they assume T and B sites, respectively. Cr atoms were found to interact more strongly with clean monolayer graphene, they are possibly incorporated at graphene lattice imperfections and have been observed to catalyze dissociation of C-C bonds. This behavior might explain the observed high frequency of Cr-cluster nucleation, and the usefulness as wetting layer, for depositing electrical contacts on graphene.

  2. Scattering of axially channeled particles by atomic strings in crystals

    Energy Technology Data Exchange (ETDEWEB)

    Cherdyntsev, V.V.; Pokhil, G.P.; Ryabov, V.A. (Moskovskij Gosudarstvennyj Univ. (USSR). Nauchno-Issledovatel' skij Inst. Yadernoj Fiziki)

    1983-06-01

    The motion of axially channeled particles at shallow depths is analytically treated. It is shown that there may exist finite trajectories for particles with energies of the order of the critical energy. The effect of focusing upon backscattering yield oscillations is examined. For the transition from axial channeling to planar one, the self-consistent solution of the equations of motion is obtained, which allows to take an exact account of the discrete arrangement of atomic rows making up a planar channel. An analysis of this solution offers a new interpretation of the processes occuring at such transitions.

  3. BiI3 Crystals for High Energy Resolution Gamma-Ray Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Nino, Juan C. [Univ. of Florida, Gainesville, FL (United States); Baciak, James [Univ. of Florida, Gainesville, FL (United States); Johns, Paul [Univ. of Florida, Gainesville, FL (United States); Sulekar, Soumitra [Univ. of Florida, Gainesville, FL (United States); Totten, James [Univ. of Florida, Gainesville, FL (United States); Nimmagadda, Jyothir [Univ. of Florida, Gainesville, FL (United States)

    2017-04-12

    BiI3 had been investigated for its unique properties as a layered compound semiconductor for many decades. However, despite the exceptional atomic, physical, and electronic properties of this material, good resolution gamma ray spectra had never been reported for BiI3. The shortcomings that previously prevented BiI3 from reaching success as a gamma ray sensor were, through this project, identified and suppressed to unlock the performance of this promising compound. Included in this work were studies on a number of methods which have, for the first time, enabled BiI3 to exhibit spectral performance rivaling many other candidate semiconductors for room temperature gamma ray sensors. New approaches to crystal growth were explored that allow BiI3 spectrometers to be fabricated with up to 2.2% spectral resolution at 662 keV. Fundamental studies on trap states, dopant incorporation, and polarization were performed to enhance performance of this compound. Additionally, advanced detection techniques were applied to display the capabilities of high quality BiI3 spectrometers. Overall, through this work, BiI3 has been revealed as a potentially transformative material for nuclear security and radiation detection sciences.

  4. High-resolution crystal structure of the human CB1 cannabinoid receptor.

    Science.gov (United States)

    Shao, Zhenhua; Yin, Jie; Chapman, Karen; Grzemska, Magdalena; Clark, Lindsay; Wang, Junmei; Rosenbaum, Daniel M

    2016-11-16

    The human cannabinoid G-protein-coupled receptors (GPCRs) CB1 and CB2 mediate the functional responses to the endocannabinoids anandamide and 2-arachidonyl glycerol (2-AG), as well as the widely consumed plant (phyto)cannabinoid Δ(9)-tetrahydrocannabinol (THC)(1). The cannabinoid receptors have been the targets of intensive drug discovery efforts owing to the therapeutic potential of modulators for controlling pain(2), epilepsy(3), obesity(4), and other maladies. Although much progress has recently been made in understanding the biophysical properties of GPCRs, investigations of the molecular mechanisms of the cannabinoids and their receptors have lacked high-resolution structural data. We used GPCR engineering and lipidic cubic phase (LCP) crystallization to determine the structure of the human CB1 receptor bound to the inhibitor taranabant at 2.6 Å resolution. The extracellular surface of CB1, including the highly conserved membrane-proximal amino-terminal (N-terminal) region, is distinct from other lipid-activated GPCRs and forms a critical part of the ligand binding pocket. Docking studies further demonstrate how this same pocket may accommodate the cannabinoid agonist THC. Our CB1 structure provides an atomic framework for studying cannabinoid receptor function, and will aid the design and optimization of cannabinoid system modulators for therapeutic ends.

  5. Atom–atom interactions around the band edge of a photonic crystal waveguide

    Science.gov (United States)

    Hood, Jonathan D.; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E.; Kimble, H. J.

    2016-01-01

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields E(x)∝e±ikxx outside the bandgap to localized fields E(x)∝e−κx|x| within the bandgap should be accompanied by a transition from largely dissipative atom–atom interactions to a regime where dispersive atom–atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the D1 line of atomic cesium for N¯=3.0±0.5 atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom–atom interactions with low dissipation into the guided mode. PMID:27582467

  6. YUP.SCX: coaxing atomic models into medium resolution electron density maps.

    Science.gov (United States)

    Tan, Robert K-Z; Devkota, Batsal; Harvey, Stephen C

    2008-08-01

    The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33A, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments.

  7. Conformational conversion during amyloid formation at atomic resolution.

    Science.gov (United States)

    Eichner, Timo; Kalverda, Arnout P; Thompson, Gary S; Homans, Steve W; Radford, Sheena E

    2011-01-21

    Numerous studies of amyloid assembly have indicated that partially folded protein species are responsible for initiating aggregation. Despite their importance, the structural and dynamic features of amyloidogenic intermediates and the molecular details of how they cause aggregation remain elusive. Here, we use ΔN6, a truncation variant of the naturally amyloidogenic protein β(2)-microglobulin (β(2)m), to determine the solution structure of a nonnative amyloidogenic intermediate at high resolution. The structure of ΔN6 reveals a major repacking of the hydrophobic core to accommodate the nonnative peptidyl-prolyl trans-isomer at Pro32. These structural changes, together with a concomitant pH-dependent enhancement in backbone dynamics on a microsecond-millisecond timescale, give rise to a rare conformer with increased amyloidogenic potential. We further reveal that catalytic amounts of ΔN6 are competent to convert nonamyloidogenic human wild-type β(2)m (Hβ(2)m) into a rare amyloidogenic conformation and provide structural evidence for the mechanism by which this conformational conversion occurs. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Crystallization of Supercooled Liquid Elements Induced by Superclusters Containing Magic Atom Numbers

    Directory of Open Access Journals (Sweden)

    Robert F. Tournier

    2014-08-01

    Full Text Available A few experiments have detected icosahedral superclusters in undercooled liquids. These superclusters survive above the crystal melting temperature Tm because all their surface atoms have the same fusion heat as their core atoms, and are melted by liquid homogeneous and heterogeneous nucleation in their core, depending on superheating time and temperature. They act as heterogeneous growth nuclei of crystallized phase at a temperature Tc of the undercooled melt. They contribute to the critical barrier reduction, which becomes smaller than that of crystals containing the same atom number n. After strong superheating, the undercooling rate is still limited because the nucleation of 13-atom superclusters always reduces this barrier, and increases Tc above a homogeneous nucleation temperature equal to Tm/3 in liquid elements. After weak superheating, the most stable superclusters containing n = 13, 55, 147, 309 and 561 atoms survive or melt and determine Tc during undercooling, depending on n and sample volume. The experimental nucleation temperatures Tc of 32 liquid elements and the supercluster melting temperatures are predicted with sample volumes varying by 18 orders of magnitude. The classical Gibbs free energy change is used, adding an enthalpy saving related to the Laplace pressure change associated with supercluster formation, which is quantified for n = 13 and 55.

  9. Density functional theory calculations of stability and diffusion mechanisms of impurity atoms in Ge crystals

    Energy Technology Data Exchange (ETDEWEB)

    Maeta, Takahiro [Graduate School of System Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan); GlobalWafers Japan Co., Ltd., Higashikou, Seirou-machi, Kitakanbara-gun, Niigata 957-0197 (Japan); Sueoka, Koji [Department of Communication Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan)

    2014-08-21

    Ge-based substrates are being developed for applications in advanced nano-electronic devices because of their higher intrinsic carrier mobility than Si. The stability and diffusion mechanism of impurity atoms in Ge are not well known in contrast to those of Si. Systematic studies of the stable sites of 2nd to 6th row element impurity atoms in Ge crystal were undertaken with density functional theory (DFT) and compared with those in Si crystal. It was found that most of the impurity atoms in Ge were stable at substitutional sites, while transition metals in Si were stable at interstitial sites and the other impurity atoms in Si were stable at substitutional sites. Furthermore, DFT calculations were carried out to clarify the mechanism responsible for the diffusion of impurity atoms in Ge crystals. The diffusion mechanism for 3d transition metals in Ge was found to be an interstitial-substitutional diffusion mechanism, while in Si this was an interstitial diffusion mechanism. The diffusion barriers in the proposed diffusion mechanisms in Ge and Si were quantitatively verified by comparing them to the experimental values in the literature.

  10. Lattice and strain analysis of atomic resolution Z-contrast images based on template matching

    Energy Technology Data Exchange (ETDEWEB)

    Zuo, Jian-Min, E-mail: jianzuo@uiuc.edu [Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801 (United States); Seitz Materials Research Laboratory, University of Illinois, Urbana, IL 61801 (United States); Shah, Amish B. [Center for Microanalysis of Materials, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Kim, Honggyu; Meng, Yifei; Gao, Wenpei [Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801 (United States); Seitz Materials Research Laboratory, University of Illinois, Urbana, IL 61801 (United States); Rouviére, Jean-Luc [CEA-INAC/UJF-Grenoble UMR-E, SP2M, LEMMA, Minatec, Grenoble 38054 (France)

    2014-01-15

    A real space approach is developed based on template matching for quantitative lattice analysis using atomic resolution Z-contrast images. The method, called TeMA, uses the template of an atomic column, or a group of atomic columns, to transform the image into a lattice of correlation peaks. This is helped by using a local intensity adjusted correlation and by the design of templates. Lattice analysis is performed on the correlation peaks. A reference lattice is used to correct for scan noise and scan distortions in the recorded images. Using these methods, we demonstrate that a precision of few picometers is achievable in lattice measurement using aberration corrected Z-contrast images. For application, we apply the methods to strain analysis of a molecular beam epitaxy (MBE) grown LaMnO{sub 3} and SrMnO{sub 3} superlattice. The results show alternating epitaxial strain inside the superlattice and its variations across interfaces at the spatial resolution of a single perovskite unit cell. Our methods are general, model free and provide high spatial resolution for lattice analysis. - Highlights: • A real space approach is developed for strain analysis using atomic resolution Z-contrast images and template matching. • A precision of few picometers is achievable in the measurement of lattice displacements. • The spatial resolution of a single perovskite unit cell is demonstrated for a LaMnO{sub 3} and SrMnO{sub 3} superlattice grown by MBE.

  11. Atomic resolution investigations of phase transformation from TaN to CrTaN in a steel matrix

    DEFF Research Database (Denmark)

    Danielsen, Hilmar Kjartansson; Hald, John

    2012-01-01

    atoms diffuse from the steel matrix into TaN precipitates and physically transform them into CrTaN. The crystal structure of the precipitates changes from that of a typical MN NaCl type crystal structure to a Z-phase crystal structure with alternating double layers of Cr and TaN. Since there is a large...

  12. Atomic resolution observation of conversion-type anode RuO 2 during the first electrochemical lithiation

    KAUST Repository

    Mao, Minmin

    2015-03-05

    Transition metal oxides have attracted great interest as alternative anode materials for rechargeable lithium-ion batteries. Among them, ruthenium dioxide is considered to be a prototype material that reacts with the Li ions in the conversion type. In situ transmission electron microscopy reveals a two-step process during the initial lithiation of the RuO2 nanowire anode at atomic resolution. The first step is characterized by the formation of the intermediate phase LixRuO2 due to the Li-ion intercalation. The following step is manifested by the solid-state amorphization reaction driven by advancing the reaction front. The crystalline/amorphous interface is consisted of {011} atomic terraces, revealing the orientation-dependent mobility. In the crystalline matrix, lattice disturbance and dislocation are identified to be two major stress-induced distortions. The latter can be effective diffusion channels, facilitating transportation of the Li ions inside the bulk RuO2 crystal and further resulting in non-uniform Li-ion distribution. It is expected that the local enrichment of the Li ions may account for the homogeneous nucleation of dislocations in the bulk RuO2 crystal and the special island-like structures. These results elucidate the structural evolution and the phase transformation during electrochemical cycling, which sheds light on engineering RuO2 anode materials.

  13. High resolution imaging of the dolomite (104) cleavage surface by atomic force microscopy

    OpenAIRE

    Pina Martínez, Carlos Manuel; Pimentel, Carlos; García Merino, Marta

    2010-01-01

    In this paper we present high resolution atomic force microscopy (AFM) images of dolomite (104) cleavage surfaces immersed in pure water. These images show a rectangular lattice with surface unit cell dimensions in general agreement with those derived from the dolomite bulk structure. Furthermore, the twodimensional fast Fourier transform (2D-FFT) plots of the high resolution images exhibit a pattern of periodicities consistent with both the alternate orientation of the carbonate ...

  14. Gamma induced atom displacements in LYSO and LuYAP crystals as used in medical imaging applications

    Energy Technology Data Exchange (ETDEWEB)

    Piñera, Ibrahin, E-mail: ipinera@ceaden.edu.cu [Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, CEADEN, 30 St. 502, Playa 11300, Havana (Cuba); Cruz, Carlos M.; Abreu, Yamiel; Leyva, Antonio [Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, CEADEN, 30 St. 502, Playa 11300, Havana (Cuba); Van Espen, Piet [University of Antwerp, CGB, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Díaz, Angelina; Cabal, Ana E. [Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, CEADEN, 30 St. 502, Playa 11300, Havana (Cuba); Van Remortel, Nick [University of Antwerp, CGB, Groenenborgerlaan 171, 2020 Antwerpen (Belgium)

    2015-08-01

    The radiation damage, in terms of atom displacements, induced by gamma irradiation in LYSO and LuYAP crystals is presented. {sup 44}Sc, {sup 22}Na and {sup 48}V are used as gamma sources for this study. The energy of gammas from the electron–positron annihilation processes (511 keV) is also included in the study. The atom displacements distributions inside each material are calculated following the Monte Carlo assisted Classical Method introduced by the authors. This procedure also allows to study the atom displacements in-depth distributions inside each crystal. The atom displacements damage in LYSO crystals is found to be higher than in LuYAP crystals, mainly provoked by the displacements of silicon and oxygen atoms. But the difference between atom displacements produced in LYSO and LuYAP decreases when more energetic sources are used. On the other hand, the correlation between the atom displacements and energy deposition in-depth distributions is excellent. The atom displacements to energy deposition ratio is found to increases with more energetic photon sources. LYSO crystals are then more liable to the atom displacements damage than LuYAP crystals.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-01

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

  16. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction.

    Science.gov (United States)

    Zhang, Xing; Settembre, Ethan; Xu, Chen; Dormitzer, Philip R; Bellamy, Richard; Harrison, Stephen C; Grigorieff, Nikolaus

    2008-02-12

    Electron cryomicroscopy (cryo-EM) yields images of macromolecular assemblies and their components, from which 3D structures can be determined, by using an image processing method commonly known as "single-particle reconstruction." During the past two decades, this technique has become an important tool for 3D structure determination, but it generally has not been possible to determine atomic models. In principle, individual molecular images contain high-resolution information contaminated by a much higher level of noise. In practice, it has been unclear whether current averaging methods are adequate to extract this information from the background. We present here a reconstruction, obtained by using recently developed image processing methods, of the rotavirus inner capsid particle ("double-layer particle" or DLP) at a resolution suitable for interpretation by an atomic model. The result establishes single-particle reconstruction as a high-resolution technique. We show by direct comparison that the cryo-EM reconstruction of viral protein 6 (VP6) of the rotavirus DLP is similar in clarity to a 3.8-A resolution map obtained from x-ray crystallography. At this resolution, most of the amino acid side chains produce recognizable density. The icosahedral symmetry of the particle was an important factor in achieving this resolution in the cryo-EM analysis, but as the size of recordable datasets increases, single-particle reconstruction also is likely to yield structures at comparable resolution from samples of much lower symmetry. This potential has broad implications for structural cell biology.

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

    Science.gov (United States)

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

    2009-05-06

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

  18. High-resolution wavefront shaping with a photonic crystal fiber for multimode fiber imaging

    NARCIS (Netherlands)

    Amitonova, Lyubov; Descloux, Adrien; Petschulat, Joerg; Frosz, Michael H.; Ahmed, Goran; Babic, Fehim; Mosk, Allard; Russell, Philip St.J.; Pinkse, Pepijn Willemszoon Harry

    2016-01-01

    We demonstrate that a high-numerical-aperture photonic crystal fiber allows lensless focusing at an unparalleled resolution by complex wavefront shaping. This paves the way toward high-resolution imaging exceeding the capabilities of imaging with multi-core single-mode optical fibers. We analyze the

  19. Broadband photon-photon interactions mediated by cold atoms in a photonic crystal fiber.

    Science.gov (United States)

    Litinskaya, Marina; Tignone, Edoardo; Pupillo, Guido

    2016-05-12

    We demonstrate theoretically that photon-photon attraction can be engineered in the continuum of scattering states for pairs of photons propagating in a hollow-core photonic crystal fiber filled with cold atoms. The atoms are regularly spaced in an optical lattice configuration and the photons are resonantly tuned to an internal atomic transition. We show that the hard-core repulsion resulting from saturation of the atomic transitions induces bunching in the photonic component of the collective atom-photon modes (polaritons). Bunching is obtained in a frequency range as large as tens of GHz, and can be controlled by the inter-atomic separation. We provide a fully analytical explanation for this phenomenon by proving that correlations result from a mismatch of the quantization volumes for atomic excitations and photons in the continuum. Even stronger correlations can be observed for in-gap two-polariton bound states. Our theoretical results use parameters relevant for current experiments and suggest a simple and feasible way to induce interactions between photons.

  20. 1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Bharat G.; Moates, Derek B. [University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233 (United States); Kim, Heung-Bok [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Green, Todd J. [University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233 (United States); Kim, Chang-Yub; Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); DeLucas, Lawrence J., E-mail: duke2@uab.edu [University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233 (United States)

    2014-03-25

    The 1.55 Å resolution X-ray crystal structure of Rv3902c from M. tuberculosis reveals a novel fold. The crystallographic structure of the Mycobacterium tuberculosis (TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overall structure similar to that of the Salmonella virulence-factor chaperone InvB, with an r.m.s.d. for main-chain atoms of 2.3 Å along an aligned domain.

  1. High resolution transmission electron microscopy studies of {sigma} phase in Ni-based single crystal superalloys

    Energy Technology Data Exchange (ETDEWEB)

    Sun Fei [Key Laboratory of Liquid Structure and Heredity of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Zhang Jianxin, E-mail: jianxin@sdu.edu.cn [Key Laboratory of Liquid Structure and Heredity of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Liu Pan [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China); Feng Qiang [National Center for Materials Service Safety, University of Science and Technology Beijing, Beijing 100083 (China); State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Han Xiaodong; Mao Shengcheng [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China)

    2012-09-25

    Graphical abstract: (a) TEM micrograph of {sigma} phase; (b) HRTEM image of {sigma}/{gamma} interface corresponding to the area of the white frame in (a); (c) an enlarged image of area from the white frame in (b). The combination of {sigma}/{gamma} interface appears very well, and a two-atomic-layer step is shown on the {sigma}/{gamma} interface. In addition, {sigma} phase has the orientation relationship of [0 0 1]{sub {gamma}}//[1 1 2{sup Macron }]{sub {sigma}}, (2{sup Macron} 2 0){sub {gamma}}//(1{sup Macron} 1 0){sub {sigma}}, (2{sup Macron }2{sup Macron} 0){sub {gamma}}//(1 1 1){sub {sigma}}; [0 1 1]{sub {gamma}}//[1 1 0]{sub {sigma}}, (1 1{sup Macron} 1){sub {gamma}}//(0 0 1{sup Macron }){sub {sigma}} with the {gamma} phase. Highlights: Black-Right-Pointing-Pointer Elemental characteristic of {sigma} phase is studied by HAADF techniques and EDS analysis. Black-Right-Pointing-Pointer Interfacial characteristics of {sigma}/{gamma} interface are revealed by HRTEM. Black-Right-Pointing-Pointer An atomic structural {sigma}/{gamma} interface with a two-atomic-layer step has been proposed. - Abstract: By means of high resolution transmission electron microscopy (HRTEM) and high-angle annular dark-field image technique (HAADF), morphological of plate-shaped {sigma} phase and interfacial characteristics between plate-shaped {sigma} phase and {gamma} phase in Ni-based single crystal superalloys have been studied. On the basis of HRTEM observations, an atomic structural interface between {sigma} phase and {gamma} phase with a step has been proposed. {sigma} Phase has the relationship of [0 0 1]{sub {gamma}}//[1 1 2{sup Macron }]{sub {sigma}}, (2{sup Macron} 2 0){sub {gamma}}//(1{sup Macron} 1 0){sub {sigma},} (2{sup Macron }2{sup Macron} 0){sub {gamma}}//(1 1 1){sub {sigma}}; [0 1 1]{sub {gamma}}//[1 1 0]{sub {sigma}}, (1 1{sup Macron} 1){sub {gamma}}//(0 0 1{sup Macron }){sub {sigma}} with the {gamma} phase. The compositional characteristics of the {sigma} phase which

  2. Atom-counting in High Resolution Electron Microscopy:TEM or STEM - That's the question.

    Science.gov (United States)

    Gonnissen, J; De Backer, A; den Dekker, A J; Sijbers, J; Van Aert, S

    2017-03-01

    In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the number of atoms in a projected atomic column. Recently, it has been demonstrated that HR TEM, when using negative spherical aberration imaging, is suitable for atom-counting as well. The capabilities of both imaging techniques are investigated and compared using the probability of error as a criterion. It is shown that for the same incoming electron dose, HR STEM outperforms HR TEM under common practice standards, i.e. when the decision is based on the probability function of the peak intensities in HR TEM and of the scattering cross-sections in HR STEM. If the atom-counting decision is based on the joint probability function of the image pixel values, the dependence of all image pixel intensities as a function of thickness should be known accurately. Under this assumption, the probability of error may decrease significantly for atom-counting in HR TEM and may, in theory, become lower as compared to HR STEM under the predicted optimal experimental settings. However, the commonly used standard for atom-counting in HR STEM leads to a high performance and has been shown to work in practice. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Imaging three-dimensional surface objects with submolecular resolution by atomic force microscopy.

    Science.gov (United States)

    Moreno, César; Stetsovych, Oleksandr; Shimizu, Tomoko K; Custance, Oscar

    2015-04-08

    Submolecular imaging by atomic force microscopy (AFM) has recently been established as a stunning technique to reveal the chemical structure of unknown molecules, to characterize intramolecular charge distributions and bond ordering, as well as to study chemical transformations and intermolecular interactions. So far, most of these feats were achieved on planar molecular systems because high-resolution imaging of three-dimensional (3D) surface structures with AFM remains challenging. Here we present a method for high-resolution imaging of nonplanar molecules and 3D surface systems using AFM with silicon cantilevers as force sensors. We demonstrate this method by resolving the step-edges of the (101) anatase surface at the atomic scale by simultaneously visualizing the structure of a pentacene molecule together with the atomic positions of the substrate and by resolving the contour and probe-surface force field on a C60 molecule with intramolecular resolution. The method reported here holds substantial promise for the study of 3D surface systems such as nanotubes, clusters, nanoparticles, polymers, and biomolecules using AFM with high resolution.

  4. Switching and counting with atomic vapors in photonic-crystal fibers

    DEFF Research Database (Denmark)

    Peyronel, Thibault; Bajcsy, Michal; Hofferberth, Sebastian

    2012-01-01

    We review our recent experiments demonstrating a hollow-core photonic-crystal fiber loaded with laser-cooled atomic vapor as a system for all-optical switching with pulses containing few hundred photons. Additionally, we discuss the outlooks for improving the efficiency of this switching scheme a...... and present preliminary results geared toward using the system as a photon-number resolving detector....

  5. Midinfrared absorption measured at a lambda/400 resolution with an atomic force microscope.

    Science.gov (United States)

    Houel, Julien; Homeyer, Estelle; Sauvage, Sébastien; Boucaud, Philippe; Dazzi, Alexandre; Prazeres, Rui; Ortéga, Jean-Michel

    2009-06-22

    Midinfrared absorption can be locally measured using a detection combining an atomic force microscope and a pulsed excitation. This is illustrated for the midinfrared bulk GaAs phonon absorption and for the midinfrared absorption of thin SiO(2) microdisks. We show that the signal given by the cantilever oscillation amplitude of the atomic force microscope follows the spectral dependence of the bulk material absorption. The absorption spatial resolution achieved with microdisks is around 50 nanometer for an optical excitation around 22 micrometer wavelength.

  6. Atomic resolution electrostatic potential mapping of graphene sheets by off-axis electron holography

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, David, E-mail: david.cooper@cea.fr [University Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054, Grenoble (France); Pan, Cheng-Ta; Haigh, Sarah [School of Materials, The University of Manchester, Manchester M13 9PL (United Kingdom)

    2014-06-21

    Off-axis electron holography has been performed at atomic resolution with the microscope operated at 80 kV to provide electrostatic potential maps from single, double, and triple layer graphene. These electron holograms have been reconstructed in order to obtain information about atomically resolved and mean inner potentials. We propose that off-axis electron holography can now be used to measure the electrical properties in a range of two-dimensional semiconductor materials and three dimensional devices comprising stacked layers of films to provide important information about their electrical properties.

  7. Optical properties of an atomic ensemble coupled to a band edge of a photonic crystal waveguide

    Science.gov (United States)

    Munro, Ewan; Kwek, Leong Chuan; Chang, Darrick E.

    2017-08-01

    We study the optical properties of an ensemble of two-level atoms coupled to a 1D photonic crystal waveguide (PCW), which mediates long-range coherent dipole-dipole interactions between the atoms. We show that the long-range interactions can dramatically alter the linear and nonlinear optical behavior, as compared to a typical atomic ensemble. In particular, in the linear regime, we find that the transmission spectrum contains multiple transmission dips, whose properties we characterize. Moreover, we show how the linear spectrum may be used to infer the number of atoms present in the system, constituting an important experimental tool in a regime where techniques for conventional ensembles break down. We also show that some of the transmission dips are associated with an effective ‘two-level’ resonance that forms due to the long-range interactions. In particular, under strong global driving and appropriate conditions, we find that the atomic ensemble is only capable of absorbing and emitting single collective excitations at a time. Our results are of direct relevance to atom-PCW experiments that should soon be realizable.

  8. Crystal-Phase Quantum Wires: One-Dimensional Heterostructures with Atomically Flat Interfaces.

    Science.gov (United States)

    Corfdir, Pierre; Li, Hong; Marquardt, Oliver; Gao, Guanhui; Molas, Maciej R; Zettler, Johannes K; van Treeck, David; Flissikowski, Timur; Potemski, Marek; Draxl, Claudia; Trampert, Achim; Fernández-Garrido, Sergio; Grahn, Holger T; Brandt, Oliver

    2018-01-10

    In semiconductor quantum-wire heterostructures, interface roughness leads to exciton localization and to a radiative decay rate much smaller than that expected for structures with flat interfaces. Here, we uncover the electronic and optical properties of the one-dimensional extended defects that form at the intersection between stacking faults and inversion domain boundaries in GaN nanowires. We show that they act as crystal-phase quantum wires, a novel one-dimensional quantum system with atomically flat interfaces. These quantum wires efficiently capture excitons whose radiative decay gives rise to an optical doublet at 3.36 eV at 4.2 K. The binding energy of excitons confined in crystal-phase quantum wires is measured to be more than twice larger than that of the bulk. As a result of their unprecedented interface quality, these crystal-phase quantum wires constitute a model system for the study of one-dimensional excitons.

  9. Characterization of single-crystal sapphire substrates by X-ray methods and atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Prokhorov, I. A.; Zakharov, B. G., E-mail: zakharov@kaluga.rosmail.com [Russian Academy of Sciences, Research Center Space Materials Science, Shubnikov Institute of Crystallography (Kaluga Branch) (Russian Federation); Asadchikov, V. E.; Butashin, A. V.; Roshchin, B. S.; Tolstikhina, A. L. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Zanaveskin, M. L.; Grishchenko, Yu. V.; Muslimov, A. E. [Russian Research Center Kurchatov Institute (Russian Federation); Yakimchuk, I. V.; Volkov, Yu. O.; Kanevskii, V. M.; Tikhonov, E. O. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2011-05-15

    The possibility of characterizing a number of practically important parameters of sapphire substrates by X-ray methods is substantiated. These parameters include wafer bending, traces of an incompletely removed damaged layer that formed as a result of mechanical treatment (scratches and marks), surface roughness, damaged layer thickness, and the specific features of the substrate real structure. The features of the real structure of single-crystal sapphire substrates were investigated by nondestructive methods of double-crystal X-ray diffraction and plane-wave X-ray topography. The surface relief of the substrates was investigated by atomic force microscopy and X-ray scattering. The use of supplementing analytical methods yields the most complete information about the structural inhomogeneities and state of crystal surface, which is extremely important for optimizing the technology of substrate preparation for epitaxy.

  10. Adiabatic preparation of Rydberg crystals in a cold lattice gas: Influence of atomic relaxations

    Science.gov (United States)

    Petrosyan, David; Molmer, Klaus; Fleischhauer, Michael

    2017-04-01

    Strong, long-range interactions between atoms in high-lying Rydberg states make them attractive systems for the studies of ordered phases and phase transitions of interacting many-body systems. Different approaches have been explored, both theoretically and experimentally, for the preparation of crystalline order of Rydberg excitations in spatially-extended ensembles of cold atoms. These include direct (near-)resonant laser excitation of interacting Rydberg states in a lattice gas, and adiabatic preparation of crystalline phases of Rydberg excitations in a one-dimensional optical lattice by adiabatic frequency sweep of the excitation laser. We show, however, that taking into account realistic relaxation processes affecting the atoms severely complicates the prospects of attaining sizable crystals of Rydberg excitations in laser-driven atomic media. Our many-body simulations well reproduce the experimental observations of spatial ordering of Rydberg excitations in driven dissipative lattice gases, as well as highly sub-Poissonian probability distribution of the excitation number. We find that the excitations essentially form liquid rather than crystal phases with long-range order.

  11. Designing exotic many-body states of atomic spin and motion in photonic crystals

    Science.gov (United States)

    Manzoni, Marco T.; Mathey, Ludwig; Chang, Darrick E.

    2017-01-01

    Cold atoms coupled to photonic crystals constitute an exciting platform for exploring quantum many-body physics. For example, such systems offer the potential to realize strong photon-mediated forces between atoms, which depend on the atomic internal (spin) states, and where both the motional and spin degrees of freedom can exhibit long coherence times. An intriguing question then is whether exotic phases could arise, wherein crystalline or other spatial patterns and spin correlations are fundamentally tied together, an effect that is atypical in condensed matter systems. Here, we analyse one realistic model Hamiltonian in detail. We show that this previously unexplored system exhibits a rich phase diagram of emergent orders, including spatially dimerized spin-entangled pairs, a fluid of composite particles comprised of joint spin-phonon excitations, phonon-induced Néel ordering, and a fractional magnetization plateau associated with trimer formation. PMID:28272466

  12. Raman, AFM and SNOM high resolution imaging of carotene crystals in a model carrot cell system.

    Science.gov (United States)

    Rygula, Anna; Oleszkiewicz, Tomasz; Grzebelus, Ewa; Pacia, Marta Z; Baranska, Malgorzata; Baranski, Rafal

    2018-02-02

    Three non-destructive and complementary techniques, Raman imaging, Atomic Force Microscopy and Scanning Near-field Optical Microscopy were used simultaneously to show for the first time chemical and structural differences of carotenoid crystals. Spectroscopic and microscopic scanning probe measurements were applied to the released crystals or to crystals accumulated in a unique, carotenoids rich callus tissue growing in vitro that is considered as a new model system for plant carotenoid research. Three distinct morphological crystal types of various carotenoid composition were identified, a needle-like, rhomboidal and helical. Raman imaging using 532 and 488 nm excitation lines provided evidence that the needle-like and rhomboidal crystals had similar carotenoid composition and that they were composed mainly of β-carotene accompanied by α-carotene. However, the presence of α-carotene was not identified in the helical crystals, which had the characteristic spatial structure. AFM measurements of crystals identified by Raman imaging revealed the crystal topography and showed the needle-like and rhomboidal crystals were planar but they differed in all three dimensions. Combining SNOM and Raman imaging enabled indication of carotenoid rich structures and visualised their distribution in the cell. The morphology of identified subcellular structures was characteristic for crystalline, membraneous and tubular chromoplasts that are plant organelles responsible for carotenoid accumulation in cells. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Atomic-resolution measurements with a new tunable diode laser-based interferometer

    DEFF Research Database (Denmark)

    Silver, R.M.; Zou, H.; Gonda, S.

    2004-01-01

    We develop a new implementation of a Michelson interferometer designed to make measurements with an uncertainty of less than 20 pm. This new method uses a tunable diode laser as the light source, with the diode laser wavelength continuously tuned to fix the number of fringes in the measured optical...... path. The diode laser frequency is measured by beating against a reference laser. High-speed, accurate frequency measurements of the beat frequency signal enables the diode laser wavelength to be measured with nominally 20-pm accuracy for the measurements described. The new interferometer design...... is lightweight and is mounted directly on an ultra-high vacuum scanning tunneling microscope capable of atomic resolution. We report the simultaneous acquisition of an atomic resolution image, while the relative lateral displacement of the tip along the sample distance is measured with the new tunable diode...

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

    Science.gov (United States)

    van den Bedem, Henry; Fraser, James S

    2015-04-01

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

  15. A design for a subminiature, low energy scanning electron microscope with atomic resolution

    Science.gov (United States)

    Eastham, D. A.; Edmondson, P.; Greene, S.; Donnelly, S.; Olsson, E.; Svensson, K.; Bleloch, A.

    2009-01-01

    We describe a type of scanning electron microscope that works by directly imaging the electron field-emission sites on a nanotip. Electrons are extracted from the nanotip through a nanoscale aperture, accelerated in a high electric field, and focused to a spot using a microscale Einzel lens. If the whole microscope (accelerating section and lens) and the focal length are both restricted in size to below 10 μm, then computer simulations show that the effects of aberration are extremely small and it is possible to have a system with approximately unit magnification at electron energies as low as 300 eV. Thus a typical emission site of 1 nm diameter will produce an image of the same size, and an atomic emission site will give a resolution of 0.1-0.2 nm (1-2 Å). Also, because the beam is not allowed to expand beyond 100 nm in diameter, the depth of field is large and the contribution to the beam spot size from chromatic aberrations is less than 0.02 nm (0.2 Å) for 500 eV electrons. Since it is now entirely possible to make stable atomic sized emitters (nanopyramids), it is expected that this instrument will have atomic resolution. Furthermore the brightness of the beam is determined only by the field emission and can be up to 1×106 times larger than in a typical (high energy) electron microscope. The advantages of this low energy, bright-beam electron microscope with atomic resolution are described and include the possibility of it being used to rapidly sequence the human genome from a single strand of DNA as well as being able to identify atomic species directly from the elastic scattering of electrons.

  16. Density functional theory study of stable configurations of substitutional and interstitial C and Sn atoms in Si and Ge crystals

    Science.gov (United States)

    Koyama, Hiroki; Sueoka, Koji

    2017-04-01

    Group IV semiconductor compounds, e.g., Si and Ge containing substitutional C (Cs) and/or Sn (Sns) atoms (mono-doping and co-doping) with contents of several % are attracting attention for application to solar cells because they are good for the environment and have an affinity with Si materials. In this study, we evaluate the stable configurations of C and/or Sn atoms in Si (Ge) crystals with a focus on the formation of interstitial C (Ci) atoms by means of density functional theory calculations. The Hakoniwa method proposed by Kamiyama et al. (2016) is applied to a 64-atom supercell to obtain the thermal equilibrium ratio of Ci to the total C atoms. The results of the analysis are fourfold. First, the isolated Cs atom is stabler than the isolated Ci atom in both Si and Ge crystals, and it is stabler in Si than in Ge. The isolated Sns atom is much stabler that Sni as well, but it is stabler in Ge than Si. Second, a Ci atom is formed in a [0 0 1] oriented Ci-Cs pair in Ge crystals with the ratio of 7.7% to total C atoms at 450 °C when the concentration of uniformly distributed C atoms is about 3%. Third, the difference of the formation energy of Ci and Cs in Si decreases to about 0.3 eV with an increase in the concentration of uniformly distributed C atoms up to 6%. Fourth, the co-doping of C and Sn suppresses the formation of Ci atoms in Si and Ge crystals. The results obtained here are useful for the prediction of possible atomic configurations of C and/or Sn in Si and Ge for solar cell application.

  17. High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

    Science.gov (United States)

    Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole

  18. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

    Science.gov (United States)

    Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from

  19. Investigating the crystal growth behavior of biodegradable polymer blend thin films using in situ atomic force microscopy

    CSIR Research Space (South Africa)

    Malwela, T

    2014-01-01

    Full Text Available This article reports the crystal growth behavior of biodegradable polylactide (PLA)/poly[(butylene succinate)-co-adipate] (PBSA) blend thin films using atomic force microscopy (AFM). Currently, polymer thin films have received increased research...

  20. Diffusion Mechanisms of Ag atom in ZnO crystal: A First Principles Study

    Science.gov (United States)

    Masoumi, Saeed; Noori, Amirreza; Nadimi, Ebrahim

    2017-12-01

    Zinc oxide (ZnO) is currently under intensive investigation, as a result of its various applications in micro, nano and optoelectronics. However, a stable and reproducible p-type doping of ZnO is still a main challenging issue. Group IB elements such as Au, Cu and Ag, are promising candidates for p-type doping. Particularly, Ag atoms has been shown to be able to easily diffuse through the crystal structure of ZnO and lead to the p-type doping of the host crystal. However, the current understanding of Ag defects and their mobility in the ZnO crystal is still not fully explored. In this work, we report the results of our first-principles calculations based on density functional theory for Ag defects, particularly the interstitial and substitutional defects in ZnO crystal. Defect formation energies are calculated in different charged states as a function of Fermi energy in order to clarify the p-type behaviour of Ag-doped ZnO. We also investigate the diffusion behaviour and migration paths of Ag in ZnO crystal in the framework of density functional theory applying climbing image (CI) nudged elastic band method (NEB).

  1. Correlative atomic force microscopy and localization-based super-resolution microscopy: revealing labelling and image reconstruction artefacts.

    Science.gov (United States)

    Monserrate, Aitor; Casado, Santiago; Flors, Cristina

    2014-03-17

    Hybrid microscopy: A correlative microscopy tool that combines in situ super-resolution fluorescence microscopy based on single-molecule localization and atomic force microscopy is presented. Direct comparison with high- resolution topography allows the authors to improve fluorescence labeling and image analysis in super-resolution imaging. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Quantitative atomic resolution mapping using high-angle annular dark field scanning transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Van Aert, S., E-mail: sandra.vanaert@ua.ac.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Verbeeck, J. [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Erni, R. [National Center for Electron Microscopy, Ernest Orlando Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 72R0150, Berkeley, CA 94720 (United States); Bals, S. [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Luysberg, M. [Institute of Solid State Research and Ernst Ruska Center for Microscopy and Spectroscopy with Electrons, Helmholtz Research Center Juelich, 52425 Juelich (Germany); Dyck, D. Van; Tendeloo, G. Van [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium)

    2009-09-15

    A model-based method is proposed to relatively quantify the chemical composition of atomic columns using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. The method is based on a quantification of the total intensity of the scattered electrons for the individual atomic columns using statistical parameter estimation theory. In order to apply this theory, a model is required describing the image contrast of the HAADF STEM images. Therefore, a simple, effective incoherent model has been assumed which takes the probe intensity profile into account. The scattered intensities can then be estimated by fitting this model to an experimental HAADF STEM image. These estimates are used as a performance measure to distinguish between different atomic column types and to identify the nature of unknown columns with good accuracy and precision using statistical hypothesis testing. The reliability of the method is supported by means of simulated HAADF STEM images as well as a combination of experimental images and electron energy-loss spectra. It is experimentally shown that statistically meaningful information on the composition of individual columns can be obtained even if the difference in averaged atomic number Z is only 3. Using this method, quantitative mapping at atomic resolution using HAADF STEM images only has become possible without the need of simultaneously recorded electron energy loss spectra.

  3. High-resolution wavefront shaping with a photonic crystal fiber for multimode fiber imaging.

    Science.gov (United States)

    Amitonova, Lyubov V; Descloux, Adrien; Petschulat, Joerg; Frosz, Michael H; Ahmed, Goran; Babic, Fehim; Jiang, Xin; Mosk, Allard P; Russell, Philip St J; Pinkse, Pepijn W H

    2016-02-01

    We demonstrate that a high-numerical-aperture photonic crystal fiber allows lensless focusing at an unparalleled resolution by complex wavefront shaping. This paves the way toward high-resolution imaging exceeding the capabilities of imaging with multi-core single-mode optical fibers. We analyze the beam waist and power in the focal spot on the fiber output using different types of fibers and different wavefront shaping approaches. We show that the complex wavefront shaping technique, together with a properly designed multimode photonic crystal fiber, enables us to create a tightly focused spot on the desired position on the fiber output facet with a subwavelength beam waist.

  4. Atomic resolution (0.97 Å) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Sekar, K., E-mail: sekar@physics.iisc.ernet.in [Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012 (India); Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012 (India); Rajakannan, V.; Gayathri, D.; Velmurugan, D. [Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025 (India); Poi, M.-J. [Department of Chemistry and Biochemistry and The Ohio State Biotechnology Program, The Ohio State University, Columbus, OH 43210 (United States); Academia Sinica,Taiwan (China); Dauter, M. [SAIC-Frederick Inc., Basic Research Program, Brookhaven National Laboratory, Building 725A-X9, Upton, NY 11973 (United States); Dauter, Z. [Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, NCI and Brookhaven National Laboratory, Building 725A-X9, Upton, NY 11973 (United States); Tsai, M.-D. [Department of Chemistry and Biochemistry and The Ohio State Biotechnology Program, The Ohio State University, Columbus, OH 43210 (United States); Academia Sinica,Taiwan (China); Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012 (India)

    2005-01-01

    The crystal structure of a triple mutant (K53,56,121M) of bovine pancreatic phospholipase A{sub 2} has been solved at atomic resolution (0.97 Å) and the refined model features the presence of a second calcium ion and a chloride ion. The enzyme phospholipase A{sub 2} catalyzes the hydrolysis of the sn-2 acyl chain of phospholipids, forming fatty acids and lysophospholipids. The crystal structure of a triple mutant (K53,56,121M) of bovine pancreatic phospholipase A{sub 2} in which the lysine residues at positions 53, 56 and 121 are replaced recombinantly by methionines has been determined at atomic resolution (0.97 Å). The crystal is monoclinic (space group P2), with unit-cell parameters a = 36.934, b = 23.863, c = 65.931 Å, β = 101.47°. The structure was solved by molecular replacement and has been refined to a final R factor of 10.6% (R{sub free} = 13.4%) using 63 926 unique reflections. The final protein model consists of 123 amino-acid residues, two calcium ions, one chloride ion, 243 water molecules and six 2-methyl-2,4-pentanediol molecules. The surface-loop residues 60–70 are ordered and have clear electron density.

  5. Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment.

    Science.gov (United States)

    Joseph, Agnel Praveen; Malhotra, Sony; Burnley, Tom; Wood, Chris; Clare, Daniel K; Winn, Martyn; Topf, Maya

    2016-05-01

    As the resolutions of Three Dimensional Electron Microscopic reconstructions of biological macromolecules are being improved, there is a need for better fitting and refinement methods at high resolutions and robust approaches for model assessment. Flex-EM/MODELLER has been used for flexible fitting of atomic models in intermediate-to-low resolution density maps of different biological systems. Here, we demonstrate the suitability of the method to successfully refine structures at higher resolutions (2.5-4.5Å) using both simulated and experimental data, including a newly processed map of Apo-GroEL. A hierarchical refinement protocol was adopted where the rigid body definitions are relaxed and atom displacement steps are reduced progressively at successive stages of refinement. For the assessment of local fit, we used the SMOC (segment-based Manders' overlap coefficient) score, while the model quality was checked using the Qmean score. Comparison of SMOC profiles at different stages of refinement helped in detecting regions that are poorly fitted. We also show how initial model errors can have significant impact on the goodness-of-fit. Finally, we discuss the implementation of Flex-EM in the CCP-EM software suite. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  6. High-resolution transmission electron microscopy of hexagonal and rhombohedral molybdenum disulfide crystals.

    Science.gov (United States)

    Isshiki, T; Nishio, K; Saijo, H; Shiojiri, M; Yabuuchi, Y; Takahashi, N

    1993-07-01

    Natural (molybdenite) and synthesized molybdenum disulfide crystals have been studied by high-resolution transmission electron microscopy. The image simulation demonstrates that the [0001] and [0110] HRTEM images of hexagonal and rhombohedral MoS2 crystals hardly disclose their stacking sequences, and that the [2110] images can distinguish the Mo and S columns along the incident electron beam and enable one to determine not only the crystal structure but also the fault structure. Observed [0001] images of cleaved molybdenite and synthesized MoS2 crystals, however, reveal the strain field around partial dislocations limiting an extended dislocation. A cross-sectional image of a single molecular (S-Mo-S) layer cleaved from molybdenite has been observed. Synthesized MoS2 flakes which were prepared by grinding have been found to be rhombohedral crystals containing many stacking faults caused by glides between S/S layers.

  7. Lithium fluoride crystal as a novel high dynamic neutron imaging detector with microns scale spatial resolution

    Energy Technology Data Exchange (ETDEWEB)

    Faenov, Anatoly; Pikuz, Tatiana [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kyoto 619-0215 (Japan); High Temperatures, Russian Academy of Sciences, Izhorskaja Street 13/19, Moscow (Russian Federation); Matsubayashi, Masahito; Yasuda, Ryo; Iikura, Hiroshi; Nojima, Takehiro; Sakai, Takuro [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195 (Japan); Fukuda, Yuji; Kando, Masaki [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kyoto 619-0215 (Japan); Shiozawa, Masahiro [Nippon SOKEN, Inc., Iwaya 14, Shimohasumi, Nishio, Aichi 445-0012 (Japan); Kato, Yoshiaki [The Graduate School for the Creation of New Photonics Industries, Hamamatsu, Shizuoka 431-1202 (Japan)

    2012-12-15

    Recently, a new field of application of optically stimulated luminescence of color centers (CCs) in lithium fluoride (LiF) crystals was proposed - using them for high-performance neutron imaging - and promising results were obtained (Matsubayashi et al., Nucl. Instrum. Methods A 622, 637 (2010) and Matsubayashi et al., Nucl. Instrum. Methods A 651, 90 (2011)). Here we present the overview of main findings, which clearly demonstrated that the LiF crystal performs efficiently as neutron imaging detector in areas, where a high spatial resolution with a high image gradation resolution is needed. It was shown that the obtained neutron images are almost free from granular noises, have spatial resolution of {proportional_to} 6 {mu}m, and have practically linear response with the dynamic range of at least 10{sup 3}. It was also found that the LiF crystal detector offers a fairly good sensitivity. Moreover, detailed evaluation using a standard sensitivity indicator for neutron radiography showed that two holes with less than 2% transmittance differences could be distinguished. Additionally, we recently demonstrated that the high resolution neutron imaging with LiF crystals could be useful for quantitative characterizations of neutron sources and electric devices, comprising of low-Z elements, for example, such as fuel cells. All of this gives new opportunity for microns scale spatial resolution imaging by neutrons (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

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

    Science.gov (United States)

    Sun, Yongfu; Gao, Shan; Xie, Yi

    2014-01-21

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

  9. Photonic quantum state transfer between a cold atomic gas and a crystal.

    Science.gov (United States)

    Maring, Nicolas; Farrera, Pau; Kutluer, Kutlu; Mazzera, Margherita; Heinze, Georg; de Riedmatten, Hugues

    2017-11-22

    Interfacing fundamentally different quantum systems is key to building future hybrid quantum networks. Such heterogeneous networks offer capabilities superior to those of their homogeneous counterparts, as they merge the individual advantages of disparate quantum nodes in a single network architecture. However, few investigations of optical hybrid interconnections have been carried out, owing to fundamental and technological challenges such as wavelength and bandwidth matching of the interfacing photons. Here we report optical quantum interconnection of two disparate matter quantum systems with photon storage capabilities. We show that a quantum state can be transferred faithfully between a cold atomic ensemble and a rare-earth-doped crystal by means of a single photon at 1,552  nanometre telecommunication wavelength, using cascaded quantum frequency conversion. We demonstrate that quantum correlations between a photon and a single collective spin excitation in the cold atomic ensemble can be transferred to the solid-state system. We also show that single-photon time-bin qubits generated in the cold atomic ensemble can be converted, stored and retrieved from the crystal with a conditional qubit fidelity of more than 85 per cent. Our results open up the prospect of optically connecting quantum nodes with different capabilities and represent an important step towards the realization of large-scale hybrid quantum networks.

  10. Crystal engineering of giant molecules based on perylene diimide conjugated polyhedral oligomeric silsesquioxane nano-atom

    Science.gov (United States)

    Ren, He

    Molecular architectures and topologies are found contributing to the formation of supramolecular structures of giant molecules. Dr. Cheng's research group developed a diverse of giant molecules via precisely controlled chemistry synthetic routes. These giant molecules can be categorized into several different families, namely giant surfactants, giant shape amphiphiles and giant polyhedron. By analyzing the hierarchical structures of these carefully designed and precisely synthesized giant molecules, the structural factors which affect, or even dominates, in some cases, the formation of supramolecular structures are revealed in these intensive researches. The results will further contribute to the understanding of dependence of supramolecular structures on molecular designs as well as molecular topology, and providing a practical solution to the scaling up of microscopic molecular functionalities to macroscopic material properties. Molecular Nano Particles (MNPs), including fullerene (C60), POSS, Polyoxometalate (POM) and proteins etc., is defined and applied as a specific type of building blocks in the design and synthesis of giant molecules. The persistence in shape and symmetry is considered as one of the major properties of MNPs. This persistence will support the construction of giant molecules for further supramolecular structures' study by introducing specific shapes, or precisely located side groups which will facilitate self-assembling behaviors with pre-programmed secondary interactions. Dictating material physical properties by its chemical composition is an attractive yet currently failed approach in the study of materials. However, the pursuit of determining material properties by microscopic molecular level properties is never seized, and found its solution when the idea of crystal engineering is raised: should each atom in the material is located exactly where it is designed to be and is properly bonded, the property of the material is hence determined

  11. A simple nonbinary scattering model applicable to atomic collisions is crystals at 1ow energies

    DEFF Research Database (Denmark)

    Andersen, Hans Henrik; Sigmund, Peter

    1966-01-01

    the projectile and each ring atom is described by a Born-Mayer potential, and the scattering is assumed to be elastic and governed by the classical equations of motion. Because of symmetry, the problem can be reduced to plane motion of a particle in a potential of elliptic symmetry. The elliptic force field...... the elliptic to the spherical potential are investigated. Special attention is paid to proper definitions of collision time and collision length which are important in collisions in crystals. Limitations to classical scattering arising from the uncertainty principle prove to be more serious than assumed...... previously. Inelastic contributions to the energy loss can easily be included. The oscillator forces binding lattice atoms turn out to influence the scattering process only at very small energies. The validity of the so-called momentum approximation and a related perturbation method are also investigated....

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

    Science.gov (United States)

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

    2016-01-01

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

  13. Combining atomic force microscope and quartz crystal microbalance studies for cell detection

    Science.gov (United States)

    Hayden, Oliver; Bindeus, Roland; Dickert, Franz L.

    2003-11-01

    The adhesion of microorganisms on a patterned polyurethane surface was studied simultaneously online and in situ with a quartz crystal microbalance (QCM) and an atomic force microscope (AFM). The specific interaction between Saccharomyces cerevisiae cells and their fingerprints formed by molecular imprinting results in a typical Sauerbrey behaviour, when adhesion events are observable with an AFM. The sensor response due to adsorption of Gram positive Leuconostoc oenus, however, shows non-Sauerbrey behaviour. Bacteria, naturally being smaller than yeast cells, were 'invisible' to liquid phase AFM-measurements, which is due to a weaker surface interaction. Thus, AFM measurements give a hint for unusual frequency enhancements in QCM microorganism measurements.

  14. The emission of atoms and molecules accompanying fracture of single-crystal MgO

    Science.gov (United States)

    Dickinson, J. T.; Jensen, L. C.; Mckay, M. R.; Freund, F.

    1986-01-01

    The emission of particles due to deformation and fracture of materials has been investigated. The emission of electrons (exoelectron emission), ions, neutral species, photons (triboluminescence), as well as long wavelength electromagnetic radiation was observed; collectively these emissions are referred to as fractoemission. This paper describes measurements of the neutral emission accompanying the fracture of single-crystal MgO. Masses detected are tentatively assigned to the emission of H2, CH4, H2O, CO, O2, CO2, and atomic Mg. Other hydrocarbons are also observed. The time dependencies of some of these emissions relative to fracture are presented for two different loading conditions.

  15. Depth of interaction resolution of LuAP and LYSO crystals

    CERN Document Server

    Trummer, J; Lecoq, P

    2009-01-01

    The Crystal Clear Collaboration (CCC) has built a prototype of a novel positron emission tomograph dedicated to functional breast imaging, the ClearPEM. One aim of the ClearPEM is to be able to depict small tumours with a diameter of 2–3 mm in the breast and axilla region. To achieve such a spatial resolution one needs to know the position of the photon interaction in the crystal—the depth of interaction (DOI) with a precision of a least 2 mm. The main component of the detector are 20 mm long LYSO crystals read out at both ends with avalanche photo diodes (APD). The method to determine the DOI in the ClearPEM is via light sharing between the two end faces of the crystal. In this work 20 mm long LuAP and LYSO crystals were used to study the spatial resolution of the DOI in the crystal. The influence of the surface state (polished and unpolished) and wrapping on the DOI resolution and the light yield were also investigated.

  16. Modulation of calcium oxalate monohydrate crystallization by citrate through selective binding to atomic steps

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, S R; Wierzbicki, A; Salter, E A; Zepeda, S; Orme, C A; Hoyer, J R; Nancollas, G H; Cody, A M; De Yoreo, J J

    2004-10-19

    The majority of human kidney stones are composed primarily of calcium oxalate monohydrate (COM) crystals. Thus, determining the molecular mechanisms by which urinary constituents modulate calcium oxalate crystallization is crucial for understanding and controlling urolithiassis in humans. A comprehensive molecular-scale view of COM shape modification by citrate, a common urinary constituent, obtained through a combination of in situ atomic force microscopy (AFM) and molecular modeling is now presented. We show that citrate strongly influences the growth morphology and kinetics on the (-101) face but has much lower effect on the (010) face. Moreover, binding energy calculations show that the strength of the citrate-COM interaction is much greater at steps than on terraces and is highly step-specific. The maximum binding energy, -166.5 kJ {center_dot} mol{sup -1}, occurs for the [101] step on the (-101) face. In contrast, the value is only -56.9 kJ {center_dot} mol-1 for the [012] step on the (010) face. The binding energies on the (-101) and (010) terraces are also much smaller, -65.4 and -48.9 kJ {center_dot} mol{sup -1} respectively. All other binding energies lie between these extremes. This high selectivity leads to preferential binding of citrate to the acute [101] atomic steps on the (-101) face. The strong citrate-step interactions on this face leads to pinning of all steps, but the anisotropy in interaction strength results in anisotropic reductions in step kinetics. These anisotropic changes in step kinetics are, in turn, responsible for changes in the shape of macroscopic COM crystals. Thus, the molecular scale growth morphology and the bulk crystal habit in the presence of citrate are similar, and the predictions of molecular simulations are fully consistent with the experimental observations.

  17. Exfoliation and characterization of bismuth telluride atomic quintuples and quasi-two-dimensional crystals.

    Science.gov (United States)

    Teweldebrhan, Desalegne; Goyal, Vivek; Balandin, Alexander A

    2010-04-14

    Bismuth telluride (Bi(2)Te(3)) and its alloys are the best bulk thermoelectric materials known today. In addition, stacked quasi-two-dimensional (2D) layers of Bi(2)Te(3) were recently identified as promising topological insulators. In this Letter we describe a method for "graphene-inspired" exfoliation of crystalline bismuth telluride films with a thickness of a few atoms. The atomically thin films were suspended across trenches in Si/SiO(2) substrates, and subjected to detail material characterization, which included atomic force microscopy and micro-Raman spectroscopy. The presence of the van der Waals gaps allowed us to disassemble Bi(2)Te(3) crystal into its quintuple building blocks-five monatomic sheets-consisting of Te((1))-Bi-Te((2))-Bi-Te((1)). By altering the thickness and sequence of atomic planes, we were able to create "designer" nonstoichiometric quasi-2D crystalline films, change their composition and doping, the type of charge carriers as well as other properties. The exfoliated quintuples and ultrathin films have low thermal conductivity, high electrical conductivity, and enhanced thermoelectric properties. The obtained results pave the way for producing stacks of crystalline bismuth telluride quantum wells with the strong spatial confinement of charge carriers and acoustic phonons, beneficial for thermoelectric devices. The developed technology for producing free-standing quasi-2D layers of Te((1))-Bi-Te((2))-Bi-Te((1)) creates an impetus for investigation of the topological insulators and their possible practical applications.

  18. High spatial resolution X-ray and gamma ray imaging system using diffraction crystals

    Science.gov (United States)

    Smither, Robert K [Hinsdale, IL

    2011-05-17

    A method and a device for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation are provided. The device comprises a plurality of arrays, with each array comprising a plurality of elements comprising a first collimator, a diffracting crystal, a second collimator, and a detector.

  19. High-resolution wavefront shaping with a photonic crystal fiber for multimode fiber imaging

    NARCIS (Netherlands)

    Amitonova, L. V.; Descloux, A.; Petschulat, J.; Frosz, M. H.; Ahmed, G.; Babic, F.; Jiang, X.; Mosk, A. P.; Russell, P. S. J.; Pinkse, P.W.H.

    2016-01-01

    We demonstrate that a high-numerical-aperture photonic crystal fiber allows lensless focusing at an unparalleled res- olution by complex wavefront shaping. This paves the way toward high-resolution imaging exceeding the capabilities of imaging with multi-core single-mode optical fibers. We analyze

  20. Tip radius preservation for high resolution imaging in amplitude modulation atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Jorge R., E-mail: jorge.rr@cea.cu [Instituto de Ciencia de Materiales de Madrid, Sor Juana Inés de la Cruz 3, Canto Blanco, 28049 Madrid, España (Spain)

    2014-07-28

    The acquisition of high resolution images in atomic force microscopy (AFM) is correlated to the cantilever's tip shape, size, and imaging conditions. In this work, relative tip wear is quantified based on the evolution of a direct experimental observable in amplitude modulation atomic force microscopy, i.e., the critical amplitude. We further show that the scanning parameters required to guarantee a maximum compressive stress that is lower than the yield/fracture stress of the tip can be estimated via experimental observables. In both counts, the optimized parameters to acquire AFM images while preserving the tip are discussed. The results are validated experimentally by employing IgG antibodies as a model system.

  1. EM-Fold: De novo atomic-detail protein structure determination from medium resolution density maps

    Science.gov (United States)

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

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-12-04

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

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

    Science.gov (United States)

    Grosely, Rosslyn; Sorgen, Paul L

    2013-02-01

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

  4. A high resolution X-ray crystal spectrometer to study electron and ...

    Indian Academy of Sciences (India)

    satellite lines of Al have been studied in collision with 3–12 keV electrons and 40 MeV. C. 4+ ions. In ion collisions as large as ... bilities to resolve complex multiplet structures in the atomic spectra. Following the first crystal spectrometer .... The Bragg's equation (nλ = 2d sin θ) and slope of the straight line (nrot vs. sin θ, not ...

  5. Low-resolution continuum source simultaneous multi-element electrothermal atomic absorption spectrometry: steps into practice

    Science.gov (United States)

    Katskov, Dmitri

    2015-03-01

    The theory and practical problems of continuum source simultaneous multi-element electrothermal atomic absorption spectrometry (SMET AAS) are discussed by the example of direct analysis of underground water. The experimental methodology is based on pulse vaporization of the sample in a fast heated graphite tube and measurement of transient absorption of continuum spectrum radiation from D2 and Xe lamps within 200-400 nm wavelengths range with a low resolution spectral instrument and linear charge-coupled device. The setup permits the acquisition of 200 spectra during 1 s atomization pulse. Respective data matrix absorbance vs wavelength/time is employed for the quantification of elements in the sample. The calculation algorithm developed includes broad band and continuum background correction, linearization of function absorbance vs. concentration of atomic vapor and integration of thus modified absorbance at the resonance lines of the elements to be determined. Practical application shows that the method can be employed for the direct simultaneous determination of about 20 elements above microgram per liter level within 3-5 orders of the magnitude concentration range. The investigated sources of measurement errors are mainly associated with the atomization and vapor transportation problems, which are aggravated for the simultaneous release of major and minor sample constituents. Respective corrections concerning the selection of analytical lines, optimal sampling volume, matrix modification and cleaning of the atomizer have been introduced in the SMET AAS analytical technology. Under the optimized experimental conditions the calibration curves in Log-Log coordinates for all the investigated analytes in the single or multi-element reference solutions are approximated by the first order equations. The use of these equations as permanent characteristics of the setup enables instant quantification of Al, Ca, Co, Cr, Cu, Fe, Mg, Mn and Ni in the underground water

  6. Application of discrete solvent reaction field model with self-consistent atomic charges and atomic polarizabilities to calculate the χ(1) and χ(2) of organic molecular crystals

    Science.gov (United States)

    Lu, Shih-I.

    2018-01-01

    We use the discrete solvent reaction field model to evaluate the linear and second-order nonlinear optical susceptibilities of 3-methyl-4-nitropyridine-1-oxyde crystal. In this approach, crystal environment is created by supercell architecture. A self-consistent procedure is used to obtain charges and polarizabilities for environmental atoms. Impact of atomic polarizabilities on the properties of interest is highlighted. This approach is shown to give the second-order nonlinear optical susceptibilities within error bar of experiment as well as the linear optical susceptibilities in the same order as experiment. Similar quality of calculations are also applied to both 4-N,N-dimethylamino-3-acetamidonitrobenzene and 2-methyl-4-nitroaniline crystals.

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

    Science.gov (United States)

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

    2017-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-25

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

  9. Robust high-resolution imaging and quantitative force measurement with tuned-oscillator atomic force microscopy

    Science.gov (United States)

    Dagdeviren, Omur E.; Götzen, Jan; Hölscher, Hendrik; Altman, Eric I.; Schwarz, Udo D.

    2016-02-01

    Atomic force microscopy (AFM) and spectroscopy are based on locally detecting the interactions between a surface and a sharp probe tip. For highest resolution imaging, noncontact modes that avoid tip-sample contact are used; control of the tip’s vertical position is accomplished by oscillating the tip and detecting perturbations induced by its interaction with the surface potential. Due to this potential’s nonlinear nature, however, achieving reliable control of the tip-sample distance is challenging, so much so that despite its power vacuum-based noncontact AFM has remained a niche technique. Here we introduce a new pathway to distance control that prevents instabilities by externally tuning the oscillator’s response characteristics. A major advantage of this operational scheme is that it delivers robust position control in both the attractive and repulsive regimes with only one feedback loop, thereby providing an easy-to-implement route to atomic resolution imaging and quantitative tip-sample interaction force measurement.

  10. Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

    Science.gov (United States)

    Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

    2014-01-01

    A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2010-12-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  14. High-Resolution Imaging and Optical Control of Bose-Einstein Condensates in an Atom Chip Magnetic Trap

    CERN Document Server

    Salim, Evan A; Pfeiffer, Jonathan B; Anderson, Dana Z

    2012-01-01

    A high-resolution projection and imaging system for ultracold atoms is implemented using a compound silicon and glass atom chip. The atom chip is metalized to enable magnetic trapping while glass regions enable high numerical aperture optical access to atoms residing in the magnetic trap about 100 microns below the chip surface. The atom chip serves as a wall of the vacuum system, which enables the use of commercial microscope components for projection and imaging. Holographically generated light patterns are used to optically slice a cigar-shaped magnetic trap into separate regions; this has been used to simultaneously generate up to four Bose-condensates. Using fluorescence techniques we have demonstrated in-trap imaging resolution down to 2.5 microns

  15. Electron dose dependence of signal-to-noise ratio, atom contrast and resolution in transmission electron microscope images

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Z., E-mail: zhongbo.lee@uni-ulm.de; Rose, H.; Lehtinen, O.; Biskupek, J.; Kaiser, U.

    2014-10-15

    In order to achieve the highest resolution in aberration-corrected (AC) high-resolution transmission electron microscopy (HRTEM) images, high electron doses are required which only a few samples can withstand. In this paper we perform dose-dependent AC-HRTEM image calculations, and study the dependence of the signal-to-noise ratio, atom contrast and resolution on electron dose and sampling. We introduce dose-dependent contrast, which can be used to evaluate the visibility of objects under different dose conditions. Based on our calculations, we determine optimum samplings for high and low electron dose imaging conditions. - Highlights: • The definition of dose-dependent atom contrast is introduced. • The dependence of the signal-to-noise ratio, atom contrast and specimen resolution on electron dose and sampling is explored. • The optimum sampling can be determined according to different dose conditions.

  16. Influence of surface relaxation of strained layers on atomic resolution ADF imaging.

    Science.gov (United States)

    Beyer, Andreas; Duschek, Lennart; Belz, Jürgen; Oelerich, Jan Oliver; Jandieri, Kakhaber; Volz, Kerstin

    2017-10-01

    Surface relaxation of thin transmission electron microscopy (TEM) specimens of strained layers results in a severe bending of lattice planes. This bending significantly displaces atoms from their ideal channeling positions which has a strong impact on the measured annular dark field (ADF) intensity. With the example of GaAs quantum wells (QW) embedded in a GaP barrier, we model the resulting displacements by elastic theory using the finite element (FE) formalism. Relaxed and unrelaxed super cells served as input for state of the art frozen phonon simulation of atomic resolution ADF images. We systematically investigate the dependencies on the sample´s geometric parameters, i.e. QW width and TEM sample thickness, by evaluating the simulated intensities at the atomic column´s positions as well as at the background positions in between. Depending on the geometry the ADF intensity can be affected in a range several nm from the actual interface. Moreover, we investigate the influence of the surface relaxation on the angular distribution of the scattered intensity. At high scattering angles we observe an intensity reduction at the interface as well as in the GaP barrier due to de-channeling. The amount of intensity reduction at an atomic column is directly proportional to its mean square displacement. On the contrary we find a clearly increased intensity at low angles caused by additional diffuse scattering. We discuss the implications for quantitative evaluations as well as strategies to compensate for the reduced intensities. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Morphology, Crystallization, and Melting of Single Crystals and Thin Films of Star-branched Polyesters with Poly(E-caprolactone) Arms as Revealed by Atomic Force Microscopy

    NARCIS (Netherlands)

    Nunez Calzado, M.E.; Nunez, E.; Vancso, Gyula J.; Gedde, U.W.

    2008-01-01

    The morphology and thermal stability of different sectors in solution- and melt-grown crystals of star-branched polyesters with poly(ε-caprolactone) (PCL) arms, and of a reference linear PCL, have been studied by tapping-mode atomic-force microscopy (AFM). Real-time monitoring of

  18. High resolution x-ray and gamma ray imaging using diffraction lenses with mechanically bent crystals

    Science.gov (United States)

    Smither, Robert K [Hinsdale, IL

    2008-12-23

    A method for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation is provided. High quality mechanically bent diffracting crystals of 0.1 mm radial width are used for focusing the radiation and directing the radiation to an array of detectors which is used for analyzing their addition to collect data as to the location of the source of radiation. A computer is used for converting the data to an image. The invention also provides for the use of a multi-component high resolution detector array and for narrow source and detector apertures.

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

    Science.gov (United States)

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

    2013-10-01

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

  20. Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kovarik, Libor; Stevens, Andrew J.; Liyu, Andrey V.; Browning, Nigel D.

    2016-10-17

    Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. The use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dose issues.

  1. Increasing 13C CP-MAS NMR resolution using single crystals: application to model octaethyl porphyrins.

    Science.gov (United States)

    Dugar, Sneha; Fu, Riqiang; Dalal, Naresh S

    2012-08-02

    Octaethyl porphyrin (OEP) and its Ni and Zn derivatives are considered as model compounds in biochemical, photophysical, and fossil fuel chemistry. They have thus been investigated by high-resolution solid-state (13)C NMR using powders, but peak assignment has been difficult because of large line widths. Arguing that a significant cause of broadening might be the anisotropic bulk magnetic susceptibility, we utilized single crystals in our (13)C cross-polarization magic angle spinning (CP-MAS) measurements and observed a nearly 2-fold line narrowing. This enhanced resolution enabled us to assign chemical shifts to each carbon for all the three compounds. The new assignments are now in agreement with X-ray structural data and allowed us to probe the motional dynamics of the methyl and methylene carbons of the OEP side chains. It is apparent that the use of single crystals in (13)C CP-MAS measurements has a significantly wider impact than previously thought.

  2. Atomic scale studies of La/Sr ordering in La2-2xSr1+2xMn2O7 single crystals

    KAUST Repository

    Roldan, Manuel

    2016-12-21

    Many fascinating properties of materials depend strongly on the local chemical environment. This is the case for many complex oxides, such as materials with colossal magnetoresistance, where small variations of composition at the atomic scale can affect drastically the macroscopic properties. The main objective of the present work is to analyze the local chemical composition with atomic resolution and to find out if any underlying chemical order is in any way connected to the magnetic properties of double perovskite La2-2xSr1+2xMn2O7 (LSMO) manganite oxides. For these compounds, charge and orbital ordering are observed for some doping values near x = 0.50 [1, 2]. For this purpose, we have use aberration corrected scanning transmission electron microscopy (STEM) combined with electron energy-loss spectroscopy (EELS) measurements and also theoretical simulations. We have compared different compositions within three distinct magnetic regions of the phase diagram: a ferromagnetic metallic sample with x=0.36, an insulating, antiferromagnetic (AF) x=0.56 and an additional AF x=0.50 sample which also exhibits charge ordering. High angle annular dark-field (HAADF) images, also known as Z-contrast, confirm that our single crystals exhibit high crystal quality. No secondary phases or defects are observed. Figure 1 displays an atomic resolution image obtained with the c-axis perpendicular to the electron beam of a x=0.50 sample. The perovskite (P)-like planes and the rock salt (R)-like planes are clearly observed, highlighted in green and red, respectively, on the image. The P-like planes exhibit a slightly high contrast, suggesting a possible La enrichment. EELS atomic resolution maps (inset) support a high degree of La segregation on those planes, while R-like planes are Sr rich. However, due to dechanneling of the beam, detailed image simulations are essential to accurately quantify the local chemical composition in an atomic column-by-atomic column fashion. For all our

  3. A versatile, highly-efficient, high-resolution von Hamos Bragg crystal x-ray spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Vane, C.R.; Smith, M.S.; Raman, S.

    1988-01-01

    An efficient, high-resolution, vertical-focusing, Bragg crystal x-ray spectrometer has been specifically designed and constructed for use in measurements of x rays produced in collisions of energetic heavy ions. In this report the design and resulting operational characteristics of the final instrument are fully described. A wide variety of sample data is also included to illustrate the utility of this device in several areas of research. 14 refs., 38 figs.

  4. Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design.

    Science.gov (United States)

    Gonnissen, J; De Backer, A; den Dekker, A J; Sijbers, J; Van Aert, S

    2016-11-01

    In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramér-Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. New multicell model for describing the atomic structure of La{sub 3}Ga{sub 5}SiO{sub 14} piezoelectric crystal: Unit cells of different compositions in the same single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Dudka, A. P., E-mail: dudka@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation)

    2017-03-15

    Accurate X-ray diffraction study of langasite (La{sub 3}Ga{sub 5}SiO{sub 14}) single crystal has been performed using the data obtained on a diffractometer equipped with a CCD area detector at 295 and 90.5 K. Within the known La{sub 3}Ga{sub 5}SiO{sub 14} model, Ga and Si cations jointly occupy the 2d site. A new model of a “multicell” consisting of two different unit cells is proposed. Gallium atoms occupy the 2d site in one of these cells, and silicon atoms occupy this site in the other cell; all other atoms correspondingly coordinate these cations. This structure implements various physical properties exhibited by langasite family crystals. The conclusions are based on processing four data sets obtained with a high resolution (sin θ/λ ≤ 1.35 Å{sup –1}), the results reproduced in repeated experiments, and the high relative precision of the study (sp. gr. P321, Z = 1; at 295 K, a = 8.1652(6) Å, c = 5.0958(5) Å, R/wR = 0.68/0.68%, 3927 independent reflections; at 90.5 K, a = 8.1559(4) Å, c = 5.0913(6) Å, R/wR = 0.92/0.93%, 3928 reflections).

  6. Synthesizing complex spin networks with spin-motion coupled neutral atoms in photonic crystals

    Science.gov (United States)

    Dong, Ying

    2017-04-01

    We develop a toolbox for realizing ``fully programmable'' d-dimensional pairwise interacting lattice spin systems with spin-motion coupled neutral atoms in the vicinity of 1D photonic crystal waveguides. The enabling platform thereby allows to synthesize a wide range of strongly interacting quantum materials by way of vacuum-engineered interatomic kinetic interactions. We demonstrate the versatility of our assembly language approach towards arbitrary SU(2)-lattice spin models with explicit constructions of familiar Hamiltonians for perfect state transfer in 1D spin chains, lattice gauge theories, and topologicallyquantum spin liquids. We further construct Dzyaloshinski-Moriya interaction for the realization ofspin liquids and long-range random quantum magnets with spin-glass phase.

  7. Time resolution deterioration with increasing crystal length in a TOF-PET system

    CERN Document Server

    Gundacker, S; Auffray, E; Jarron, P; Meyer, T; Lecoq, P

    2014-01-01

    Highest time resolution in scintillator based detectors is becoming more and more important. In medical detector physics L(Y)SO scintillators are commonly used for time of flight positron emission tomography (TOF-PET). Coincidence time resolutions (CTRs) smaller than 100 ps FWHM are desirable in order to improve the image signal to noise ratio and thus give benefit to the patient by shorter scanning times. Also in high energy physics there is the demand to improve the timing capabilities of calorimeters down to 10 ps. To achieve these goals it is important to study the whole chain, i.e. the high energy particle interaction in the crystal, the scintillation process itself, the scintillation light transfer in the crystal, the photodetector and the electronics. Time resolution measurements for a PET like system are performed with the time-over-threshold method in a coincidence setup utilizing the ultra-fast amplifier-discriminator NINO. With 2×2×3 mm3 LSO:Ce codoped 0.4%Ca crystals coupled to commercially avai...

  8. Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution.

    Science.gov (United States)

    Chen, Xuehui; Sun, Yunxiang; An, Xiongbo; Ming, Dengming

    2011-10-14

    Normal mode analysis of large biomolecular complexes at atomic resolution remains challenging in computational structure biology due to the requirement of large amount of memory space and central processing unit time. In this paper, we present a method called virtual interface substructure synthesis method or VISSM to calculate approximate normal modes of large biomolecular complexes at atomic resolution. VISSM introduces the subunit interfaces as independent substructures that join contacting molecules so as to keep the integrity of the system. Compared with other approximate methods, VISSM delivers atomic modes with no need of a coarse-graining-then-projection procedure. The method was examined for 54 protein-complexes with the conventional all-atom normal mode analysis using CHARMM simulation program and the overlap of the first 100 low-frequency modes is greater than 0.7 for 49 complexes, indicating its accuracy and reliability. We then applied VISSM to the satellite panicum mosaic virus (SPMV, 78,300 atoms) and to F-actin filament structures of up to 39-mer, 228,813 atoms and found that VISSM calculations capture functionally important conformational changes accessible to these structures at atomic resolution. Our results support the idea that the dynamics of a large biomolecular complex might be understood based on the motions of its component subunits and the way in which subunits bind one another. © 2011 American Institute of Physics

  9. The resolution dependence of optimal exposures in liquid nitrogen temperature electron cryomicroscopy of catalase crystals.

    Science.gov (United States)

    Baker, Lindsay A; Smith, Eric A; Bueler, Stephanie A; Rubinstein, John L

    2010-03-01

    Electron beam damage is the fundamental limit to resolution in electron cryomicroscopy (cryo-EM) of frozen, hydrated specimens. Radiation damage increases with the number of electrons used to obtain an image and affects information at higher spatial frequencies before low-resolution information. For the experimentalist, a balance exists between electron exposures sufficient to obtain a useful signal-to-noise ratio (SNR) in images and exposures that limit the damage to structural features. In single particle cryo-EM this balance is particularly delicate: low-resolution features must be imaged with a sufficient SNR to allow image alignment so that high-resolution features recorded below the noise level can be recovered by averaging independent images. By measuring the fading of Fourier components from images obtained at 200 kV of thin crystals of catalase embedded in ice, we have determined the electron exposures that will maximize the SNR at resolutions between 86 and 2.9A. These data allow for a rational choice of exposure for single particle cryo-EM. For example, for 20A resolution, the SNR is maximized at approximately 20e(-)/A(2), whereas for 3A resolution, it is maximized at approximately 10 e(-)/A(2). We illustrate the effects of exposure in single particle cryo-EM with data collected at approximately 12-15 and approximately 24-30 e(-)/A(2). (c) 2009 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Wang, J.; Beyerlein, I. J.

    2012-03-01

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

  11. 'Big Bang' tomography as a new route to atomic-resolution electron tomography.

    Science.gov (United States)

    Van Dyck, Dirk; Jinschek, Joerg R; Chen, Fu-Rong

    2012-06-13

    Until now it has not been possible to image at atomic resolution using classical electron tomographic methods, except when the target is a perfectly crystalline nano-object imaged along a few zone axes. The main reasons are that mechanical tilting in an electron microscope with sub-ångström precision over a very large angular range is difficult, that many real-life objects such as dielectric layers in microelectronic devices impose geometrical constraints and that many radiation-sensitive objects such as proteins limit the total electron dose. Hence, there is a need for a new tomographic scheme that is able to deduce three-dimensional information from only one or a few projections. Here we present an electron tomographic method that can be used to determine, from only one viewing direction and with sub-ångström precision, both the position of individual atoms in the plane of observation and their vertical position. The concept is based on the fact that an experimentally reconstructed exit wave consists of the superposition of the spherical waves that have been scattered by the individual atoms of the object. Furthermore, the phase of a Fourier component of a spherical wave increases with the distance of propagation at a known 'phase speed'. If we assume that an atom is a point-like object, the relationship between the phase and the phase speed of each Fourier component is linear, and the distance between the atom and the plane of observation can therefore be determined by linear fitting. This picture has similarities with Big Bang cosmology, in which the Universe expands from a point-like origin such that the distance of any galaxy from the origin is linearly proportional to the speed at which it moves away from the origin (Hubble expansion). The proof of concept of the method has been demonstrated experimentally for graphene with a two-layer structure and it will work optimally for similar layered materials, such as boron nitride and molybdenum disulphide.

  12. CHARACTERIZATION OF SURFACE OF THE (010 FACE OF BORAX CRYSTALS USING EX SITU ATOMIC FORCE MICROSCOPY (AFM:

    Directory of Open Access Journals (Sweden)

    Suharso Suharso

    2010-06-01

    Full Text Available The surface topology of borax crystals grown at a relative supersaturation of 0.21 has been investigated using ex situ atomic force microscopy (AFM. It was found that the cleavage of borax crystals along the (010 face planes has features of the cleavage of layered compounds, exhibiting cleavage steps of low heights. The step heights of the cleavage of the (010 face of borax crystal are from one unit cell to three unit cells of this face.   Keywords: AFM, cleavage, borax.

  13. Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.

    Science.gov (United States)

    Shalev-Benami, Moran; Zhang, Yan; Rozenberg, Haim; Nobe, Yuko; Taoka, Masato; Matzov, Donna; Zimmerman, Ella; Bashan, Anat; Isobe, Toshiaki; Jaffe, Charles L; Yonath, Ada; Skiniotis, Georgios

    2017-11-17

    Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL). The structure reveals the mechanism by which the drug induces its deleterious effects on the parasite. We further show that PAR interferes with several aspects of cytosolic translation, thus highlighting the cytosolic rather than the mitochondrial ribosome as the primary drug target. The results also highlight unique as well as conserved elements in the PAR-binding pocket that can serve as hotspots for the development of novel therapeutics.

  14. Toward atomic resolution diffractive imaging of isolated molecules with x-ray free-electron lasers

    DEFF Research Database (Denmark)

    Stern, Stephan; Holmegaard, Lotte; Filsinger, Frank

    2014-01-01

    We give a detailed account of the theoretical analysis and the experimental results of an x-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Cohere...... Light Source [Phys. Rev. Lett. 112, 083002 (2014)]. This experiment is the first step toward coherent diffractive imaging of structures and structural dynamics of isolated molecules at atomic resolution, i. e., picometers and femtoseconds, using x-ray free-electron lasers.......We give a detailed account of the theoretical analysis and the experimental results of an x-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Coherent...

  15. Cryo-electron microscopy and the amazing race to atomic resolution.

    Science.gov (United States)

    Binshtein, Elad; Ohi, Melanie D

    2015-05-26

    Cryo-electron microscopy (cryo-EM), the structural analysis of samples embedded in vitreous ice, is a powerful approach for determining three-dimensional (3D) structures of biological specimens. Over the past two decades, this technique has been used to successfully calculate subnanometer (electron microscopes with automated data collection capabilities and robust direct electron detection cameras, as well as new powerful image processing algorithms, has dramatically expanded the number of biological macromolecules amenable for study using cryo-EM. In addition, these new technological and computational developments have been used to successfully determine cryo-EM. With these exciting new advances, cryo-EM is now on pace to determine atomic resolution 3D structures.

  16. High-resolution x-ray characterization of mosaic crystals for hard x-ray astronomy

    Science.gov (United States)

    Ferrari, Claudio; Buffagni, Elisa; Marchini, Laura; Zappettini, Andrea

    2012-04-01

    GaAs, Cu, CdTe, and CdZnTe crystals have been studied as optical elements for lenses for hard x-ray astronomy. High-resolution x-ray diffraction at 8 keV in Bragg geometry and at synchrotron at energies up to 500 keV in Laue geometry has been used. A good agreement was found between the mosaicity evaluated in Bragg geometry at 8 keV with x-ray penetration of the order of few tens of micrometers and that derived at synchrotron in transmission Laue geometry at higher x-ray energies. Mosaicity values in a range between a few to 150 arcsec were found in all the samples but, due to the presence of crystal grains in the cm range, CdTe and CdZnTe crystals were found not suitable. Cu crystals exhibit a mosaicity of the order of several arcmin; they indeed were found to be severely affected by cutting damage which could only be removed with a very deep etching. The full width at half maximum of the diffraction peaks decreased at higher x-ray energies showing that the peak broadening is affected by crystallite size. GaAs crystals grown by Czochralski method showed a mosaic spread up to 30 arcsec and good diffraction efficiency up to energies of 500 keV. The use of thermal treatments as a possible method to increase the mosaic spread was also evaluated.

  17. Elemental mapping in achromatic atomic-resolution energy-filtered transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Forbes, B.D. [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia); Houben, L. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Mayer, J. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Central Facility for Electron Microscopy, RWTH Aachen University, D-52074 Aachen (Germany); Dunin-Borkowski, R.E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Allen, L.J., E-mail: lja@unimelb.edu.au [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia)

    2014-12-15

    We present atomic-resolution energy-filtered transmission electron microscopy (EFTEM) images obtained with the chromatic-aberration-corrected FEI Titan PICO at the Ernst-Ruska Centre, Jülich, Germany. We find qualitative agreement between experiment and simulation for the background-subtracted EFTEM images of the Ti–L{sub 2,3} and O–K edges for a specimen of SrTiO{sub 3} oriented down the [110] zone axis. The simulations utilize the transition potential formulation for inelastic scattering, which permits a detailed investigation of contributions to the EFTEM image. We find that energy-filtered images of the Ti–L{sub 2,3} and O–K edges are lattice images and that the background-subtracted core-loss maps may not be directly interpretable as elemental maps. Simulations show that this is a result of preservation of elastic contrast, whereby the qualitative details of the image are determined primarily by elastic, coherent scattering. We show that this effect places a constraint on the range of specimen thicknesses which could theoretically yield directly useful elemental maps. In general, interpretation of EFTEM images is ideally accompanied by detailed simulations. - Highlights: • Achromatic atomic-resolution EFTEM images were obtained for STO 〈110〉. • Simulations were in qualitative agreement with Ti–L{sub 2,3} and O–K edge maps. • The experimental EFTEM maps are not directly interpretable as elemental maps. • Image intensities are strongly determined by preservation of elastic contrast. • Interpretation of EFTEM images is ideally accompanied by detailed simulations.

  18. He atom-surface scattering: Surface dynamics of insulators, overlayers and crystal growth

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    Investigations in this laboratory have focused on the surface structure and dynamics of ionic insulators and on epitaxial growth onto alkali halide crystals. In the later the homoepitaxial growth of NaCl/NaCl(001) and the heteroepitaxial growth of KBr/NaCl(001), NaCl/KBr(001) and KBr/RbCl(001) have been studied by monitoring the specular He scattering as a function of the coverage and by measuring the angular and energy distributions of the scattered He atoms. These data provide information on the surface structure, defect densities, island sizes and surface strain during the layer-by-layer growth. The temperature dependence of these measurements also provides information on the mobilities of the admolecules. He atom scattering is unique among surface probes because the low-energy, inert atoms are sensitive only to the electronic structure of the topmost surface layer and are equally applicable to all crystalline materials. It is proposed for the next year to exploit further the variety of combinations possible with the alkali halides in order to carry out a definitive study of epitaxial growth in the ionic insulators. The work completed so far, including measurements of the Bragg diffraction and surface dispersion at various stages of growth, appears to be exceptionally rich in detail, which is particularly promising for theoretical modeling. In addition, because epitaxial growth conditions over a wide range of lattice mismatches is possible with these materials, size effects in growth processes can be explored in great depth. Further, as some of the alkali halides have the CsCl structure instead of the NaCl structure, we can investigate the effects of the heteroepitaxy with materials having different lattice preferences. Finally, by using co-deposition of different alkali halides, one can investigate the formation and stability of alloys and even alkali halide superlattices.

  19. Application of spatially resolved high resolution crystal spectrometry to inertial confinement fusion plasmas.

    Science.gov (United States)

    Hill, K W; Bitter, M; Delgado-Aparacio, L; Pablant, N A; Beiersdorfer, P; Schneider, M; Widmann, K; Sanchez del Rio, M; Zhang, L

    2012-10-01

    High resolution (λ∕Δλ ∼ 10 000) 1D imaging x-ray spectroscopy using a spherically bent crystal and a 2D hybrid pixel array detector is used world wide for Doppler measurements of ion-temperature and plasma flow-velocity profiles in magnetic confinement fusion plasmas. Meter sized plasmas are diagnosed with cm spatial resolution and 10 ms time resolution. This concept can also be used as a diagnostic of small sources, such as inertial confinement fusion plasmas and targets on x-ray light source beam lines, with spatial resolution of micrometers, as demonstrated by laboratory experiments using a 250-μm (55)Fe source, and by ray-tracing calculations. Throughput calculations agree with measurements, and predict detector counts in the range 10(-8)-10(-6) times source x-rays, depending on crystal reflectivity and spectrometer geometry. Results of the lab demonstrations, application of the technique to the National Ignition Facility (NIF), and predictions of performance on NIF will be presented.

  20. [Determination of sulfur in plant using a high-resolution continuum source atomic absorption spectrometer].

    Science.gov (United States)

    Wang, Yu; Li, Jia-xi

    2009-05-01

    A method for the analysis of sulfur (S) in plant by molecular absorption of carbon monosulfide (CS) using a high-resolution continuum source atomic absorption spectrometer (CS AAS) with a fuel-rich air/acetylene flame has been devised. The strong CS absorption band was found around 258 nm. The half-widths of some absorption bands were of the order of picometers, the same as the common atomic absorption lines. The experimental procedure in this study provided optimized instrumental conditions (the ratio of acetylene to air, the burner height) and parameters, and researched the spectral interferences and chemical interferences. The influence of the organic solvents on the CS absorption signals and the different digestion procedures for the determination of sulfur were also investigated. The limit of detection achieved for sulfur was 14 mg x L(-1), using the CS wavelength of 257. 961 nm and a measurement time of 3 s. The accuracy and precision were verified by analysis of two plant standard reference materials. The major applications of this method have been used for the determination of sulfur in plant materials, such as leaves. Compared to the others, this method for the analysis of sulfur is rapid, easy and simple for sulfur determination in plant.

  1. Analysis and Calibration of in situ scanning tunnelling microscopy Images with atomic Resolution Influenced by Surface Drift Phenomena

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov; Møller, Per

    1994-01-01

    The influence of surface drift velocities on in situ scanning tunnelling microscopy (STM) experiments with atomic resolution is analysed experimentally and mathematically. Constant drift velocities much smaller than the speed of scanning can in many in situ STM experiments with atomic resolution...... result in an apparent surface reconstruction. It is shown that a surface atomic structure can be distorted and observed as another atomic structure entirely owing to a constant drift velocity in the plane of the surface. The image can be resolved mathematically and the components of the drift velocity...... as well as the vectors of the non-distorted surface lattice can be determined. The calibration of distances can thus be carried out also when the image is influenced by drift. Results with gold surfaces and graphite surfaces are analysed and discussed....

  2. Crystallization and atomic diffusion behavior of high coercive Ta/Nd-Fe-B/Ta-based permanent magnetic thin film

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Na; Zhang, Xiao; You, Caiyin; Fu, Huarui [Xi' an University of Technology, School of Materials Science and Engineering, Xi' an (China); Shen, Qianlong [Logistics University of People' s Armed Police Force, Tianjin (China)

    2017-06-15

    A high coercivity of about 20.4 kOe was obtained through post-annealing the sputtered Ta/Nd-Fe-B/Ta-based permanent magnetic thin films. Transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS) analyses were performed to investigate the crystallization and atomic diffusion behaviors during post-annealing. The results show that the buffer and capping Ta layers prefered to intermix with Fe and B atoms, and Nd tends to be combined with O atoms. The preferred atomic combination caused the appearance of the soft magnetic phase of Fe-Ta-B, resulting in a kink of the second quadratic magnetic hysteresis loop. The preferred atomic diffusion and phase formation of the thin films were well explained in terms of the formation enthalpy of the various compounds. (orig.)

  3. Atomic force microscopy with nanoelectrode tips for high resolution electrochemical, nanoadhesion and nanoelectrical imaging

    Science.gov (United States)

    Nellist, Michael R.; Chen, Yikai; Mark, Andreas; Gödrich, Sebastian; Stelling, Christian; Jiang, Jingjing; Poddar, Rakesh; Li, Chunzeng; Kumar, Ravi; Papastavrou, Georg; Retsch, Markus; Brunschwig, Bruce S.; Huang, Zhuangqun; Xiang, Chengxiang; Boettcher, Shannon W.

    2017-03-01

    Multimodal nano-imaging in electrochemical environments is important across many areas of science and technology. Here, scanning electrochemical microscopy (SECM) using an atomic force microscope (AFM) platform with a nanoelectrode probe is reported. In combination with PeakForce tapping AFM mode, the simultaneous characterization of surface topography, quantitative nanomechanics, nanoelectronic properties, and electrochemical activity is demonstrated. The nanoelectrode probe is coated with dielectric materials and has an exposed conical Pt tip apex of ∼200 nm in height and of ∼25 nm in end-tip radius. These characteristic dimensions permit sub-100 nm spatial resolution for electrochemical imaging. With this nanoelectrode probe we have extended AFM-based nanoelectrical measurements to liquid environments. Experimental data and numerical simulations are used to understand the response of the nanoelectrode probe. With PeakForce SECM, we successfully characterized a surface defect on a highly-oriented pyrolytic graphite electrode showing correlated topographical, electrochemical and nanomechanical information at the highest AFM-SECM resolution. The SECM nanoelectrode also enabled the measurement of heterogeneous electrical conductivity of electrode surfaces in liquid. These studies extend the basic understanding of heterogeneity on graphite/graphene surfaces for electrochemical applications.

  4. Phase measurement of atomic resolution image using transport of intensity equation.

    Science.gov (United States)

    Ishizuka, Kazuo; Allman, Brendan

    2005-06-01

    Since the Transport Intensity Equation (TIE) has been applied to electron microscopy only recently, there are controversial discussions in the literature regarding the theoretical concepts underlying the equation and the practical techniques to solve the equation. In this report we explored some of the issues regarding the TIE, especially bearing electron microscopy in mind, and clarified that: (i) the TIE for electrons exactly corresponds to the Schrödinger equation for high-energy electrons in free space, and thus the TIE does not assume weak scattering; (ii) the TIE can give phase information at any distance from the specimen, not limited to a new field; (iii) information transfer in the TIE for each spatial frequency g will be multiplied by g2 and thus low frequency components will be dumped more with respect to high frequency components; (vi) the intensity derivative with respect to the direction of wave propagation is well approximated by using a set of three symmetric images; and (v) a substantially larger defocus distance than expected before can be used for high-resolution electron microscopy. In the second part of this report we applied the TIE down to atomic resolution images to obtain phase information and verified the following points experimentally: (i) although low frequency components are attenuated in the TIE, all frequencies will be recovered satisfactorily except the very low frequencies; and (ii) using a reconstructed phase and the measured image intensity we can correct effectively the defects of imaging, such as spherical aberrations as well as partial coherence.

  5. Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

    Science.gov (United States)

    Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

    2015-02-02

    Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Implementing an accurate and rapid sparse sampling approach for low-dose atomic resolution STEM imaging

    Science.gov (United States)

    Kovarik, L.; Stevens, A.; Liyu, A.; Browning, N. D.

    2016-10-01

    While aberration correction for scanning transmission electron microscopes (STEMs) dramatically increased the spatial resolution obtainable in the images of materials that are stable under the electron beam, the practical resolution of many STEM images is now limited by the sample stability rather than the microscope. To extract physical information from the images of beam sensitive materials, it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here, we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in the scan coils, we show that a sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by at least a factor of 5× relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. The use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected the Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dosage issues.

  7. Many-particle interactions and rainbow effects in grazing scattering of Ar atoms on the Al(1 1 1), Ag(1 1 1) crystals

    Science.gov (United States)

    Babenko, P. Yu.; Meluzova, D. S.; Shergin, A. P.; Zinoviev, A. N.

    2017-09-01

    Computer simulation of rainbow and ;ion focusing; effects taking place in scattering of Ar atoms on Al(1 1 1) and Ag(1 1 1) crystal surfaces have been performed. The trajectory calculation and vector summation of forces of the projectile atom interaction with crystal atoms have been shown to provide good fitting of the available experimental data. The thermal vibration amplitude for atoms located on the surface of crystals under study has been determined. A functional form of the potential has been proposed that fits well the experimental data.

  8. Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

    Directory of Open Access Journals (Sweden)

    Morita Mizuki

    2011-12-01

    Full Text Available Abstract Background Protein-lipid interactions play essential roles in the conformational stability and biological functions of membrane proteins. However, few of the previous computational studies have taken into account the atomic details of protein-lipid interactions explicitly. Results To gain an insight into the molecular mechanisms of the recognition of lipid molecules by membrane proteins, we investigated amino acid propensities in membrane proteins for interacting with the head and tail groups of lipid molecules. We observed a common pattern of lipid tail-amino acid interactions in two different data sources, crystal structures and molecular dynamics simulations. These interactions are largely explained by general lipophilicity, whereas the preferences for lipid head groups vary among individual proteins. We also found that membrane and water-soluble proteins utilize essentially an identical set of amino acids for interacting with lipid head and tail groups. Conclusions We showed that the lipophilicity of amino acid residues determines the amino acid preferences for lipid tail groups in both membrane and water-soluble proteins, suggesting that tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner. In contrast, interactions between lipid head groups and amino acids showed a more variable pattern, apparently constrained by each protein's specific molecular function.

  9. Crystal interface and high-resolution electron microscopy—the best partner

    Directory of Open Access Journals (Sweden)

    H Ichinose

    2000-01-01

    Full Text Available Several contributions of HRTEM on the interface science are reviewed in chronological order. The first contribution of HRTEM is the observation of gold (113Σ°11 boundary, giving experimental proof of the CSL model. An observation of the asymmetric (112Σ°3 boundary follows. A SiC grain boundary is effectively assessed not by the density of CSL point but the number of dangling bonds in the boundary. A ZnO/Pd interface provides an example that a misfit dislocation does not necessarily accommodate the lattice mismatch. Segregated interface shows characteristic HRTEM image contrast, suggesting change in atomic bonding. An atomic height step in the semiconductor hetero interface is observed by the Chemical Lattice Image technique. In the diamond grain boundary a dangling bond may not elevate the boundary energy, being contradictory of the least dangling bond rule. Super-high resolution of the HVHRTEM enable us to determine atomic species in the grain boundary. Combined use of HRTEM and EELSE allows us to discuss the correlation between atomic structure and nature of the corresponding interface. It is not exaggeration to say that modern interface science does not exist witout HRTEM. On the other hand, many complicated interfaces found by HRTEM remained as unaswered questions. An innovative structural model is requested to appear on the scene.

  10. Note: High-speed Z tip scanner with screw cantilever holding mechanism for atomic-resolution atomic force microscopy in liquid

    OpenAIRE

    Mohammad Reza Akrami, Seyed; Miyata, Kazuki; Asakawa, Hitoshi; Fukuma, Takeshi

    2014-01-01

    High-speed atomic force microscopy has attracted much attention due to its unique capability of visualizing nanoscale dynamic processes at a solid/liquid interface. However, its usability and resolution have yet to be improved. As one of the solutions for this issue, here we present a design of a high-speed Z-tip scanner with screw holding mechanism. We perform detailed comparison between designs with different actuator size and screw arrangement by finite element analysis. Based on the desig...

  11. Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

    Science.gov (United States)

    Mondal, Pradip Kumar; Yadav, Hare Ram; Choudhury, Angshuman Roy; Chopra, Deepak

    2017-10-01

    Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp 2 -H...F-Csp 2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp 2 -F...F-Csp 2 contacts.

  12. Endlessly single-mode photonic crystal fiber as a high resolution probe.

    Science.gov (United States)

    Valtna-Lukner, Heli; Repän, Jaagup; Valdma, Sandhra-Mirella; Piksarv, Peeter

    2016-11-20

    We sample ultra-broadband light, focused onto a diffraction-limited spot, to an endlessly single-mode photonic crystal fiber (ESM) and detect both the field amplitude and phase using a SEA TADPOLE interferometer. We resolve spatial features up to 2.5 times finer than the fiber mode size while sampling the periodic features of the bipolar oscillating field in the transverse section. The resolution enhancement is expected also in other types of single-mode fibers in intensity measurements and leads to an inexpensive method for characterizing the point-spread function of such optical fields, e.g., diffraction-limited spots from microscope objectives. In addition, we demonstrate the guidance of a high-NA light field in the fine structure of an ESM fiber mode. The results are especially valuable for devices where a fiber tip acts as an input slit and defines the spatial resolution, e.g., fiber-based interferometers, spectrometers, and sensors.

  13. Low frequency Raman spectroscopy of few-atomic-layer thick hBN crystals

    Science.gov (United States)

    Stenger, I.; Schué, L.; Boukhicha, M.; Berini, B.; Plaçais, B.; Loiseau, A.; Barjon, J.

    2017-09-01

    Hexagonal boron nitride (hBN) has recently gained a strong interest as a strategic component in engineering van der Waals heterostructures built with 2D crystals such as graphene. This work reports micro-Raman measurements on hBN flakes made of a few atomic layers, prepared by mechanical exfoliation. The temperature dependence of the Raman scattering in hBN is investigated first such as to define appropriate measurements conditions suitable for thin layers avoiding undesirable heating induced effects. We further focus on the low frequency Raman mode corresponding to the rigid shearing oscillation between adjacent layers, found to be equal to 52.5 cm-1 in bulk hBN. For hBN sheets with thicknesses below typically 4 nm, the frequency of this mode presents discrete values, which are found to decrease down to 46.0(5) cm-1 for a three-layer hBN, in good agreement with the linear-chain model. This makes Raman spectroscopy a relevant tool to quantitatively determine in a non destructive way the number of layers in ultra thin hBN sheets, below 8 L, prior to their integration in van der Waals heterostructures.

  14. Quasi-mosaic Crystals For High-resolution Focusing Of Hard X-rays Through A Laue Lens

    Science.gov (United States)

    Camattari, R.; Guidi, V.; Bellucci, V.; Neri, I.

    2011-09-01

    We propose the usage of bent crystals exploiting the Quasi-Mosaicity for high-resolution focusing of hard X-rays. Quasi-Mosaicity is an effect of anisotropy in crystals that manifests itself along selected crystallographic directions. As a result of primary curvature imparted to the crystal, a secondary curvature (Quasi-Mosaic curvature) occurs. We demonstrated that a combination of primary and Quasi-Mosaic curvatures allows high-efficiency diffraction and high-resolution focusing of diffracted photons. As compared to traditional mosaic crystals with same size and energy passband, Quasi-Mosaic crystals would increases the signal-to-noise ratio by about an order of magnitude and no mosaic defocusing would occur.

  15. Atomic resolution imaging of YAlO{sub 3}: Ce in the chromatic and spherical aberration corrected PICO electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Lei [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich (Germany); Barthel, Juri [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich (Germany); Central Facility for Electron Microscopy, RWTH Aachen University, 52074 Aachen (Germany); Jia, Chun-Lin [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich (Germany); School of Electronic and Information Engineering and State Key Laboratory for Mechanical Behaviour of Materials, Xi' an Jiaotong University, Xi' an 710049 (China); Urban, Knut W., E-mail: k.urban@fz-juelich.de [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich-Aachen Research Alliance (JARA), Forschungszentrum Jülich GmbH, 52425 Jülich, (Germany); School of Electronic and Information Engineering and State Key Laboratory for Mechanical Behaviour of Materials, Xi' an Jiaotong University, Xi' an 710049 (China)

    2017-05-15

    Highlights: • First time resolution of 57 pm atom separations by HRTEM with 200 keV electrons. • Quantification of the image spread by absolute matching of experiment and simulation. • An information limit of 52 pm is deduced from the determined image spread. • Substantial deviations from the bulk structure are observed for the ultra-thin sample. - Abstract: The application of combined chromatic and spherical aberration correction in high-resolution transmission electron microscopy enables a significant improvement of the spatial resolution down to 50 pm. We demonstrate that such a resolution can be achieved in practice at 200 kV. Diffractograms of images of gold nanoparticles on amorphous carbon demonstrate corresponding information transfer. The Y atom pairs in [010] oriented yttrium orthoaluminate are successfully imaged together with the Al and the O atoms. Although the 57 pm pair separation is well demonstrated separations between 55 pm and 80 pm are measured. This observation is tentatively attributed to structural relaxations and surface reconstruction in the very thin samples used. Quantification of the resolution limiting effective image spread is achieved based on an absolute match between experimental and simulated image intensity distributions.

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

    Directory of Open Access Journals (Sweden)

    Shane D. Trask

    2010-06-01

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

  17. Elemental mapping in achromatic atomic-resolution energy-filtered transmission electron microscopy.

    Science.gov (United States)

    Forbes, B D; Houben, L; Mayer, J; Dunin-Borkowski, R E; Allen, L J

    2014-12-01

    We present atomic-resolution energy-filtered transmission electron microscopy (EFTEM) images obtained with the chromatic-aberration-corrected FEI Titan PICO at the Ernst-Ruska Centre, Jülich, Germany. We find qualitative agreement between experiment and simulation for the background-subtracted EFTEM images of the Ti-L2,3 and O-K edges for a specimen of SrTiO3 oriented down the [110] zone axis. The simulations utilize the transition potential formulation for inelastic scattering, which permits a detailed investigation of contributions to the EFTEM image. We find that energy-filtered images of the Ti-L2,3 and O-K edges are lattice images and that the background-subtracted core-loss maps may not be directly interpretable as elemental maps. Simulations show that this is a result of preservation of elastic contrast, whereby the qualitative details of the image are determined primarily by elastic, coherent scattering. We show that this effect places a constraint on the range of specimen thicknesses which could theoretically yield directly useful elemental maps. In general, interpretation of EFTEM images is ideally accompanied by detailed simulations. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. High resolution gamma-ray spectroscopy and the fascinating angular momentum realm of the atomic nucleus

    Science.gov (United States)

    Riley, M. A.; Simpson, J.; Paul, E. S.

    2016-12-01

    In 1974 Aage Bohr and Ben Mottelson predicted the different ‘phases’ that may be expected in deformed nuclei as a function of increasing angular momentum and excitation energy all the way up to the fission limit. While admitting their picture was highly conjectural they confidently stated ‘...with the ingenious experimental approaches that are being developed, we may look forward with excitement to the detailed spectroscopic studies that will illuminate the behaviour of the spinning quantised nucleus’. High resolution gamma-ray spectroscopy has indeed been a major tool in studying the structure of atomic nuclei and has witnessed numerous significant advances over the last four decades. This article will select highlights from investigations at the Niels Bohr Institute, Denmark, and Daresbury Laboratory, UK, in the late 1970s and early 1980s, some of which have continued at other national laboratories in Europe and the USA to the present day. These studies illustrate the remarkable diversity of phenomena and symmetries exhibited by nuclei in the angular momentum-excitation energy plane that continue to surprise and fascinate scientists.

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

    Science.gov (United States)

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

    2017-08-01

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

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

    OpenAIRE

    Raji Heyrovska

    2011-01-01

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

  1. Compact Single Site Resolution Cold Atom Experiment for Adiabatic Quantum Computing

    Science.gov (United States)

    2016-02-03

    Specifically, we will design and construct a set of compact single atom traps with integrated optics, suitable for heralded entanglement and loophole...technical development is to achieve fast loading and qubit manipulation in the single- atom traps, which will enable our scientific investigation. The...goal of our scientific investigation is to demonstrate high fidelity and fast atom - atom entanglement between physically 1. REPORT DATE (DD-MM-YYYY) 4

  2. DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein.

    Science.gov (United States)

    Duan, Ming-Rui; Nan, Jie; Liang, Yu-He; Mao, Peng; Lu, Lu; Li, Lanfen; Wei, Chunhong; Lai, Luhua; Li, Yi; Su, Xiao-Dong

    2007-01-01

    WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be involved in the salicylic acid signaling pathway and partially dependent on NPR1; a C-terminal domain of WRKY1, AtWRKY1-C, was constructed for structural studies. Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs. The crystal structure of the AtWRKY1-C determined at 1.6 A resolution has revealed that this domain is composed of a globular structure with five beta strands, forming an antiparallel beta-sheet. A novel zinc-binding site is situated at one end of the beta-sheet, between strands beta4 and beta5. Based on this high-resolution crystal structure and site-directed mutagenesis, we have defined and confirmed that the DNA-binding residues of AtWRKY1-C are located at beta2 and beta3 strands. These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins.

  3. Investigations of the dynamics and growth of insulator films by high resolution helium atom scattering. Final report, May 1, 1985--April 30, 1997

    Energy Technology Data Exchange (ETDEWEB)

    Safron, S.A.; Skofronick, J.G.

    1997-07-01

    Over the twelve years of this grant from the U.S. Department of Energy, DE-FG05-85ER45208, the over-reaching aims of this work have been to explore and to attempt to understand the fundamental physics and chemistry of surfaces and interfaces. The instrument we have employed m in this work is high-resolution helium atom scattering (HAS) which we have become even more convinced is an exceptionally powerful and useful tool for surface science. One can follow the evolution of the development and progress of the experiments that we have carried out by the evolution of the proposal titles for each of the four three-year periods. At first, m in 1985-1988, the main objective of this grant was to construct the HAS instrument so that we could begin work on the surface vibrational dynamics of crystalline materials; the title was {open_quotes}Helium Atom-Surface Scattering Apparatus for Studies of Crystalline Surface Dynamics{close_quotes}. Then, as we became more interested m in the growth of films and interfaces the title m in 1988-1991 became {open_quotes}Helium Atom Surface Spectroscopy: Surface Lattice Dynamics of Insulators, Metal and Metal Overlayers{close_quotes}. In 1991-1994, we headed even more m in this direction, and also recognized that we should focus more on insulator materials as very few techniques other than helium atom scattering could be applied to insulators without causing surface damage. Thus, the proposal title became {open_quotes}Helium Atom-Surface Scattering: Surface Dynamics of Insulators, Overlayers and Crystal Growth{close_quotes}. M in the final period of this grant the title ended up {open_quotes}Investigations of the Dynamics and Growth of Insulator Films by High Resolution Helium Atom Scattering{close_quotes} m in 1994-1997. The list of accomplishments briefly discussed in this report are: tests of the shell model; multiphoton scattering; physisorbed monolayer films; other surface phase transitions; and surface magnetic effects.

  4. Upgrades of the high resolution imaging x-ray crystal spectrometers on experimental advanced superconducting tokamaka)

    Science.gov (United States)

    Lu, B.; Wang, F.; Shi, Y.; Bitter, M.; Hill, K. W.; Lee, S. G.; Fu, J.; Li, Y.; Wan, B.

    2012-10-01

    Two imaging x-ray crystal spectrometers, the so-called "poloidal" and "tangential" spectrometers, were recently implemented on experimental advanced superconducting tokamak (EAST) to provide spatially and temporally resolved impurity ion temperature (Ti), electron temperature (Te) and rotation velocity profiles. They are derived from Doppler width of W line for Ti, the intensity ratio of Li-like satellites to W line for Te, and Doppler shift of W line for rotation. Each spectrometer originally consisted of a spherically curved crystal and a two-dimensional multi-wire proportional counter (MWPC) detector. Both spectrometers have now been upgraded. The layout of the tangential spectrometer was modified, since it had to be moved to a different port, and the spectrometer was equipped with two high count rate Pilatus detectors (Model 100 K) to overcome the count rate limitation of the MWPC and to improve its time resolution. The poloidal spectrometer was equipped with two spherically bent crystals to record the spectra of He-like and H-like argon simultaneously and side by side on the original MWPC. These upgrades are described, and new results from the latest EAST experimental campaign are presented.

  5. Upgrades of the high resolution imaging x-ray crystal spectrometers on experimental advanced superconducting tokamak.

    Science.gov (United States)

    Lu, B; Wang, F; Shi, Y; Bitter, M; Hill, K W; Lee, S G; Fu, J; Li, Y; Wan, B

    2012-10-01

    Two imaging x-ray crystal spectrometers, the so-called "poloidal" and "tangential" spectrometers, were recently implemented on experimental advanced superconducting tokamak (EAST) to provide spatially and temporally resolved impurity ion temperature (T(i)), electron temperature (T(e)) and rotation velocity profiles. They are derived from Doppler width of W line for Ti, the intensity ratio of Li-like satellites to W line for Te, and Doppler shift of W line for rotation. Each spectrometer originally consisted of a spherically curved crystal and a two-dimensional multi-wire proportional counter (MWPC) detector. Both spectrometers have now been upgraded. The layout of the tangential spectrometer was modified, since it had to be moved to a different port, and the spectrometer was equipped with two high count rate Pilatus detectors (Model 100 K) to overcome the count rate limitation of the MWPC and to improve its time resolution. The poloidal spectrometer was equipped with two spherically bent crystals to record the spectra of He-like and H-like argon simultaneously and side by side on the original MWPC. These upgrades are described, and new results from the latest EAST experimental campaign are presented.

  6. Large Area Atomically Flat Surfaces via Exfoliation of Bulk Bi 2 Se 3 Single Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Melamed, Celeste L. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Colorado School of Mines, 1500; Ortiz, Brenden R. [Colorado School of Mines, 1500; Gorai, Prashun [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Colorado School of Mines, 1500; Martinez, Aaron D. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Colorado School of Mines, 1500; McMahon, William E. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Miller, Elisa M. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Stevanović, Vladan [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Colorado School of Mines, 1500; Tamboli, Adele C. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Norman, Andrew G. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Toberer, Eric S. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Colorado School of Mines, 1500

    2017-09-27

    In this work, we present an exfoliation method that produces cm2-area atomically flat surfaces from bulk layered single crystals, with broad applications such as for the formation of lateral heterostructures and for use as substrates for van der Waals epitaxy. Single crystals of Bi2Se3 were grown using the Bridgman method and examined with X-ray reciprocal space maps, Auger spectroscopy, low-energy electron diffraction, and X-ray photoelectron spectroscopy. An indium-bonding exfoliation technique was developed that produces multiple ~100 um thick atomically flat, macroscopic (>1 cm2) slabs from each Bi2Se3 source crystal. Two-dimensional X-ray diffraction and reciprocal space maps confirm the high crystalline quality of the exfoliated surfaces. Atomic force microscopy reveals that the exfoliated surfaces have an average root-mean-square (RMS) roughness of ~0.04 nm across 400 um2 scans and an average terrace width of 70 um between step edges. First-principles calculations reveal exfoliation energies of Bi2Se3 and a number of other layered compounds, which demonstrate relevance of our method across the field of 2D materials. While many potential applications exist, excellent lattice matching with the III-V alloy space suggests immediate potential for the use of these exfoliated layered materials as epitaxial substrates for photovoltaic development.

  7. High-magnification super-resolution FINCH microscopy using birefringent crystal lens interferometers

    Science.gov (United States)

    Siegel, Nisan; Lupashin, Vladimir; Storrie, Brian; Brooker, Gary

    2016-12-01

    Fresnel incoherent correlation holography (FINCH) microscopy is a promising approach for high-resolution biological imaging but has so far been limited to use with low-magnification, low-numerical-aperture configurations. We report the use of in-line incoherent interferometers made from uniaxial birefringent α-barium borate (α-BBO) or calcite crystals that overcome the aberrations and distortions present with previous implementations that employed spatial light modulators or gradient refractive index lenses. FINCH microscopy incorporating these birefringent elements and high-numerical-aperture oil immersion objectives could outperform standard wide-field fluorescence microscopy, with, for example, a 149 nm lateral point spread function at a wavelength of 590 nm. Enhanced resolution was confirmed with sub-resolution fluorescent beads. Taking the Golgi apparatus as a biological example, three different proteins labelled with GFP and two other fluorescent dyes in HeLa cells were resolved with an image quality that is comparable to similar samples captured by structured illumination microscopy.

  8. High-resolution Laue-type DuMond curved crystal spectrometer.

    Science.gov (United States)

    Szlachetko, M; Berset, M; Dousse, J-Cl; Hoszowska, J; Szlachetko, J

    2013-09-01

    We report on a high-resolution transmission-type curved crystal spectrometer based on the modified DuMond slit geometry. The spectrometer was developed at the University of Fribourg for the study of photoinduced X-ray spectra. K and L X-ray transitions with energies above about 10 keV can be measured with an instrumental resolution comparable to their natural linewidths. Construction details and operational characteristics of the spectrometer are presented. The variation of the energy resolution as a function of the focal distance and diffraction order is discussed. The high sensitivity of the spectrometer is demonstrated via the 2s-1s dipole-forbidden X-ray transition of Gd which could be observed despite its extremely low intensity. The precision of the instrument is illustrated by comparing the sum of the energies of the Au K-L2 and L2-M3 cascading transitions with the energy of the crossover K-M3 transition as well as by considering the energy differences of the Gd Kα1 X-ray line measured at five different diffraction orders. Finally, to demonstrate the versatility of the spectrometer, it is shown that the latter can also be used for in-house extended X-ray absorption fine structure measurements.

  9. Bulk Crystal Growth, and High-Resolution X-ray Diffraction Results of LiZnAs Semiconductor Material

    Science.gov (United States)

    Montag, Benjamin W.; Reichenberger, Michael A.; Sunder, Madhana; Ugorowski, Philip B.; Nelson, Kyle A.; Henson, Luke C.; McGregor, Douglas S.

    2017-08-01

    LiZnAs is being explored as a candidate for solid-state neutron detectors. The compact form, solid-state device would have greater efficiency than present day gas-filled 3He and 10BF3 detectors. Devices fabricated from LiZnAs having either natural Li (nominally 7.5% 6Li) or enriched 6Li (usually 95% 6Li) as constituent atoms may provide a material for compact high efficiency neutron detectors. The 6Li( n, t)4He reaction yields a total Q-value of 4.78 MeV, an energy larger than that of the 10B reaction, which can easily be identified above background radiations. LiZnAs material was synthesized by preparing equimolar portions of Li, Zn, and As sealed under vacuum (10-6 Torr) in quartz ampoules lined with boron nitride and subsequently reacted in a compounding furnace (Montag et al. in J Cryst Growth 412:103, 2015). The raw synthesized LiZnAs was purified by a static vacuum sublimation in quartz (Montag et al. in J Cryst Growth 438:99, 2016). Bulk crystalline LiZnAs ingots were grown from the purified material with a high-temperature Bridgman-style growth process described here. One of the largest LiZnAs ingots harvested was 9.6 mm in diameter and 4.2 mm in length. Samples were harvested from the ingot and were characterized for crystallinity using a Bruker AXS Inc. D8 AXS Inc. D2 CRYSO, energy dispersive x-ray diffractometer, and a Bruker AXS Inc. D8 DISCOVER, high-resolution x-ray diffractometer equipped with molybdenum radiation, Gobel mirror, four bounce germanium monochromator and a scintillation detector. The primary beam divergence was determined to be 0.004°, using a single crystal Si standard. The x-ray based characterization revealed that the samples nucleated in the (110) direction and a high-resolution open detector rocking curve recorded on the (220) LiZnAs yielded a full width at half maximum (FWHM) of 0.235°. Sectional pole figures using off-axis reflections of the (211) LiZnAs confirmed in-plane ordering, and also indicated the presence of multiple

  10. Observation of selective desorption of one-phonon inelastically scattered He atoms from a LiF crystal surface

    Science.gov (United States)

    Brusdeylins, G.; Doak, R. Bruce; Toennies, J. Peter

    1981-08-01

    Measurements of angular distributions for scattering of low energy (≊20 meV) monoenergetic (Δv/v = 0.8% FWHM) He beams from a LiF (001) crystal along the and directions and from a NaF (001) crystal along the direction reveal a large number of mostly small maxima and minima between the specular and diffraction peaks. Typical intensities of these features are about 10-3 of the specular peak. Time-of-flight spectra of the scattered atoms at the incident angles corresponding to the maxima reveal that the atoms were inelastically scattered by single phonons. From the known bound state energies for both systems He-LiF and He-NaF, we find that most of the maxima can be explained by a two step process in which the atoms are first elastically selectively adsorbed by diffraction into an in-plane bound state and then are subsequently desorbed as a result of a single phonon inelastic process. From the observed half-widths the lifetimes of atoms in the trapped states are found to depend on the vibrational quantum number and for the weakest bound state is as large as 60×10-12 sec. Evidence for minima involving selective adsorption into out-of-plane states is also presented.

  11. Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.

    Science.gov (United States)

    Malinska, Maura; Dauter, Zbigniew

    2016-06-01

    In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.

  12. Composition measurement in substitutionally disordered materials by atomic resolution energy dispersive X-ray spectroscopy in scanning transmission electron microscopy.

    Science.gov (United States)

    Chen, Z; Taplin, D J; Weyland, M; Allen, L J; Findlay, S D

    2017-05-01

    The increasing use of energy dispersive X-ray spectroscopy in atomic resolution scanning transmission electron microscopy invites the question of whether its success in precision composition determination at lower magnifications can be replicated in the atomic resolution regime. In this paper, we explore, through simulation, the prospects for composition measurement via the model system of AlxGa1-xAs, discussing the approximations used in the modelling, the variability in the signal due to changes in configuration at constant composition, and the ability to distinguish between different compositions. Results are presented in such a way that the number of X-ray counts, and thus the expected variation due to counting statistics, can be gauged for a range of operating conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. StatSTEM: An efficient program for accurate and precise model-based quantification of atomic resolution electron microscopy images

    Science.gov (United States)

    De Backer, A.; van den Bos, K. H. W.; Van den Broek, W.; Sijbers, J.; Van Aert, S.

    2017-09-01

    An efficient model-based estimation algorithm is introduced in order to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for the overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, is investigated. The highest attainable precision is reached even for low dose images. Furthermore, advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.

  14. Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

    Science.gov (United States)

    DiMaio, F; Chiu, W

    2016-01-01

    Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

  15. Lightweight and High-Resolution Single Crystal Silicon Optics for X-ray Astronomy

    Science.gov (United States)

    Zhang, William W.; Biskach, Michael P.; Chan, Kai-Wing; Mazzarella, James R.; McClelland, Ryan S.; Riveros, Raul E.; Saha, Timo T.; Solly, Peter M.

    2016-01-01

    We describe an approach to building mirror assemblies for next generation X-ray telescopes. It incorporates knowledge and lessons learned from building existing telescopes, including Chandra, XMM-Newton, Suzaku, and NuSTAR, as well as from our direct experience of the last 15 years developing mirror technology for the Constellation-X and International X-ray Observatory mission concepts. This approach combines single crystal silicon and precision polishing, thus has the potential of achieving the highest possible angular resolution with the least possible mass. Moreover, it is simple, consisting of several technical elements that can be developed independently in parallel. Lastly, it is highly amenable to mass production, therefore enabling the making of telescopes of very large photon collecting areas.

  16. Aberration production using a high-resolution liquid-crystal spatial light modulator.

    Science.gov (United States)

    Schmidt, Jason D; Goda, Matthew E; Duncan, Bradley D

    2007-05-01

    Phase-only liquid-crystal spatial light modulators provide a powerful means of wavefront control. With high resolution and diffractive (modulo 2pi) operation, they can accurately represent large-dynamic-range phase maps. As a result, they provide an excellent means of producing electrically controllable, dynamic, and repeatable aberrations. However, proper calibration is critical to achieving accurate phase maps. Several calibration methods from previous literature were considered. With simplicity and accuracy in mind, we selected one method for each type of necessary calibration. We augmented one of the selected methods with a new step that improves its accuracy. After calibrating our spatial light modulator with our preferred methods, we evaluated its ability to produce aberrations in the laboratory. We studied Zernike polynomial aberrations using interferometry and Fourier-transform-plane images, and atmospheric aberrations using a Shack-Hartmann wavefront sensor. These measurements show the closest agreement with theoretical expectations that we have seen to date.

  17. High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus.

    Science.gov (United States)

    Clifton, Matthew C; Bruhn, Jessica F; Atkins, Kateri; Webb, Terry L; Baydo, Ruth O; Raymond, Amy; Lorimer, Donald D; Edwards, Thomas E; Myler, Peter J; Saphire, Erica Ollmann

    2015-10-01

    Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. High-resolution magnetic field imaging with a nitrogen-vacancy diamond sensor integrated with a photonic-crystal fiber.

    Science.gov (United States)

    Fedotov, I V; Blakley, S M; Serebryannikov, E E; Hemmer, P; Scully, M O; Zheltikov, A M

    2016-02-01

    We demonstrate high-resolution magnetic field imaging with a scanning fiber-optic probe which couples nitrogen-vacancy (NV) centers in diamond to a high-numerical-aperture photonic-crystal fiber integrated with a two-wire microwave transmission line. Magnetic resonance excitation of NV centers driven by the microwave field is read out through optical interrogation through the photonic-crystal fiber to enable high-speed, high-sensitivity magnetic field imaging with sub 30 μm spatial resolution.

  19. Hybrid Young interferometer for high resolution measurement of dynamic speckle using high birefringence liquid crystal

    Science.gov (United States)

    Bennis, N.; Holdynski, Z.; Merta, I.; Marc, P.; Kula, P.; Mazur, R.; Piecek, W.; Jaroszewicz, L. R.

    2015-08-01

    It is well known that the Young interference experiment is the fundamental setup to combine two beams and to construct the phase modulated light. Moreover, homodyne phase demodulator is based on signal decoding in back Fourier focal plane using bicell photodetector (B-PD). On the above base, we propose a novel experimental approach to the signals demodulation by using the optical interferometer which operates in homodyne mode, combined with liquid crystal spatial light modulators operating both phase as speckle modulator. Dynamic phase changes between the two beams can be controlled by monopixel liquid crystals cell placed in one branch of the interferometer. A phase modulation effect in a signal arm of interferometer is observed as a dynamic shift of the speckle pattern. Simple arithmetic combination of signals from B-PD placed in speckle pattern plane is only one necessary numerical manipulation to obtain exactly phase difference. Concept of signals demodulation in the Fourier focal plane can be only used for exactly defined geometrical (B-PD as well as Young interferometer) and physical parameters (polarization, wavelength). We optimize the setup geometry to obtain extremely high measurement resolution. In this paper we focus on the principles of operation of each part of the system as well as discussion their requirement in order to increase the signal to noise ratio.

  20. High-resolution continuum source electrothermal atomic absorption spectrometry - An analytical and diagnostic tool for trace analysis

    Energy Technology Data Exchange (ETDEWEB)

    Welz, Bernhard [Instituto de Quimica, Departamento de Quimica Analitica, Universidade Federal da Bahia, Campus Universitario de Ondina, 40170-290 Salvador - BA (Brazil); Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis - SC (Brazil)], E-mail: w.bernardo@terra.com.br; Borges, Daniel L.G.; Lepri, Fabio G. [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis - SC (Brazil); Vale, Maria Goreti R. [Instituto de Quimica, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves 9500, 91501-970 Porto Alegre - RS (Brazil); Heitmann, Uwe [ISAS - Institute for Analytical Sciences, Department of Interface Spectroscopy, Albert-Einstein-Str. 9, 12489 Berlin (Germany)

    2007-09-15

    The literature about applications of high-resolution continuum source atomic absorption spectrometry (HR-CS AAS) with electrothermal atomization is reviewed. The historic development of HR-CS AAS is briefly summarized and the main advantages of this technique, mainly the 'visibility' of the spectral environment around the analytical line at high resolution and the unequaled simultaneous background correction are discussed. Simultaneous multielement CS AAS has been realized only in a very limited number of cases. The direct analysis of solid samples appears to have gained a lot from the special features of HR-CS AAS, and the examples from the literature suggest that calibration can be carried out against aqueous standards. Low-temperature losses of nickel and vanadyl porphyrins could be detected and avoided in the analysis of crude oil due to the superior background correction system. The visibility of the spectral environment around the analytical line revealed that the absorbance signal measured for phosphorus at the 213.6 nm non-resonance line without a modifier is mostly due to the PO molecule, and not to atomic phosphorus. The future possibility to apply high-resolution continuum source molecular absorption for the determination of non-metals is discussed.

  1. Solution of the phase problem at non-atomic resolution by the phantom derivative method.

    Science.gov (United States)

    Giacovazzo, Carmelo

    2015-09-01

    For a given unknown crystal structure (the target), n random structures, arbitrarily designed without any care for their chemical consistency and usually uncorrelated with the target, are sheltered in the same unit cell as the target structure and submitted to the same space-group symmetry. (These are called ancil structures.) The composite structures, whose electron densities are the sum of the target and of the ancil electron densities, are denoted derivatives. No observed diffraction amplitudes are available for them: in order to emphasize their unreal nature, the term phantom is added. The paper describes the theoretical basis by which the phantom derivative method may be used to phase the target structure. It may be guessed that 100-300 ancil structures may be sufficient for phasing a target structure, so that the phasing technique may be denoted as the multiple phantom derivative method. Ancil phases and amplitudes may be initially combined with observed target magnitudes to estimate amplitudes and phases of the corresponding phantom derivative. From them suitable algorithms allow one to obtain poor target phase estimates, which are often improved by combining the indications arising from each derivative. Probabilistic criteria are described to recognize the most reliable target phase estimates. The method is cyclic: the target phase estimates just obtained are used to improve amplitudes and phases of each derivative, which, in their turn, are employed to provide better target phase estimates. The method is a fully ab initio method, because it needs only the experimental data of the target structure. The term derivative is maintained with reference to SIR-MIR (single isomorphous replacement-multiple isomorphous replacement) techniques, even if its meaning is different: therefore the reader should think of the phantom derivative method more as a new method than as a variant of SIR-MIR techniques. The differences are much greater than the analogies. The paper

  2. High Resolution X-ray Characterization Of Mosaic Crystals For Hard X- And Gamma-ray Astronomy

    Science.gov (United States)

    Marchini, L.; Ferrari, C.; Buffagni, E.; Zappettini, A.

    2011-09-01

    For hard X-ray astronomy in the 70-1000 keV energy range Laue lenses have been proposed where the focusing elements are made of single mosaic crystals, in order to increase the diffraction efficiency with respect to perfect crystals. Suitable crystals to be used for such application should have a sufficient density to increase the diffraction efficiency and a mosaicity ranging between 30 arcsec and 1-2 arcmin, depending on the lens focusing distance and resolution. In the past germanium and copper crystals, often employed as monochromators for neutrons, have been considered. In this work we propose several crystalline materials of different degree of crystal perfection such as GaAs, Cu, CdTe, and CdZnTe as possible mosaic crystals for hard X-ray astronomy. They were analyzed by high resolution X-ray diffraction at 8 keV and by diffraction at energies up to 700 keV at synchrotron. It was found that: CdTe and CdZnTe crystals exhibit low angle grain boundaries preventing the formation of a single diffracted X-ray beam; Cu crystals exhibit mosaicity of the order of several arcmin, however a deep etching is needed to remove the cutting damage; GaAs crystals grown by LEC method show mosaicity between 15 and 30 arcsec and good diffraction efficiency up to energies of 700 keV. Annealing and surface damage were considered as possible methods to increase the GaAs crystal mosaicity.

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

    Directory of Open Access Journals (Sweden)

    Akihiko Nakatsuka

    2015-09-01

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

  4. Comment on "Atomic force microscopy characterization of stable faces in cubic C60 single crystals": possible evidence for growth-promoting cross-twinning

    NARCIS (Netherlands)

    van de Waal, B.W.

    1994-01-01

    An explanation is given for a molecular arrangement on a face of a C60 fcc single crystal as observed recently with atomic force microscopy (B. Keita et al., Chem. Phys. 179 (1994) 595). The explanation relies on a cross-twinning model of fcc crystal growth, and involves local fivefold symmetry.

  5. Visualization of drug-nucleic acid interactions at atomic resolution. VIII. Structures of two ethidium/dinucleoside monophosphate crystalline complexes containing ethidium: cytidylyl(3'-5') guanosine

    Energy Technology Data Exchange (ETDEWEB)

    Jain, S.C.; Sobell, H.M.

    1984-01-01

    This paper describes two complexes containing ethidium and the dinucleoside monophosphate, cytidylyl(3'-5')guanosine (CpG). Both crystals are monoclinic, space group P2/sub 1/, with unit cell dimensions as follows: modification 1: a = 13.64 A, b = 32.16 A, c = 14.93 A, ..beta.. = 114.8/sup 0/ and modification 2: a = 13.79 A, b = 31.94 A, c = 15.66 A, ..beta.. = 117.5 /sup 0/. Each structure has been solved to atomic resolution and refined by Fourier and least squares methods; the first has been refined to a residual of 0.187 on 1903 reflections, while the second has been refined to a residual of 0.187 on 1001 reflections. The asymmetric unit in both structures contains two ethidium molecules and two CpG molecules; the first structure has 30 water molecules (a total of 158 non-hydrogen atoms), while the second structure has 19 water molecules (a total of 147 non-hydrogen atoms). Both structures demonstrate intercalation of ethidium between base-paired CpG dimers. In addition, ethidium molecules stack on either side of the intercalated duplex, being related by a unit cell translation along the a axis. The basic feature of the sugar-phosphate chains accompanying ethidium intercalation in both structures is: C3' endo (3'-5') C2' endo. This mixed sugar-puckering pattern has been observed in all previous studies of ethidium intercalation and is a feature common to other drug-nucleic acid structural studies carried out in the authors laboratory. The authors discussed this further in this paper and in the accompanying papers.

  6. Visualization of drug-nucleic acid interactions at atomic resolution. VII. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: uridylyl(3'-5')adenosine

    Energy Technology Data Exchange (ETDEWEB)

    Jain, S.C.; Sobell, H.M.

    1984-01-01

    Ethidium forms a crystalline complex with the dinucleoside monophosphate, uridylyl (3'-5') adenosine (UpA). The complex crystallizes in the monoclinic space group P2/sub 1/ with unit cell dimensions, a = 13.704 A, b = 31.674 A, c = 15.131 A, ..beta.. = 113.8/sup 0/. This light atom structure has been solved to atomic resolution and refined by full matrix least squares to a residual of 0.12, using 3034 observed reflections. The asymmetric unit consists of two ethidium molecules, two UpA molecules and 19 solvent molecules, a total of 145 non-hydrogen atoms. The two UPa molecules are hydrogen-bonded together by Watson-Crick base pairing. Base-pairs in this duplex are separated by 6.7 A; this reflects intercalative binding by one of the ethidium molecules. The other ethidium molecule stacks on either side of the intercalated base-paired dinucleoside monophosphate, being related by a unit cell translation along the a axis. The conformation of the sugar-phosphate backbone accompanying intercalation has been accurately determined in this analysis, and contains the mixed sugar-puckering pattern: C3' endo (3'-5') C2' endo. This same structural feature has been observed in the ethidium-iodoUpA and ethidium-iodoCpG complexes, and exists in two additional structures containing ethidium-CpG. Taken together, these studies confirm the authors earlier sugar-puckering assignments and demonstrate that iodine covalently bound to the C5 position on uridine or cytosine does not alter the basic sugar-phosphate geometry or the mode of ethidium intercalation in these model studies. The authors have proposed this stereochemistry to explain the intercalation of ethidium into both DNA and into double-helical RNA. 15 references, 10 figures, 2 tables.

  7. Protein Crystallization

    Science.gov (United States)

    Chernov, Alexander A.

    2005-01-01

    Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

  8. Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution

    DEFF Research Database (Denmark)

    Niefind, K; Guerra, B; Pinna, L A

    1998-01-01

    CK2alpha is the catalytic subunit of protein kinase CK2, an acidophilic and constitutively active eukaryotic Ser/Thr kinase involved in cell proliferation. A crystal structure, at 2.1 A resolution, of recombinant maize CK2alpha (rmCK2alpha) in the presence of ATP and Mg2+, shows the enzyme in an ...

  9. Crystal structure of recombinant tyrosinase-binding protein MtaL at 1.35 Å resolution

    NARCIS (Netherlands)

    Lai, X.; Soler-Lopez, M.; Ismaya, W.T.; Wichers, H.J.; Dijkstra, B.W.

    2016-01-01

    Mushroom tyrosinase-associated lectin-like protein (MtaL) binds to mature Agaricus bisporus tyrosinase in vivo, but the exact physiological function of MtaL is unknown. In this study, the crystal structure of recombinant MtaL is reported at 1.35 Å resolution. Comparison of its structure with that of

  10. Atomic scale study of surface orientations and energies of Ti 2 O 3 crystals

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Meng [Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen, Guangdong 518055, China; Wang, Zhiguo [School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu 610054, People' s Republic of China; Wang, Chongmin [Environmental Molecular Science Laboratory, 902 Battelle Boulevard, Richland, Washington 99352, USA; Zheng, Jianming [Energy and Environmental Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352, USA

    2017-10-30

    For nanostructured particles, the faceting planes and their terminating chemical species are two critical factors that govern the chemical behavior of the particle. The surface atomistic structure and termination of the Ti2O3 crystals were analyzed using atomic-scale aberration-corrected scanning transmission electron microscopy (STEM) combining with density functional theory (DFT) calculations. STEM imaging reveals that the Ti2O3 crystal are most often faceted along (001), (012), (-114) and (1-20) planes. DFT calculation indicates that the (012) surface with TiO-termination have the lowest cleavage energy and correspondingly the lowest surface energy, indicating that (012) will be the most stable and prevalent surfaces in Ti2O3 nanocrystals. These observations provide insights for exploring the interfacial process involving Ti2O3 nanoparticles.

  11. A new 28Si single crystal: counting the atoms for the new kilogram definition

    Science.gov (United States)

    Bartl, G.; Becker, P.; Beckhoff, B.; Bettin, H.; Beyer, E.; Borys, M.; Busch, I.; Cibik, L.; D'Agostino, G.; Darlatt, E.; Di Luzio, M.; Fujii, K.; Fujimoto, H.; Fujita, K.; Kolbe, M.; Krumrey, M.; Kuramoto, N.; Massa, E.; Mecke, M.; Mizushima, S.; Müller, M.; Narukawa, T.; Nicolaus, A.; Pramann, A.; Rauch, D.; Rienitz, O.; Sasso, C. P.; Stopic, A.; Stosch, R.; Waseda, A.; Wundrack, S.; Zhang, L.; Zhang, X. W.

    2017-10-01

    A new single crystal from isotopically enriched silicon was used to determine the Avogadro constant N A by the x-ray-crystal density method. The new crystal, named Si28-23Pr11, has a higher enrichment than the former ‘AVO28’ crystal allowing a smaller uncertainty of the molar mass determination. Again, two 1 kg spheres were manufactured from this crystal. The crystal and the spheres were measured with improved and new methods. One sphere, Si28kg01a, was measured at NMIJ and PTB with very consistent results. The other sphere, Si28kg01b, was measured only at PTB and yielded nearly the same Avogadro constant value. The mean result for both 1 kg spheres is N A  =  6.022 140 526(70)  ×  1023 mol-1 with a relative standard uncertainty of 1.2  ×  10-8. This value deviates from the Avogadro value published in 2015 for the AVO28 crystal by about 3.9(2.1)  ×  10-8. Possible reasons for this difference are discussed and additional measurements are proposed.

  12. The study on the nanomachining property and cutting model of single-crystal sapphire by atomic force microscopy.

    Science.gov (United States)

    Huang, Jen-Ching; Weng, Yung-Jin

    2014-01-01

    This study focused on the nanomachining property and cutting model of single-crystal sapphire during nanomachining. The coated diamond probe is used to as a tool, and the atomic force microscopy (AFM) is as an experimental platform for nanomachining. To understand the effect of normal force on single-crystal sapphire machining, this study tested nano-line machining and nano-rectangular pattern machining at different normal force. In nano-line machining test, the experimental results showed that the normal force increased, the groove depth from nano-line machining also increased. And the trend is logarithmic type. In nano-rectangular pattern machining test, it is found when the normal force increases, the groove depth also increased, but rather the accumulation of small chips. This paper combined the blew by air blower, the cleaning by ultrasonic cleaning machine and using contact mode probe to scan the surface topology after nanomaching, and proposed the "criterion of nanomachining cutting model," in order to determine the cutting model of single-crystal sapphire in the nanomachining is ductile regime cutting model or brittle regime cutting model. After analysis, the single-crystal sapphire substrate is processed in small normal force during nano-linear machining; its cutting modes are ductile regime cutting model. In the nano-rectangular pattern machining, due to the impact of machined zones overlap, the cutting mode is converted into a brittle regime cutting model. © 2014 Wiley Periodicals, Inc.

  13. Atomic resolution elemental mapping using energy-filtered imaging scanning transmission electron microscopy with chromatic aberration correction.

    Science.gov (United States)

    Krause, F F; Rosenauer, A; Barthel, J; Mayer, J; Urban, K; Dunin-Borkowski, R E; Brown, H G; Forbes, B D; Allen, L J

    2017-10-01

    This paper addresses a novel approach to atomic resolution elemental mapping, demonstrating a method that produces elemental maps with a similar resolution to the established method of electron energy-loss spectroscopy in scanning transmission electron microscopy. Dubbed energy-filtered imaging scanning transmission electron microscopy (EFISTEM) this mode of imaging is, by the quantum mechanical principle of reciprocity, equivalent to tilting the probe in energy-filtered transmission electron microscopy (EFTEM) through a cone and incoherently averaging the results. In this paper we present a proof-of-principle EFISTEM experimental study on strontium titanate. The present approach, made possible by chromatic aberration correction, has the advantage that it provides elemental maps which are immune to spatial incoherence in the electron source, coherent aberrations in the probe-forming lens and probe jitter. The veracity of the experiment is supported by quantum mechanical image simulations, which provide an insight into the image-forming process. Elemental maps obtained in EFTEM suffer from the effect known as preservation of elastic contrast, which, for example, can lead to a given atomic species appearing to be in atomic columns where it is not to be found. EFISTEM very substantially reduces the preservation of elastic contrast and yields images which show stability of contrast with changing thickness. The experimental application is demonstrated in a proof-of-principle study on strontium titanate. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Robust High-Resolution Imaging and Quantitative Force Spectroscopy in Vacuum with Tuned-Oscillator Atomic Force Microscopy.

    Science.gov (United States)

    Schwarz, Udo; Dagdeviren, Omur; GöTzen, Jan; HöLscher, Hendrik; Altman, Eric

    Atomic force microscopy and spectroscopy are based on locally detecting the interactions between a surface and a sharp probe tip. For highest resolution imaging, noncontact modes that avoid tip-sample contact are used; control of the tip's vertical position is accomplished by oscillating the tip and detecting perturbations induced by its interaction with the surface potential. Due to this potential's nonlinear nature, however, achieving reliable control of the tip-sample distance is challenging, so much so that despite its power vacuum-based noncontact atomic force microscopy has remained a niche technique. Here we introduce a new pathway to distance control that prevents instabilities by externally tuning the oscillator's response characteristics. A major advantage of this operational scheme is that it delivers robust position control in both the attractive and repulsive regimes with only one feedback loop, thereby providing an easy-to-implement route to atomic resolution imaging and quantitative tip-sample interaction force measurement. Financial support from National Science Foundation through the Yale Materials Research Science and Engineering Center (Grant No. MRSEC DMR-1119826) is gratefully acknowledged.

  15. Atomic mechanism for the growth of wafer-scale single-crystal graphene: theoretical perspective and scanning tunneling microscopy investigations

    Science.gov (United States)

    Niu, Tianchao; Zhang, Jialin; Chen, Wei

    2017-12-01

    Chemical vapor deposition (CVD) is the most promising approach for producing low-cost, high-quality, and large area graphene. Revealing the graphene growth mechanism at the atomic-scale is of great importance for realizing single crystal graphene (SCG) over wafer scale. Density functional theoretical (DFT) calculations are playing an increasingly important role in revealing the structure of the most stable carbon species, understanding the evolution processes, and disclosing the active sites. Scanning tunneling microscopy (STM) is a powerful surface characterization tool to illustrate the real space distribution and atomic structures of growth intermediates during the CVD process. Combining them together can provide valuable information to improve the atomically controlled growth of SCG. Starting from a basic concept of the substrate effect on realizing SCG, this review covers the progress made in theoretical investigations on various carbon species during graphene growth on different transition metal substrates, in the STM study of the structural intermediates on transition metal surfaces, and in synthesizing graphene nanoribbons with atomic-precise width and edge structure, ending with a perspective on the future development of 2D materials beyond graphene.

  16. Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

    KAUST Repository

    Zhu, Yihan

    2012-08-28

    The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex inhomogeneities. Here, we report an atomic structure study of an important MoVTeO complex metal oxide catalyst that is potentially useful for the industrially relevant propane-based BP/SOHIO process. We combined aberration-corrected scanning transmission electron microscopy with synchrotron powder X-ray crystallography to explore the structure at both nanoscopic and macroscopic scales. At the nanoscopic scale, this material exhibits structural and compositional order within nanosized "domains", while the domains show disordered distribution at the macroscopic scale. We proposed that the intradomain compositional ordering and the interdomain electric dipolar interaction synergistically induce the displacement of Te atoms in the Mo-V-O channels, which determines the geometry of the multifunctional metal oxo-active sites.

  17. Imaging screw dislocations at atomic resolution by aberration-corrected electron optical sectioning.

    Science.gov (United States)

    Yang, H; Lozano, J G; Pennycook, T J; Jones, L; Hirsch, P B; Nellist, P D

    2015-06-04

    Screw dislocations play an important role in materials' mechanical, electrical and optical properties. However, imaging the atomic displacements in screw dislocations remains challenging. Although advanced electron microscopy techniques have allowed atomic-scale characterization of edge dislocations from the conventional end-on view, for screw dislocations, the atoms are predominantly displaced parallel to the dislocation line, and therefore the screw displacements are parallel to the electron beam and become invisible when viewed end-on. Here we show that screw displacements can be imaged directly with the dislocation lying in a plane transverse to the electron beam by optical sectioning using annular dark field imaging in a scanning transmission electron microscope. Applying this technique to a mixed [a+c] dislocation in GaN allows direct imaging of a screw dissociation with a 1.65-nm dissociation distance, thereby demonstrating a new method for characterizing dislocation core structures.

  18. THE CRYSTAL UNIVERSE?... (A New theory on “Atom and element”)

    OpenAIRE

    M.Arulmani; V.R.Hema Latha

    2014-01-01

    A Scientific research in this article focus that the “Material Universe” which accommodates Various Planets, Comets, Asteroids, life organisms shall be considered as “SINGLE CRYSTAL HOUSE” deriving soul from “WHITE ELEMENT” (or) “WHITE IONS” and free from “ATOM”. It is focused that “BLACK CRYSTAL” shall be considered as the absolutely perfect body exist in the early Universe and material Universe shall be considered as the integral part of black crystal.

  19. Polymeric spatial resolution test patterns for mass spectrometry imaging using nano-thermal analysis with atomic force microscopy.

    Science.gov (United States)

    Tai, Tamin; Kertesz, Vilmos; Lin, Ming-Wei; Srijanto, Bernadeta R; Hensley, Dale K; Xiao, Kai; Van Berkel, Gary J

    2017-07-30

    As the spatial resolution of mass spectrometry imaging technologies has begun to reach into the nanometer regime, finding readily available or easily made resolution reference materials has become particularly challenging for molecular imaging purposes. This paper describes the fabrication, characterization and use of vertical line array polymeric spatial resolution test patterns for nano-thermal analysis/atomic force microscopy/mass spectrometry chemical imaging. Test patterns of varied line width (0.7 or 1.0 μm) and spacing (0.7 or 1.0 μm) were created in an ~1-μm-thick poly(methyl methacrylate) thin film using electron beam lithography. The patterns were characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy, atomic force microscopy topography and nano-thermal analysis/mass spectrometry imaging. The efficacy of these polymeric test patterns for the advancement of chemical imaging techniques was illustrated by their use to judge the spatial resolution improvement achieved by heating the ionization interface of the current instrument platform. The spatial resolution of the mass spectral chemical images was estimated to be 1.4 μm, based on the ability to statistically distinguish 0.7-μm-wide lines separated by 0.7-μm-wide spacings in those images when the interface cross was heated to 200°C. This work illustrates that e-beam lithography is a viable method to create spatial resolution test patterns in a thin film of high molecular weight polymer to allow unbiased judgment of intra-laboratory advancement and/or inter-laboratory comparison of instrument advances in nano-thermal analysis/atomic force microscopy/mass spectrometry chemical imaging. Published in 2017. This article is a U.S. Government work and is in the public domain in the USA. Published in 2017. This article is a U.S. Government work and is in the public domain in the USA.

  20. Compositional Analysis With Atomic Column Spatial Resolution by 5th Order Aberration-corrected Scanning Transmission Electron Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez-Maldonado, David [Universidad de Cadiz, Spain; Herrera, Miriam [Universidad de Cadiz, Spain; Alonso-Gonzalez, Pablo [Instituto de Microelectronica de Madrid (CNM, CSIC); Gonzalez, Yolanda [Instituto de Microelectronica de Madrid (CNM, CSIC); Gonzalez, Luisa [Instituto de Microelectronica de Madrid (CNM, CSIC); Gazquez Alabart, Jaume [ORNL; Varela del Arco, Maria [ORNL; Pennycook, Stephen J [ORNL; Guerrero, M. P. [Universidad de Cadiz, Spain; Pizarro, Joaquin [Universidad de Cadiz, Spain; Galindo, Pedro [Universidad de Cadiz, Spain; Molina, S. I. [Universidad de Cadiz, Spain

    2011-01-01

    We show in this article that it is possible to obtain elemental compositional maps and profiles with atomic-column resolution across an In{sub x}Ga{sub 1-x}As multilayer structure from 5th-order aberration-corrected high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) images. The compositional profiles obtained from the analysis of HAADF-STEM images describe accurately the distribution of In in the studied multilayer in good agreement with Muraki's segregation model [Muraki, K., Fukatsu, S., Shiraki, Y. & Ito, R. (1992)]. Surface segregation of In atoms during molecular beam epitaxy and its influence on the energy levels in InGaAs/GaAs quantums wells.

  1. About vortex-like atomic motion in a loaded single crystal

    Science.gov (United States)

    Dmitriev, A. I.; Nikonov, A. Yu.

    2017-12-01

    The paper presents a molecular dynamics study of internal stress and atomic displacement redistributions in a preliminary loaded solid. The study demonstrates the possibility of self-organized vortices as dynamic defects of typical size 1-5 nm due to atomic motion in the elastic region at the stage of relaxation. The simulation results agree well with experimental data on strain localization in elastic distortion regions which gives rise to nanodipoles of partial disclinations.

  2. Atomic-resolution imaging in liquid by frequency modulation atomic force microscopy using small cantilevers with megahertz-order resonance frequencies.

    Science.gov (United States)

    Fukuma, T; Onishi, K; Kobayashi, N; Matsuki, A; Asakawa, H

    2012-04-06

    In this study, we have investigated the performance of liquid-environment FM-AFM with various cantilevers having different dimensions from theoretical and experimental aspects. The results show that reduction of the cantilever dimensions provides improvement in the minimum detectable force as long as the tip height is sufficiently long compared with the width of the cantilever. However, we also found two important issues to be overcome to achieve this theoretically expected performance. The stable photothermal excitation of a small cantilever requires much higher pointing stability of the exciting laser beam than that for a long cantilever. We present a way to satisfy this stringent requirement using a temperature controlled laser diode module and a polarization-maintaining optical fiber. Another issue is associated with the tip. While a small carbon tip formed by electron beam deposition (EBD) is desirable for small cantilevers, we found that an EBD tip is not suitable for atomic-scale applications due to the weak tip-sample interaction. Here we show that the tip-sample interaction can be greatly enhanced by coating the tip with Si. With these improvements, we demonstrate atomic-resolution imaging of mica in liquid using a small cantilever with a megahertz-order resonance frequency. In addition, we experimentally demonstrate the improvement in the minimum detectable force obtained by the small cantilever in measurements of oscillatory hydration forces.

  3. Viscoelasticity of Living Cells Allows High Resolution Imaging by Tapping Mode Atomic Force Microscopy

    NARCIS (Netherlands)

    Putman, C.A.J.; Putman, Constant A.J.; van der Werf, Kees; de Grooth, B.G.; van Hulst, N.F.; Greve, Jan

    1994-01-01

    Application of atomic force microscopy (AFM) to biological objects and processes under physiological conditions has been hampered so far by the deformation and destruction of the soft biological materials invoked. Here we describe a new mode of operation in which the standard V-shaped silicon

  4. Atomic resolution imaging of precipitate transformation from cubic TaN to tetragonal CrTaN

    DEFF Research Database (Denmark)

    Danielsen, Hilmar Kjartansson; Hald, John; Somers, Marcel A. J.

    2012-01-01

    In 9–12% Cr creep-resistant steels Cr(V,Nb,Ta)N Z-phase is known to replace metastable (V,Nb,Ta)N MN precipitates at high temperatures. The precipitation process of Z-phase does not follow the classical nucleation theory, where dissolving MN particles provide constituents for Z-phase nucleation...... in the matrix. Using atomic resolution transmission electron microscopy, the current work demonstrates that metastable cubic TaN precipitates in a complex steel gradually transform compositionally and crystallographically into stable tetragonal CrTaN precipitates under the influence of Cr indiffusion from...... the steel matrix....

  5. Analytical calculation of the lower bound on timing resolution for PET scintillation detectors comprising high-aspect-ratio crystal elements

    Science.gov (United States)

    Cates, Joshua W.; Vinke, Ruud; Levin, Craig S.

    2015-07-01

    Excellent timing resolution is required to enhance the signal-to-noise ratio (SNR) gain available from the incorporation of time-of-flight (ToF) information in image reconstruction for positron emission tomography (PET). As the detector’s timing resolution improves, so does SNR, reconstructed image quality, and accuracy. This directly impacts the challenging detection and quantification tasks in the clinic. The recognition of these benefits has spurred efforts within the molecular imaging community to determine to what extent the timing resolution of scintillation detectors can be improved and develop near-term solutions for advancing ToF-PET. Presented in this work, is a method for calculating the Cramér-Rao lower bound (CRLB) on timing resolution for scintillation detectors with long crystal elements, where the influence of the variation in optical path length of scintillation light on achievable timing resolution is non-negligible. The presented formalism incorporates an accurate, analytical probability density function (PDF) of optical transit time within the crystal to obtain a purely mathematical expression of the CRLB with high-aspect-ratio (HAR) scintillation detectors. This approach enables the statistical limit on timing resolution performance to be analytically expressed for clinically-relevant PET scintillation detectors without requiring Monte Carlo simulation-generated photon transport time distributions. The analytically calculated optical transport PDF was compared with detailed light transport simulations, and excellent agreement was found between the two. The coincidence timing resolution (CTR) between two 3× 3× 20 mm3 LYSO:Ce crystals coupled to analogue SiPMs was experimentally measured to be 162+/- 1 ps FWHM, approaching the analytically calculated lower bound within 6.5%.

  6. High-Resolution Imaging of Polyethylene Glycol Coated Dendrimers via Combined Atomic Force and Scanning Tunneling Microscopy

    Directory of Open Access Journals (Sweden)

    Shawn Riechers

    2015-01-01

    Full Text Available Dendrimers have shown great promise as drug delivery vehicles in recent years because they can be synthesized with designed size and functionalities for optimal transportation, targeting, and biocompatibility. One of the most well-known termini used for biocompatibility is polyethylene glycol (PEG, whose performance is affected by its actual conformation. However, the conformation of individual PEG bound to soft materials such as dendrimers has not been directly observed. Using atomic force microscopy (AFM and scanning tunneling microscopy (STM, this work characterizes the structure adopted by PEGylated dendrimers with the highest resolution reported to date. AFM imaging enables visualization of the individual dendrimers, as well as the differentiation and characterization of the dendrimer core and PEG shell. STM provides direct imaging of the PEG extensions with high-resolution. Collectively, this investigation provides important insight into the structure of coated dendrimers, which is crucial for the design and development of better drug delivery vehicles.

  7. The limit of time resolution in frequency modulation atomic force microscopy by a pump-probe approach

    Science.gov (United States)

    Schumacher, Zeno; Spielhofer, Andreas; Miyahara, Yoichi; Grutter, Peter

    2017-01-01

    Atomic force microscopy (AFM) routinely achieves structural information in the sub-nm length scale. Measuring time resolved properties on this length scale to understand kinetics at the nm scale remains an elusive goal. We present a general analysis of the lower limit for time resolution in AFM. Our finding suggests that the time resolution in AFM is ultimately limited by the well-known thermal limit of AFM and not as often proposed by the mechanical response time of the force sensing cantilever. We demonstrate a general pump-probe approach using the cantilever as a detector responding to the averaged signal. This method can be applied to any excitation signal such as electrical, thermal, magnetic or optical. Experimental implementation of this method allows us to measure a photocarrier decay time of ˜1 ps in low temperature grown GaAs using a cantilever with a resonant frequency of 280 kHz.

  8. Improving the intrinsic spatial resolution performance of the continuous miniature crystal element (cMiCE) detector.

    Science.gov (United States)

    Ling, Tao; Lewellen, Tom K; Miyaoka, Robert S

    2007-10-26

    We have previously reported performance characteristics of a cMiCE detector composed of a 50 mm by 50 mm by 8 mm thick slab of LYSO, coupled to a 64 channel flat-panel PMT. In that work, all 64 PMT channels were digitized and a statistics-based positioning method was used for event positioning. In characterizing the detector, the intrinsic spatial resolution performance for the corner sections of the crystal was degraded compared to the central section of the crystal, even when using our SBP method. It is our belief that the poorer positioning performance at the corners is because much of the light is lost (i.e., not collected by our PMT). To offset this problem, we propose to place light sensors (i.e., micro-pixel avalanche photo diodes, MAPD) at the corners along the short edge of the crystal. The new design would require an additional 8 MAPD devices. Monte Carlo simulation was used to compare the performance of the original cMiCE design and this new enhanced design. Simulation results using DETECT2000 are presented. In addition to doing light ray tracing, GEANT was used to track gamma interactions (i.e., Compton scatter and photoelectric absorption) in the crystal. Thus the simulations include the effects of Compton scatter in the detector. Results indicate that adding the sensors improves the intrinsic spatial resolution performance from 0.99 mm FWHM to 0.79 mm FWHM for the corner section of the crystal, thereby nearly matching the intrinsic spatial resolution of the center section of the crystal (i.e., 0.73 mm FWHM). These results are based upon using dual-DOI look up tables. Additional results were that energy histograms were better using just the 64 channels from the flat panel PMT than using all 72 signal channels.

  9. Atomic-Resolution Transmission Electron Microscopic Movies for Study of Organic Molecules, Assemblies, and Reactions: The First 10 Years of Development.

    Science.gov (United States)

    Nakamura, Eiichi

    2017-06-20

    A molecule is a quantum mechanical entity. "Watching motions and reactions of a molecule with our eyes" has therefore been a dream of chemists for a century. This dream has come true with the aid of the movies of atomic-resolution transmission electron microscopic (AR-TEM) molecular images through real-time observation of dynamic motions of single organic molecules (denoted hereafter as single-molecule atomic-resolution real-time (SMART) TEM imaging). Since 2007, we have reported movies of a variety of single organic molecules, organometallic molecules, and their assemblies, which are rotating, stretching, and reacting. Like movies in the theater, the atomic-resolution molecular movies provide us information on the 3-D structures of the molecules and also their time evolution. The success of the SMART-TEM imaging crucially depends on the development of "chemical fishhooks" with which fish (organic molecules) in solution can be captured on a single-walled carbon nanotube (CNT, serving as a "fishing rod"). The captured molecules are connected to a slowly vibrating CNT, and their motions are displayed on a monitor in real time. A "fishing line" connecting the fish and the rod may be a σ-bond, a van der Waals force, or other weak connections. Here, the molecule/CNT system behaves as a coupled oscillator, where the low-frequency anisotropic vibration of the CNT is transmitted to the molecules via the weak chemical connections that act as an energy filter. Interpretation of the observed motions of the molecules at atomic resolution needs us to consider the quantum mechanical nature of electrons as well as bond rotation, letting us deviate from the conventional statistical world of chemistry. What new horizons can we explore? We have so far carried out conformational studies of individual molecules, assigning anti or gauche conformations to each C-C bond in conformers that we saw. We can also determine the structures of van der Waals assemblies of organic molecules

  10. Accurate model annotation of a near-atomic resolution cryo-EM map.

    Science.gov (United States)

    Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah

    2017-03-21

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

  11. StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images

    Energy Technology Data Exchange (ETDEWEB)

    De Backer, A.; Bos, K.H.W. van den [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Van den Broek, W. [AG Strukturforschung/Elektronenmikroskopie, Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Sijbers, J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium)

    2016-12-15

    An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. - Highlights: • An efficient model-based method for quantitative electron microscopy is introduced. • Images are modelled as a superposition of 2D Gaussian peaks. • Overlap between neighbouring columns is taken into account. • Structure parameters can be obtained with the highest precision and accuracy. • StatSTEM, auser friendly program (GNU public license) is developed.

  12. Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution

    Directory of Open Access Journals (Sweden)

    Xiaojun Xu

    2015-01-01

    Full Text Available While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM and small angle X-ray scattering (SAXS have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrative modeling approaches aim to provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM or SAXS. Specifically, we focus on the popular molecular dynamics flexible fitting (MDFF method, which has been widely used for flexible fitting into cryo-EM maps. Second, we describe hybrid molecular dynamics, Rosetta Monte-Carlo and minimum ensemble search (MES methods that can be used to incorporate SAXS into pseudoatomic structural models. We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair.

  13. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

    DEFF Research Database (Denmark)

    Cherezov, Vadim; Rosenbaum, Daniel M; Hanson, Michael A

    2007-01-01

    Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors constitute the largest family of eukaryotic signal transduction proteins that communicate across the membrane. We report the crystal structure of a human beta2-adrenergic receptor-T4 lysozyme fusion protein bound...... to the partial inverse agonist carazolol at 2.4 angstrom resolution. The structure provides a high-resolution view of a human G protein-coupled receptor bound to a diffusible ligand. Ligand-binding site accessibility is enabled by the second extracellular loop, which is held out of the binding cavity by a pair...

  14. Objectives and Layout of a High-Resolution X-ray Imaging Crystal Spectrometer for the Large Helical Device (LHD)

    Energy Technology Data Exchange (ETDEWEB)

    Bitter, M; Gates, D; Monticello, D; Neilson, H; Reiman, A; Roquemore, A L; Morita, S; Goto, M; Yamada, H

    2010-07-29

    A high-resolution X-ray imaging crystal spectrometer, whose concept was tested on NSTX and Alcator C-Mod, is being designed for LHD. This instrument will record spatially resolved spectra of helium-like Ar16+ and provide ion temperature profiles with spatial and temporal resolutions of < 2 cm and ≥ 10 ms. The stellarator equilibrium reconstruction codes, STELLOPT and PIES, will be used for the tomographic inversion of the spectral data. The spectrometer layout and instrumental features are largely determined by the magnetic field structure of LHD.

  15. Objectives and layout of a high-resolution x-ray imaging crystal spectrometer for the large helical device

    Energy Technology Data Exchange (ETDEWEB)

    Bitter, M.; Hill, K.; Gates, D.; Monticello, D.; Neilson, H.; Reiman, A.; Roquemore, A. L. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States); Morita, S.; Goto, M.; Yamada, H. [National Institute for Fusion Science, Toki 509-5292, Gifu (Japan); Rice, J. E. [Plasma Fusion Center, MIT, Cambridge, Massachusetts 02139-4307 (United States)

    2010-10-15

    A high-resolution x-ray imaging crystal spectrometer, whose concept was tested on NSTX and Alcator C-Mod, is being designed for the large helical device (LHD). This instrument will record spatially resolved spectra of helium-like Ar{sup 16+} and will provide ion temperature profiles with spatial and temporal resolutions of <2 cm and {>=}10 ms, respectively. The spectrometer layout and instrumental features are largely determined by the magnetic field structure of LHD. The stellarator equilibrium reconstruction codes, STELLOPT and PIES, will be used for the tomographic inversion of the spectral data.

  16. Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible 3He/10 T cryostat

    Science.gov (United States)

    von Allwörden, H.; Ruschmeier, K.; Köhler, A.; Eelbo, T.; Schwarz, A.; Wiesendanger, R.

    2016-07-01

    The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped 3He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambers are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).

  17. Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible (3)He/10 T cryostat.

    Science.gov (United States)

    von Allwörden, H; Ruschmeier, K; Köhler, A; Eelbo, T; Schwarz, A; Wiesendanger, R

    2016-07-01

    The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped (3)He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambers are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).

  18. Pattern of Hydroxyapatite Crystal Growth on Bleached Enamel Following the Application of Two Antioxidants: An Atomic Force Microscope Study.

    Science.gov (United States)

    Bhusari, Chitra P; Sharma, Divya S

    This study observed the topographical pattern of hydroxyapatite deposition and growth (D&G) on bleached enamel following application of two antioxidants (sodium ascorbate and catalase) using atomic force microscope. Twenty enamel specimens (4×3×2mm), prepared from extracted impacted third molars, were mounted in self-cure acrylic and randomly grouped as: Group I-untreated; Group II- 35%H2O2; Group III- 35%H2O2 + artificial saliva; Group IV- 35%H2O2 + catalase+ artificial saliva; Group V- 35%H2O2 + sodium ascorbate+ artificial saliva. Groups I and II were observed immediately after treatment. Groups III-V were observed after 72 hrs. Roughness average was also calculated and analyzed with non-parametric Kruskall-Wallis ANOVA and Mann-Whitney tests. H2O2 dissolved matrix, exposed hydroxyapatite crystals (HACs), causing dissolution on the sides of and within HACs and opening up of nano-spaces. Artificial saliva showed growth of dissoluted crystals. Antioxidants+saliva showed potentiated remineralization by D&G on dissoluted HACs of bleached enamel. Catalase potentiated blockshaped, while sodium ascorbate the needle-shaped crystals with stair-pattern of crystallization. Evidence of oxygen bubbles was a new finding with catalase. Maximum roughness average was in group V followed by group II > group IV > group III > group I. Post-bleaching application of catalase and sodium ascorbate potentiated remineralization by saliva, but in different patterns. None of the tested antioxidant could return the original topography of enamel.

  19. Near-field optical and atomic force microscopy studies on RbTiOPO4 single crystal with ferroelectric domains

    Directory of Open Access Journals (Sweden)

    Diaz, F.

    2006-06-01

    Full Text Available We have developed a Scanning Near-Field Optic Microscope (SNOM, which is based on a commercial tuning-fork sensor, capable of measuring the topography and the optical signal, at the same time. We have measured the SNOM transmission, as well as the topography, of an RbTiOPO4 single crystal, which exhibits two kinds of macroscopic ferroelectric domains. A chemical selective attack has been performed to distinguish them. As a consequence, we obtained zones with a noticeable roughness (C- in comparison with the flat aspect of the other ones (C+. The SNOM topography images have been compared to Atomic Force Microscopy ones, which has a better resolution. The changes observed in the transmission measurements are due to different effects: i variations of the dielectric constant at the interface walls between domains; ii light scattering, wavelength dependent, at the grains in the C- face. Finally, we have determined the angles formed at the domain-walls between inverted domains, which are measured to be higher than 90º and close to 135º, as could be expected, because of the combination between [1 1 0], [-1 1 0], [1 0 0] and [0 1 0] directions of the orthorhombic lattice.Hemos desarrollado un Microscopio Óptico de Campo Cercano (SNOM que es capaz de adquirir una señal óptica, al mismo tiempo que la topografía, basado en un sensor de fuerza lateral comercial. Con este microscopio hemos medido la transmisión óptica en campo cercano, así como la topografía, de un cristal de RbTiOPO4, que exhibe dos tipos de dominios ferroeléctricos macroscópicos. Previamente, la muestra había sido sometida a un ataque químico selectivo, con el que se pueden distinguir dos zonas diferentes, una con una rugosidad apreciable (C- y otra con aspecto perfectamente plano (C+, aspecto que tenía la superficie antes del ataque. Hemos comparado las imágenes de topografía del SNOM con otras tomadas usando un Microscopio de Fuerzas Atómicas, con mayor resoluci

  20. Ab Initio Structure Determination of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A(2) at Atomic and High Resolution Using ACORN

    Energy Technology Data Exchange (ETDEWEB)

    Velmurugan,D.; Rajakannan, V.; Gayathri, D.; Banumathi, S.; Yamane, T.; Dauter, Z.; Dauter, M.; Sekar, K.

    2006-01-01

    Atomic resolution (0.97 Angstroms) data were collected for the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A{sub 2} at 100 K and data extending to 1.0 Angstroms resolution were used for the present study. Accuracy of the data at high resolution allowed the structure to be solved using the program ACORN, with a random single-atom start in an ab initio manner. The phases obtained from ACORN are of good quality and revealed most of the amino acid residues. Single wavelength Anomalous Diffraction (SAD) data were also used to locate the position of the sulphurs and ACORN was run with these atomic positions as a source of phasing information. The effect of truncating the data to 1.4 and 1.45 Angstroms for input to ACORN is also examined. Larger fragments are required to trigger successful phase refinement at these lower resolutions.

  1. Determination of silicon and aluminum in silicon carbide nanocrystals by high-resolution continuum source graphite furnace atomic absorption spectrometry.

    Science.gov (United States)

    Dravecz, Gabriella; Bencs, László; Beke, Dávid; Gali, Adam

    2016-01-15

    The determination of Al contaminant and the main component Si in silicon carbide (SiC) nanocrystals with the size-distribution of 1-8nm dispersed in an aqueous solution was developed using high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS-GFAAS). The vaporization/atomization processes were investigated in a transversally heated graphite atomizer by evaporating solution samples of Al and Si preserved in various media (HCl, HNO3). For Si, the best results were obtained by applying a mixture of 5µg Pd plus 5µg Mg, whereas for Al, 10µg Mg (each as nitrate solution) was dispensed with the samples, but the results obtained without modifier were found to be better. This way a maximum pyrolysis temperature of 1200°C for Si and 1300°C for Al could be used, and the optimum (compromise) atomization temperature was 2400°C for both analytes. The Si and Al contents of different sized SiC nanocrystals, dispersed in aqueous solutions, were determined against aqueous (external) calibration standards. The correlation coefficients (R values) of the calibrations were found to be 0.9963 for Si and 0.9991 for Al. The upper limit of the linear calibration range was 2mg/l Si and 0.25mg/l Al. The limit of detection was 3µg/l for Si and 0.5µg/l for Al. The characteristic mass (m0) was calculated to be 389pg Si and 6.4pg Al. The Si and Al content in the solution samples were found to be in the range of 1.0-1.7mg/l and 0.1-0.25mg/l, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Crystallization and preliminary crystallographic studies of Schizolobium parahyba chymotrypsin inhibitor (SPCI) at 1.8 Å resolution

    Energy Technology Data Exchange (ETDEWEB)

    Teles, Rozeni Chagas Lima; Esteves, Gisele Ferreira; Araújo, Marcus Aurélio Miranda [Laboratório de Biofísica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília-DF, 70910-900 (Brazil); Bloch, Carlos Jr [Laboratório de Espectrometria de Massa, Empresa Brasileira de Pesquisa Agropecuária - Recursos Genéticos e Biotecnologia, Brasília-DF, 70770-900 (Brazil); Barbosa, João Alexandre Ribeiro Gonçalves, E-mail: joao@lnls.br [Center for Structural Molecular Biology (CeBiME), Brazilian Synchrotron Light Laboratory (LNLS), CP-6192, Campinas-SP, 13084-971 (Brazil); Freitas, Sonia Maria de, E-mail: joao@lnls.br [Laboratório de Biofísica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília-DF, 70910-900 (Brazil)

    2007-11-01

    Crystallization and preliminary crystallographic studies of Schizolobium parahyba chymotrypsin inhibitor (SPCI) at 1.8 Å resolution. SPCI, a Kunitz-type chymotrypsin inhibitor, is a 180-amino-acid polypeptide isolated from Schizolobium parahyba seeds. This inhibitor has been characterized as a highly stable protein over a broad pH and temperature range. SPCI was crystallized using a solution containing 0.1 M sodium acetate trihydrate buffer pH 4.6, 33%(v/v) PEG 2000 and 0.2 M ammonium sulfate. Data were collected to 1.80 Å resolution from a single crystal of SPCI under cryogenic conditions. The protein crystallized in space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 40.01, b = 71.58, c = 108.68 Å and an R{sub merge} of 0.052. The structure of SPCI has been solved by molecular replacement using the known structure of the Kunitz-type trypsin inhibitor from Delonix regia (PDB code) as the search model.

  3. Ultra-high-resolution time projection chambers with liquid crystal backplanes

    Energy Technology Data Exchange (ETDEWEB)

    Monreal, Benjamin

    2014-10-15

    We investigated the possibility of incorporating a liquid-crystal device into a gas ionization detector. After extensive R&D on several candidate liquid-crystal technologies, we developed some novel materials allowing twisted nematic liquid-crystal layers to be coupled directly to gas ionization counters. However, the resulting structures were unsuitable for large-scale or practical use. We tested several technologies known to result in mechanically-robust liquid crystal electrooptic layers, but found poor behavior in the detector context.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-04-12

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

  5. C atom endohedral doping effect on the bond lengths in the crystal structure of fcc-C60

    Directory of Open Access Journals (Sweden)

    S Javanbakht

    2011-03-01

    Full Text Available Single and double equilibrium bond lengths of the fcc-C60 crystal were calculated in the absence and presence of the endohedral C atom as an impurity doped into each C60 cluster, i.e., fcc-C@C60, by means of fully-relaxed self-consistent calculations within the density functtional theory (DFT employing the full potential-augmented plane waves plus local orbital (FP-APW+lo method. The result shows that the single and double bond lengths were decreased for the doped case of fcc-C@C60 when compared with the pure fcc-C60. The reduction in the bond lengths by the carbon impurity doping is attributed to the bond alternation effect and reduction of the symmetry in the C60 molecule. The result shows that the impurity injection gives rise to change in the electron charge distribution and as a result to change in electronic properties.

  6. High-resolution x-ray characterization of mosaic crystals for hard x-and gamma-ray astronomy

    Science.gov (United States)

    Ferrari, Claudio; Buffagni, Elisa; Marchini, Laura; Zappettini, Andrea

    2011-09-01

    We have analyzed GaAs, Cu, CdTe, and CdZnTe crystals as possible optical elements for hard x-ray lenses for x-ray astronomy. We used high resolution x-ray diffraction at 8keV in Bragg geometry and Laue transmission diffraction at synchrotron at energies up to 500 keV. A good agreement was found between the mosaicity evaluated in Bragg diffraction geometry with x-ray penetration of the order of few tens micrometers and in Laue transmission geometry at synchrotron. All the analyzed crystals showed mosaicity values in a range between a few to 150 arcseconds and suitable for the application. Nevertheless -CdTe and CdZnTe crystals exhibit non-uniformity due to the presence of low angle grain boundaries; -Cu crystals exhibit mosaicity of the order of several arcminutes; they indeed suffer by a severe cutting damage that had to be removed with a very deep etching. The FWHM was also rapidly decreasing with the x-ray energy showing that the mosaic spread is not the only origin of peak broadening; -GaAs crystals grown by Czochralski method show mosaicity up to 30 arcseconds and good diffraction efficiency up to energies of 500 keV. The use of thermal treatments as a possible method to increase the mosaic spread is also evaluated.

  7. Atomic resolution on the (111 )B surface of mercury cadmium telluride by scanning tunneling microscopy

    Science.gov (United States)

    Zha, Fang-Xing; Hong, Feng; Pan, Bi-Cai; Wang, Yin; Shao, Jun; Shen, Xue-Chu

    2018-01-01

    The real-space atomic surface structure of mercury cadmium telluride was successfully achieved on the (111 )B surface of H g0.78C d0.22Te by ultrahigh-vacuum scanning tunneling microscopy (STM). The work casts light on the reconstructions of the (111 )B surface unraveling a (2 ×2 ) surface reconstruction induced by adatom adsorption of Cd. The other (2 ×2 ) surface reconstruction is clarified to be induced by the single Te vacancy, which is more stable than the reconstruction of multivacancies in contrast to the prevailing view. The simulated STM images are in good agreement with the experiments. We also observed an in situ morphology transition from the (1 ×1 ) structure to those (2 ×2 ) reconstructions, implying the stability of the reconstructions.

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

    Science.gov (United States)

    Wang, Jian; Beyerlein, Irene J.

    2012-10-01

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

  9. High time resolution measurements of the thermosphere from Fabry-Perot Interferometer measurements of atomic oxygen

    Directory of Open Access Journals (Sweden)

    E. A. K. Ford

    2007-06-01

    Full Text Available Recent advances in the performance of CCD detectors have enabled a high time resolution study of the high latitude upper thermosphere with Fabry-Perot Interferometers (FPIs to be performed. 10-s integration times were used during a campaign in April 2004 on an FPI located in northern Sweden in the auroral oval. The FPI is used to study the thermosphere by measuring the oxygen red line emission at 630.0 nm, which emits at an altitude of approximately 240 km. Previous time resolutions have been 4 min at best, due to the cycle of look directions normally observed. By using 10 s rather than 40 s integration times, and by limiting the number of full cycles in a night, high resolution measurements down to 15 s were achievable. This has allowed the maximum variability of the thermospheric winds and temperatures, and 630.0 nm emission intensities, at approximately 240 km, to be determined as a few minutes. This is a significantly greater variability than the often assumed value of 1 h or more. A Lomb-Scargle analysis of this data has shown evidence of gravity wave activity with waves with short periods. Gravity waves are an important feature of mesosphere-lower thermosphere (MLT dynamics, observed using many techniques and providing an important mechanism for energy transfer between atmospheric regions. At high latitudes gravity waves may be generated in-situ by localised auroral activity. Short period waves were detected in all four clear nights when this experiment was performed, in 630.0 nm intensities and thermospheric winds and temperatures. Waves with many periodicities were observed, from periods of several hours, down to 14 min. These waves were seen in all parameters over several nights, implying that this variability is a typical property of the thermosphere.

  10. Optimizing timing resolution for TOF PET detectors based on monolithic scintillation crystals using fast photosensor arrays

    NARCIS (Netherlands)

    Vinke, Ruud; Lohner, Herbert; Schaart, Dennis R.; van Dam, Herman T.; Seifert, Stefan; Beekman, Freek J.; Dendooven, Peter

    2009-01-01

    We have investigated the time-of-flight (TOF) capability of a monolithic 20 rum x 20 mm x 12 mm LYSO crystal coupled to a Hamamatsu position-sensitive H8711-03 4x4 multi-anode photomultiplier tube. The x-, y-, and z-coordinates of the photoconversion location inside the crystal are determined using

  11. High Resolution Vibrational Spectroscopy at the Atomic Scale: CO on Au(110) and Cu(100), and C2H2 on Cu(100)

    Science.gov (United States)

    Xu, Chen; Jiang, Chilun; Zhang, Yanning; Wu, Ruqian; Ho, Wilson

    2012-11-01

    STM-IETS has been regarded as the ultimate tool to identify and characterize single molecules adsorbed on solid surfaces with atomic spatial resolution. With the improvement of the energy resolution obtained at ˜600 mK, STM-IETS is able to reveal subtle interactions between the molecule and its environment which was previously not possible at higher temperatures. Here we demonstrate the capability of sub-Kelvin STM on detecting the influence of the tip as well as the anisotropy of the reconstructed Au(110) surface on the low energy hindered vibrational motions of single adsorbed CO molecule. In the case of acetylene, more vibrational modes are resolved due to the enhanced spectral resolution. Single molecule vibrational spectroscopy with atomic scale spatial resolution opens new possibilities to probe molecular interactions with high spectral resolution.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-03-15

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

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

    DEFF Research Database (Denmark)

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

    1998-01-01

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

  14. Van der Waals Epitaxial Growth of Atomic Layered HfS2Crystals for Ultrasensitive Near-Infrared Phototransistors.

    Science.gov (United States)

    Fu, Lei; Wang, Feng; Wu, Bin; Wu, Nian; Huang, Wei; Wang, Hanlin; Jin, Chuanhong; Zhuang, Lin; He, Jun; Fu, Lei; Liu, Yunqi

    2017-08-01

    As a member of the group IVB transition metal dichalcogenides (TMDs) family, hafnium disulfide (HfS 2 ) is recently predicted to exhibit higher carrier mobility and higher tunneling current density than group VIB (Mo and W) TMDs. However, the synthesis of high-quality HfS 2 crystals, sparsely reported, has greatly hindered the development of this new field. Here, a facile strategy for controlled synthesis of high-quality atomic layered HfS 2 crystals by van der Waals epitaxy is reported. Density functional theory calculations are applied to elucidate the systematic epitaxial growth process of the S-edge and Hf-edge. Impressively, the HfS 2 back-gate field-effect transistors display a competitive mobility of 7.6 cm 2 V -1 s -1 and an ultrahigh on/off ratio exceeding 10 8 . Meanwhile, ultrasensitive near-infrared phototransistors based on the HfS 2 crystals (indirect bandgap ≈1.45 eV) exhibit an ultrahigh responsivity exceeding 3.08 × 10 5 A W -1 , which is 10 9 -fold higher than 9 × 10 -5 A W -1 obtained from the multilayer MoS 2 in near-infrared photodetection. Moreover, an ultrahigh photogain exceeding 4.72 × 10 5 and an ultrahigh detectivity exceeding 4.01 × 10 12 Jones, superior to the vast majority of the reported 2D-materials-based phototransistors, imply a great promise in TMD-based 2D electronic and optoelectronic applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Simultaneous determination of rhodium and ruthenium by high-resolution continuum source graphite furnace atomic absorption spectrometry

    Science.gov (United States)

    Zambrzycka-Szelewa, Elżbieta; Lulewicz, Marta; Godlewska-Żyłkiewicz, Beata

    2017-07-01

    In the present paper a fast, simple and sensitive analytical method for simultaneous determination of rhodium and ruthenium by high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS GFAAS) was developed. Among six pairs of absorption atomic lines of Rh and Ru, which are close enough to enable their simultaneous detection, two pairs were selected for further studies. Best results were obtained for measurements of the resonance line of rhodium at 343.489 nm and the adjacent secondary line of ruthenium at 343.674 nm (23% intensity of this line). For evaluated lines, the absorbance values were obtained using three pixels. The pyrolysis and atomization temperatures were 1200 °C and 2600 °C, respectively. Under these conditions the limits of detection achieved for Rh and Ru were found to be 1.0 μg L- 1 and 1.9 μg L- 1, respectively. The characteristic mass was 12.9 pg for Rh and 71.7 pg for Ru. Repeatability of the results expressed as a relative standard deviation was typically below 6%. The trueness of the method was confirmed by analysis of the certified reference material - platinum ore (SARM 76). The recovery of Rh and Ru from the platinum ore was 93.0 ± 4.6% and 90.1 ± 2.5%, respectively. The method was successfully applied to the direct simultaneous determination of trace amounts of rhodium and ruthenium in spiked river water, road runoff, and municipal sewage. Separation of interfering matrix on cation exchange resin was required before analysis of road dust and tunnel dust (CW-7) by HR-CS GFAAS.

  16. Alcohol-Binding Sites in Distinct Brain Proteins: The Quest for Atomic Level Resolution

    Science.gov (United States)

    Howard, Rebecca J.; Slesinger, Paul A.; Davies, Daryl L.; Das, Joydip; Trudell, James R.; Harris, R. Adron

    2011-01-01

    Defining the sites of action of ethanol on brain proteins is a major prerequisite to understanding the molecular pharmacology of this drug. The main barrier to reaching an atomic-level understanding of alcohol action is the low potency of alcohols, ethanol in particular, which is a reflection of transient, low-affinity interactions with their targets. These mechanisms are difficult or impossible to study with traditional techniques such as radioligand binding or spectroscopy. However, there has been considerable recent progress in combining X-ray crystallography, structural modeling, and site-directed mutagenesis to define the sites and mechanisms of action of ethanol and related alcohols on key brain proteins. We review such insights for several diverse classes of proteins including inwardly rectifying potassium, transient receptor potential, and neurotransmit-ter-gated ion channels, as well as protein kinase C epsilon. Some common themes are beginning to emerge from these proteins, including hydrogen bonding of the hydroxyl group and van der Waals interactions of the methylene groups of ethanol with specific amino acid residues. The resulting binding energy is proposed to facilitate or stabilize low-energy state transitions in the bound proteins, allowing ethanol to act as a “molecular lubricant” for protein function. We discuss evidence for characteristic, discrete alcohol-binding sites on protein targets, as well as evidence that binding to some proteins is better characterized by an interaction region that can accommodate multiple molecules of ethanol. PMID:21676006

  17. Smoking and fluidity of erythrocyte membranes: a high resolution scanning electron and atomic force microscopy investigation.

    Science.gov (United States)

    Pretorius, Etheresia; du Plooy, Jeanette N; Soma, Prashilla; Keyser, Ina; Buys, Antoinette V

    2013-11-30

    Smoking affects the general health of an individual, however, the red blood cells (RBCs) and their architecture are particularly vulnerable to inhaled toxins related to smoking. Smoking is one of the lifestyle diseases that are responsible for the most deaths worldwide and an individual who smokes is exposed to excessive amounts of oxidants and toxins which generate up to 10(18) free radicals in the human body. Recently, it was reported that smoking decreases RBC membrane fluidity. Here we confirm this and we show changes visible in the topography of RBC membranes, using scanning electron microscopy (SEM). RBC membranes show bubble formation of the phospholipid layer, as well as balloon-like smooth areas; while their general discoid shapes are changed to form pointed extensions. We also investigate membrane roughness using atomic force microscopy (AFM) and these results confirm SEM results. Due to the vast capability of RBCs to be adaptable, their state of well-being is a major indication for the general health status of an individual. We conclude that these changes, using an old technique in a novel application, may provide new insights and new avenues for future improvements in clinical medicine pertaining to conditions like COPD. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Role of organoclay in controlling the morphology and crystal-growth behavior of biodegradable polymer-blend thin films studied using atomic force microscopy

    CSIR Research Space (South Africa)

    Malwela, T

    2014-09-01

    Full Text Available clays, their organic modifications and their initial d(sub001)-spacing on the morphology and crystal growth behavior of the PLA/PBSA blend were studied. An atomic force microscopy equipped with a hot-stage scanner was used to examine the crystalline...

  19. Curved crystals for high-resolution focusing of X and gamma rays through a Laue lens

    Science.gov (United States)

    Guidi, Vincenzo; Bellucci, Valerio; Camattari, Riccardo; Neri, Ilaria

    2013-08-01

    Crystals with curved diffracting planes have been investigated as high-efficiency optical components for the realization of a Laue lens for satellite-borne experiments in astrophysics. At Sensor and Semiconductor Laboratory (Ferrara, Italy) a research and development plan to implement Si and Ge curved crystals by surface grooving technique has been undertaken. The method of surface grooving allows obtaining Si and Ge curved crystals with self-standing curvature, i.e., with no need for external bending device, which is a mandatory issue in satellite-borne experiments. Si and Ge grooved crystals have been characterized by X-ray diffraction at ESRF and ILL to prove their functionality for a high-reflectivity Laue lens.

  20. Optimizing 1-μs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope.

    Science.gov (United States)

    Edwards, Devin T; Faulk, Jaevyn K; Sanders, Aric W; Bull, Matthew S; Walder, Robert; LeBlanc, Marc-Andre; Sousa, Marcelo C; Perkins, Thomas T

    2015-10-14

    Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is widely used to mechanically measure the folding and unfolding of proteins. However, the temporal resolution of a standard commercial cantilever is 50-1000 μs, masking rapid transitions and short-lived intermediates. Recently, SMFS with 0.7-μs temporal resolution was achieved using an ultrashort (L = 9 μm) cantilever on a custom-built, high-speed AFM. By micromachining such cantilevers with a focused ion beam, we optimized them for SMFS rather than tapping-mode imaging. To enhance usability and throughput, we detected the modified cantilevers on a commercial AFM retrofitted with a detection laser system featuring a 3-μm circular spot size. Moreover, individual cantilevers were reused over multiple days. The improved capabilities of the modified cantilevers for SMFS were showcased by unfolding a polyprotein, a popular biophysical assay. Specifically, these cantilevers maintained a 1-μs response time while eliminating cantilever ringing (Q ≅ 0.5). We therefore expect such cantilevers, along with the instrumentational improvements to detect them on a commercial AFM, to accelerate high-precision AFM-based SMFS studies.

  1. Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jae-Mun; Hutson, Anne M.; Estes, Mary K.; Prasad, B.V. Venkataram (Baylor)

    2008-07-28

    Members of Norovirus, a genus in the family Caliciviridae, are causative agents of epidemic diarrhea in humans. Susceptibility to several noroviruses is linked to human histo-blood type, and its determinant histo-blood group antigens (HBGAs) are regarded as receptors for these viruses. Specificity for these carbohydrates is strain-dependent. Norwalk virus (NV) is the prototype genogroup I norovirus that specifically recognizes A- and H-type HBGA, in contrast to genogroup II noroviruses that exhibit a more diverse HBGA binding pattern. To understand the structural basis for how HBGAs interact with the NV capsid protein, and how the specificity is achieved, we carried out x-ray crystallographic analysis of the capsid protein domain by itself and in complex with A- and H-type HBGA at a resolution of {approx}1.4 {angstrom}. Despite differences in their carbohydrate sequence and linkage, both HBGAs bind to the same surface-exposed site in the capsid protein and project outward from the capsid surface, substantiating their possible role in initiating cell attachment. Precisely juxtaposed polar side chains that engage the sugar hydroxyls in a cooperative hydrogen bonding and a His/Trp pair involved in a cation-p interaction contribute to selective and specific recognition of A- and H-type HBGAs. This unique binding epitope, confirmed by mutational analysis, is highly conserved, but only in the genogroup I noroviruses, suggesting that a mechanism by which noroviruses infect broader human populations is by evolving different sites with altered HBGA specificities.

  2. Probing the Active Site of Candida Glabrata Dihydrofolate Reductase with High Resolution Crystal Structures and the Synthesis of New Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.; Bolstad, D; Smith, A; Priestley, N; Wright, D; Anderson, A

    2009-01-01

    Candida glabrata, a fungal strain resistant to many commonly administered antifungal agents, has become an emerging threat to human health. In previous work, we validated that the essential enzyme, dihydrofolate reductase, is a drug target in C. glabrata. Using a crystal structure of dihydrofolate reductase from C. glabrata bound to an initial lead compound, we designed a class of biphenyl antifolates that potently and selectively inhibit both the enzyme and the growth of the fungal culture. In this work, we explore the structure-activity relationships of this class of antifolates with four new high resolution crystal structures of enzyme:inhibitor complexes and the synthesis of four new inhibitors. The designed inhibitors are intended to probe key hydrophobic pockets visible in the crystal structure. The crystal structures and an evaluation of the new compounds reveal that methyl groups at the meta and para positions of the distal phenyl ring achieve the greatest number of interactions with the pathogenic enzyme and the greatest degree of selectivity over the human enzyme. Additionally, antifungal activity can be tuned with substitution patterns at the propargyl and para-phenyl positions.

  3. Composition and (in)homogeneity of carotenoid crystals in carrot cells revealed by high resolution Raman imaging

    Science.gov (United States)

    Roman, Maciej; Marzec, Katarzyna M.; Grzebelus, Ewa; Simon, Philipp W.; Baranska, Malgorzata; Baranski, Rafal

    2015-02-01

    Three categories of roots differing in both β/α-carotene ratio and in total carotenoid content were selected based on HPLC measurements: high α- and β-carotene (HαHβ), low α- and high β-carotene (LαHβ), and low α- and low β-carotene (LαLβ). Single carotenoid crystals present in the root cells were directly measured using high resolution Raman imaging technique with 532 nm and 488 nm lasers without compound extraction. Crystals of the HαHβ root had complex composition and consisted of β-carotene accompanied by α-carotene. In the LαHβ and LαLβ roots, measurements using 532 nm laser indicated the presence of β-carotene only, but measurements using 488 nm laser confirmed co-occurrence of xanthophylls, presumably lutein. Thus the results show that independently on carotenoid composition in the root, carotenoid crystals are composed of more than one compound. Individual spectra extracted from Raman maps every 0.2-1.0 μm had similar shapes in the 1500-1550 cm-1 region indicating that different carotenoid molecules were homogeneously distributed in the whole crystal volume. Additionally, amorphous carotenoids were identified and determined as composed of β-carotene molecules but they had a shifted the ν1 band probably due to the effect of bonding of other plant constituents like proteins or lipids.

  4. High-resolution spectroscopy, crystal-field calculations, and quadrupole helix chirality of DyFe3(BO34

    Directory of Open Access Journals (Sweden)

    Popova M.N.

    2017-01-01

    Full Text Available High-resolution polarized transmission spectra of DyFe3(BO34 single crystals were investigated in broad spectral (10-23000 cm−1 and temperature (3.5-300 K ranges. Energies of the dysprosium levels in the paramagnetic and antiferromagnetic phases were determined. On the basis of these data and preliminary calculations in the frameworks of the exchange-charge model, we determined the crystal-field and Dy-Fe exchange interaction parameters of the Dy3+ ions at sites with the point C2 symmetry corresponding to the enantiomorphic P3121 and P3221 space groups. The values of electronic quadrupole moments of the Dy3+ ions were calculated, which enabled us to interpret results of the work [Usui et al., Nature Mater. 13, 611 (2014] on the observation of domains of different quadrupole chirality in DyFe3(BO34.

  5. Visualization of drug-nucleic acid interactions at atomic resolution v. structure of two aminoacridine/dinucleoside monophosphate crystalline complexes, proflavine: 5-iodocytidylyl(3'-5') guanosine and acridine orange: 5-iodocytidylyl(3'-5') guanosine

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, B.S.; Seshadri, T.P.; Sakore, T.D.; Sobell, H.M.

    1979-01-01

    Acridine orange and proflavine form complexes with the dinucleoside monophosphate, 5-iodocytidylyl(3'-5') guanosine (iodoCpG). The acridine orange-iodoCpG crystals are monoclinic, space group P2/sub 1/, with unit cell dimensions a = 14.36 A, b = 19.64 A, c = 20.67 A, ..beta.. = 102.5. The proflavine-iodoCpG crystals are monoclinic, space group C2, with unit cell dimensions a = 32.14 A, b = 22.23 A, c = 18.42 A, ..beta.. = 123.3. Both structures have been solved to atomic resolution by Patterson and Fourier methods, and refined by full matrix least squares. Acridine orange forms an intercalative structure with iodoCpG but the acridine nucleus lies asymmetrically in the intercalation site. This asymmetric intercalation is accompanied by a sliding of base-pairs upon the acridine nucleus. Base-pairs above and below the drug are separated by about 6.8 A and are twisted about 10/sup 0/. Proflavine demonstrates symmetric intercalation with iodoCpG. Hydrogen bonds connect amino- groups on proflavine with phosphate oxygen atoms on the dinucleotide. Base-pairs above and below the intercalative proflavine molecule are twisted about 36/sup 0/. The altered magnitude of this angular twist reflects the sugar puckering pattern that is observed. We propose a proflavine-DNA and an acridine orange-DNA binding model. We will describe these models in detail in this paper.

  6. Dependence of Ion Transport on the Electronegativity of the Constituting Atoms in Ionic Crystals.

    Science.gov (United States)

    Zhang, Qian; Kaghazchi, Payam

    2017-04-19

    Ion transport in electrode and electrolyte materials is a key process in Li-based batteries. In this work, we study the mechanism and activation energy of ion transport (Ea ) in rock-salt Li-based LiX (X=Cl, Br, and I) materials. It is found that Ea at low external voltages, where Li-X Schottky pairs are the most favorable defect types, is about 0.42 times the Gibbs energy of formation of LiX compound (ΔGf ). The value of 0.42 is the slope of the electronegativity of anions of binary Li-based materials as a function of ΔGf . At high voltages, where the Fermi level is located very close to the valence band maximum (VBM), electrons can be excited from the VB to Li vacancy-induced states close to the Fermi level. Under this condition, the formation of Li vacancies that are compensated by holes is energetically more favorable than that of Li-X Schottky pairs, and therefore, the activation energies are lower in the former case. The wide range of reported experimental values of activation energies lies between calculated values at low and high voltage regimes. This work motivates further studies on the relation between the activation energy for ionic conductivity in solid materials and the intrinsic ground-state properties of their free atoms. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Feasibility of atomic force microscopy for determining crystal growth rates of nifedipine at the surface of amorphous solids with and without polymers.

    Science.gov (United States)

    Miyazaki, Tamaki; Aso, Yukio; Kawanishi, Toru

    2011-10-01

    Amorphous nifedipine (NFD), which has a smooth surface immediately after preparation, was shown to have structures resembling clusters of curling and branching fibers approximately 1 μm wide by atomic force microscopy (AFM) after storage at 25°C. The size of the cluster-like structures increased with storage over time, implying crystal growth. The average elongation rate of the fibers determined by AFM at ambient room temperature was 1.1 × 10(-9) m/s, and this agreed well with the crystal growth rate of 1.6 × 10(-9) m/s determined by polarized light microscopy. The crystal growth rate of NFD in solid dispersions with 5% polyethylene glycol (PEG) was found to be 5.0 × 10(-8) m/s by AFM. Although this value was approximately the same as that obtained by polarized light microscopy, three-dimensional information obtained by AFM for the crystallization of NFD in a solid dispersion with PEG revealed that the changes in topography were not a consequence of surface crystal growth, but rather attributable to the growth of crystals formed in the amorphous bulk. For solid dispersions with α,β-poly(N-5-hydroxypentyl)-l-aspartamide, acceleration of NFD crystallization by tapping with an AFM probe was observed. The present study has demonstrated the feasibility and application of AFM for interpretation of surface crystallization data. Copyright © 2011 Wiley-Liss, Inc.

  8. Thermal equilibrium concentration of intrinsic point defects in heavily doped silicon crystals - Theoretical study of formation energy and formation entropy in area of influence of dopant atoms-

    Science.gov (United States)

    Kobayashi, K.; Yamaoka, S.; Sueoka, K.; Vanhellemont, J.

    2017-09-01

    It is well known that p-type, neutral and n-type dopants affect the intrinsic point defect (vacancy V and self-interstitial I) behavior in single crystal Si. By the interaction with V and/or I, (1) growing Si crystals become more V- or I-rich, (2) oxygen precipitation is enhanced or retarded, and (3) dopant diffusion is enhanced or retarded, depending on the type and concentration of dopant atoms. Since these interactions affect a wide range of Si properties ranging from as-grown crystal quality to LSI performance, numerical simulations are used to predict and to control the behavior of both dopant atoms and intrinsic point defects. In most cases, the thermal equilibrium concentrations of dopant-point defect pairs are evaluated using the mass action law by taking only the binding energy of closest pair to each other into account. The impacts of dopant atoms on the formation of V and I more distant than 1st neighbor and on the change of formation entropy are usually neglected. In this study, we have evaluated the thermal equilibrium concentrations of intrinsic point defects in heavily doped Si crystals. Density functional theory (DFT) calculations were performed to obtain the formation energy (Ef) of the uncharged V and I at all sites in a 64-atom supercell around a substitutional p-type (B, Ga, In, and Tl), neutral (C, Ge, and Sn) and n-type (P, As, and Sb) dopant atom. The formation (vibration) entropies (Sf) of free I, V and I, V at 1st neighboring site from B, C, Sn, P and As atoms were also calculated with the linear response method. The dependences of the thermal equilibrium concentrations of trapped and total intrinsic point defects (sum of free I or V and I or V trapped with dopant atoms) on the concentrations of B, C, Sn, P and As in Si were obtained. Furthermore, the present evaluations well explain the experimental results of the so-called ;Voronkov criterion; in B and C doped Si, and also the observed dopant dependent void sizes in P and As doped Si

  9. Determination of silicon in biomass and products of pyrolysis process via high-resolution continuum source atomic absorption spectrometry.

    Science.gov (United States)

    Nakadi, Flávio V; Prodanov, Caroline; Boschetti, Wiliam; Vale, Maria Goreti R; Welz, Bernhard; de Andrade, Jailson B

    2018-03-01

    Thermochemical processes can convert the biomass into fuels, such as bio-oil. The biomass submitted to pyrolysis process, such as fibers, are generally rich in silicon, an element that can lead to damages in an engine when there is high concentration in a fuel. High-resolution continuum source atomic absorption spectrometry (HR-CS AAS) is an interesting alternative for Si determination in the products and byproducts of the pyrolysis process because, besides the flame (F) and graphite furnace (GF) atomizers, it has enhanced the application of direct analysis of solid samples (SS) within GF. This study aimed the development of methods to determine Si in biomass samples, their products and byproducts using HR-CS AAS. A high-resolution continuum source atomic absorption spectrometer contrAA 700 equipped with F and GF atomizers was used throughout the study. HR-CS F AAS (λ = 251.611nm, 1 detection pixel, N2O/C2H2 flame) was used to evaluate Si content in biomass and ash, after a microwave-assisted acid digestion with HNO3 and HF. HR-CS GF AAS (Tpyr = 1400°C, Tatom = 2650°C) has evaluated Si in pyrolysis water and bio-oil at 251.611nm, and in peach pit biomass and ash at 221.174nm using SS, both wavelengths with 1 detection pixel. Rhodium (300μg) was applied as permanent modifier and 10μgPd + 6μg Mg were pipetted onto the standards/samples at each analysis. Three different biomass samples were studied: palm tree fiber, coconut fiber and peach pit, and three certified reference materials (CRM) were used to verify the accuracy of the methods. The figures of merit were LOD 0.09-20mgkg-1, and LOQ 0.3-20mgkg-1, considering all the methods. There were no significant differences between the CRM certified values and the determined ones, using a Student t-test with a confidence interval of 95% (n = 5). Si concentration ranged from 0.11-0.92% mm-1, 1.1-1.7mgkg-1, 3.3-13mgkg-1, and 0.41-1.4%mm-1, in biomass, bio-oil, pyrolysis water and ash, respectively. Si remained mostly

  10. The molecular structure of the IsiA-Photosystem I supercomplex, modelled from high-resolution, crystal structures of Photosystem I and the CP43 protein.

    Science.gov (United States)

    Zhang, Yinan; Chen, Min; Church, W Bret; Lau, Kwok Wai; Larkum, Anthony W D; Jermiin, Lars S

    2010-04-01

    We present the molecular structure of the IsiA-Photosystem I (PSI) supercomplex, inferred from high-resolution, crystal structures of PSI and the CP43 protein. The structure of iron-stress-induced A protein (IsiA) is similar to that of CP43, albeit with the difference that IsiA is associated with 15 chlorophylls (Chls), one more than previously assumed. The membrane-spanning helices of IsiA contain hydrophilic residues many of which bind Chl. The optimal structure of the IsiA-PSI supercomplex was inferred by systematically rearranging the IsiA monomers and PSI trimer in relation to each other. For each of the 6,969,600 structural configurations considered, we counted the number of optimal Chl-Chl connections (i.e., cases where Chl-bound Mg atoms are 228% the energy-transfer potential. In conclusion, our model allows us to explain how the IsiA-PSI supercomplex may act as an efficient light-harvesting structure under low-light conditions and as an efficient dissipater of excess energy under high-light conditions.

  11. Surface-initiated dehydrogenative polymerization of monolignols: a quartz crystal microbalance with dissipation monitoring and atomic force microscopy study.

    Science.gov (United States)

    Wang, Chao; Qian, Chen; Roman, Maren; Glasser, Wolfgang G; Esker, Alan R

    2013-11-11

    This work highlights a real-time and label-free method to monitor the dehydrogenative polymerization of monolignols initiated by horseradish peroxidase (HRP) physically immobilized on surfaces using a quartz crystal microbalance with dissipation monitoring (QCM-D). The dehydrogenative polymer (DHP) films are expected to provide good model substrates for studying ligninolytic enzymes. The HRP was adsorbed onto gold or silica surfaces or onto and within porous desulfated nanocrystalline cellulose films from an aqueous solution. Surface-immobilized HRP retained its activity and selectivity for monolignols as coniferyl and p-coumaryl alcohol underwent dehydrogenative polymerization in the presence of hydrogen peroxide, whereas sinapyl alcohol polymerization required the addition of a nucleophile. The morphologies of the DHP layers on the surfaces were investigated via atomic force microscopy (AFM). Data from QCM-D and AFM showed that the surface-immobilized HRP-initiated dehydrogenative polymerization of monolignols was greatly affected by the support surface, monolignol concentration, hydrogen peroxide concentration, and temperature.

  12. Design of a self-aligned, wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with 10 nm magnetic force microscope resolution

    Energy Technology Data Exchange (ETDEWEB)

    Karcı, Özgür [NanoMagnetics Instruments Ltd., Hacettepe - İvedik OSB Teknokent, 1368. Cad., No: 61/33, 06370, Yenimahalle, Ankara (Turkey); Department of Nanotechnology and Nanomedicine, Hacettepe University, Beytepe, 06800 Ankara (Turkey); Dede, Münir [NanoMagnetics Instruments Ltd., Hacettepe - İvedik OSB Teknokent, 1368. Cad., No: 61/33, 06370, Yenimahalle, Ankara (Turkey); Oral, Ahmet, E-mail: orahmet@metu.edu.tr [Department of Physics, Middle East Technical University, 06800 Ankara (Turkey)

    2014-10-01

    We describe the design of a wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with a self-aligned fibre-cantilever mechanism. An alignment chip with alignment groves and a special mechanical design are used to eliminate tedious and time consuming fibre-cantilever alignment procedure for the entire temperature range. A low noise, Michelson fibre interferometer was integrated into the system for measuring deflection of the cantilever. The spectral noise density of the system was measured to be ~12 fm/√Hz at 4.2 K at 3 mW incident optical power. Abrikosov vortices in BSCCO(2212) single crystal sample and a high density hard disk sample were imaged at 10 nm resolution to demonstrate the performance of the system.

  13. Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg2+ channel MgtE.

    Science.gov (United States)

    Takeda, Hironori; Hattori, Motoyuki; Nishizawa, Tomohiro; Yamashita, Keitaro; Shah, Syed T A; Caffrey, Martin; Maturana, Andrés D; Ishitani, Ryuichiro; Nureki, Osamu

    2014-11-04

    Magnesium is the most abundant divalent cation in living cells and is crucial to several biological processes. MgtE is a Mg(2+) channel distributed in all domains of life that contributes to the maintenance of cellular Mg(2+) homeostasis. Here we report the high-resolution crystal structures of the transmembrane domain of MgtE, bound to Mg(2+), Mn(2+) and Ca(2+). The high-resolution Mg(2+)-bound crystal structure clearly visualized the hydrated Mg(2+) ion within its selectivity filter. Based on those structures and biochemical analyses, we propose a cation selectivity mechanism for MgtE in which the geometry of the hydration shell of the fully hydrated Mg(2+) ion is recognized by the side-chain carboxylate groups in the selectivity filter. This is in contrast to the K(+)-selective filter of KcsA, which recognizes a dehydrated K(+) ion. Our results further revealed a cation-binding site on the periplasmic side, which regulate channel opening and prevents conduction of near-cognate cations.

  14. High-resolution crystal structure of human Mapkap kinase 3 in complex with a high affinity ligand.

    Science.gov (United States)

    Cheng, Robert; Felicetti, Brunella; Palan, Shilpa; Toogood-Johnson, Ian; Scheich, Christoph; Barker, John; Whittaker, Mark; Hesterkamp, Thomas

    2010-01-01

    The Mapkap kinases 2 and 3 (MK2 and MK3) have been implicated in intracellular signaling pathways leading to the production of the pro-inflammatory cytokine tumor necrosis factor alpha. MK2 has been pursued by the biopharmaceutical industry for many years for the development of a small molecule anti-inflammatory treatment and drug-like inhibitors have been described. The development of some of these compounds, however, has been slowed by the absence of a high-resolution crystal structure of MK2. Herein we present a high-resolution (1.9 A) crystal structure of the highly homologous MK3 in complex with a pharmaceutical lead compound. While all of the canonical features of Ser/Thr kinases in general and MK2 in particular are recapitulated in MK3, the detailed analysis of the binding interaction of the drug-like ligand within the adenine binding pocket allows relevant conclusions to be drawn for the further design of potent and selective drug candidates.

  15. Crystallization and preliminary X-ray analysis of RsbS from Moorella thermoacetica at 2.5 A resolution.

    Science.gov (United States)

    Quin, Maureen; Newman, Joseph; Firbank, Susan; Lewis, Richard J; Marles-Wright, Jon

    2008-03-01

    The thermophilic bacterium Moorella thermoacetica possesses an rsb operon that is related to the genetic locus common to many Gram-positive bacteria that regulates the activity of the stress-responsive sigma factor sigma(B). One of the gene products of this operon is RsbS, a single STAS-domain protein that is a component of higher order assemblies in Bacillus subtilis known as 'stressosomes'. It is expected that similar complexes are found in M. thermoacetica, but in this instance regulating the biosynthesis of cyclic di-GMP, a ubiquitous secondary messenger. Selenomethionine-labelled MtRsbS protein was crystallized at room temperature using the hanging-drop vapour-diffusion method. Crystals belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.07, b = 60.52, c = 89.28 A, diffracted to 2.5 A resolution on beamline I04 of the Diamond Light Source. The selenium substructure was solved using SHELX and it is believed that this represents the first reported ab initio crystal structure to be solved using diffraction data collected at DLS.

  16. Acoustic emission and magnification of atomic lines resolution for laser breakdown of salt water in ultrasound field

    Energy Technology Data Exchange (ETDEWEB)

    Bulanov, Alexey V., E-mail: a-bulanov@me.com [Far Eastern Federal University, Vladivostok, Russia 690950 (Russian Federation); V.I. Il’ichev Pacific Oceanological Institute, Vladivostok, Russia 690041 (Russian Federation); Nagorny, Ivan G., E-mail: ngrn@mail.ru [Far Eastern Federal University, Vladivostok, Russia 690950 (Russian Federation); Institute for automation and control processes, Vladivostok, Russia 690041 (Russian Federation)

    2015-10-28

    Researches of the acoustic effects accompanying optical breakdown in a water, generated by the focused laser radiation with power ultrasound have been carried out. Experiments were performed by using 532 nm pulses from Brilliant B Nd:YAG laser. Acoustic radiation was produced by acoustic focusing systems in the form hemisphere and ring by various resonance frequencies of 10.7 kHz and 60 kHz. The experimental results are obtained, that show the sharply strengthens effects of acoustic emission from a breakdown zone by the joint influence of a laser and ultrasonic irradiation. Essentially various thresholds of breakdown and character of acoustic emission in fresh and sea water are found out. The experimental result is established, testifying that acoustic emission of optical breakdown of sea water at presence and at absence of ultrasound essentially exceeds acoustic emission in fresh water. Atomic lines of some chemical elements like a Sodium, Magnesium and so on were investigated for laser breakdown of water with ultrasound field. The effect of magnification of this lines resolution for salt water in ultrasound field was obtained.

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

    Science.gov (United States)

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

    2016-10-01

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

  18. Fast sequential determination of antimony and lead in pewter alloys using high-resolution continuum source flame atomic absorption spectrometry.

    Science.gov (United States)

    Dessuy, Morgana B; de Jesus, Robson M; Brandao, Geovani C; Ferreira, Sergio L C; Vale, Maria Goreti R; Welz, Bernhard

    2013-01-01

    A simple method has been developed to determine antimony and lead in pewter alloy cups produced in Brazil, using fast sequential determination by high-resolution continuum source flame atomic absorption spectrometry. The samples were dissolved in HCl and H(2)O(2), employing a cold finger system in order to avoid analyte losses. The main resonance line of lead at 217.001 nm and a secondary line of antimony at 212.739 nm were used. The limits of detection for lead and antimony were 0.02 and 5.7 mg L(-1), respectively. The trueness of the method was established by recovery tests and comparing the results obtained by the proposed method with those obtained by inductively coupled plasma optical emission spectrometry. The results were compared using a student's t-test and there was no significant difference at a 95% confidence interval. With the developed methods, it was possible to determine accurately antimony and lead in pewter samples. The lead concentration found in the analysed samples was around 1 mg g(-1), which means that they are not lead free; however, the content was below the maximum allowed level of 5 mg g(-1). The antimony content, which was found to be between 40 and 46 mg g(-1), is actually of greater concern, as antimony is known to be potentially toxic already at very low concentrations, although there is no legislation yet for this element.

  19. Deterministic tuning of slow-light in photonic-crystal waveguides through the C and L bands by atomic layer deposition

    CERN Document Server

    Chen, Charlton J; Meric, Inanc; Shepard, Ken L; Wong, Chee Wei; Green, William M J; Vlasov, Yurii A; Assefa, Solomon

    2009-01-01

    We demonstrate digital tuning of the slow-light regime in silicon photonic-crystal waveguides by performing atomic layer deposition of hafnium oxide. The high group-index regime was deterministically controlled (red-shift of 140 +/- 10 pm per atomic layer) without affecting the group-velocity dispersion and third-order dispersion. Additionally, differential tuning of 110 +/- 30 pm per monolayer of the slow-light TE-like and TM-like modes was observed. This passive post-fabrication process has potential applications including the tuning of chip-scale optical interconnects, as well as Raman and parametric amplification.

  20. Studying the InAs quantum points on the vicinal surface of a GaAs crystal by the atomic force microscopy

    CERN Document Server

    Evtikhiev, V P; Kotelnikov, E Y; Matveentsev, A V; Titkov, A N; Shkolnik, A S

    2002-01-01

    The methodology for processing the images, obtained through the atomic force microscopy, is proposed. It is shown by the concrete example, how the parameters of the InAs clusters on the vicinal surface of the GaAs crystal are determined. This makes it possible to calculate the energy levels of the electrons and holes in the quantum point with application of the previously developed cluster spherical model

  1. Development of high-resolution gamma detector using sub-mm GAGG crystals coupled to TSV-MPPC array

    Science.gov (United States)

    Lipovec, A.; Shimazoe, K.; Takahashi, H.

    2016-03-01

    In this study a high-resolution gamma detector based on an array of sub-millimeter Ce:GAGG (Cerium doped Gd3Al2Ga3O12) crystals read out by an array of surface-mount type of TSV-MPPC was developed. MPPC sensor from Hamamatsu which has a 26 by 26 mm2 detector area with 64 channels was used. One channel has a 3 by 3 mm2 photosensitive area with 50 μ m pitch micro cells. MPPC sensor provides 576 mm2 sensing area and was used to decode 48 by 48 array with 0.4 by 0.4 by 20 mm3 Ce:GAGG crystals of 500 μ m pitch. The base of the detector with the crystal module was mounted to a read out board which consists of charge division circuit, thus allowing for a read out of four channels to identify the position of the incident event on the board. The read out signals were amplified using charge sensitive amplifiers. The four amplified signals were digitized and analyzed to produce a position sensitive event. For the performance analysis a 137Cs source was used. The produced events were used for flood histogram and energy analysis. The effects of the glass thickness between the Ce:GAGG and MPPC were analyzed using the experimental flood diagrams and Geant4 simulations. The glass between the scintillator and the detector allows the spread of the light over different channels and is necessary if the channel's sensitive area is bigger than the scintillator's area. The initial results demonstrate that this detector module is promising and could be used for applications requiring compact and high-resolution detectors. Experimental results show that the detectors precision increases using glass guide thickness of 1.35 mm and 1.85 mm; however the precision using 2.5 mm are practically the same as if using 0.8 mm or 1.0 mm glass guide thicknesses. In addition, simulations using Geant4 indicate that the light becomes scarcer if thicker glass is used, thus reducing the ability to indicate which crystal was targeted. When 2.5 mm glass thickness is used, the scarce light effect becomes

  2. The crystal structure of human dopamine  β-hydroxylase at 2.9 Å resolution

    DEFF Research Database (Denmark)

    Vendelboe, Trine Vammen; Harris, Pernille; Zhao, Y.

    2016-01-01

    The norepinephrine pathway is believed to modulate behavioral and physiological processes, such as mood, overall arousal, and attention. Furthermore, abnormalities in the pathway have been linked to numerous diseases, for example hypertension, depression, anxiety, Parkinson’s disease, schizophrenia......, Alzheimer’s disease, attention deficit hyperactivity disorder, and cocaine dependence. We report the crystal structure of human dopamine β-hydroxylase, which is the enzyme converting dopamine to norepinephrine. The structure of the DOMON (dopamine β-monooxygenase N-terminal) domain, also found in >1600...

  3. Crystal structure of haemoglobin from donkey (Equus asinus) at 3A resolution.

    Science.gov (United States)

    Balasundaresan, D; Saraboji, K; Ponnuswamy, M N

    2006-06-01

    Haemoglobin from donkey was purified and crystallized in space group C2. The present donkey haemoglobin model comprises of two subunits alpha and beta. These alpha and beta subunits comprise of 141 and 146 amino acid residues, respectively, and the haem groups. The donkey haemoglobin differs from horse only in two amino acids of alpha-chain (His20 to Asn and Tyr24 to Phe) and these substitutions do not significantly change the secondary structural features of donkey haemoglobin. The haem group region and subunit contacts are closely resemble with that of horse methaemoglobin.

  4. Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy.

    Science.gov (United States)

    Yan, Si; Guo, Changmiao; Hou, Guangjin; Zhang, Huilan; Lu, Xingyu; Williams, John Charles; Polenova, Tatyana

    2015-11-24

    Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

  5. Crystal Structure of Human Adenovirus at 3.5 Å Resolution

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Vijay S.; Natchiar, S. Kundhavai; Stewart, Phoebe L.; Nemerow, Glen R. (Scripps); (Vanderbilt)

    2010-09-27

    Rational development of adenovirus vectors for therapeutic gene transfer is hampered by the lack of accurate structural information. Here, we report the x-ray structure at 3.5 angstrom resolution of the 150-megadalton adenovirus capsid containing nearly 1 million amino acids. We describe interactions between the major capsid protein (hexon) and several accessory molecules that stabilize the capsid. The virus structure also reveals an altered association between the penton base and the trimeric fiber protein, perhaps reflecting an early event in cell entry. The high-resolution structure provides a substantial advance toward understanding the assembly and cell entry mechanisms of a large double-stranded DNA virus and provides new opportunities for improving adenovirus-mediated gene transfer.

  6. Gas-phase ion-molecule reactions for resolution of atomic isobars: AMS and ICP-MS perspectives

    Science.gov (United States)

    Bandura, Dmitry R.; Baranov, Vladimir I.; Litherland, A. E.; Tanner, Scott D.

    2006-09-01

    Ion-molecule reactions that can be used for resolution of spectral overlaps of long-lived or stable (T1/2 > 100 years) atomic isobars on the long-lived radio-isotopes (100 < T1/2 < 1012 years) in mass spectrometry are considered. Results for the separations of isobaric overlaps via cation reactions with NO, N2O, O2, CO2, C2H2, CH3F studied with the Inductively Coupled Plasma Dynamic Reaction Cell(TM) Mass Spectrometer (ICP-DRC(TM)-MS) with use of stable isotopes are presented. Overview of potential and reported reactions for separation of 35 isobars is given. Potential for the following isobaric pairs separation is shown (reaction gas and the extent of separation achieved to date in parenthesis): 32Si+/32S+(NO, 5 x 104), 40K+/40Ar+(N2O, 1.9 x 103), 40K+/40Ca+(N2O, 50), 59Ni+/59Co+(N2O, 6), 79Se+/79Br+(O2, 7.2 x 103), 81Kr+/81Br+(C2H2, 1.5 x 104), 93Mo+/93Nb+(N2O, 100), 93Mo+/93Zr+(N2O, 150), 135Cs+/135Ba+(N2O, 8 x 104), 137,138La+/137,138Ba+(O2, 40), 146Sm+/146Nd+(CO2, 1.5 x 105), 176Lu+/176Hf+(NO, 2.8 x 103), 187Re+/187Os+(N2O, 2.8 x 104). Effect of instrumental parameters on reactivity is discussed. The relevance of this work to accelerator mass spectrometry is discussed briefly.

  7. Separate-type scanner and wideband high-voltage amplifier for atomic-resolution and high-speed atomic force microscopy

    OpenAIRE

    Miyata, Kazuki; Usho, Satoshi; Yamada, Satoshi; Furuya, Shoji; Yoshida, Kiyonori; Asakawa, Hitoshi; Fukuma, Takeshi

    2013-01-01

    We have developed a liquid-environment atomic force microscope with a wideband and low-noise scanning system for atomic-scale imaging of dynamic processes at solid/liquid interfaces. The developed scanning system consists of a separate-type scanner and a wideband high-voltage amplifier (HVA). By separating an XY-sample scanner from a Z-tip scanner, we have enabled to use a relatively large sample without compromising the high resonance frequency. We compared various cantilever- and sample-hol...

  8. High resolution time-to-space conversion of sub-picosecond pulses at 1.55µm by non-degenerate SFG in PPLN crystal.

    Science.gov (United States)

    Shayovitz, Dror; Herrmann, Harald; Sohler, Wolfgang; Ricken, Raimund; Silberhorn, Christine; Marom, Dan M

    2012-11-19

    We demonstrate high resolution and increased efficiency background-free time-to-space conversion using spectrally resolved non-degenerate and collinear SFG in a bulk PPLN crystal. A serial-to-parallel resolution factor of 95 and a time window of 42 ps were achieved. A 60-fold increase in conversion efficiency slope compared with our previous work using a BBO crystal [D. Shayovitz and D. M. Marom, Opt. Lett. 36, 1957 (2011)] was recorded. Finally the measured 40 GHz narrow linewidth of the output SFG signal implies the possibility to extract phase information by employing coherent detection techniques.

  9. Calibration of the OHREX high-resolution imaging crystal spectrometer at the Livermore electron beam ion traps

    Energy Technology Data Exchange (ETDEWEB)

    Hell, N. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Dr. Remeis-Sternwarte and ECAP, Universität Erlangen-Nürnberg, Bamberg 96049 (Germany); Beiersdorfer, P.; Magee, E. W.; Brown, G. V. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)

    2016-11-15

    We report the calibration of the Orion High-Resolution X-ray (OHREX) imaging crystal spectrometer at the EBIT-I electron beam ion trap at Livermore. Two such instruments, dubbed OHREX-1 and OHREX-2, are fielded for plasma diagnostics at the Orion laser facility in the United Kingdom. The OHREX spectrometer can simultaneously house two spherically bent crystals with a radius of curvature of r = 67.2 cm. The focusing properties of the spectrometer allow both for larger distance to the source due to the increase in collected light and for observation of extended sources. OHREX is designed to cover a 2.5°–3° spectral range at Bragg angles around 51.3°. The typically high resolving powers at these large Bragg angles are ideally suited for line shape diagnostics. For instance, the nominal resolving power of the instrument (>10 000) is much higher than the effective resolving power associated with the Doppler broadening due to the temperature of the trapped ions in EBIT-I. The effective resolving power is only around 3000 at typical EBIT-I conditions, which nevertheless is sufficient to set up and test the instrument’s spectral characteristics. We have calibrated the spectral range for a number of crystals using well known reference lines in the first and second order and derived the ion temperatures from these lines. We have also made use of the 50 μm size of the EBIT-I source width to characterize the spatial focusing of the spectrometer.

  10. Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations.

    Science.gov (United States)

    Peng, Junhui; Zhang, Zhiyong

    2016-07-05

    Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1-3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.

  11. Stripping scattering of fast atoms on surfaces of metal-oxide crystals and ultrathin films; Streifende Streuung schneller Atome an Oberflaechen von Metalloxid-Kristallen und ultraduennen Filmen

    Energy Technology Data Exchange (ETDEWEB)

    Blauth, David

    2010-03-11

    In the framework of the present dissertation the interactions of fast atoms with surfaces of bulk oxides, metals and thin films on metals were studied. The experiments were performed in the regime of grazing incidence of atoms with energies of some keV. The advantage of this scattering geometry is the high surface sensibility and thus the possibility to determine the crystallographic and electronic characteristics of the topmost surface layer. In addition to these experiments, the energy loss and the electron emission induced by scattered projectiles was investigated. The energy for electron emission and exciton excitation on Alumina/NiAl(110) and SiO{sub 2}/Mo(112) are determined. By detection of the number of projectile induced emitted electrons as function of azimuthal angle for the rotation of the target surface, the geometrical structure of atoms forming the topmost layer of different adsorbate films on metal surfaces where determined via ion beam triangulation. (orig.)

  12. Energy resolution of the CdTe-XPAD detector: calibration and potential for Laue diffraction measurements on protein crystals.

    Science.gov (United States)

    Medjoubi, Kadda; Thompson, Andrew; Bérar, Jean-François; Clemens, Jean-Claude; Delpierre, Pierre; Da Silva, Paulo; Dinkespiler, Bernard; Fourme, Roger; Gourhant, Patrick; Guimaraes, Beatriz; Hustache, Stéphanie; Idir, Mourad; Itié, Jean-Paul; Legrand, Pierre; Menneglier, Claude; Mercere, Pascal; Picca, Frederic; Samama, Jean-Pierre

    2012-05-01

    The XPAD3S-CdTe, a CdTe photon-counting pixel array detector, has been used to measure the energy and the intensity of the white-beam diffraction from a lysozyme crystal. A method was developed to calibrate the detector in terms of energy, allowing incident photon energy measurement to high resolution (approximately 140 eV), opening up new possibilities in energy-resolved X-ray diffraction. In order to demonstrate this, Laue diffraction experiments were performed on the bending-magnet beamline METROLOGIE at Synchrotron SOLEIL. The X-ray energy spectra of diffracted spots were deduced from the indexed Laue patterns collected with an imaging-plate detector and then measured with both the XPAD3S-CdTe and the XPAD3S-Si, a silicon photon-counting pixel array detector. The predicted and measured energy of selected diffraction spots are in good agreement, demonstrating the reliability of the calibration method. These results open up the way to direct unit-cell parameter determination and the measurement of high-quality Laue data even at low resolution. Based on the success of these measurements, potential applications in X-ray diffraction opened up by this type of technology are discussed.

  13. High resolution crystal structure of a fluoride-inhibited organophosphate-degrading metallohydrolase.

    Science.gov (United States)

    Selleck, Christopher; Guddat, Luke W; Ollis, David L; Schenk, Gerhard; Pedroso, Marcelo Monteiro

    2017-12-01

    Metal ion-dependent, organophosphate-degrading enzymes (OP hydrolases) have received increasing attention due to their ability to degrade and thus detoxify commonly used pesticides and nerve agents such as sarin and VX. These enzymes thus garner strong potential as bioremediators. The OP hydrolase from Agrobacterium radiobacter (OpdA) is one of the most efficient members of this group of enzymes. Previous studies have indicated that the choice of the hydrolysis-initiating nucleophile may depend on the pH of the reaction, with a metal ion-bridging hydroxide being preferred at lower pH (i.e. pH≤8.5), and a terminally coordinated hydroxide at higher pH (i.e. pH>9.0). Furthermore, fluoride was shown to be a potent inhibitor of the reaction, but only at low pH. Here, the crystal structure (1.3Å, pH6) of OpdA in presence of fluoride is described. While the first coordination sphere in the active site displays minimal changes in the presence of fluoride, the hydrogen bonding network that connects the dimetallic metal center to the substrate binding pocket is disrupted. Thus, the structure of fluoride-inhibited OpdA demonstrates the significance of this hydrogen bond network in controlling the mechanism and function of this enzyme. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Aspirin induces its anti-inflammatory effects through its specific binding to phospholipase A2: crystal structure of the complex formed between phospholipase A2 and aspirin at 1.9 angstroms resolution.

    Science.gov (United States)

    Singh, Rajendra Kumar; Ethayathulla, A S; Jabeen, Talat; Sharma, Sujata; Kaur, Punit; Singh, Tej P

    2005-02-01

    Phospholipase A2 is potentially an important target for structure-based rational drug design. In order to determine the involvement of phospholipase A2 in the action of non-steroidal anti-inflammatory drugs (NSAIDs), the crystal structure of the complex formed between phospholipase A2 and aspirin has been determined at 1.9 angstroms resolution. The structure contains 915 protein atoms, 1 calcium ion, 13 atoms of aspirin and 105 water molecules. The observed electron density of the aspirin molecule in the structure was of very high quality thus allowing the precise determination of its atomic coordinates leading to the clear description of its interactions with the enzyme. The structure of the complex clearly shows that aspirin is literally embedded in the hydrophobic environment of PLA2. It is so placed in the substrate binding channel that it forms several important attractive interactions with calcium ion, His 48 and Asp 49. Thus, the structure of the complex clearly shows that aspirin occupies a favourable place in the specific binding site of PLA2. The binding studies have shown that acetyl salicylate (aspirin) binds to PLA2 enzyme specifically with a dissociation constant of 6.4 x 10(-6) M. The structural details and binding data suggest that the inhibition of PLA2 by aspirin is of pharmacological

  15. Crystal-structure analysis of four mineral samples of anhydrite, CaSO[subscript 4], using synchrotron high-resolution powder X-ray diffraction data

    Energy Technology Data Exchange (ETDEWEB)

    Antao, Sytle M. (Calgary)

    2014-05-28

    The crystal structures of four samples of anhydrite, CaSO{sub 4}, were obtained by Rietveld refinements using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and space group Amma. As an example, for one sample of anhydrite from Hants County, Nova Scotia, the unit-cell parameters are a = 7.00032(2), b = 6.99234(1), c = 6.24097(1) {angstrom}, and V = 305.487(1) {angstrom}{sup 3} with a > b. The eight-coordinated Ca atom has an average distance of 2.4667(4) {angstrom}. The tetrahedral SO{sub 4} group has two independent S-O distances of 1.484(1) to O1 and 1.478(1) {angstrom} to O2 and an average distance of 1.4810(5) {angstrom}. The three independent O-S-O angles [108.99(8) x 1, 110.38(3) x 4, 106.34(9){sup o} x 1; average [6] = 109.47(2){sup o}] and S-O distances indicate that the geometry of the SO{sub 4} group is quite distorted in anhydrite. The four anhydrite samples have structural trends where the a, b, and c unit-cell parameters increase linearly with increasing unit-cell volume, V, and their average and distances are nearly constant. The grand mean = 2.4660(2) {angstrom}, and grand mean = 1.4848(3) {angstrom}, the latter is longer than 1.480(1) {angstrom} in celestite, SrSO{sub 4}, as expected.

  16. Determination of total mercury for marine environmental monitoring studies by solid sampling continuum source high resolution atomic absorption spectrometry

    Science.gov (United States)

    Mandjukov, Petko; Orani, Anna Maria; Han, Eunmi; Vassileva, Emilia

    2015-01-01

    The most critical step in almost all commonly used analytical procedures for Hg determination is the sample preparation due to its extreme volatility. One of the possible solutions of this problem is the application of methods for direct analysis of solid samples. The possibilities for solid sampling high resolution continuum source atomic absorption spectrometry (HR CS AAS) determination of total mercury in various marine environmental samples e.g. sediments and biota are object of the present study. The instrumental parameters were optimized in order to obtain reproducible and interference free analytical signal. A calibration technique based on the use of solid standard certified reference materials similar to the nature of the analyzed sample was developed and applied to various CRMs and real samples. This technique allows simple and reliable evaluation of the uncertainty of the result and the metrological characteristics of the method. A validation approach in line with the requirements of ISO 17025 standard and Eurachem guidelines was followed. With this in mind, selectivity, working range (0.06 to 25 ng for biota and 0.025 to 4 ng for sediment samples, expressed as total Hg) linearity (confirmed by Student's t-test), bias (1.6-4.3%), repeatability (4-9%), reproducibility (9-11%), and absolute limit of detection (0.025 ng for sediment, 0.096 ng for marine biota) were systematically assessed using solid CRMs. The relative expanded uncertainty was estimated at 15% for sediment sample and 8.5% for marine biota sample (k = 2). Demonstration of traceability of measurement results is also presented. The potential of the proposed analytical procedure, based on solid sampling HR CS AAS technique was demonstrated by direct analysis of sea sediments form the Caribbean region and various CRMs. Overall, the use of solid sampling HR CS AAS permits obtaining significant advantages for the determination of this complex analyte in marine samples, such as straightforward

  17. Determination of total mercury for marine environmental monitoring studies by solid sampling continuum source high resolution atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Mandjukov, Petko; Orani, Anna Maria; Han, Eunmi; Vassileva, Emilia, E-mail: e.vasileva-veleva@iaea.org

    2015-01-01

    The most critical step in almost all commonly used analytical procedures for Hg determination is the sample preparation due to its extreme volatility. One of the possible solutions of this problem is the application of methods for direct analysis of solid samples. The possibilities for solid sampling high resolution continuum source atomic absorption spectrometry (HR CS AAS) determination of total mercury in various marine environmental samples e.g. sediments and biota are object of the present study. The instrumental parameters were optimized in order to obtain reproducible and interference free analytical signal. A calibration technique based on the use of solid standard certified reference materials similar to the nature of the analyzed sample was developed and applied to various CRMs and real samples. This technique allows simple and reliable evaluation of the uncertainty of the result and the metrological characteristics of the method. A validation approach in line with the requirements of ISO 17025 standard and Eurachem guidelines was followed. With this in mind, selectivity, working range (0.06 to 25 ng for biota and 0.025 to 4 ng for sediment samples, expressed as total Hg) linearity (confirmed by Student's t-test), bias (1.6–4.3%), repeatability (4–9%), reproducibility (9–11%), and absolute limit of detection (0.025 ng for sediment, 0.096 ng for marine biota) were systematically assessed using solid CRMs. The relative expanded uncertainty was estimated at 15% for sediment sample and 8.5% for marine biota sample (k = 2). Demonstration of traceability of measurement results is also presented. The potential of the proposed analytical procedure, based on solid sampling HR CS AAS technique was demonstrated by direct analysis of sea sediments form the Caribbean region and various CRMs. Overall, the use of solid sampling HR CS AAS permits obtaining significant advantages for the determination of this complex analyte in marine samples, such as

  18. Statistical studies on the light output and energy resolution of small LSO single crystals with different surface treatments combined with various reflector materials

    CERN Document Server

    Heinrichs, U; Bussmann, N; Engels, R; Kemmerling, G; Weber, S; Ziemons, K

    2002-01-01

    The optimization of light output and energy resolution of scintillators is of special interest for the development of high resolution and high sensitivity PET. The aim of this work is to obtain statistically reliable results concerning optimal surface treatment of scintillation crystals and the selection of reflector material. For this purpose, raw, mechanically polished and etched LSO crystals (size 2x2x10 mm sup 3) were combined with various reflector materials (Teflon tape, Teflon matrix, BaSO sub 4) and exposed to a sup 2 sup 2 Na source. In order to ensure the statistical reliability of the results, groups of 10 LSO crystals each were measured for all combinations of surface treatment and reflector material. Using no reflector material the light output increased up to 551+-35% by mechanical polishing the surface compared to 100+-5% for raw crystals. Etching the surface increased the light output to 441+-29%. The untreated crystals had an energy resolution of 24.6+-4.0%. By mechanical polishing the surfac...

  19. A dead-zone free 4He atomic magnetometer with intensity-modulated linearly polarized light and a liquid crystal polarization rotator

    Science.gov (United States)

    Wu, T.; Peng, X.; Lin, Z.; Guo, H.

    2015-10-01

    We demonstrate an all-optical 4He atomic magnetometer experimental scheme based on an original Bell-Bloom configuration. A single intensity-modulated linearly polarized laser beam is used both for generating spin polarization within a single 4He vapor and probing the spin precessing under a static magnetic field. The transmitted light signal from the vapor is then phase-sensitively detected at the modulation frequency and its harmonics, which lead to the atomic magnetic resonance signals. Based on this structure, a liquid crystal is added in our magnetometer system and constitutes a polarization rotator. By controlling the voltage applied on the liquid crystal, the light linear polarization vector can be kept perpendicular with the ambient magnetic field direction, which in turn provides the maximum resonance signal amplitude. Moreover, the system exhibits a magnetic-field noise floor of about 2 pT / √{ Hz } , which is not degraded due to the presence of the liquid crystal and varying magnetic field direction. The experiment results prove that our method can eliminate the dead-zone effect, improve the system spatial isotropy, and thus be suitable in mobile applications.

  20. A dead-zone free ⁴He atomic magnetometer with intensity-modulated linearly polarized light and a liquid crystal polarization rotator.

    Science.gov (United States)

    Wu, T; Peng, X; Lin, Z; Guo, H

    2015-10-01

    We demonstrate an all-optical (4)He atomic magnetometer experimental scheme based on an original Bell-Bloom configuration. A single intensity-modulated linearly polarized laser beam is used both for generating spin polarization within a single (4)He vapor and probing the spin precessing under a static magnetic field. The transmitted light signal from the vapor is then phase-sensitively detected at the modulation frequency and its harmonics, which lead to the atomic magnetic resonance signals. Based on this structure, a liquid crystal is added in our magnetometer system and constitutes a polarization rotator. By controlling the voltage applied on the liquid crystal, the light linear polarization vector can be kept perpendicular with the ambient magnetic field direction, which in turn provides the maximum resonance signal amplitude. Moreover, the system exhibits a magnetic-field noise floor of about 2pT/√Hz, which is not degraded due to the presence of the liquid crystal and varying magnetic field direction. The experiment results prove that our method can eliminate the dead-zone effect, improve the system spatial isotropy, and thus be suitable in mobile applications.

  1. CRYSTAL-STRUCTURE OF RECOMBINANT HUMAN TRIOSEPHOSPHATE ISOMERASE AT 2.8 ANGSTROM RESOLUTION - TRIOSEPHOSPHATE ISOMERASE-RELATED HUMAN GENETIC-DISORDERS AND COMPARISON WITH THE TRYPANOSOMAL ENZYME

    NARCIS (Netherlands)

    MANDE, SC; MAINFROID, [No Value; KALK, KH; GORAJ, K; MARTIAL, JA; HOL, WGJ

    The crystal structure of recombinant human triosephosphate isomerase (hTIM) has been determined complexed with the transition-state analogue 2-phosphoglycolate at a resolution of 2.8 Angstrom. After refinement, the R-factor is 16.7% with good geometry. The asymmetric unit contains 1 complete dimer

  2. High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand

    DEFF Research Database (Denmark)

    Taskinen, Jukka P; van Aalten, Daan M; Knudsen, Jens

    2007-01-01

    The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described...

  3. Crystal structures at 2.5 Angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate

    DEFF Research Database (Denmark)

    Belrhali, H.; Yaremchuk, A.; Tukalo, M.

    1994-01-01

    Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 Angstrom resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically...

  4. CRYSTAL-STRUCTURE OF DEOXYGENATED LIMULUS-POLYPHEMUS SUBUNIT-II HEMOCYANIN AT 2.18-ANGSTROM RESOLUTION - CLUES FOR A MECHANISM FOR ALLOSTERIC REGULATION

    NARCIS (Netherlands)

    HAZES, B; MAGNUS, KA; BONAVENTURA, C; BONAVENTURA, J; DAUTER, Z; KALK, KH; HOL, WGJ

    The crystal structure of Limulus polyphemus subunit type II hemocyanin in the deoxygenated state has been determined to a resolution of 2.18 angstrom. Phase information for this first structure of a cheliceratan hemocyanin was obtained by molecular replacement using the crustacean hemocyanin

  5. Atomic-resolution studies of In{sub 2}O{sub 3}-ZnO compounds on aberration-corrected electron microscopes

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Wentao

    2009-10-23

    In this work, the characteristic inversion domain microstructures of In{sub 2}O{sub 3}(ZnO){sub m} (m=30) compounds were investigated by TEM methods. At bright-atom contrast condition, atomically resolved HR-TEM images of In{sub 2}O{sub 3}(ZnO){sub 30} were successfully acquired in [1 anti 100] zone axis of ZnO, with projected metal columns of {proportional_to}1.6 A well resolved. From contrast maxima in the TEM images, local lattice distortions at the pyramidal inversion domain boundaries were observed for the first time. Lattice displacements and the strain field in two-dimensions were visualized and measured using the 'DALI' algorithm. Atomically resolved single shot and focal series images of In{sub 2}O{sub 3}(ZnO){sub 30} were achieved in both zone axes of ZnO, [1 anti 100] and [2 anti 1 anti 10], respectively. The electron waves at the exit-plane were successfully reconstructed using the software package 'TrueImage'. Finally, a three dimensional atomic structure model for the pyramidal IDB was proposed, with an In distribution of 10%, 20%, 40%, 20% and 10% of In contents over 5 atom columns along basal planes, respectively. Through a detailed structural study of In{sub 2}O{sub 3}(ZnO){sub m} compounds by using phase-contrast and Z-contrast imaging at atomic resolution, In{sup 3+} atoms are determined with trigonal bi-pyramidal co-ordination and are distributed at the pyramidal IDBs. (orig.)

  6. High-resolution water window X-ray imaging of in vivo cells and their products using LiF crystal detectors.

    Science.gov (United States)

    Bonfigli, Francesca; Faenov, Anatoly; Flora, Francesco; Francucci, Massimo; Gaudio, Pasqualino; Lai, Antonia; Martellucci, Sergio; Montereali, Rosa Maria; Pikuz, Tania; Reale, Lucia; Richetta, Maria; Vincenti, Maria Aurora; Baldacchini, Giuseppe

    2008-01-01

    High contrast imaging of in vivo Chlorella sorokiniana cells with submicron spatial resolution was obtained with a contact water window X-ray microscopy technique using a point-like, laser-plasma produced, water-window X-ray radiation source, and LiF crystals as detectors. This novel type of X-ray imaging detectors is based on photoluminescence of stable electronic point defects, characterized by high intrinsic resolution. The fluorescence images obtained on LiF crystals exposed in single-shot experiments demonstrate the high sensitivity and dynamic range of this new detector. The powerful performances of LiF crystals allowed us to detect the exudates of Chlorella cells in their living medium and their spatial distribution in situ, without any special sample preparation. 2007 Wiley-Liss, Inc

  7. Near-Atomic Resolution Structure Determination in Over-Focus with Volta Phase Plate by Cs-Corrected Cryo-EM.

    Science.gov (United States)

    Fan, Xiao; Zhao, Lingyun; Liu, Chuan; Zhang, Jin-Can; Fan, Kelong; Yan, Xiyun; Peng, Hai-Lin; Lei, Jianlin; Wang, Hong-Wei

    2017-10-03

    Volta phase plate (VPP) is a recently developed transmission electron microscope (TEM) apparatus that can significantly enhance the image contrast of biological samples in cryoelectron microscopy, and therefore provide the possibility to solve structures of relatively small macromolecules at high-resolution. In this work, we performed theoretical analysis and found that using phase plate on objective lens spherical aberration (Cs)-corrected TEM may gain some interesting optical properties, including the over-focus imaging of macromolecules. We subsequently evaluated the imaging strategy of frozen-hydrated apo-ferritin with VPP on a Cs-corrected TEM and obtained the structure of apo-ferritin at near-atomic resolution from both under- and over-focused dataset, illustrating the feasibility and new potential of combining VPP with Cs-corrected TEM for high-resolution cryo-EM. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. [Connection of magnetic antisense probe with SK-Br-3 oncocyte mRNA nucleotide detected by high resolution atomic force microscope].

    Science.gov (United States)

    Tan, Shude; Ouyang, Yu; Li, Xinyou; Wen, Ming; Li, Shaolin

    2011-06-01

    The present paper is aimed to detect superparamagnetic iron oxide labeled c-erbB2 oncogene antisense oligonucleotide probe (magnetic antisense probe) connected with SK-Br-3 oncocyte mRNA nucleotide by high resolution atomic force microscope (AFM). We transfected SK-Br-3 oncocyte with magnetic antisense probe, then observed the cells by AFM with high resolution and detected protein expression and magnetic resonance imagine (MRI). The high resolution AFM clearly showed the connection of the oligonucleotide remote end of magnetic antisense probe with the mRNA nucleotide of oncocyte. The expression of e-erbB2 protein in SK-Br3 cells were highly inhibited by using magnetic antisense probe. We then obtained the lowest signal to noise ratio (SNR) of SK-Br-3 oncocyte transfected with magnetic antisense probe by MRI (Pmagnetic antisense probe and SK-Br-3 mRNA of tumor cell nuclear.

  9. Study of morphology and crystal growth behaviour of nanoclay-containing biodegradable polymer blend thin films using atomic force microscopy

    CSIR Research Space (South Africa)

    Malwela, T

    2012-04-01

    Full Text Available Thin films of unmodified and nanoclay-modified polylactide/poly(butylene succinate) (PLA/PBS) blends were prepared on a glass substrate with a spin coater. The morphology and crystal growth behaviours for the films, crystallized at different...

  10. Hirshfeld atom refinement.

    Science.gov (United States)

    Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

    2014-09-01

    Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

  11. High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-l-arabinofuranosidase activity

    Energy Technology Data Exchange (ETDEWEB)

    Hassan, Noor [KTH Royal Institute of Technology, Stockholm (Sweden); Karolinska Institutet, Stockholm (Sweden); Kori, Lokesh D. [Griffith University, Brisbane, QLD 4111 (Australia); Baylor College of Medicine, Houston, TX 77030 (United States); Gandini, Rosaria [KTH Royal Institute of Technology, Stockholm (Sweden); Karolinska Institutet, Stockholm (Sweden); Patel, Bharat K. C. [Griffith University, Brisbane, QLD 4111 (Australia); Divne, Christina; Tan, Tien Chye, E-mail: tantc@kth.se [KTH Royal Institute of Technology, Stockholm (Sweden); Karolinska Institutet, Stockholm (Sweden)

    2015-02-19

    The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. A gene from the heterotrophic, halothermophilic marine bacterium Halothermothrix orenii has been cloned and overexpressed in Escherichia coli. This gene encodes the only glycoside hydrolase of family 43 (GH43) produced by H. orenii. The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. As for other GH43 members, the enzyme folds as a five-bladed β-propeller. The structure features a metal-binding site on the propeller axis, near the active site. Based on thermal denaturation data, the H. orenii glycosidase depends on divalent cations in combination with high salt for optimal thermal stability against unfolding. A maximum melting temperature of 76°C was observed in the presence of 4 M NaCl and Mn{sup 2+} at pH 6.5. The gene encoding the H. orenii GH43 enzyme has previously been annotated as a putative α-l-arabinofuranosidase. Activity was detected with p-nitrophenyl-α-l-arabinofuranoside as a substrate, and therefore the name HoAraf43 was suggested for the enzyme. In agreement with the conditions for optimal thermal stability against unfolding, the highest arabinofuranosidase activity was obtained in the presence of 4 M NaCl and Mn{sup 2+} at pH 6.5, giving a specific activity of 20–36 µmol min{sup −1} mg{sup −1}. The active site is structurally distinct from those of other GH43 members, including arabinanases, arabinofuranosidases and xylanases. This probably reflects the special requirements for degrading the unique biomass available in highly saline aqueous ecosystems, such as halophilic algae and halophytes. The amino-acid distribution of HoAraf43 has similarities to those of mesophiles, thermophiles and halophiles, but also has unique features, for example more hydrophobic amino acids on the surface and fewer buried charged residues.

  12. Comparison of precursor infiltration into polymer thin films via atomic layer deposition and sequential vapor infiltration using in-situ quartz crystal microgravimetry

    Energy Technology Data Exchange (ETDEWEB)

    Padbury, Richard P.; Jur, Jesse S., E-mail: jsjur@ncsu.edu [Department of Textile Engineering, Chemistry and Science, North Carolina State University, Raleigh, North Carolina 27695 (United States)

    2014-07-01

    Previous research exploring inorganic materials nucleation behavior on polymers via atomic layer deposition indicates the formation of hybrid organic–inorganic materials that form within the subsurface of the polymer. This has inspired adaptations to the process, such as sequential vapor infiltration, which enhances the diffusion of organometallic precursors into the subsurface of the polymer to promote the formation of a hybrid organic–inorganic coating. This work highlights the fundamental difference in mass uptake behavior between atomic layer deposition and sequential vapor infiltration using in-situ methods. In particular, in-situ quartz crystal microgravimetry is used to compare the mass uptake behavior of trimethyl aluminum in poly(butylene terephthalate) and polyamide-6 polymer thin films. The importance of trimethyl aluminum diffusion into the polymer subsurface and the subsequent chemical reactions with polymer functional groups are discussed.

  13. Electron diffraction and high-resolution transmission electron microscopy of the high temperature crystal structures of GexSb2Te3+x (x=1,2,3) phase change material

    NARCIS (Netherlands)

    Kooi, B.J.; de Hosson, J.T.M.

    2002-01-01

    The crystal structures of GeSb2Te4, Ge2Sb2Te5, and Ge3Sb2Te6 were determined using electron diffraction and high-resolution transmission electron microscopy. The structure determined for the former two crystals deviates from the ones proposed in the literature. These crystal structures were

  14. Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of C(alpha atoms.

    Directory of Open Access Journals (Sweden)

    Rupali A Gadkari

    Full Text Available BACKGROUND: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C(alpha atoms which are modeled with modest accuracy. METHODOLOGY/PRINCIPAL FINDINGS: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C(alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C(alpha. We extend the method further to recognize potential protein-protein interface residues. CONCLUSION/ SIGNIFICANCE: Our approach to identify buried and exposed residues solely from the positions of C(alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C(alpha positions and all-atom models suggested that, recognition of interfacial residues using C(alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only (alpha positions are available as, for example, in the cases of integration of cryo

  15. Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment: comparison of atom-centered charge, extra-point and polarizable force fields.

    Science.gov (United States)

    Baucom, Jason; Transue, Thomas; Fuentes-Cabrera, Miguel; Krahn, Joseph; Darden, Thomas; Sagui, Celeste

    2004-03-01

    Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)2 were used to study the relationship between DNA sequence and structure. Three different force fields were used: a traditional description based on atomic point charges, a polarizable force field and an ``extra-point" force field (with additional charges on extra-nuclear sites). It is found that in crystal environment all the force fields reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force fields, however, outperforms the other two, pointing out to the need of the inclusion of polarization for accurate descriptions of DNA.

  16. DFT study of the effect of fluorine atoms on the crystal structure and semiconducting properties of poly(arylene-ethynylene) derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Moral, Mónica, E-mail: monica.moral@uclm.es [Renewable Energy Research Institute, University of Castilla-La Mancha, Paseo de la Investigación 1, 02071 Albacete (Spain); García, Gregorio [Department of Chemistry, University of Burgos, Plaza Misael Bañuelos, s/n, 09001 Burgos (Spain); Garzón, Andrés [Department of Physical Chemistry, Faculty of Pharmacy, University of Castilla-La Mancha, Paseo de los Estudiantes, 02071 Albacete (Spain); Granadino-Roldán, José M.; Fernández-Gómez, Manuel [Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, s/n, 23071 Jaén (Spain)

    2016-04-21

    The effect of fluorine substitution on the molecular structure, crystal packing, and n-type semiconducting properties of a set of poly(arylene-ethynylene) polymers based on alternating thiadiazole and phenyl units linked through ethynylene groups has been studied by means of Density Functional Theory. As a result, an enlargement in the interplanar distance between cofacial polymer chains, as well as a decrease of the electronic coupling and electron mobility is predicted. On the other hand, fluorination could facilitate electron injection into the material. A polymer containing both alkoxy pendant chains and fluorine atoms is proposed as a compromise solution between efficiency of electron injection and charge transport within the material.

  17. Two Keggin-type heteropolytungstates with transition metal as a central atom: Crystal structure and magnetic study with 2D-IR correlation spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chai, Feng [Department of Chemistry, Fuzhou University, Fuzhou 350108 (China); Chen, YiPing, E-mail: ypchen007@sina.com [Department of Chemistry, Fuzhou University, Fuzhou 350108 (China); State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002 (China); You, ZhuChai; Xia, ZeMin; Ge, SuZhi; Sun, YanQiong; Huang, BiHua [Department of Chemistry, Fuzhou University, Fuzhou 350108 (China)

    2013-06-01

    Two Keggin-type heteropolytungstates, [Co(phen)₃]₃[CoW₁₂O₄₀]·9H₂O 1 (phen=1,10-phenanthroline) and [Fe(phen)₃]₂[FeW₁₂O₄₀]·H₃O·H₂O 2, have been synthesized via the hydrothermal technique and characterized by single crystal X-ray diffraction analyses, IR, XPS, TG analysis, UV–DRS, XRD, thermal-dependent and magnetic-dependent 2D-COS IR (two-dimensional infrared correlation spectroscopy). Crystal structure analysis reveals that the polyanions in compound 1 are linked into 3D supramolecule through hydrogen bonding interactions between lattice water molecules and terminal oxygen atoms of polyanion units, and [Co(phen)₃]²⁺ cations distributed in the polyanion framework with many hydrogen bonding interactions. The XPS spectra indicate that all the Co atoms in 1 are +2 oxidation state, the Fe atoms in 2 existing with +2 and +3 mixed oxidation states. - Graphical abstract: The magnetic-dependent synchronous 2D correlation IR spectra of 1 (a), 2 (b) over 0–50 mT in the range of 600–1000 cm⁻¹, the obvious response indicate two Keggin polyanions skeleton susceptible to applied magnetic field. Highlights: • Two Keggin-type heteropolytungstates with transition metal as a central atom has been obtained. • Compound 1 forms into 3D supramolecular architecture through hydrogen bonding between water molecules and polyanions. • Magnetic-dependent 2D-IR correlation spectroscopy was introduced to discuss the magnetism of polyoxometalate.

  18. Ductile-brittle behavior at blunted cavities in 3D iron crystals uncovered and covered by copper atoms

    Directory of Open Access Journals (Sweden)

    Pelikán V.

    2010-12-01

    Full Text Available This paper is devoted to studies of the mechanical response of an atomically blunted cavity uncovered and covered by copper atoms by means 3D molecular dynamic (MD simulations. The cavity is loaded uni-axially in tension mode I. Our question is how the copper atoms influence the ductile-brittle behavior at the crack front of the blunted cavity in comparison with the blunted cavity in pure bcc iron. We show that the dislocation emission is easier in the Fe–Cu system in comparison with pure bcc iron. However, stability of the blunted cavities seems to be weaker in copper region than in pure bcc iron.

  19. Combined High Spectral Resolution Lidar and Millimeter Wavelength Radar Measurement of Ice Crystal Precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Eloranta, Edwin [Univ. of Wisconsin, Madison, WI (United States)

    2016-10-28

    The goal of this research has been to improve measurements of snowfall using a combination of millimeter-wavelength radar and High Spectral Resolution Lidar (HSRL) Observations. Snowflakes are large compared to the 532nm HSRL wavelength and small compared to the 3.2 and 8.6 mm wavelength radars used in this study. This places the particles in the optical scattering regime of the HSRL, where extinction cross-section is proportional to the projected area of the particles, and in the Rayleigh regime for the radar, where the backscatter cross-section is proportional to the mass-squared of the particles. Forming a ratio of the radar measured cross-section to the HSRL measured cross section eliminates any dependence on the number of scattering particles, yielding a quantity proportional to the average mass-squared of the snowflakes over the average area of the flakes. Using simultaneous radar measurements of particle fall velocities, which are dependent particle mass and cross-sectional area it is possible to derive the average mass of the snow flakes, and with the radar measured fall velocities compute the snowfall rate. Since this retrieval requires the optical extinction cross-section we began by considering errors this quantity. The HSRL is particularly good at measuring the backscatter cross-section. In previous studies of snowfall in the high Arctic were able to estimate the extinction cross-section directly as a fixed ratio to the backscatter cross-section. Measurements acquired in the STORMVEX experiment in Colorado showed that this approach was not valid in mid-latitude snowfalls and that direct measurement of the extinction cross-section is required. Attempts to measure the extinction directly uncovered shortcomings in thermal regulation and mechanical stability of the newly deployed DOE HSRL systems. These problems were largely mitigated by modifications installed in both of the DOE systems. We also investigated other sources of error in the HSRL direct

  20. Organometallic Bonding in an Ullmann-Type On-Surface Chemical Reaction Studied by High-Resolution Atomic Force Microscopy.

    Science.gov (United States)

    Kawai, Shigeki; Sadeghi, Ali; Okamoto, Toshihiro; Mitsui, Chikahiko; Pawlak, Rémy; Meier, Tobias; Takeya, Jun; Goedecker, Stefan; Meyer, Ernst

    2016-10-01

    The on-surface Ullmann-type chemical reaction synthesizes polymers by linking carbons of adjacent molecules on solid surfaces. Although an organometallic compound is recently identified as the reaction intermediate, little is known about the detailed structure of the bonded organometallic species and its influence on the molecule and the reaction. Herein atomic force microscopy at low temperature is used to study the reaction with 3,9-diiododinaphtho[2,3-b:2',3'-d]thiophene (I-DNT-VW), which is polymerized on Ag(111) in vacuum. Thermally sublimated I-DNT-VW picks up a Ag surface atom, forming a CAg bond at one end after removing an iodine. The CAg bond is usually short-lived, and a CAgC organometallic bond immediately forms with an adjacent molecule. The existence of the bonded Ag atoms strongly affects the bending angle and adsorption height of the molecular unit. Density functional theory calculations reveal the bending mechanism, which reveals that charge from the terminus of the molecule is transferred via the Ag atom into the organometallic bond and strengths the local adsorption to the substrate. Such deformations vanish when the Ag atoms are removed by annealing and CC bonds are established. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state

    Energy Technology Data Exchange (ETDEWEB)

    Blankenship, Elise; Vukoti, Krishna [Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Miyagi, Masaru, E-mail: mxm356@cwru.edu [Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Lodowski, David T., E-mail: mxm356@cwru.edu [Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States)

    2014-03-01

    This work reports the first sub-angstrom resolution structure of S. erythraeus trypsin. The detailed model of a prototypical serine protease at a catalytically relevant pH with an unoccupied active site is presented and is compared with other high-resolution serine protease structures. With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.

  2. A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

    Energy Technology Data Exchange (ETDEWEB)

    Yap, Thai Leong [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore); Chen, Yen Liang; Xu, Ting; Wen, Daying; Vasudevan, Subhash G. [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); Lescar, Julien, E-mail: julien@ntu.edu.sg [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)

    2007-02-01

    Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents an interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration.

  3. Monolayer resolution in Rutherford backscattering spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kimura, K. [Kyoto Univ. (Japan). Dept. of Engineering Science; Ohshima, K. [Kyoto Univ. (Japan). Dept. of Engineering Science; Nakajima, K. [Kyoto Univ. (Japan). Dept. of Engineering Science; Fujii, Y. [Kyoto Univ. (Japan). Dept. of Engineering Science; Mannami, M. [Kyoto Univ. (Japan). Dept. of Engineering Science; Gossmann, H.J. [AT and T Bell Laboratories, Murray Hill, NJ 07974 (United States)

    1995-05-01

    Conditions for to obtain monolayer resolution in Rutherford backscattering spectroscopy are discussed. It is shown that both high energy resolution and the grazing angle technique are essential to achieve monolayer resolution. A 90 sector magnetic spectrometer ({delta}E/E similar 0.1%) is utilized for high-resolution Rutherford backscattering spectroscopy (HRBS). Energy spectra of scattered 300-keV He ions from single crystals are measured with the spectrometer at grazing exit angles. The ions scattered from successive atomic layers can be resolved as separated peaks in the energy spectra. Results of some applications of HRBS are presented. (orig.).

  4. Single-particle cryo-EM at crystallographic resolution

    Science.gov (United States)

    Cheng, Yifan

    2015-01-01

    Until only a few years ago, single-particle electron cryo-microscopy (cryo-EM) was usually not the first choice for many structural biologists due to its limited resolution in the range of nanometer to subnanometer. Now, this method rivals X-ray crystallography in terms of resolution and can be used to determine atomic structures of macromolecules that are either refractory to crystallization or difficult to crystallize in specific functional states. In this review, I discuss the recent breakthroughs in both hardware and software that transformed cryo-microscopy, enabling understanding of complex biomolecules and their functions at atomic level. PMID:25910205

  5. Cytochrome c3 from Desulfovibrio gigas: crystal structure at 1.8 A resolution and evidence for a specific calcium-binding site.

    OpenAIRE

    Matias, P. M.; Morais, J.; Coelho, R.; Carrondo, M. A.; Wilson, K. Van; Dauter, Z.; Sieker, L

    1996-01-01

    Crystals of the tetraheme cytochrome c3 from sulfate-reducing bacteria Desulfovibrio gigas (Dg) (MW 13 kDa, 111 residues, four heme groups) were obtained and X-ray diffraction data collected to 1.8 A resolution. The structure was solved by the method of molecular replacement and the resulting model refined to a conventional R-factor of 14.9%. The three-dimensional structure shows many similarities to other known crystal structures of tetraheme c3 cytochromes, but it also shows some remarkable...

  6. Calcite biomineralization in coccoliths: Evidence from atomic force microscopy (AFM)

    DEFF Research Database (Denmark)

    Henriksen, Karen; Stipp, S.L.S.

    2002-01-01

    geochemistry, crystal orientation, coccolith function, biomineralization, biological calcite, atomic force microscopy......geochemistry, crystal orientation, coccolith function, biomineralization, biological calcite, atomic force microscopy...

  7. Optimal experimental design for the detection of light atoms from high-resolution scanning transmission electron microscopy images

    NARCIS (Netherlands)

    Gonnissen, J.; De Backer, A.; Den Dekker, A.J.; Martinez, G.T.; Rosenauer, A.; Sijbers, J.; Van Aert, S.

    2014-01-01

    We report an innovative method to explore the optimal experimental settings to detect light atoms from scanning transmission electron microscopy (STEM) images. Since light elements play a key role in many technologically important materials, such as lithium-battery devices or hydrogen storage

  8. A new approach for the determination of sulphur in food samples by high-resolution continuum source flame atomic absorption spectrometer.

    Science.gov (United States)

    Ozbek, N; Baysal, A

    2015-02-01

    The new approach for the determination of sulphur in foods was developed, and the sulphur concentrations of various fresh and dried food samples determined using a high-resolution continuum source flame atomic absorption spectrometer with an air/acetylene flame. The proposed method was optimised and the validated using standard reference materials, and certified values were found to be within the 95% confidence interval. The sulphur content of foods ranged from less than the LOD to 1.5mgg(-1). The method is accurate, fast, simple and sensitive. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  10. Two-step high-resolution laser spectroscopy of the Stark substates of the n = 33 level in atomic hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Delsart, C.; Cabaret, L.; Blondel, C.; Champeau, R.J.

    1987-09-28

    Two synchronised pulsed single-mode tunable laser systems are used to excite atomic hydrogen in an atomic beam. A vacuum ultraviolet laser populates first the 2p /sup 2/Psub(3/2) sublevel from the ground 1s/sup 2/Ssub(1/2) state. A second-step UV laser selects substates of the n = 33 manifold in the presence of a weak electric field. Stark patterns of this manifold are recorded for different polarisation configurations of the exciting light beams. The measured relative intensities of the Stark components agree with the theoretical excitation probabilities in the two-step process, calculated to the first order of perturbation theory. Varying the field value of the ionisation field pulse also makes it possible to plot the ionisation threshold against the parabolic quantum number in the n = 33 manifold. The results agree with an asymptotic formula of ionisation probabilities for hydrogen perturbed by an electric field.

  11. Exploiting the high-resolution crystal structure of Staphylococcus aureus MenH to gain insight into enzyme activity

    Directory of Open Access Journals (Sweden)

    Gillet Florian

    2011-04-01

    Full Text Available Abstract Background MenH (2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase is a key enzyme in the biosynthesis of menaquinone, catalyzing an unusual 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate. Results The crystal structure of Staphylococcus aureus MenH has been determined at 2 Å resolution. In the absence of a complex to inform on aspects of specificity a model of the enzyme-substrate complex has been used in conjunction with previously published kinetic analyses, site-directed mutagenesis studies and comparisons with orthologues to investigate the structure and reactivity of MenH. Conclusions The overall basic active site displays pronounced hydrophobic character on one side and these properties complement those of the substrate. A complex network of hydrogen bonds involving well-ordered water molecules serves to position key residues participating in the recognition of substrate and subsequent catalysis. We propose a proton shuttle mechanism, reliant on a catalytic triad consisting of Ser89, Asp216 and His243. The reaction is initiated by proton abstraction from the substrate by an activated Ser89. The propensity to form a conjugated system provides the driving force for pyruvate elimination. During the elimination, a methylene group is converted to a methyl and we judge it likely that His243 provides a proton, previously acquired from Ser89 for that reduction. A conformational change of the protonated His243 may be encouraged by the presence of an anionic intermediate in the active site.

  12. High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-L-arabinofuranosidase activity.

    Science.gov (United States)

    Hassan, Noor; Kori, Lokesh D; Gandini, Rosaria; Patel, Bharat K C; Divne, Christina; Tan, Tien Chye

    2015-03-01

    A gene from the heterotrophic, halothermophilic marine bacterium Halothermothrix orenii has been cloned and overexpressed in Escherichia coli. This gene encodes the only glycoside hydrolase of family 43 (GH43) produced by H. orenii. The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. As for other GH43 members, the enzyme folds as a five-bladed β-propeller. The structure features a metal-binding site on the propeller axis, near the active site. Based on thermal denaturation data, the H. orenii glycosidase depends on divalent cations in combination with high salt for optimal thermal stability against unfolding. A maximum melting temperature of 76°C was observed in the presence of 4 M NaCl and Mn(2+) at pH 6.5. The gene encoding the H. orenii GH43 enzyme has previously been annotated as a putative α-L-arabinofuranosidase. Activity was detected with p-nitrophenyl-α-L-arabinofuranoside as a substrate, and therefore the name HoAraf43 was suggested for the enzyme. In agreement with the conditions for optimal thermal stability against unfolding, the highest arabinofuranosidase activity was obtained in the presence of 4 M NaCl and Mn(2+) at pH 6.5, giving a specific activity of 20-36 µmol min(-1) mg(-1). The active site is structurally distinct from those of other GH43 members, including arabinanases, arabinofuranosidases and xylanases. This probably reflects the special requirements for degrading the unique biomass available in highly saline aqueous ecosystems, such as halophilic algae and halophytes. The amino-acid distribution of HoAraf43 has similarities to those of mesophiles, thermophiles and halophiles, but also has unique features, for example more hydrophobic amino acids on the surface and fewer buried charged residues.

  13. DoI position resolution in a continuous LaBr{sub 3}(Ce) scintillation crystal for {gamma}-ray imaging

    Energy Technology Data Exchange (ETDEWEB)

    Pani, R., E-mail: roberto.pani@uniroma1.it [NFN, Istituto Nazionale di Fisica Nucleare (Italy); Molecular Medicine Dept., ' Sapienza' University of Rome (Italy); Nourbakhsh, S.; Pani, P. [NFN, Istituto Nazionale di Fisica Nucleare (Italy); Physics Dept, ' Sapienza' University, Rome (Italy); Bennati, P. [NFN, Istituto Nazionale di Fisica Nucleare (Italy); EDEMOM PhD School of Electronics, ' Roma Tre' University, Rome (Italy); Pellegrini, R.; Cinti, M.N.; Scafe, R. [NFN, Istituto Nazionale di Fisica Nucleare (Italy); Molecular Medicine Dept., ' Sapienza' University of Rome (Italy); Cassano, B. [NFN, Istituto Nazionale di Fisica Nucleare (Italy); Physics Dept, ' Sapienza' University, Rome (Italy); Navarria, F.; Lo Meo, S.; Lanconelli, N. [NFN, Istituto Nazionale di Fisica Nucleare (Italy); Physics Dept, Bologna University (Italy); Moschini, G.; Boccaccio, P. [NFN, Istituto Nazionale di Fisica Nucleare (Italy); LNL-INFN, Padua (Italy); Fabbri, A. [NFN, Istituto Nazionale di Fisica Nucleare (Italy); Physics Dept, ' Sapienza' University, Rome (Italy); Cencelli, V.O.; De Notaristefani, F. [NFN, Istituto Nazionale di Fisica Nucleare (Italy); Physics Dept, ' Roma Tre' University, Rome (Italy)

    2011-06-15

    A Monte Carlo simulation of a 50mmx50mmx4mm continuous crystal has been developed to investigate the correlation between the scintillation light width ({sigma}) and the Depth of Interaction (DoI) within the crystal. Our studies are based on a LaBr{sub 3}(Ce) crystal, in order to take advantage of its high light yield to reduce the statistic uncertainties on the estimators of the {sigma}. The first one, the standard deviation of the light distribution, has demonstrated a poor, though linear, correlation to DoI, that is not experimentally detectable. Otherwise, the second estimator, N/I , is the ratio of the total number of photoelectrons to the maximum number of photoelectrons collected from a single anode, in a scintillation event. N/I has been found to have the best correlation to DoI, that provides 2 mm resolution.

  14. Coke Formation in a Zeolite Crystal During the Methanol-to- Hydrocarbons Reaction as Studied with Atom Probe Tomography

    NARCIS (Netherlands)

    Schmidt, Joel E; Poplawsky, Jonathan D; Mazumder, Baishakhi; Attila, Özgün; Fu, Donglong; Winter, D A Matthijs De; Meirer, Florian; Bare, Simon R; Weckhuysen, Bert M

    2016-01-01

    Understanding the formation of carbon deposits in zeolites is vital to developing new,superior materials for various applications,including oil and gas conversion pro- cesses.Herein, atom probe tomography (APT) has been used to spatially resolve the 3D compositional changes at the sub- nm length

  15. Investigating effects of sample pretreatment on protein stability using size-exclusion chromatography and high-resolution continuum source atomic absorption spectrometry.

    Science.gov (United States)

    Rakow, Tobias; El Deeb, Sami; Hahne, Thomas; El-Hady, Deia Abd; AlBishri, Hassan M; Wätzig, Hermann

    2014-09-01

    In this study, size-exclusion chromatography and high-resolution atomic absorption spectrometry methods have been developed and evaluated to test the stability of proteins during sample pretreatment. This especially includes different storage conditions but also adsorption before or even during the chromatographic process. For the development of the size exclusion method, a Biosep S3000 5 μm column was used for investigating a series of representative model proteins, namely bovine serum albumin, ovalbumin, monoclonal immunoglobulin G antibody, and myoglobin. Ambient temperature storage was found to be harmful to all model proteins, whereas short-term storage up to 14 days could be done in an ordinary refrigerator. Freezing the protein solutions was always complicated and had to be evaluated for each protein in the corresponding solvent. To keep the proteins in their native state a gentle freezing temperature should be chosen, hence liquid nitrogen should be avoided. Furthermore, a high-resolution continuum source atomic absorption spectrometry method was developed to observe the adsorption of proteins on container material and chromatographic columns. Adsorption to any container led to a sample loss and lowered the recovery rates. During the pretreatment and high-performance size-exclusion chromatography, adsorption caused sample losses of up to 33%. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Trial wave functions for ring-trapped ions and neutral atoms: Microscopic description of the quantum space-time crystal

    Science.gov (United States)

    Yannouleas, Constantine; Landman, Uzi

    2017-10-01

    A constructive theoretical platform for the description of quantum space-time crystals uncovers for N interacting and ring-confined rotating particles the existence of low-lying states with proper space-time crystal behavior. The construction of the corresponding many-body trial wave functions proceeds first via symmetry breaking at the mean-field level followed by symmetry restoration using projection techniques. The ensuing correlated many-body wave functions are stationary states and preserve the rotational symmetries, and at the same time they reflect the point-group symmetries of the mean-field crystals. This behavior results in the emergence of sequences of select magic angular momenta Lm. For angular-momenta away from the magic values, the trial functions vanish. Symmetry breaking beyond the mean-field level can be induced by superpositions of such good-Lm many-body stationary states. We show that superposing a pair of adjacent magic angular momenta states leads to formation of special broken-symmetry states exhibiting quantum space-time-crystal behavior. In particular, the corresponding particle densities rotate around the ring, showing undamped and nondispersed periodic crystalline evolution in both space and time. The experimental synthesis of such quantum space-time-crystal wave packets is predicted to be favored in the vicinity of ground-state energy crossings of the Aharonov-Bohm-type spectra accessed via an externally applied, natural or synthetic, magnetic field. These results are illustrated here for Coulomb-repelling fermionic ions and for a lump of contact-interaction attracting bosons.

  17. Micro-sampling method based on high-resolution continuum source graphite furnace atomic absorption spectrometry for calcium determination in blood and mitochondrial suspensions.

    Science.gov (United States)

    Gómez-Nieto, Beatriz; Gismera, Mª Jesús; Sevilla, Mª Teresa; Satrústegui, Jorgina; Procopio, Jesús R

    2017-08-01

    A micro-sampling and straightforward method based on high resolution continuum source atomic absorption spectrometry (HR-CS AAS) was developed to determine extracellular and intracellular Ca in samples of interest in clinical and biomedical analysis. Solid sampling platforms were used to introduce the micro-samples into the graphite furnace atomizer. The secondary absorption line for Ca, located at 239.856nm, was selected to carry out the measurements. Experimental parameters such as pyrolysis and atomization temperatures and the amount of sample introduced for the measurements were optimized. Calibration was performed using aqueous standards and the approach to measure at the wings of the absorption lines was employed for the expansion of the linear response range. The limit of detection was of 0.02mgL-1 Ca (0.39ng Ca) and the upper limit of linear range was increased up to 8.0mgL-1 Ca (160ng Ca). The proposed method was used to determine Ca in mitochondrial suspensions and whole blood samples with successful results. Adequate recoveries (within 91-107%) were obtained in the tests performed for validation purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Visualization of drug-nucleic acid interactions at atomic resolution. II. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodocytidylyl(3'5')guanosine

    Energy Technology Data Exchange (ETDEWEB)

    Jain, S.C.; Tsair, C.C.; Sobell, H.M.

    1977-01-01

    Ethidium forms a second crystalline complex with the dinucleoside monophosphate 5-iodocytidyl(3'-5')guanosine (iodoCpG). These crystals are monoclinic, P2/sub 1/, with a = 14.06 A, b = 32.34 A, c = 16.53 A, ..beta.. = 117.8/sup 0/. The structure has been solved to atomic resolution using rigid-body Patterson vector search and Fourier methods, and refined by full matrix least-squares to a residual of 0.16 on 3180 observed reflections. Both iodoCpG molecules are hydrogen-bonded together by guanine.cytosine Watson--Crick base-pairing. Adjacent base-pairs within this paired iodoCpG structure and between neighboring iodoCpG molecules in adjoining unit cells are separated by 6.7 A. Approximate 2-fold symmetry is used in the interaction; this reflects the pseudo-2-fold symmetry axis of the phenanthridinium ring system in ethidium coinciding with the approximate 2-fold axis relating base-paired iodoCpG molecules. The phenyl and ethyl groups of the intercalated ethidium molecule lie in the narrow groove of the miniature iodoCpG double-helix. The stacked ethidium, however, lies in the opposite direction, its phenyl and ethyl groups neighboring iodine atoms on cytosine residues. Base-pairs within the paired nucleotide units are related by a twist of about 8/sup 0/. The magnitude of this angular twist reflects conformational changes in the sugar--phosphate chains accompanying intercalation. These primarily reflect the differences in ribose sugar ring puckering that are observed (i.e., both iodocytidine residues have C3' endo sugar conformations, while both guanosine residues have C2' endo sugar conformations), and alterations in the glycosidic torsional angles that describe the base-sugar orientation.

  19. Visualization of drug-nucleic acid interactions at atomic resolution. I. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodouridylyl(3'5')adenosine

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, C.C.; Jain, S.C.; Sobell, H.M.

    1977-01-01

    Ethidium forms a crystalline complex with the dinucleoside monophosphate 5-iodouridyly(3'-5')adenosine (iodoUpA). These crystals are monoclinic, space group C2, with unit cell dimensions, a = 28.45 A, b = 13.54 A, c = 34.13 A, ..beta.. = 98.6/sup 0/. The structure has been solved to atomic resolution by Patterson and Fourier methods, and refined by full matrix least-squares to a residual of 0.20 on 2017 observed reflections. The asymmetric unit contains two ethidium molecules, two iodoUpA molecules and 27 water molecules, a total of 155 atoms excluding hydrogens. The two iodoUpA molecules are held together by adenine.uracil Watson--Crick-type base-pairing. Adjacent base-pairs within this paired iodoUpA structure and between neighboring iodoUpA molecules in adjoining unit cells are separated by about 6.7 A; this separation results from intercalative binding by one ethidium molecule and stacking by the other ethidium molecule above and below the base-pairs. Non-crystallographic 2-fold symmetry is utilized in this model drug--nucleic acid interaction, the intercalated ethidium molecule being oriented such that its phenyl and ethyl groups lie in the narrow groove of the miniature nucleic acid double-helix. Base-pairs within the paired nucleotide units are related by a twist of 8/sup 0/. The magnitude of this angular twist is related to conformational changes in the sugar--phosphate chains that accompany drug intercalation. These changes partly reflect the differences in ribose sugar ring puckering that are observed. Additional small but systematic changes occur in torsional angles that involve the phosphodiester linkages and the C4'--C5' bond. Solution studies have indicated a marked sequence-specific binding preference in ethidium--dinucleotide interactions, and a probable structural explanation for this is provided by this study.

  20. Visualization of drug-nucleic acid interactions at atomic resolution. IV. Structure of an aminoacridine/dinucleoside monophosphate crystalline complex, 9-aminoacridine: 5-iodocytidylyl(3'-5')guanosine

    Energy Technology Data Exchange (ETDEWEB)

    Sakore, T.D.; Reddy, B.S.; Sobell, H.M.

    1979-01-01

    9-Aminoacridine forms a crystalline complex with the dinucleoside monophosphate, 5-iodocytidylyl(3'-5')guanosine (iodoCpG). These crystals are monoclinic, space group P2/sub 1/, with a = 13.98 A, b = 30.58 A, c = 22.47 A and ..beta.. = 113.9. The structure has been solved to atomic resolution by Patterson and Fourier methods, and refined by a combination of Fourier and sum function Fourier methods. The asymmetric unit contains four 9-aminoacridine molecules, four iodoCpG molecules and 21 water molecules, a total of 245 atoms. 9-Aminoacridine demonstrates two different intercalative binding modes and, along with these, two slightly different intercalative geometries in this model system. The first of these is very nearly symmetric, the 9-amino- group lying in the narrow groove of the intercalated base-paired nucleotide structure. The second shows grossly asymmetric binding to the dinucleotide, the 9-amino- group lying in the wide groove of the structure. Associated with these two different intercalative binding modes is a difference in geometries in the structures. Although both structures demonstrate C3' endo (3'-5') C2' endo mixed sugar puckering patterns, with corresponding twist angles between base-pairs of about 10/sup 0/, they differ in the magnitude of the helical screw axis dislocation accompanying intercalation. In the pseudosymmetric intercalative structure, this value is about +0.5 A, whereas in the asymmetric intercalative structure this value is about +2.7 A. These conformational differences can be best described as a sliding of base-pairs on the intercalated acridine molecule.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-03-01

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

  2. Atomic Resolution Structural and Chemical Imaging Revealing the Sequential Migration of Ni, Co, and Mn upon the Battery Cycling of Layered Cathode.

    Science.gov (United States)

    Yan, Pengfei; Zheng, Jianming; Zhang, Ji-Guang; Wang, Chongmin

    2017-06-14

    Layered lithium transition metal oxides (LTMO) are promising candidate cathode materials for next-generation high-energy density lithium ion battery. The challenge for using this category of cathode is the capacity and voltage fading, which is believed to be associated with the layered structure disordering, a process that is initiated from the surface or solid-electrolyte interface and facilitated by transition metal (TM) reduction and oxygen vacancy formation. However, the atomic level dynamic mechanism of such a layered structure disordering is still not fully clear. In this work, utilizing atomic resolution electron energy loss spectroscopy (EELS), we map, for the first time at atomic scale, the spatial evolution of Ni, Co and Mn in a cycled LiNi1/3Mn1/3Co1/3O2 layered cathode. In combination with atomic level structural imaging, we discovered the direct correlation of TM ions migration behavior with lattice disordering, featuring the residing of TM ions in the tetrahedral site and a sequential migration of Ni, Co, and Mn upon the increased lattice disordering of the layered structure. This work highlights that Ni ions, though acting as the dominant redox species in many LTMO, are labile to migrate to cause lattice disordering upon battery cycling, while the Mn ions are more stable as compared with Ni and Co and can act as pillar to stabilize layered structure. Direct visualization of the behavior of TM ions during the battery cycling provides insight for designing of cathode with high structural stability and correspondingly a superior performance.

  3. Atomic Resolution Structural and Chemical Imaging Revealing the Sequential Migration of Ni, Co, and Mn upon the Battery Cycling of Layered Cathode

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Pengfei; Zheng, Jianming; Zhang, Ji-Guang; Wang, Chongmin

    2017-05-11

    Layered lithium transition metal oxides (LTMO) are promising candidate cathode materials for next generation high energy density lithium ion battery. The challenge for using this category of cathode is the capacity and voltage fading, which is believed to be associated with the layered structure disordering, a process that is initiated from the surface or solid-electrolyte interface and facilitated by transition metal (TM) reduction and oxygen vacancy formation. However, the atomic level dynamic mechanism of such a layered structure disordering is still not fully clear. In this work, utilizing atomic resolution electron energy loss spectroscopy (EELS), we map, for the first time at atomic scale, the spatial evolution of Ni, Co and Mn in a cycled LiNi1/3M1/3Co1/3O2 layered cathode. In combination with atomic level structural imaging, we discovered the direct correlation of TM ions migration behavior with lattice disordering, featuring the residing of TM ions in the tetrahedral site and a sequential migration of Ni, Co, and Mn upon the increased lattice disordering of the layered structure. This work highlights that Ni ions, though acting as the dominant redox species in many LTMO, are labile to migrate to cause lattice disordering upon battery cycling; while the Mn ions are more stable as compared with Ni and Co and can act as pillar to stabilize layered structure. Direct visualization of the behavior of TM ions during the battery cycling provides insight for designing of cathode with structural stability and correspondingly a superior performance.

  4. Double Nuclear Magnetic Resonance and Crystal Chemistry at the Lattice Positions of Diamagnetic Atoms, Both Structural, and Foreign

    NARCIS (Netherlands)

    Shchepkin, V.D.; Vainshtein, D.I.; Dautov, R.A.; Vinokurov, V.M.

    1980-01-01

    Double nuclear magnetic resonance (DNMR) with Jeener's pulsed sequence on proton and fluorine frequencies was used to investigate the electric quadrupole interactions of (i) 23Na in Na2Cd(SO4)2·2H2O, B20=±218.5±1 kHz, B22=±98±5 kHz, (ii) of 23Na, which enter the crystal, CaF2:Na+ (0.07 wt. %)

  5. Atomic-resolution study of dislocation structures and interfaces in poly-crystalline thin film CdTe using aberration-corrected STEM

    Science.gov (United States)

    Paulauskas, Tadas; Colegrove, Eric; Buurma, Chris; Kim, Moon; Klie, Robert

    2014-03-01

    Commercial success of CdTe-based thin film photovoltaic devices stems from its nearly ideal direct band gap which very effectively couples to Sun's light spectrum as well as ease of manufacturing and low cost of these modules. However, to further improve the conversion efficiency beyond 20 percent, it is important to minimize the harmful effects of grain boundaries and lattice defects in CdTe. Direct atomic-scale characterization is needed in order identify the carrier recombination centers. Likewise, it is necessary to confirm that passivants in CdTe, such as Cl, are able to diffuse and bind to the target defects. In this study, we characterize dislocation structures and grain boundaries in poly-crystalline CdTe using aberration-corrected cold-field emission scanning transmission electron microscopy (STEM). The chemical composition of Shockley partial, Frank and Lomer-Cottrell dislocations is examined via atomic column-resolved X-ray energy dispersive (XEDS) and electron energy-loss spectroscopies (EELS). Segregation of Cl towards dislocation cores and grain boundaries is shown in CdCl2 treated samples. We also investigate interfaces in ultra-high-vacuum bonded CdTe bi-crystals with pre-defined misorientation angles which are intended to mimic grain boundaries. Funded by: DOE EERE Sunshot Award EE0005956.

  6. Study of atomic jumps in quasi-crystals; Etude des sauts atomiques dans les quasi-cristaux

    Energy Technology Data Exchange (ETDEWEB)

    Lyonnard, S

    1997-05-07

    The terminology phason used in quasicrystals to refer to atomic jumps. The study of the hopping process is important for the understanding of many basic issues in quasi-crystallography: structure, stability, diffusion, phase transitions between quasicrystals and approximants, mechanical properties. Quasi-elastic neutron scattering allows to find the characteristics of each elementary jump: chemical species involves, relaxation times, activation energies, jump distances and orientations. We performed a series of experiments in the perfect icosahedral phases AlFeCu and AlMnPd, on both powders and single domain samples, using time-of-flight, backscattering and triple axis spectrometers. We evidenced the existence of very fast phason hopping, and studied about ten different atomic jumps. An unusual temperature dependence has been found systematically: each process is assisted by a thermally activated mechanism. The assistance process has to be determined case by case, but the more plausible explanation invokes assistance by phonons or phason clouds. Moreover, the dependence of the quasi elastic signal as a function of the momentum transfer shows that the jumps are local and do not give rise to any long-range diffusion. Phason hopping mainly corresponds to the atom moving forwards and backwards between two energetically equivalent sites. Finally, we have been able to show that the jumps occur along the various quasi-crystalline symmetry axes. (author) 91 refs.

  7. Crystal Dislocations

    Directory of Open Access Journals (Sweden)

    Ronald W. Armstrong

    2016-01-01

    Full Text Available Crystal dislocations were invisible until the mid-20th century although their presence had been inferred; the atomic and molecular scale dimensions had prevented earlier discovery. Now they are normally known to be just about everywhere, for example, in the softest molecularly-bonded crystals as well as within the hardest covalently-bonded diamonds. The advent of advanced techniques of atomic-scale probing has facilitated modern observations of dislocations in every crystal structure-type, particularly by X-ray diffraction topography and transmission electron microscopy. The present Special Issue provides a flavor of their ubiquitous presences, their characterizations and, especially, their influence on mechanical and electrical properties.

  8. Electrochemically assisted localized etching of ZnO single crystals in water using a catalytically active Pt-coated atomic force microscopy probe

    Science.gov (United States)

    Shibata, Takayuki; Yamamoto, Kota; Sasano, Junji; Nagai, Moeto

    2017-09-01

    This paper presents a nanofabrication technique based on the electrochemically assisted chemical dissolution of zinc oxide (ZnO) single crystals in water at room temperature using a catalytically active Pt-coated atomic force microscopy (AFM) probe. Fabricated grooves featured depths and widths of several tens and several hundreds of nanometers, respectively. The material removal rate of ZnO was dramatically improved by controlling the formation of hydrogen ions (H+) on the surface of the catalytic Pt-coated probe via oxidation of H2O molecules; this reaction can be enhanced by applying a cathodic potential to an additional Pt-wire working electrode in a three-electrode configuration. Consequently, ZnO can be dissolved chemically in water as a soluble Zn2+ species via a reaction with H+ species present in high concentrations in the immediate vicinity of the AFM tip apex.

  9. Analytical atomic spectroscopy of plutonium—I. High resolution spectra of plutonium emitted in an inductively coupled plasma

    Science.gov (United States)

    Edelson, M. C.; DeKalb, E. L.; Winge, R. K.; Fassel, V. A.

    In the atomic emission spectrum of Pu-242 emitted in an inductively coupled plasma (ICP) 23 lines with detection limits of less than 100 ng/ml were identified in the 200-700 nm spectral range. The line at 453.614 nm had the best detection limit of 15 ng/ml. The isotopic splittings of several Pu emission lines were resolved with a commercial 1.5m spectrometer. The line at 398.988 nm (Pu-240 wavelength) had the greatest isotope shift, but was interfered with by neighboring Pu lines. Other lines were shown to be useful for Pu isotopic analysis. The hyperfine splitting of some intense Pu-239 lines was measured; the Pu 453.614 nm line exhibited the widest splitting (5.9 pm).

  10. Building Atomic Models of the Ion Channels Based on Low Resolution Electron Microscopy Maps and Homology Modeling.

    Science.gov (United States)

    Novoseletsky, Valery; Malak, Olfat A; Loussouarn, Gildas; Sokolova, Olga S

    2018-01-01

    Voltage-gated potassium channels play pivotal roles in excitable and non-excitable cells. For many decades, structural properties and molecular mechanisms of these channels were inferred from functional observations. At the turn of the twenty-first century, structural biology revealed major aspects in the structural basis of ion channel organization, permeation, and gating. Among the available tools, homology modeling associated with low resolution microscopy helps in delineating the different structural elements of voltage-gated channels. Here, we describe in detail the methodology of homology modeling, using the 3D structure of the Kv2.1ΔCTA ion channel as a reference.

  11. Resolution of crystal structures by X-ray and neutrons powder diffraction using global optimisation methods; Resolution des structures cristallines par diffraction des rayons X et neutrons sur poudres en utilisant les methodes d'optimisation globale

    Energy Technology Data Exchange (ETDEWEB)

    Palin, L

    2005-03-15

    We have shown in this work that X-ray diffraction on powder is a powerful tool to analyze crystal structure. The purpose of this thesis is the resolution of crystal structures by X-ray and neutrons diffraction on powder using global optimisation methods. We have studied 3 different topics. The first one is the order-disorder phenomena observed in some globular organic molecular solids. The second is the opiate family of neuropeptides. These neurotransmitters regulate sensory functions including pain and control of respiration in the central nervous system. The aim of our study was to try to determine the crystal structure of Leu-enkephalin and some of its sub-fragments. The determination of the crystal structures has been done performing Monte Carlo simulations. The third one is the location of benzene in a sodium-X zeolite. The zeolite framework was already known and the benzene has been localized by simulated annealing and by the use of maximum entropy maps.

  12. Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.

    Science.gov (United States)

    Sun, Lei; Zhang, Xinzheng; Gao, Song; Rao, Prashant A; Padilla-Sanchez, Victor; Chen, Zhenguo; Sun, Siyang; Xiang, Ye; Subramaniam, Sriram; Rao, Venigalla B; Rossmann, Michael G

    2015-07-06

    The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.

  13. The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex

    Energy Technology Data Exchange (ETDEWEB)

    Olczak, A.; Glówka, M.L.; Szczesio, M.; Bojarska, J.; Wawrzak, Z.; Duax, W.L. (Poland); (NWU); (HWMRI)

    2010-11-15

    The crystal structure of the nonstoichiometric complex of gramicidin D with NaI has been studied using synchrotron radiation at 100 K. The limiting resolution was 1.25 {angstrom} and the R factor was 16% for 19,883 observed reflections. The general architecture of the antiparallel two-stranded gramicidin dimers in the studied crystal was a right-handed antiparallel double-stranded form that closely resembles the structures of other right-handed species published to date. However, there were several surprising observations. In addition to the significantly different composition of linear gramicidins identified in the crystal structure, including the absence of the gramicidin C form, only two cationic sites were found in each of the two independent dimers (channels), which were partially occupied by sodium, compared with the seven sites found in the RbCl complex of gramicidin. The sum of the partial occupancies of Na{sup +} was only 1.26 per two dimers and was confirmed by the similar content of iodine ions (1.21 ions distributed over seven sites), which was easily visible from their anomalous signal. Another surprising observation was the significant asymmetry of the distributions and occupancies of cations in the gramicidin dimers, which was in contrast to those observed in the high-resolution structures of the complexes of heavier alkali metals with gramicidin D, especially that of rubidium.

  14. He atom-surface scattering: Surface dynamics of insulators, overlayers and crystal growth. Progress report, May 1, 1991--April 30, 1992

    Energy Technology Data Exchange (ETDEWEB)

    1992-05-01

    Investigations in this laboratory have focused on the surface structure and dynamics of ionic insulators and on epitaxial growth onto alkali halide crystals. In the later the homoepitaxial growth of NaCl/NaCl(001) and the heteroepitaxial growth of KBr/NaCl(001), NaCl/KBr(001) and KBr/RbCl(001) have been studied by monitoring the specular He scattering as a function of the coverage and by measuring the angular and energy distributions of the scattered He atoms. These data provide information on the surface structure, defect densities, island sizes and surface strain during the layer-by-layer growth. The temperature dependence of these measurements also provides information on the mobilities of the admolecules. He atom scattering is unique among surface probes because the low-energy, inert atoms are sensitive only to the electronic structure of the topmost surface layer and are equally applicable to all crystalline materials. It is proposed for the next year to exploit further the variety of combinations possible with the alkali halides in order to carry out a definitive study of epitaxial growth in the ionic insulators. The work completed so far, including measurements of the Bragg diffraction and surface dispersion at various stages of growth, appears to be exceptionally rich in detail, which is particularly promising for theoretical modeling. In addition, because epitaxial growth conditions over a wide range of lattice mismatches is possible with these materials, size effects in growth processes can be explored in great depth. Further, as some of the alkali halides have the CsCl structure instead of the NaCl structure, we can investigate the effects of the heteroepitaxy with materials having different lattice preferences. Finally, by using co-deposition of different alkali halides, one can investigate the formation and stability of alloys and even alkali halide superlattices.

  15. Determination of macro- and micronutrients in plant leaves by high-resolution continuum source flame atomic absorption spectrometry combining instrumental and sample preparation strategies

    Science.gov (United States)

    Oliveira, Silvana R.; Gomes Neto, José A.; Nóbrega, Joaquim A.; Jones, Bradley T.

    2010-04-01

    A method for determination of B, Ca, Cu, Fe, K, Mg, Mn, Mo, P, S and Zn in plant tissues by high-resolution continuum source flame atomic absorption spectrometry (HR-CS FAAS) is proposed. This method is based on special features of HR-CS-AAS, such as side pixel registration, wavelength integrated absorbance, and molecular absorption bands, for determining macro- and micronutrients in foliar analysis without requiring several different strategies for sample preparation and adjustment of the analytes concentration ranges. Plant samples were analyzed and results for certified materials were in agreement at a 95% confidence level (paired t-test) with reference values. Recoveries of analytes added to plant digests varied within the 82-112% interval. Relative standard deviations ( n = 12) were lower than or equal to 5.7% for all analytes in all concentration ranges.

  16. Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole.

    Science.gov (United States)

    Asztalos, Peter; Müller, Astrid; Hölke, Werner; Sobek, Harald; Rudolph, Markus G

    2014-07-01

    Lysobacter enzymogenes lysyl endoproteinase (LysC) is a trypsin-type serine protease with a high pH optimum that hydrolyses all Lys-Xaa peptide bonds. The high specificity of LysC renders it useful for biotechnological purposes. The K30R variant of a related lysyl endoproteinase from Achromobacter lyticus has favourable enzymatic properties that might be transferrable to LysC. To visualize structural differences in the substrate-binding sites, the crystal structures of wild-type and the K30R variant of LysC were determined. The mutation is located at a distance of 12 Å from the catalytic triad and subtly changes the surface properties of the substrate-binding site. The high pH optimum of LysC can be attributed to electrostatic effects of an aromatic Tyr/His stack on the catalytic aspartate and is a general feature of this enzyme subfamily. LysC crystals in complex with the covalent inhibitor N(α)-p-tosyl-lysyl chloromethylketone yielded data to 1.1 and 0.9 Å resolution, resulting in unprecedented precision of the active and substrate-binding sites for this enzyme subfamily. Error estimates on bond lengths and difference electron density indicate that instead of the expected oxyanion a hydroxyl group binds to the partially solvent-exposed oxyanion hole. Protonation of the alkoxide catalytic intermediate might be a recurring feature during serine protease catalysis.

  17. Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis.

    Science.gov (United States)

    Zeytuni, Natalie; Hong, Chuan; Flanagan, Kelly A; Worrall, Liam J; Theiltges, Kate A; Vuckovic, Marija; Huang, Rick K; Massoni, Shawn C; Camp, Amy H; Yu, Zhiheng; Strynadka, Natalie C

    2017-08-22

    Bacterial sporulation allows starving cells to differentiate into metabolically dormant spores that can survive extreme conditions. Following asymmetric division, the mother cell engulfs the forespore, surrounding it with two bilayer membranes. During the engulfment process, an essential channel, the so-called feeding tube apparatus, is thought to cross both membranes to create a direct conduit between the mother cell and the forespore. At least nine proteins are required to create this channel, including SpoIIQ and SpoIIIAA-AH. Here, we present the near-atomic resolution structure of one of these proteins, SpoIIIAG, determined by single-particle cryo-EM. A 3D reconstruction revealed that SpoIIIAG assembles into a large and stable 30-fold symmetric complex with a unique mushroom-like architecture. The complex is collectively composed of three distinctive circular structures: a 60-stranded vertical β-barrel that forms a large inner channel encircled by two concentric rings, one β-mediated and the other formed by repeats of a ring-building motif (RBM) common to the architecture of various dual membrane secretion systems of distinct function. Our near-atomic resolution structure clearly shows that SpoIIIAG exhibits a unique and dramatic adaptation of the RBM fold with a unique β-triangle insertion that assembles into the prominent channel, the dimensions of which suggest the potential passage of large macromolecules between the mother cell and forespore during the feeding process. Indeed, mutation of residues located at key interfaces between monomers of this RBM resulted in severe defects both in vivo and in vitro, providing additional support for this unprecedented structure.

  18. Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations

    DEFF Research Database (Denmark)

    Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit

    2012-01-01

    resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates...... in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable...... to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A...

  19. Visualization of drug-nucleic acid interactions at atomic resolution. IX. Structures of two N,N-dimethylproflavine: 5-iodocytidylyl (3'-5') guanosine crystalline complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bhandary, K.K.; Sakore, T.D.; Sobell, H.M.; King, D.; Gabbay, E.J.

    1984-01-01

    This paper describes two complexes containing N,N-dimethylproflavine and the dinucleoside monophosphate, 5-iodocytidylyl(3'-5')guanosine (iodoCpG). The first complex is triclinic, space group P1, with unit cell dimensions a = 11.78 A, b = 14.55 A, c = 15.50 A, ..cap alpha.. = 89.2/sup 0/, ..beta.. 86.2/sup 0/, ..gamma.. = 96.4/sup 0/. The second complex is monoclinic, space group P2/sub 1/, with a = 14.20 A, b = 19.00 A, c = 20.73 A, ..beta.. = 103.6/sup 0/. Both structures have been solved to atomic resolution and refined by Fourier and least squares methods. The first structure has been refined anisotropically to a residual of 0.09 on 5025 observed reflections using block diagonal least squares, while the second structure has been refined isotropically to a residual of 0.13 on 2888 reflections with full matrix least squares. The asymmetric unit in both structures contains two dimethylproflavine molecules and two iodoCpG molecules; the first structure has 16 water molecules (a total of 134 non-hydrogen atoms), while the second structure has 18 water molecules (a total of 136 non-hydrogen atoms). Both structures demonstrate intercalation of dimethylproflavine between base-paired iodoCpG dimers. In addition, dimethylproflavine molecules stack on either side of the intercalated duplex, being related by a unit cell translation along b and a axes, respectively. 16 references, 13 figures, 5 tables.

  20. Investigation of chemical modifiers for the direct determination of arsenic in fish oil using high-resolution continuum source graphite furnace atomic absorption spectrometry.

    Science.gov (United States)

    Pereira, Éderson R; de Almeida, Tarcísio S; Borges, Daniel L G; Carasek, Eduardo; Welz, Bernhard; Feldmann, Jörg; Campo Menoyo, Javier Del

    2016-04-01

    High-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS GF AAS) has been applied for the development of a method for the determination of total As in fish oil samples using direct analysis. The method does not use any sample pretreatment, besides dilution with 1-propanole, in order to decrease the oil viscosity. The stability and sensitivity of As were evaluated using ruthenium and iridium as permanent chemical modifiers and palladium added in solution over the sample. The best results were obtained with ruthenium as the permanent modifier and palladium in solution added to samples and standard solutions. Under these conditions, aqueous standard solutions could be used for calibration for the fish oil samples diluted with 1-propanole. The pyrolysis and atomization temperatures were 1400 °C and 2300 °C, respectively, and the limit of detection and characteristic mass were 30 pg and 43 pg, respectively. Accuracy and precision of the method have been evaluated using microwave-assisted acid digestion of the samples with subsequent determination by HR-CS GF AAS and ICP-MS; the results were in agreement (95% confidence level) with those of the proposed method. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Evaluation of solid sampling for determination of Mo, Ni, Co, and V in soil by high-resolution continuum source graphite furnace atomic absorption spectrometry

    Science.gov (United States)

    Babos, Diego Victor; Barros, Ariane Isis; Ferreira, Edilene Cristina; Neto, José Anchieta Gomes

    2017-04-01

    New methods are proposed for the determination of Mo, Ni, Co, and V in soils using high-resolution continuum source graphite furnace atomic absorption spectrometry with direct solid sampling. Cobalt and V were simultaneously determined, and different analytical lines of Ni and V were monitored to adjust sensitivity for each sample. Accuracy was checked by means of soil certified reference materials, and also by flame atomic absorption spectrometry as comparative technique. The results for Mo, Ni, Co, and V found by proposed methods were in agreement with certified values and with those obtained by the comparative technique at 95% confidence level. The concentrations found in different soil samples were in the ranges 0.19-1.84 mg kg- 1 (Mo), 9.2-22.7 mg kg- 1 (Ni), 1.1-10.7 mg kg- 1 (Co), and 35.6-426.1 mg kg- 1 (V). The relative standard deviations were in the ranges 3.2-10% (Mo), 2.8-9.8% (Ni), 4.0-9.2% (Co), and 1.2-8.0% (V). The limits of quantification for Mo, Ni, Co, and V were 0.027, 0.071, 0.15, and 1.43 ng, respectively.

  2. A simple and fast method for assessment of the nitrogen-phosphorus-potassium rating of fertilizers using high-resolution continuum source atomic and molecular absorption spectrometry

    Science.gov (United States)

    Bechlin, Marcos André; Fortunato, Felipe Manfroi; da Silva, Ricardo Moutinho; Ferreira, Edilene Cristina; Gomes Neto, José Anchieta

    2014-11-01

    The determination of N, P, and K in fertilizers by high-resolution continuum source flame atomic and molecular absorption spectrometry is proposed. Under optimized conditions, measurements of the diatomic molecules NO and PO at 215.360 and 247.620 nm, respectively, and K using the wing of the alternative line at 404.722 nm allowed calibration curves to be constructed in the ranges 500-5000 mg L- 1 N (r = 0.9994), 100-2000 mg L- 1 P (r = 0.9946), and 100-2500 mg L- 1 K (r = 0.9995). Commercial fertilizers were analyzed by the proposed method and the concentrations of N, P, and K were found to be in agreement with those obtained by Kjeldahl, spectrophotometric, and flame atomic emission spectrometry methods, respectively, at a 95% confidence level (paired t-test). A phosphate rock certified reference material (CRM) was analyzed and the results for P and K were in agreement with the reference values. Recoveries from spiked CRM were in the ranges 97-105% (NO3--N), 95-103% (NH4+-N), 93-103% (urea-N), 99-108% (P), and 99-102% (K). The relative standard deviations (n = 12) for N, P, and K were 6, 4, and 2%, respectively.

  3. Evaluation of solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry for direct determination of chromium in medicinal plants

    Energy Technology Data Exchange (ETDEWEB)

    Virgilio, Alex; Nobrega, Joaquim A. [Department of Chemistry, Federal University of Sao Carlos, Post Office Box 676, 13560-970, Sao Carlos-SP (Brazil); Rego, Jardes F. [Department of Analytical Chemistry, Institute of Chemistry, Sao Paulo State University-UNESP, Post Office Box 355, 14801-970, Araraquara-SP (Brazil); Neto, Jose A. Gomes, E-mail: anchieta@iq.unesp.br [Department of Analytical Chemistry, Institute of Chemistry, Sao Paulo State University-UNESP, Post Office Box 355, 14801-970, Araraquara-SP (Brazil)

    2012-12-01

    A method for Cr determination in medicinal plants using direct solid sampling graphite furnace high-resolution continuum source atomic absorption spectrometry was developed. Modifiers were dispensable. Pyrolysis and atomization temperatures were 1500 Degree-Sign C and 2400 Degree-Sign C, respectively. Slopes of calibration curves (50-750 pg Cr, R{sup 2} > 0.999) using aqueous and solid standards coincides in 96%, indicated feasibility of aqueous calibration for solid sampling of medicinal plants. Accuracy was checked by analysis of four plant certified reference materials. Results were in agreement at 95% confidence level with certified and non-certified values. Ten samples of medicinal plants were analyzed and Cr contents were in the 1.3-17.7 {mu}g g{sup -1} Cr range. The highest RSD (n = 5) was 15.4% for the sample Melissa officinalis containing 13.9 {+-} 2.1 {mu}g g{sup -1} Cr. The limit of detection was 3.3 ng g{sup -1} Cr. - Highlights: Black-Right-Pointing-Pointer Direct solid sampling is first time employed for Cr in plant materials. Black-Right-Pointing-Pointer Calibration curves with liquids and solids are coincident. Black-Right-Pointing-Pointer Microanalysis of plants for Cr is validated by reference materials. Black-Right-Pointing-Pointer The proposed HR-CS GF AAS method is environmental friendly.

  4. SINGLE CRYSTAL NEUTRON DIFFRACTION.

    Energy Technology Data Exchange (ETDEWEB)

    KOETZLE,T.F.

    2001-03-13

    Single-crystal neutron diffraction measures the elastic Bragg reflection intensities from crystals of a material, the structure of which is the subject of investigation. A single crystal is placed in a beam of neutrons produced at a nuclear reactor or at a proton accelerator-based spallation source. Single-crystal diffraction measurements are commonly made at thermal neutron beam energies, which correspond to neutron wavelengths in the neighborhood of 1 Angstrom. For high-resolution studies requiring shorter wavelengths (ca. 0.3-0.8 Angstroms), a pulsed spallation source or a high-temperature moderator (a ''hot source'') at a reactor may be used. When complex structures with large unit-cell repeats are under investigation, as is the case in structural biology, a cryogenic-temperature moderator (a ''cold source'') may be employed to obtain longer neutron wavelengths (ca. 4-10 Angstroms). A single-crystal neutron diffraction analysis will determine the crystal structure of the material, typically including its unit cell and space group, the positions of the atomic nuclei and their mean-square displacements, and relevant site occupancies. Because the neutron possesses a magnetic moment, the magnetic structure of the material can be determined as well, from the magnetic contribution to the Bragg intensities. This latter aspect falls beyond the scope of the present unit; for information on magnetic scattering of neutrons see Unit 14.3. Instruments for single-crystal diffraction (single-crystal diffractometers or SCDs) are generally available at the major neutron scattering center facilities. Beam time on many of these instruments is available through a proposal mechanism. A listing of neutron SCD instruments and their corresponding facility contacts is included in an appendix accompanying this unit.

  5. DHS Internship Summary-Crystal Assembly at Different Length Scales

    Energy Technology Data Exchange (ETDEWEB)

    Mishchenko, L

    2009-08-06

    I was part of a project in which in situ atomic force microscopy (AFM) was used to monitor growth and dissolution of atomic and colloidal crystals. At both length scales, the chemical environment of the system greatly altered crystal growth and dissolution. Calcium phosphate was used as a model system for atomic crystals. A dissolution-reprecipitation reaction was observed in this first system, involving the conversion of brushite (DCPD) to octacalcium phosphate (OCP). In the second system, polymeric colloidal crystals were dissolved in an ionic solvent, revealing the underlying structure of the crystal. The dissolved crystal was then regrown through an evaporative step method. Recently, we have also found that colloids can be reversibly deposited in situ onto an ITO (indium tin oxide) substrate via an electrochemistry setup. The overall goal of this project was to develop an understanding of the mechanisms that control crystallization and order, so that these might be controlled during material synthesis. Controlled assembly of materials over a range of length scales from molecules to nanoparticles to colloids is critical for designing new materials. In particular, developing materials for sensor applications with tailorable properties and long range order is important. In this work, we examine two of these length scales: small molecule crystallization of calcium phosphate (whose crystal phases include DCPD, OCP, and HAP) and colloidal crystallization of Poly(methyl methacrylate) beads. Atomic Force Microscopy is ideal for this line of work because it allows for the possibility of observing non-conducting samples in fluid during growth with high resolution ({approx} 10 nm). In fact, during atomic crystal growth one can observe changes in atomic steps, and with colloidal crystals, one can monitor the individual building blocks of the crystal. Colloids and atoms crystallize under the influence of different forces acting at different length scales as seen in Table 1

  6. High-resolution high-speed dynamic mechanical spectroscopy of cells and other soft materials with the help of atomic force microscopy

    Science.gov (United States)

    Dokukin, M.; Sokolov, I.

    2015-07-01

    Dynamic mechanical spectroscopy (DMS), which allows measuring frequency-dependent viscoelastic properties, is important to study soft materials, tissues, biomaterials, polymers. However, the existing DMS techniques (nanoindentation) have limited resolution when used on soft materials, preventing them from being used to study mechanics at the nanoscale. The nanoindenters are not capable of measuring cells, nanointerfaces of composite materials. Here we present a highly accurate DMS modality, which is a combination of three different methods: quantitative nanoindentation (nanoDMA), gentle force and fast response of atomic force microscopy (AFM), and Fourier transform (FT) spectroscopy. This new spectroscopy (which we suggest to call FT-nanoDMA) is fast and sensitive enough to allow DMS imaging of nanointerfaces, single cells, while attaining about 100x improvements on polymers in both spatial (to 10-70 nm) and temporal resolution (to 0.7s/pixel) compared to the current art. Multiple frequencies are measured simultaneously. The use of 10 frequencies are demonstrated here (up to 300 Hz which is a rather relevant range for biological materials and polymers, in both ambient conditions and liquid). The method is quantitatively verified on known polymers and demonstrated on cells and polymers blends. Analysis shows that FT-nanoDMA is highly quantitative. The FT-nanoDMA spectroscopy can easily be implemented in the existing AFMs.

  7. High-resolution high-speed dynamic mechanical spectroscopy of cells and other soft materials with the help of atomic force microscopy.

    Science.gov (United States)

    Dokukin, M; Sokolov, I

    2015-07-28

    Dynamic mechanical spectroscopy (DMS), which allows measuring frequency-dependent viscoelastic properties, is important to study soft materials, tissues, biomaterials, polymers. However, the existing DMS techniques (nanoindentation) have limited resolution when used on soft materials, preventing them from being used to study mechanics at the nanoscale. The nanoindenters are not capable of measuring cells, nanointerfaces of composite materials. Here we present a highly accurate DMS modality, which is a combination of three different methods: quantitative nanoindentation (nanoDMA), gentle force and fast response of atomic force microscopy (AFM), and Fourier transform (FT) spectroscopy. This new spectroscopy (which we suggest to call FT-nanoDMA) is fast and sensitive enough to allow DMS imaging of nanointerfaces, single cells, while attaining about 100x improvements on polymers in both spatial (to 10-70 nm) and temporal resolution (to 0.7 s/pixel) compared to the current art. Multiple frequencies are measured simultaneously. The use of 10 frequencies are demonstrated here (up to 300 Hz which is a rather relevant range for biological materials and polymers, in both ambient conditions and liquid). The method is quantitatively verified on known polymers and demonstrated on cells and polymers blends. Analysis shows that FT-nanoDMA is highly quantitative. The FT-nanoDMA spectroscopy can easily be implemented in the existing AFMs.

  8. Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations.

    Science.gov (United States)

    Kraft, Johan F; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea

    2012-05-08

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A. Kukol fails to maintain stable micelles, whereas the most recent CHARMM36 lipid parameters and GROMOS96 with the so-called Berger lipid parameters both succeed in this regard.

  9. Hirshfeld atom refinement

    Directory of Open Access Journals (Sweden)

    Silvia C. Capelli

    2014-09-01

    Full Text Available Hirshfeld atom refinement (HAR is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's, all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules, the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

  10. An Overview of Biological Macromolecule Crystallization

    Science.gov (United States)

    Krauss, Irene Russo; Merlino, Antonello; Vergara, Alessandro; Sica, Filomena

    2013-01-01

    The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality. PMID:23727935

  11. Hybrid gold single crystals incorporating amino acids

    CERN Document Server

    Chen, Linfeng; Weber, Eva; Fitch, Andy N; Pokroy, Boaz

    2016-01-01

    Composite hybrid gold crystals are of profound interest in various research areas ranging from materials science to biology. Their importance is due to their unique properties and potential implementation, for example in sensing or in bio-nanomedicine. Here we report on the formation of hybrid organic-metal composites via the incorporation of selected amino acids histidine, aspartic acid, serine, glutamine, alanine, cysteine, and selenocystine into the crystal lattice of single crystals of gold. We used electron microscopy, chemical analysis and high-resolution synchrotron powder X ray diffraction to examine these composites. Crystal shape, as well as atomic concentrations of occluded amino acids and their impact on the crystal structure of gold, were determined. Concentration of the incorporated amino acid was highest for cysteine, followed by serine and aspartic acid. Our results indicate that the incorporation process probably occurs through a complex interaction of their individual functional groups with ...

  12. High resolution, low hν photoelectron spectroscopy with the use of a microwave excited rare gas lamp and ionic crystal filters.

    Science.gov (United States)

    Suga, S; Sekiyama, A; Funabashi, G; Yamaguchi, J; Kimura, M; Tsujibayashi, M; Uyama, T; Sugiyama, H; Tomida, Y; Kuwahara, G; Kitayama, S; Fukushima, K; Kimura, K; Yokoi, T; Murakami, K; Fujiwara, H; Saitoh, Y; Plucinski, L; Schneider, C M

    2010-10-01

    The need for not only bulk sensitive but also extremely high resolution photoelectron spectroscopy for studying detailed electronic structures of strongly correlated electron systems is growing rapidly. Moreover, easy access to such a capability in one's own laboratory is desirable. Demonstrated here is the performance of a microwave excited rare gas (Xe, Kr, and Ar) lamp combined with ionic crystal filters (sapphire, CaF(2), and LiF), which can supply three strong lines near the photon energy of hnyu hν=8.4, 10.0, and 11.6 eV, with the hν resolution of better than 600 μeV for photoelectron spectroscopy. Its performance is demonstrated on some materials by means of both angle-integrated and angle-resolved measurements.

  13. Design Parameters and Objectives of a High-­Resolution X-­ray Imaging Crystal Spectrometer for the Large Helical Device (LHD)

    Energy Technology Data Exchange (ETDEWEB)

    Bitter, M; Gates, D; Neilson, H; Reiman, A; Roquemore, A L; Morita, S; Goto, M; Yamada, H

    2010-05-19

    A high-resolution X-ray imaging crystal spectrometer, whose instrumental concept was thoroughly tested on NSTX and Alcator C-Mod, is presently being designed for LHD. The instrument will record spatially resolved spectra of helium-like Ar16+ and provide ion temperature profiles with spatial and temporal resolutions of 1 cm and > 10 ms which are obtained by a tomographic inversion of the spectral data, using the stellarator equilibrium reconstruction codes, STELLOPT and PIES. Since the spectrometer will be equipped with radiation hardened, high count rate, PILATUS detectors,, it is expected to be operational for all experimental conditions on LHD, which include plasmas of high density and plasmas with auxiliary RF and neutral beam heating. The special design features required by the magnetic field structure at LHD will be described.

  14. Raman spectroscopy adds complementary detail to the high-resolution x-ray crystal structure of photosynthetic PsbP from Spinacia oleracea.

    Science.gov (United States)

    Kopecky, Vladimir; Kohoutova, Jaroslava; Lapkouski, Mikalai; Hofbauerova, Katerina; Sovova, Zofie; Ettrichova, Olga; González-Pérez, Sergio; Dulebo, Alexander; Kaftan, David; Smatanova, Ivana Kuta; Revuelta, Jose L; Arellano, Juan B; Carey, Jannette; Ettrich, Rüdiger

    2012-01-01

    Raman microscopy permits structural analysis of protein crystals in situ in hanging drops, allowing for comparison with Raman measurements in solution. Nevertheless, the two methods sometimes reveal subtle differences in structure that are often ascribed to the water layer surrounding the protein. The novel method of drop-coating deposition Raman spectropscopy (DCDR) exploits an intermediate phase that, although nominally "dry," has been shown to preserve protein structural features present in solution. The potential of this new approach to bridge the structural gap between proteins in solution and in crystals is explored here with extrinsic protein PsbP of photosystem II from Spinacia oleracea. In the high-resolution (1.98 Å) x-ray crystal structure of PsbP reported here, several segments of the protein chain are present but unresolved. Analysis of the three kinds of Raman spectra of PsbP suggests that most of the subtle differences can indeed be attributed to the water envelope, which is shown here to have a similar Raman intensity in glassy and crystal states. Using molecular dynamics simulations cross-validated by Raman solution data, two unresolved segments of the PsbP crystal structure were modeled as loops, and the amino terminus was inferred to contain an additional beta segment. The complete PsbP structure was compared with that of the PsbP-like protein CyanoP, which plays a more peripheral role in photosystem II function. The comparison suggests possible interaction surfaces of PsbP with higher-plant photosystem II. This work provides the first complete structural picture of this key protein, and it represents the first systematic comparison of Raman data from solution, glassy, and crystalline states of a protein.

  15. Raman spectroscopy adds complementary detail to the high-resolution x-ray crystal structure of photosynthetic PsbP from Spinacia oleracea.

    Directory of Open Access Journals (Sweden)

    Vladimir Kopecky

    Full Text Available Raman microscopy permits structural analysis of protein crystals in situ in hanging drops, allowing for comparison with Raman measurements in solution. Nevertheless, the two methods sometimes reveal subtle differences in structure that are often ascribed to the water layer surrounding the protein. The novel method of drop-coating deposition Raman spectropscopy (DCDR exploits an intermediate phase that, although nominally "dry," has been shown to preserve protein structural features present in solution. The potential of this new approach to bridge the structural gap between proteins in solution and in crystals is explored here with extrinsic protein PsbP of photosystem II from Spinacia oleracea. In the high-resolution (1.98 Å x-ray crystal structure of PsbP reported here, several segments of the protein chain are present but unresolved. Analysis of the three kinds of Raman spectra of PsbP suggests that most of the subtle differences can indeed be attributed to the water envelope, which is shown here to have a similar Raman intensity in glassy and crystal states. Using molecular dynamics simulations cross-validated by Raman solution data, two unresolved segments of the PsbP crystal structure were modeled as loops, and the amino terminus was inferred to contain an additional beta segment. The complete PsbP structure was compared with that of the PsbP-like protein CyanoP, which plays a more peripheral role in photosystem II function. The comparison suggests possible interaction surfaces of PsbP with higher-plant photosystem II. This work provides the first complete structural picture of this key protein, and it represents the first systematic comparison of Raman data from solution, glassy, and crystalline states of a protein.

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

    Science.gov (United States)

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

    2017-08-01

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

  17. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un [Ithaca, NY; Gruner, Sol M [Ithaca, NY

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  18. High-resolution insights into episodes of crystallization, hydrothermal alteration and remelting in the Skaergaard intrusive complex

    DEFF Research Database (Denmark)

    Wotzlaw, Joern-Frederik; Bindeman, Ilya N.; Schaltegger, Urs

    2012-01-01

    intrusions, and related remelting events, which cause the generation of low-delta O-18 magmas. Our precise temporal framework for intrusion crystallization also provides constraints for the timing of coeval flood basalt volcanism and its synchronicity with the Paleocene-Eocene thermal maximum....

  19. Role of atomic-level defects and electronic energy loss on amorphization in LiNbO3 single crystals

    Science.gov (United States)

    Sellami, N.; Crespillo, M. L.; Xue, H.; Zhang, Y.; Weber, W. J.

    2017-08-01

    Understanding complex non-equilibrium defect processes, where multiple irradiation mechanisms may take place simultaneously, is a long standing subject in material science. The separate and combined effects of elastic and inelastic energy loss are a very complicated and challenging topic. In this work, LiNbO3 has been irradiated with 0.9 MeV Si+ and 8 MeV O3+, which are representative of regimes where nuclear (S n) and electronic (S e) energy loss are dominant, respectively. The evolution of damage has been investigated by Rutherford backscattering spectrometry (RBS) in channeling configuration. Pristine samples were irradiated with 0.9 MeV Si+ ions to create different pre-existing damage states. Below the threshold (S e,th  =  5-6 keV nm-1) for amorphous track formation in this material, irradiation of the pristine samples with a highly ionizing beam of 8 MeV O3+ ions, with nearly constant S e of about 3 keV nm-1, induces a crystalline to amorphous phase transition at high ion fluences. In the pre-damaged samples, the electronic energy loss from the 8 MeV O3+ ions interacts synergistically with the pre-existing damage, resulting in a rapid, non-linear increase in damage production. There is a significant reduction in the incubation fluence for rapid amorphization with the increasing amount of pre-existing damage. These results highlight the important role of atomic-level defects on increasing the sensitivity of some oxides to amorphization induced by electronic energy loss. Controlling the nature and amount of pre-damage may provide a new approach to tuning optical properties for photonic device applications.

  20. A novel gamma-ray detector with submillimeter resolutions using a monolithic MPPC array with pixelized Ce:LYSO and Ce:GGAG crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kato, T., E-mail: katou.frme.8180@asagi.waseda.jp [Research Institute for Science and Engineering, Waseda University, 3-4-1, Ohkubo, Shinjuku, Tokyo (Japan); Kataoka, J.; Nakamori, T.; Miura, T.; Matsuda, H.; Kishimoto, A. [Research Institute for Science and Engineering, Waseda University, 3-4-1, Ohkubo, Shinjuku, Tokyo (Japan); Sato, K.; Ishikawa, Y.; Yamamura, K.; Nakamura, S.; Kawabata, N. [Solid State Division, Hamamatsu Photonics K. K., 1126-1, Ichino-cho, Hamamatsu, Shizuoka (Japan); Ikeda, H. [ISAS/JAXA, 3-1-1, Yoshinodai, Chuo-ku, Sagamihara-shi, Kanagawa (Japan); Yamamoto, S. [Kobe City College of Technology, 8-3, Gakuenhigashimati, Nishi-ku, Kobe-shi, Hyougo 651-2194 (Japan); Kamada, K. [Materials Research Laboratory, Furukawa Co., Ltd., 1-25-13, Kannondai, Tsukuba, Ibaraki 305-0856 (Japan)

    2013-01-21

    We have developed a large-area monolithic Multi-Pixel Photon Counter (MPPC) array consisting of 4×4 channels with a three-side buttable package. Each channel has a photosensitive area of 3×3 mm{sup 2} and 3600 Geiger mode avalanche photodiodes (APDs). For typical operational gain of 7.5×10{sup 5} at +20 °C, gain fluctuation over the entire MPPC device is only ±5.6%, and dark count rates (as measured at the 1 p.e. level) amount to ≤400kcps per channel. We first fabricated a gamma-ray camera consisting of the MPPC array with one-to-one coupling to a Ce-doped (Lu,Y){sub 2}(SiO{sub 4})O (Ce:LYSO) crystal array (4×4 array of 3×3×10 mm{sup 3} crystals). Energy and time resolutions of 11.5±0.5% (FWHM at 662 keV) and 493±22ps were obtained, respectively. When using the charge division resistor network, which compiles signals into four position-encoded analog outputs, the ultimate positional resolution is estimated as 0.19 mm in both X and Y directions, while energy resolution of 10.2±0.4% (FWHM) was obtained. Finally, we fabricated submillimeter Ce:LYSO and Ce-doped Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12} (Ce:GGAG) scintillator matrices each consisting of 1.0×1.0, 0.7×0.7 and 0.5×0.5 mm{sup 2} pixels, to further improve the spatial resolution. In all types of Ce:LYSO and Ce:GGAG matrices, each crystal was clearly resolved in the position histograms when irradiated by a {sup 137}Cs source. The energy resolutions for 662 keV gamma-rays for each Ce:LYSO and Ce:GGAG scintillator matrix were ≤14.3%. These results suggest excellent potential for its use as a high spatial medical imaging device, particularly in positron emission tomography (PET). -- Highlights: ► We developed a newly designed large-area monolithic MPPC array. ► We obtained fine gain uniformity, and good energy and time resolutions when coupled to the LYSO scintillator. ► We fabricated gamma-ray camera consisting of the MPPC array and submillimeter pixelized LYSO and GGAG scintillators. ► In

  1. Layout And Results From The Initial Operation Of The High-resolution X-ray Imaging Crystal Spectrometer On The Large Helical Device

    Energy Technology Data Exchange (ETDEWEB)

    Pablant, N A [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Delgado-Apricio, L [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Goto, M [National Institute for Fusion Science, Toki 509-5292, Gifu, Japan; Hill, K W [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Lzerson, S [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Morita, S [National Institute for Fusion Science, Toki 509-5292, Gifu, Japan; Roquemore, A L [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Gates, D [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Monticello, D [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Neilson, H [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Reiman, A [Princeton Plasma Physics Laboratory, Princeton, New Jersey (United States); Reinke, M [Plasma Science Fusion Center, MIT, Cambridge, Massachusetts (United States); Rice, J E [Plasma Science Fusion Center, MIT, Cambridge, Massachusetts (United States)

    2012-04-05

    First results of ion and electron temperature pro le measurements from the x-ray imaging crystal spectrometer (XICS) diagnostic on the Large Helical Device (LHD) are presented. This diagnostic system has been operational since the beginning of the 2011 LHD experimental campaign and is the rst application of the XICS diagnostic technique to helical plasma geometry. The XICS diagnostic provides measurements of ion and electron temperature pro les in LHD with a spatial resolution of 2cm and a time resolution of ≥ 10ms. Ion temperature pro les from the XICS diagnostic are possible under conditions where charge exchange recombination spectroscopy (CXRS) is not possible (high density) or is perturbative to the plasma (low density or radio frequency heated plasmas). Measurements are made by using a spherically bent crystal to provide a spectrally resolved 1D image of the plasma from line integrated emission of helium-like Ar16+. The nal hardware design and con guration are detailed along with the calibration procedures. Line-integrated ion and electron temperature measurements are presented, and the measurement accuracy is discussed. Finally central temperature measurements from the XICS system are compared to measurements from the Thomson scattering and CXRS systems, showing excellent agreement.

  2. Layout and results from the initial operation of the high-resolution x-ray imaging crystal spectrometer on the Large Helical Device

    Energy Technology Data Exchange (ETDEWEB)

    Pablant, N. A.; Bitter, M.; Delgado-Aparicio, L.; Hill, K. W.; Lazerson, S.; Roquemore, A. L.; Gates, D.; Monticello, D.; Nielson, H.; Reiman, A. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States); Goto, M.; Morita, S.; Yamada, H. [National Institute for Fusion Science, Toki 509-5292, Gifu (Japan); Reinke, M.; Rice, J. E. [Plasma Science Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307 (United States)

    2012-08-15

    First results of ion and electron temperature profile measurements from the x-ray imaging crystal spectrometer (XICS) diagnostic on the Large Helical Device (LHD) are presented. This diagnostic system has been operational since the beginning of the 2011 LHD experimental campaign and is the first application of the XICS diagnostic technique to helical plasma geometry. The XICS diagnostic provides measurements of ion and electron temperature profiles in LHD with a spatial resolution of 2 cm and a maximum time resolution of 5 ms (typically 20 ms). Ion temperature profiles from the XICS diagnostic are possible under conditions where charge exchange recombination spectroscopy (CXRS) is not possible (high density) or is perturbative to the plasma (low density or radio frequency heated plasmas). Measurements are made by using a spherically bent crystal to provide a spectrally resolved 1D image of the plasma from line integrated emission of helium-like Ar{sup 16+}. The final hardware design and configuration are detailed along with the calibration procedures. Line-integrated ion and electron temperature measurements are presented, and the measurement accuracy is discussed. Finally central temperature measurements from the XICS system are compared to measurements from the Thomson scattering and CXRS systems, showing excellent agreement.

  3. Light-Induced Fluorescence Modulation of Quantum Dot-Crystal Violet Conjugates: Stochastic Off-On-Off Cycles for Multicolor Patterning and Super-Resolution.

    Science.gov (United States)

    Jung, Sungwook; Park, Joonhyuck; Bang, Jiwon; Kim, Jae-Yeol; Kim, Cheolhee; Jeon, Yongmoon; Lee, Seung Hwan; Jin, Ho; Choi, Sukyung; Kim, Bomi; Lee, Woo Jin; Pack, Chan-Gi; Lee, Jong-Bong; Lee, Nam Ki; Kim, Sungjee

    2017-06-07

    Photoswitching or modulation of quantum dots (QDs) can be promising for many fields that include display, memory, and super-resolution imaging. However, such modulations have mostly relied on photomodulations of conjugated molecules in QD vicinity, which typically require high power of high energy photons at UV. We report a visible light-induced facile modulation route for QD-dye conjugates. QD crystal violets conjugates (QD-CVs) were prepared and the crystal violet (CV) molecules on QD quenched the fluorescence efficiently. The fluorescence of QD-CVs showed a single cycle of emission burst as they go through three stages of (i) initially quenched "off" to (ii) photoactivated "on" as the result of chemical change of CVs induced by photoelectrons from QD and (iii) back to photodarkened "off" by radical-associated reactions. Multicolor on-demand photopatterning was demonstrated using QD-CV solid films. QD-CVs were introduced into cells, and excitation with visible light yielded photomodulation from "off" to "on" and "off" by nearly ten fold. Individual photoluminescence dynamics of QD-CVs was investigated using fluorescence correlation spectroscopy and single QD emission analysis, which revealed temporally stochastic photoactivations and photodarkenings. Exploiting the stochastic fluorescence burst of QD-CVs, simultaneous multicolor super-resolution localizations were demonstrated.

  4. High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Shuxia, E-mail: pengsx@ihep.ac.cn; Zhou, Ke; Wang, Wenjia; Gao, Zengqiang; Dong, Yuhui; Liu, Quansheng

    2014-10-31

    Highlights: • Crystal structure of the C-terminal (CT) domain of Swt1 was determined at 2.3 Å. • Structure of the CT domain was identified as HEPN domain superfamily member. • Low-resolution envelope of Swt1 full-length in solution was analyzed by SAXS. • The middle and CT domains gave good fit to SAXS structural model. - Abstract: Swt1 is an RNA endonuclease that plays an important role in quality control of nuclear messenger ribonucleoprotein particles (mRNPs) in eukaryotes; however, its structural details remain to be elucidated. Here, we report the crystal structure of the C-terminal (CT) domain of Swt1 from Saccharomyces cerevisiae, which shares common characteristics of higher eukaryotes and prokaryotes nucleotide binding (HEPN) domain superfamily. To study in detail the full-length protein structure, we analyzed the low-resolution architecture of Swt1 in solution using small angle X-ray scattering (SAXS) method. Both the CT domain and middle domain exhibited a good fit upon superimposing onto the molecular envelope of Swt1. Our study provides the necessary structural information for detailed analysis of the functional role of Swt1, and its importance in the process of nuclear mRNP surveillance.

  5. Simultaneous determination of Cd and Fe in grain products using direct solid sampling and high-resolution continuum source electrothermal atomic absorption spectrometry.

    Science.gov (United States)

    dos Santos, Lisia M G; Araujo, Rennan G O; Welz, Bernhard; Jacob, Silvana do C; Vale, Maria Goreti R; Becker-Ross, Helmut

    2009-04-30

    Cadmium and iron are antagonistic elements in the sense that they produce different effects in the human body. Both elements have to be determined routinely in grain products, cadmium because of its toxicity, and iron because all grain products, according to Brazilian law, have to contain a minimum of 42 mg kg(-1) Fe to combat anemia. A routine screening method has been developed for the quasi simultaneous determination of cadmium and iron using high-resolution continuum source electrothermal atomic absorption spectrometry and direct solid sampling. The primary absorption line at 228.802 nm has been used for Cd, and an adjacent secondary line at 228.726 nm for the determination of Fe. Various chemical modifiers have been investigated, and a mixture of tungsten and iridium, applied as a permanent modifier, showed the best performance; it stabilized Cd up to a pyrolysis temperature of 700 degrees C and did not over-stabilize Fe. Two atomization temperatures were used sequentially, 1700 degrees C for Cd and 2600 degrees C for Fe, because of their significantly different volatilities. The characteristic masses obtained were 0.9 pg for Cd and 1.2 ng for Fe. The limits of detection (3 sigma, n=10) were 0.6 microg kg(-1) for Cd and 0.5 mg kg(-1) for Fe. The relative standard deviation ranged from 3 to 7% for Cd and from 4 to 13% for Fe, which is satisfactory for the purpose. The accuracy of the method was confirmed by the analysis of three certified reference materials; the results were in agreement with the certified values at a 95% confidence interval. The Cd content in the investigated grain products was between 0.9 and 10.5 microg kg(-1), but most of them did not contain the required minimum amount of iron.

  6. Determination of mercury in airborne particulate matter collected on glass fiber filters using high-resolution continuum source graphite furnace atomic absorption spectrometry and direct solid sampling

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Rennan G.O., E-mail: rgoa01@terra.com.br [Laboratorio de Quimica Analitica Ambiental, Departamento de Quimica, Universidade Federal de Sergipe, Campus Sao Cristovao, 49.100-000, Sao Cristovao, SE (Brazil); Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900, Florianopolis, SC (Brazil); Vignola, Fabiola; Castilho, Ivan N.B. [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900, Florianopolis, SC (Brazil); Borges, Daniel L.G.; Welz, Bernhard [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900, Florianopolis, SC (Brazil); Instituto Nacional de Ciencia e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador, BA (Brazil); Vale, Maria Goreti R. [Instituto Nacional de Ciencia e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador, BA (Brazil); Instituto de Quimica, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS (Brazil); Smichowski, Patricia [Comision Nacional de Energia Atomica (CNEA) and Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires (Argentina); Ferreira, Sergio L.C. [Instituto Nacional de Ciencia e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador, BA (Brazil); Instituto de Quimica, Universidade Federal da Bahia, 40170-290, Salvador, BA (Brazil); Becker-Ross, Helmut [Leibniz-Institut fuer Analytische Wissenschaften-ISAS-e.V., Department Berlin, 12489 Berlin (Germany)

    2011-05-15

    A study has been undertaken to assess the capability of high-resolution continuum source graphite furnace atomic absorption spectrometry for the determination of mercury in airborne particulate matter (APM) collected on glass fiber filters using direct solid sampling. The main Hg absorption line at 253.652 nm was used for all determinations. The certified reference material NIST SRM 1648 (Urban Particulate Matter) was used to check the accuracy of the method, and good agreement was obtained between published and determined values. The characteristic mass was 22 pg Hg. The limit of detection (3{sigma}), based on ten atomizations of an unexposed filter, was 40 ng g{sup -1}, corresponding to 0.12 ng m{sup -3} in the air for a typical air volume of 1440 m{sup 3} collected within 24 h. The limit of quantification was 150 ng g{sup -1}, equivalent to 0.41 ng m{sup -3} in the air. The repeatability of measurements was better than 17% RSD (n = 5). Mercury concentrations found in filter samples loaded with APM collected in Buenos Aires, Argentina, were between < 40 ng g{sup -1} and 381 {+-} 24 ng g{sup -1}. These values correspond to a mercury concentration in the air between < 0.12 ng m{sup -3} and 1.47 {+-} 0.09 ng m{sup -3}. The proposed procedure was found to be simple, fast and reliable, and suitable as a screening procedure for the determination of mercury in APM samples.

  7. A simple and fast method for assessment of the nitrogen–phosphorus–potassium rating of fertilizers using high-resolution continuum source atomic and molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Bechlin, Marcos André; Fortunato, Felipe Manfroi; Moutinho da Silva, Ricardo; Ferreira, Edilene Cristina; Gomes Neto, José Anchieta, E-mail: anchieta@iq.unesp.br

    2014-11-01

    The determination of N, P, and K in fertilizers by high-resolution continuum source flame atomic and molecular absorption spectrometry is proposed. Under optimized conditions, measurements of the diatomic molecules NO and PO at 215.360 and 247.620 nm, respectively, and K using the wing of the alternative line at 404.722 nm allowed calibration curves to be constructed in the ranges 500–5000 mg L{sup −1} N (r = 0.9994), 100–2000 mg L{sup −1} P (r = 0.9946), and 100–2500 mg L{sup −1} K (r = 0.9995). Commercial fertilizers were analyzed by the proposed method and the concentrations of N, P, and K were found to be in agreement with those obtained by Kjeldahl, spectrophotometric, and flame atomic emission spectrometry methods, respectively, at a 95% confidence level (paired t-test). A phosphate rock certified reference material (CRM) was analyzed and the results for P and K were in agreement with the reference values. Recoveries from spiked CRM were in the ranges 97–105% (NO{sub 3}{sup −}-N), 95–103% (NH{sub 4}{sup +}-N), 93–103% (urea-N), 99–108% (P), and 99–102% (K). The relative standard deviations (n = 12) for N, P, and K were 6, 4, and 2%, respectively. - Highlights: • A single technique is proposed to analyze NPK fertilizer. • HR-CS FAAS is proposed for the first time for N, P and K determination in fertilizers. • The method employs the same sample preparation and dilution for the three analytes. • Addition of H{sub 2}O{sub 2} allows analysis of fertilizers with different nitrogen species. • Proposal provides advantages over traditional methods in terms of cost and time.

  8. Direct determination of chromium in infant formulas employing high-resolution continuum source electrothermal atomic absorption spectrometry and solid sample analysis.

    Science.gov (United States)

    Silva, Arlene S; Brandao, Geovani C; Matos, Geraldo D; Ferreira, Sergio L C

    2015-11-01

    The present work proposed an analytical method for the direct determination of chromium in infant formulas employing the high-resolution continuum source electrothermal atomic absorption spectrometry combined with the solid sample analysis (SS-HR-CS ET AAS). Sample masses up to 2.0mg were directly weighted on a solid sampling platform and introduced into the graphite tube. In order to minimize the formation of carbonaceous residues and to improve the contact of the modifier solution with the solid sample, a volume of 10 µL of a solution containing 6% (v/v) H2O2, 20% (v/v) ethanol and 1% (v/v) HNO3 was added. The pyrolysis and atomization temperatures established were 1600 and 2400 °C, respectively, using magnesium as chemical modifier. The calibration technique was evaluated by comparing the slopes of calibration curves established using aqueous and solid standards. This test revealed that chromium can be determined employing the external calibration technique using aqueous standards. Under these conditions, the method developed allows the direct determination of chromium with limit of quantification of 11.5 ng g(-1), precision expressed as relative standard deviation (RSD) in the range of 4.0-17.9% (n=3) and a characteristic mass of 1.2 pg of chromium. The accuracy was confirmed by analysis of a certified reference material of tomato leaves furnished by National Institute of Standards and Technology. The method proposed was applied for the determination of chromium in five different infant formula samples. The chromium content found varied in the range of 33.9-58.1 ng g(-1) (n=3). These samples were also analyzed employing ICP-MS. A statistical test demonstrated that there is no significant difference between the results found by two methods. The chromium concentrations achieved are lower than the maximum limit permissible for chromium in foods by Brazilian Legislation. Copyright © 2015. Published by Elsevier B.V.

  9. Visualization of drug-nucleic acid interactions at atomic resolution. X. Structure of a N,N-dimethylproflavine: deoxycytidylyl(3'-5')deoxyguanosine crystalline complex

    Energy Technology Data Exchange (ETDEWEB)

    Sakore, T.D.; Bhandary, K.K.; Sobell, H.M.

    1984-01-01

    N,N-dimethylproflavine forms a crystalline complex with deoxycytidylyl(3'-5')deoxyguanosine (d-CpG), space group P2/sub 1/,2/sub 1/2, with a = 21.37 A, b = 34.05 A, c = 13.63 A. The structure has been solved to atomic resolution and refined by Fourier and least squares methods to a residual of 0.18 of 2032 observed reflections. The structure consists of two N,N-dimethylproflavine molecules, two deoxycytidylyl (3'-5')deoxyguanosine molecules and 16 water molecules, a total of 128 nonhydrogen atoms. As with other structures of this type, N,N-dimethylproflavine molecules intercalate between base-paired d-CpG dimers. In addition, dimethylproflavine molecules stack on either side of the intercalated duplex, being related by a unit cell translation along the c axis. Both sugar-phosphate chains demonstrate the mixed sugar puckering geometry: C3' endo (3'-5') C2' endo. The same intercalative geometry has been seen in two other complexes containing N,N-dimethylproflavine and iodoCpG, described in the accompanying paper. Taken together, these studies indicate a common intercalative geometry present in both RNA- and DNA- model systems. Again, N,N-dimethylproflavine behaves as a simple intercalator, intercalating asymmetrically between guanine-cytosine base-pairs. The free amino- group on the intercalated dimethylproflavine molecule does not hydrogen bond directly to the phosphate oxygen. Other aspects of the structure will be presented. 4 references, 5 figures, 2 tables.

  10. High-resolution crystal structure of Streptococcus pyogenes β-NAD{sup +} glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin [Seoul National University, Seoul 151-747 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Sang Jae [Seoul National University, Seoul 151-742 (Korea, Republic of); Im, Ha Na; Jang, Jun Young [Seoul National University, Seoul 151-747 (Korea, Republic of); Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-747 (Korea, Republic of)

    2013-11-01

    The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD{sup +} glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD{sup +} glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN{sub ct}–IFS complex, which consists of the SPN C-terminal domain (SPN{sub ct}; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN{sub ct} and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

  11. Breakthrough to Non-Vacuum Deposition of Single-Crystal, Ultra-Thin, Homogeneous Nanoparticle Layers: A Better Alternative to Chemical Bath Deposition and Atomic Layer Deposition

    Directory of Open Access Journals (Sweden)

    Yu-Kuang Liao

    2017-04-01

    Full Text Available Most thin-film techniques require a multiple vacuum process, and cannot produce high-coverage continuous thin films with the thickness of a few nanometers on rough surfaces. We present a new ”paradigm shift” non-vacuum process to deposit high-quality, ultra-thin, single-crystal layers of coalesced sulfide nanoparticles (NPs with controllable thickness down to a few nanometers, based on thermal decomposition. This provides high-coverage, homogeneous thickness, and large-area deposition over a rough surface, with little material loss or liquid chemical waste, and deposition rates of 10 nm/min. This technique can potentially replace conventional thin-film deposition methods, such as atomic layer deposition (ALD and chemical bath deposition (CBD as used by the Cu(In,GaSe2 (CIGS thin-film solar cell industry for decades. We demonstrate 32% improvement of CIGS thin-film solar cell efficiency in comparison to reference devices prepared by conventional CBD deposition method by depositing the ZnS NPs buffer layer using the new process. The new ZnS NPs layer allows reduction of an intrinsic ZnO layer, which can lead to severe shunt leakage in case of a CBD buffer layer. This leads to a 65% relative efficiency increase.

  12. Breakthrough to Non-Vacuum Deposition of Single-Crystal, Ultra-Thin, Homogeneous Nanoparticle Layers: A Better Alternative to Chemical Bath Deposition and Atomic Layer Deposition.

    Science.gov (United States)

    Liao, Yu-Kuang; Liu, Yung-Tsung; Hsieh, Dan-Hua; Shen, Tien-Lin; Hsieh, Ming-Yang; Tzou, An-Jye; Chen, Shih-Chen; Tsai, Yu-Lin; Lin, Wei-Sheng; Chan, Sheng-Wen; Shen, Yen-Ping; Cheng, Shun-Jen; Chen, Chyong-Hua; Wu, Kaung-Hsiung; Chen, Hao-Ming; Kuo, Shou-Yi; Charlton, Martin D B; Hsieh, Tung-Po; Kuo, Hao-Chung

    2017-04-06

    Most thin-film techniques require a multiple vacuum process, and cannot produce high-coverage continuous thin films with the thickness of a few nanometers on rough surfaces. We present a new "paradigm shift" non-vacuum process to deposit high-quality, ultra-thin, single-crystal layers of coalesced sulfide nanoparticles (NPs) with controllable thickness down to a few nanometers, based on thermal decomposition. This provides high-coverage, homogeneous thickness, and large-area deposition over a rough surface, with little material loss or liquid chemical waste, and deposition rates of 10 nm/min. This technique can potentially replace conventional thin-film deposition methods, such as atomic layer deposition (ALD) and chemical bath deposition (CBD) as used by the Cu(In,Ga)Se₂ (CIGS) thin-film solar cell industry for decades. We demonstrate 32% improvement of CIGS thin-film solar cell efficiency in comparison to reference devices prepared by conventional CBD deposition method by depositing the ZnS NPs buffer layer using the new process. The new ZnS NPs layer allows reduction of an intrinsic ZnO layer, which can lead to severe shunt leakage in case of a CBD buffer layer. This leads to a 65% relative efficiency increase.

  13. Measurement of absolute density of N atom in sputtering plasma for epitaxial growth ZnO films via nitrogen mediated crystallization

    Science.gov (United States)

    Ide, Tomoaki; Matsushima, Koichi; Takasaki, Toshiyuki; Takeda, Keigo; Hori, Masaru; Yamashita, Daisuke; Seo, Hyuwoong; Koga, Kazunori; Shiratani, Masaharu; Itagaki, Naho

    2015-09-01

    ZnO has attracted attention as a potential alternative to GaN in light emitting diodes because of the wide band gap and large exciton binding energy. Recently, we have developed a fabrication method of ZnO by sputtering, nitrogen mediated crystallization (NMC), enabling us to make epitaxial films with low defect density. By utilizing the buffer layers fabricated by NMC method, we have succeeded in fabrication of single crystalline ZnO films even on 18% lattice mismatched substrates. Here, aiming to clarify effects of nitrogen during NMC process, we measured absolute density of N atom in sputtering plasma by means of vacuum ultra violet absorption spectroscopy. First, NMC-ZnO buffer layers were deposited in Ar/N2 atmosphere. Then, ZnO films were deposited in Ar/O2 atmosphere. With increasing N2 flow rate ratio from 4 to 12%, the N density increases from 3.2 × 1010 to 1.4 × 1011 cm-3. By utilizing the NMC-ZnO buffer layer fabricated at under these conditions, single crystalline ZnO films are grown. However, large number of pits are observed on the surface of ZnO films under N-rich conditions, indicating that N density is of importance in controlling the morphology of ZnO films. This work was supported in part by Japan Society for the Promotion of Science KAKENHI Grant Number 15H05431.

  14. Atomic-resolution structure of the α-galactosyl binding Lyophyllum decastes lectin reveals a new protein family found in both fungi and plants.

    Science.gov (United States)

    van Eerde, André; Grahn, Elin M; Winter, Harry C; Goldstein, Irwin J; Krengel, Ute

    2015-05-01

    The crystal structure of the α-galactosyl binding Lyophyllum decastes lectin (LDL) was determined to 1.0 Å resolution by sulfur single-wavelength anomalous diffraction (SAD). The 10 kDa protein exhibits no sequence similarity to any protein with known structure and adopts a unique lectin fold, where a core of two antiparallel β-sheets at the heart of the homodimer is connected to the periphery of the structure by intramolecular disulfide bridges. This fold suggests that LDL is secreted, which sets it apart from other mushroom lectins. Structures of complexes between LDL and the ligands α-methylgalactoside and globotriose shed light on the binding specificity. Sequence comparison suggests a location and function of LDL and homologous proteins in or at the fungal cell wall. Structural comparison allows the identification of a superfamily of secreted proteins with the LDL fold, which may play a role at the interface between fungi and their environment. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Fast arsenic speciation in water by on-site solid phase extraction and high-resolution continuum source graphite furnace atomic absorption spectrometry

    Science.gov (United States)

    Mihucz, Victor G.; Bencs, László; Koncz, Kornél; Tatár, Enikő; Weiszburg, Tamás; Záray, Gyula

    2017-02-01

    A method of high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS-GFAAS), combined with on-site separation/solid phase extraction (SPE) has been developed for the speciation of inorganic As (iAs) in geothermal and drinking water samples. The HR-CS-GFAAS calibration curves were linear up to 200 μg/L As, but using second order polynomial fitting, accurate calibration could be performed up to 500 μg/L. It has been demonstrated that sample pH should not be higher than 8 for an accurate speciation of As(V) with a recovery of ≈ 95%. Geothermal water had fairly high salt content (≈ 2200 mg/L) due to the presence of chlorides and sulfates at mg/L levels. Therefore, a two-fold dilution of these types of samples before SPE is recommended, especially, for total As determinations, when the As concentration is as high as 400 μg/L. For drinking water, sampled from public wells with records of As concentrations higher than the 10 μg/L in the past, the reduction of As contamination below the WHO's health limit value could be observed. However, the electrical conductivity was close to 2500 μS/cm, i.e., the guideline limit for drinking water, which was due to their higher chloride content. The proposed fit-for-purpose SPE-HR-CS-GFAAS method could be a candidate for screening drinking water quality.

  16. The role of symmetry in the theory of inelastic high-energy electron scattering and its application to atomic-resolution core-loss imaging

    Energy Technology Data Exchange (ETDEWEB)

    Dwyer, C., E-mail: c.dwyer@fz-juelich.de [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich D-52425 (Germany); Peter Grünberg Institute, Forschungszentrum Jülich, Jülich D-52425 (Germany)

    2015-04-15

    The inelastic scattering of a high-energy electron in a solid constitutes a bipartite quantum system with an intrinsically large number of excitations, posing a considerable challenge for theorists. It is demonstrated how and why the utilization of symmetries, or approximate symmetries, can lead to significant improvements in both the description of the scattering physics and the efficiency of numerical computations. These ideas are explored thoroughly for the case of core-loss excitations, where it is shown that the coupled angular momentum basis leads to dramatic improvements over the bases employed in previous work. The resulting gains in efficiency are demonstrated explicitly for K-, L- and M-shell excitations, including such excitations in the context of atomic-resolution imaging in the scanning transmission electron microscope. The utilization of other symmetries is also discussed. - Highlights: • It is explained how and why symmetry improves the efficiency of inelastic scattering calculations in general. • This includes approximate symmetries, which are often easier to specify. • Specific examples are given for core-loss scattering in STEM. • The utilization of approximate symmetries associated with ELNES, the detector geometry, and the energy loss are also discussed.

  17. The electronic structure of the primary electron donor of reaction centers of purple bacteria at atomic resolution as observed by photo-CIDNP 13C NMR.

    Science.gov (United States)

    Daviso, Eugenio; Prakash, Shipra; Alia, A; Gast, Peter; Neugebauer, Johannes; Jeschke, Gunnar; Matysik, Jörg

    2009-12-29

    Composed of the two bacteriochlorophyll cofactors, P(L) and P(M), the special pair functions as the primary electron donor in bacterial reaction centers of purple bacteria of Rhodobacter sphaeroides. Under light absorption, an electron is transferred to a bacteriopheophytin and a radical pair is produced. The occurrence of the radical pair is linked to the production of enhanced nuclear polarization called photochemically induced dynamic nuclear polarization (photo-CIDNP). This effect can be used to study the electronic structure of the special pair at atomic resolution by detection of the strongly enhanced nuclear polarization with laser-flash photo-CIDNP magic-angle spinning NMR on the carotenoid-less mutant R26. In the electronic ground state, P(L) is strongly disturbed, carrying a slightly negative charge. In the radical cation state, the ratio of total electron spin densities between P(L) and P(M) is 2:1, although it is 2.5:1 for the pyrrole carbons, 2.2:1 for all porphyrinic carbons, and 4:1 for the pyrrole nitrogen. It is shown that the symmetry break between the electronic structures in the electronic ground state and in the radical cation state is an intrinsic property of the special pair supermolecule, which is particularly attributable to a modification of the structure of P(L). The significant difference in electron density distribution between the ground and radical cation states is explained by an electric polarization effect of the nearby histidine.

  18. Multivariate optimization of ultrasound-assisted extraction for determination of Cu, Fe, Ni and Zn in vegetable oils by high-resolution continuum source atomic absorption spectrometry.

    Science.gov (United States)

    Trindade, Alex S N; Dantas, Alailson F; Lima, Daniel C; Ferreira, Sérgio L C; Teixeira, Leonardo S G

    2015-10-15

    An assisted liquid-liquid extraction of copper, iron, nickel and zinc from vegetable oil samples with subsequent determination by high-resolution continuum source flame atomic absorption spectrometry (HR-CS FAAS) was optimized by applying a full factorial design in two levels and the response surface methodology, Box-Behnken. The effects of the acid concentration and the amplitude, cycle and time of sonication on the extraction of the analytes, as well as their interactions, were assessed. In the selected condition (sonication amplitude = 66%, sonication time = 79 s, sonication cycle = 74%), using 0.5 mol L(-1) HCl as the extractant, the limits of quantification were 0.14, 0.20, 0.21 and 0.04 μg g(-1) for Cu, Fe, Ni and Zn, respectively, with R.S.D. ranging from 1.4% to 3.6%. The proposed method was applied for the determination of the analytes in soybean, canola and sunflower oils. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Determination of Chlorine in Milk via Molecular Absorption of SrCl Using High-Resolution Continuum Source Graphite Furnace Atomic Absorption Spectrometry.

    Science.gov (United States)

    Ozbek, Nil; Akman, Suleyman

    2016-07-20

    Total chlorine in milk was determined via the molecular absorption of diatomic strontium monochloride at 635.862 nm using high-resolution continuum source graphite furnace atomic absorption spectrometry. The effects of coating the graphite furnace, using different modifiers, amount of molecule-forming element, and different calibrants were investigated and optimized. Chlorine concentrations in milk samples were determined in a Zr-coated graphite furnace using 25 μg of Sr as the molecule-forming reagent and applying a pyrolysis temperature of 600 °C and a molecule-forming temperature of 2300 °C. Linearity was maintained up to 500 μg mL(-1) of Cl. The method was tested by analyzing a certified reference wastewater. The results were in the uncertainty limits of the certified value. The limit of detection of the method was 1.76 μg mL(-1). The chlorine concentrations in various cow milk samples taken from the market were found in the range of 588-1472 mg L(-1).

  20. Determination of macro and trace elements in multivitamin dietary supplements by high-resolution continuum source graphite furnace atomic absorption spectrometry with slurry sampling.

    Science.gov (United States)

    Krawczyk, Magdalena

    2014-01-01

    In this research, three different commercially available multivitamin dietary supplements were analyzed by high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS GFAAS) with slurry sampling. The concentrations of Cr, Cu, Fe, Mn, and Se were determined and compared to the amounts stated by producers. The safety of multivitamin dietary supplements depends on various factors including the manufacturing process and the purity and origins of the raw ingredients. For this reason, this research determined concentrations of several toxic elements (As, Cd, and Pb). Microwave-assisted high pressure Teflon bomb digestion was used to determine total amounts of elements in samples. Samples were prepared as slurries at a concentration of 0.1% (m/v) for macro elements (Cr, Cu, Fe, Mn, and Se) and at a concentration of % (m/v) for trace elements (As, Cd, and Pb) in acidic media (3M HNO3). The influence of acid concentration, Triton X-100 addition, sonication time, and sonication power on absorbance was investigated. The accuracy of this method was validated by analyses of NRCC LUTS-1 (Lobster hepatopancreas), NRCC DORM-1 (Dogfish Muscle), NRCC DOLT-2 (Dogfish Liver), NBS SRM 1570 (Spinach Leaves) and NBS SRM 1573 (Tomato Leaves) certified reference materials. The measured elements contents in these reference materials (except NRCC DOLT-2) were in satisfactory agreement with the certified values according to the t-test for a 95% confidence level. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry for gold determination in geological samples after preconcentration onto carbon nanotubes

    Science.gov (United States)

    Dobrowolski, Ryszard; Mróz, Agnieszka; Dąbrowska, Marzena; Olszański, Piotr

    2017-06-01

    A novelty method for the determination of gold in geological samples by solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry (SS HR CS GF AAS) after solid-phase extraction onto modified carbon nanotubes (CNT) was described. The methodology developed is based on solid phase extraction of Au(III) ions from digested samples to eliminate strong interference caused by iron compounds and problems related to inhomogeneities of the samples. The use of aqueous or solid standard for calibration was studied and the slope of calibration curve was the same for both of these modes. This statement indicates the possibility to perform the calibration of the method using aqueous standard solutions. Under optimum conditions the absolute detection limit for gold was equal to 2.24 · 10- 6 μg g- 1 while the adsorption capacity of modified carbon nanotubes was 264 mg g- 1. The proposed procedure was validated by the application of certified reference materials (CRMs) with different content of gold and different matrix, the results were in good agreement with certified values. The method was successfully applied for separation and determination of gold ions in complex geological samples, with precision generally better than 8%.

  2. Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

    Science.gov (United States)

    Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

    2013-04-01

    When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. Local structure and lattice dynamics study of low dimensional materials using atomic pair distribution function and high energy resolution inelastic x-ray scattering

    Science.gov (United States)

    Shi, Chenyang

    Structure and dynamics lie at the heart of the materials science. A detailed knowledge of both subjects would be foundational in understanding the materials' properties and predicting their potential applications. However, the task becomes increasingly dicult as the particle size is reduced to the nanometer scale. For nanostructured materials their laboratory x-ray scattering patterns are overlapped and broadened, making structure determination impossible. Atomic pair distribution function technique based on either synchrotron x-ray or neutron scattering data is known as the tool of choice for probing local structures. However, to solve the "structure problem" in low-dimensional materials with PDF is still challenging. For example for 2D materials of interest in this thesis the crystallographic modeling approach often yields unphysical thermal factors along stacking direction where new chemical intuitions about their actual structures and new modeling methodology/program are needed. Beyond this, lattice dynamical investigations on nanosized particles are extremely dicult. Laboratory tools such as Raman and infra-red only probe phonons at Brillouin zone center. Although in literature there are a great number of theoretical studies of their vibrational properties based on either empirical force elds or density functional theory, various approximations made in theories make the theoretical predictions less reliable. Also, there lacks the direct experiment result to validate the theory against. In this thesis, we studied the structure and dynamics of a wide variety of technologically relevant low-dimensional materials through synchrotron based x-ray PDF and high energy resolution inelastic x-ray scattering (HERIX) techniques. By collecting PDF data and employing advanced modeling program such as DiPy-CMI, we successfully determined the atomic structures of (i) emerging Ti3C2, Nb4C3 MXenes (transition metal carbides and/or nitrides) that are promising for energy storage

  4. Structural characterization of K sub 3 Li sub 2 Nb sub 5 O sub 1 sub 5 single crystals by combining high-resolution X-ray diffractometry and topography

    CERN Document Server

    Kaigawa, K; Honda, A; Imaeda, M; Sakai, H; Tsurumi, T

    2002-01-01

    High-resolution multiple-crystal multiple-reflection X-ray diffractometry is used for the structural characterization of nonlinear optical single crystals of K sub 3 Li sub 2 Nb sub 5 O sub 1 sub 5 (KLN) grown by the micro-pulling-down (mu-PD) method. The combination of high-resolution X-ray diffractometry and topography shows that the lattice parameters along the c-axis (c-parameters) decrease towards the seed crystals, because of the decrease in the K content and increase in the Nb content. However, the KLN single crystals exhibit multi domain structures in which discontinuous changes in the c-parameters are periodically observed along the growth direction, despite the compositional change being continuous. Large mosaic structures due to discontinuous tilt in the lattice planes are also observed at the boundaries between the domains.

  5. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus. Purification, Crystallization and Structure Determination

    Energy Technology Data Exchange (ETDEWEB)

    Clemons, William M.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki (MRC); (Utah); (MRC)

    2009-10-07

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 {angstrom} resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 {angstrom} resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  6. Investigation of spectral interferences in the determination of lead in fertilizers and limestone samples using high-resolution continuum source graphite furnace atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Borges, Aline R. [Instituto de Química, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq — INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Becker, Emilene M.; François, Luciane L.; Jesus, Alexandre de [Instituto de Química, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS (Brazil); Vale, Maria Goreti R. [Instituto de Química, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq — INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Welz, Bernhard [Instituto Nacional de Ciência e Tecnologia do CNPq — INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC (Brazil); Dessuy, Morgana B., E-mail: mbdessuy@ufrgs.br [Instituto de Química, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS (Brazil); Andrade, Jailson B. de [Instituto Nacional de Ciência e Tecnologia do CNPq — INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil)

    2014-11-01

    In the present work, spectral interferences on the determination of lead in fertilizer and limestone samples were investigated using high-resolution continuum source graphite furnace atomic absorption spectrometry at the main analytical lines: 217.001 and 283.306 nm. For these investigations, samples were introduced into the furnace as slurry together with a mixture of Pd and Mg as chemical modifier. Spectral interferences were observed for some samples at both analytical lines. In order to verify whether a wet digestion procedure would avoid these interferences, a reference method for wet digestion of fertilizers was employed as an alternative sample preparation procedure. However, the same interferences were also observed in the digested samples. In order to identify and eliminate the fine-structured background using a least-squares background correction, reference spectra were generated using the combination of different species. The use of the latter technique allowed the elimination of spectral interferences for most of the investigated samples, making possible the determination of lead in fertilizer and limestone samples free of interferences. The best results were found using a reference spectrum of NH{sub 4}H{sub 2}PO{sub 4} at 217.001 nm, and a mixture of H{sub 2}SO{sub 4} + Ca and HNO{sub 3} + Ca at the 283.306 nm line. The accuracy of the method was evaluated using a certified reference material “Trace Elements in Multi-Nutrient Fertilizer”. Similar results were obtained using line source graphite furnace atomic absorption spectrometry with Zeeman-effect background correction, indicating that the latter technique was also capable to correct the spectral interferences, at least in part. - Highlights: • Spectral interferences on the determination of lead in fertilizers and limestone. • The analytical lines at 217.001 nm and 283.306 nm using HR-CS GF AAS. • Various combinations of compounds were used to create reference spectra. • LSBC

  7. High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

    Science.gov (United States)

    Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.; Park, YongKeun

    2014-01-01

    We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated.

  8. High-resolution electron-energy-loss spectroscopy and photoelectron-diffraction studies of the geometric structure of adsorbates on single-crystal metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Rosenblatt, D.H.

    1982-11-01

    Two techniques which have made important contributions to the understanding of surface phenomena are high resolution electron energy loss spectroscopy (EELS) and photoelectron diffraction (PD). EELS is capable of directly measuring the vibrational modes of clean and adsorbate covered metal surfaces. In this work, the design, construction, and performance of a new EELS spectrometer are described. These results are discussed in terms of possible structures of the O-Cu(001) system. Recommendations for improvements in this EELS spectrometer and guidelines for future spectrometers are given. PD experiments provide accurate quantitative information about the geometry of atoms and molecules adsorbed on metal surfaces. The technique has advantages when used to study disordered overlayers, molecular overlayers, multiple site systems, and adsorbates which are weak electron scatterers. Four experiments were carried out which exploit these advantages.

  9. Determination of the {ital S}-wave scattering length in pionic deuterium with a high resolution crystal spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Chatellard, D.; Egger, J.; Jeannet, E. [Institut de Physique de l`Universite, Breguet 1, CH-2000 Neuchatel (Switzerland); Badertscher, A.; Bogdan, M.; Goudsmit, P.F.A.; Leisi, H.J.; Matsinos, E.; Schroeder, H.; Sigg, D.; Zhao, Z.G. [Institut fuer Teilchenphysik der Eidgenoessische Technische Hochschule Zuerich, CH-5232 Villigen PSI (Switzerland); Aschenauer, E.C.; Gabathuler, K.; Hauser, P.; Simons, L.M. [Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); Rusi, A.J.; Hassani, E. [Ecole Mohammadia des Ingenieurs, Rabat (Morocco)

    1995-05-22

    The pionic deuterium 3{ital P}{minus}1{ital S} x-ray transition was measured with a quartz crystal spectrometer in combination with a cyclotron trap and charge coupled device detectors. The strong interaction shift and total decay width of the 1{ital S} level are {epsilon}{sub 1{ital S}}(shift)=2.48{plus_minus}0.10 eV (repulsive), {Gamma}{sub 1{ital S}}(width)=1.02{plus_minus}0.21 eV, where the statistical and systematic errors were added linearly. They yield the total pionic deuterium {ital S}-wave scattering length: {ital a}{sub {pi}{sup {minus}}{ital d}}= {minus}0.0264({plus_minus}0.0011)+{ital i}0.0054({plus_minus}0.0011){ital m}{sub {pi}}{sup {minus}1}.

  10. Determination of crystal growth rates during rapid solidification of polycrystalline aluminum by nano-scale spatio-temporal resolution in situ transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Zweiacker, K., E-mail: Kai@zweiacker.org; Liu, C.; Wiezorek, J. M. K. [Department of Mechanical Engineering and Materials Science, University of Pittsburgh, 648 Benedum Hall, 3700 OHara Street, Pittsburgh, Pennsylvania 15261 (United States); McKeown, J. T.; LaGrange, T.; Reed, B. W.; Campbell, G. H. [Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551 (United States)

    2016-08-07

    In situ investigations of rapid solidification in polycrystalline Al thin films were conducted using nano-scale spatio-temporal resolution dynamic transmission electron microscopy. Differences in crystal growth rates and asymmetries in melt pool development were observed as the heat extraction geometry was varied by controlling the proximity of the laser-pulse irradiation and the associated induced melt pools to the edge of the transmission electron microscopy support grid, which acts as a large heat sink. Experimental parameters have been established to maximize the reproducibility of the material response to the laser-pulse-related heating and to ensure that observations of the dynamical behavior of the metal are free from artifacts, leading to accurate interpretations and quantifiable measurements with improved precision. Interface migration rate measurements revealed solidification velocities that increased consistently from ∼1.3 m s{sup −1} to ∼2.5 m s{sup −1} during the rapid solidification process of the Al thin films. Under the influence of an additional large heat sink, increased crystal growth rates as high as 3.3 m s{sup −1} have been measured. The in situ experiments also provided evidence for development of a partially melted, two-phase region prior to the onset of rapid solidification facilitated crystal growth. Using the experimental observations and associated measurements as benchmarks, finite-element modeling based calculations of the melt pool evolution after pulsed laser irradiation have been performed to obtain estimates of the temperature evolution in the thin films.

  11. High-resolution heat-transfer-coefficient maps applicable to compound-curve surfaces using liquid crystals in a transient wind tunnel

    Science.gov (United States)

    Jones, Terry V.; Hippensteele, Steven A.

    1988-01-01

    Tests were performed in a transient heat transfer tunnel in which the model under test was preheated prior to allowing room temperature air to be suddenly drawn over the model. The resulting movement of isothermal contours on the model is revealed using a surface coating of thermochromic liquid crystals that display distinctive colors at particular temperatures. A video record is obtained of a temperature and time data pair for all points on the model during a single test. Experiments on a duct model are reported in which the model was preheated using a hot air stream. A manner in which initial model temperature nonuniformities could be taken into account was investigated. The duct model was also tested with a steady-state measurement technique and results were compared with the transient measurements, but recognizing that differences existed between the upstream thermal boundary conditions. The steady-state and transient measurements were shown to be consistent with predicted values. The main advantage of this transient heat transfer technique using liquid crystals is that since the test model need not be actively heated, high-resolution measurements on surfaces with complex shapes may be obtained.

  12. Super-resolution biomolecular crystallography with low-resolution data.

    Science.gov (United States)

    Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

    2010-04-22

    X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X

  13. Ultrasound-assisted single-drop microextraction for the determination of cadmium in vegetable oils using high-resolution continuum source electrothermal atomic absorption spectrometry

    Science.gov (United States)

    Almeida, Jorge S.; Anunciação, Taiana A.; Brandão, Geovani C.; Dantas, Alailson F.; Lemos, Valfredo A.; Teixeira, Leonardo S. G.

    2015-05-01

    This work presents an ultrasound-assisted single-drop microextraction procedure for the determination of cadmium in vegetable oils using high-resolution continuum source electrothermal atomic absorption spectrometry. Some initial tests showed that the best extraction efficiency was obtained when using ultrasound instead of mechanical agitation, indicating that acoustic cavitation improved the extraction process. Nitric, hydrochloric and acetic acids were evaluated for use in the extraction process, and HNO3 gave the best results. A two-level full-factorial design was applied to investigate the best conditions for the extraction of Cd from the oil samples. The influences of the sonication amplitude, time and temperature of the extraction were evaluated. The results of the design revealed that all of the variables had a significant effect on the experimental results. Afterward, a Box-Behnken design was applied to determine the optimum conditions for the determination of cadmium in vegetable oil samples. According to a multivariate study, the optimum conditions were as follows: sonication amplitude of 60%, extraction time of 15 min, extraction temperature of 46 °C and 0.1 mol L- 1 HNO3 as the extractor solution. Under optimized conditions, the developed method allows for the determination of Cd in oil samples with a limit of quantification of 7.0 ng kg- 1. Addition and recovery experiments were performed in vegetable oil samples to evaluate the accuracy of the method, and the recoveries obtained varied from 90% to 115%. The samples were also analyzed after the acid digestion procedure, and the paired t-test (95% confidence level) did not show significant differences from the proposed method.

  14. Ultrasound-assisted single-drop microextraction for the determination of cadmium in vegetable oils using high-resolution continuum source electrothermal atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Jorge S.; Anunciação, Taiana A. [Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador, Bahia 40170-280 (Brazil); Brandão, Geovani C. [Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador, Bahia 40170-280 (Brazil); INCT de Energia e Ambiente, Instituto de Química, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador, Bahia 40170-280 (Brazil); Dantas, Alailson F. [Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador, Bahia 40170-280 (Brazil); Lemos, Valfredo A. [Laboratório de Química Analítica (LQA), Universidade Estadual do Sudoeste da Bahia, Campus de Jequié, Jequié, Bahia 45506-191 (Brazil); and others

    2015-05-01

    This work presents an ultrasound-assisted single-drop microextraction procedure for the determination of cadmium in vegetable oils using high-resolution continuum source electrothermal atomic absorption spectrometry. Some initial tests showed that the best extraction efficiency was obtained when using ultrasound instead of mechanical agitation, indicating that acoustic cavitation improved the extraction process. Nitric, hydrochloric and acetic acids were evaluated for use in the extraction process, and HNO{sub 3} gave the best results. A two-level full-factorial design was applied to investigate the best conditions for the extraction of Cd from the oil samples. The influences of the sonication amplitude, time and temperature of the extraction were evaluated. The results of the design revealed that all of the variables had a significant effect on the experimental results. Afterward, a Box–Behnken design was applied to determine the optimum conditions for the determination of cadmium in vegetable oil samples. According to a multivariate study, the optimum conditions were as follows: sonication amplitude of 60%, extraction time of 15 min, extraction temperature of 46 °C and 0.1 mol L{sup −1} HNO{sub 3} as the extractor solution. Under optimized conditions, the developed method allows for the determination of Cd in oil samples with a limit of quantification of 7.0 ng kg{sup −1}. Addition and recovery experiments were performed in vegetable oil samples to evaluate the accuracy of the method, and the recoveries obtained varied from 90% to 115%. The samples were also analyzed after the acid digestion procedure, and the paired t-test (95% confidence level) did not show significant differences from the proposed method. - Highlights: • The determination of cadmium in vegetable oils was developed using UA-SDME. • HR-CS ET-AAS was employed as a detection technique with direct drop sampling. • The procedure allowed for a reduction in the consumption of reagents and

  15. Speciation analysis of volatile and non-volatile vanadium compounds in Brazilian crude oils using high-resolution continuum source graphite furnace atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Lepri, Fabio G. [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis, SC (Brazil); Welz, Bernhard [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis, SC (Brazil)]. E-mail: welz@qmc.ufsc.br; Borges, Daniel L.G. [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis, SC (Brazil); Silva, Alessandra F. [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis, SC (Brazil); Vale, Maria Goreti R. [Instituto de Quimica, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves 9500, 91501-970 Porto Alegre, RS (Brazil); Heitmann, Uwe [ISAS - Institute of Analytical Sciences, Department Berlin, Albert-Einstein-Str. 9, 12489 Berlin (Germany)

    2006-02-03

    A method is proposed that makes possible determining total and 'thermally stable' vanadium in crude oil without prior separation, and to calculate 'volatile' vanadium by difference. The volatile fraction is believed to be largely vanadyl porphyrine complexes. The method is based on the unsurpassed background correction capability of high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS GF AAS), which allows pyrolysis temperatures as low as 300 deg. C to be used. The samples were prepared as oil-in-water emulsions, and aqueous standards emulsified in the same way were used for calibration. Total vanadium has been determined using a pyrolysis temperature of 400 deg. C, and 'thermally stable' vanadium using a pyrolysis temperature of 800 deg. C. The content of total vanadium in 12 Brazilian crude oil samples was found to be between less than 0.04 and about 30 mg kg{sup -1}. The volatile fraction was between 5 and 51% of the total content, and there was no correlation between the total and the volatile vanadium content. The limits of detection and quantification were 0.04 and 0.12 mg kg{sup -1} of V in crude oil, respectively, based on a mass of 2 g of oil in 10 mL of emulsion. The precision was better than 4% at the 3 mg kg{sup -1} level and better than 1.5% at the 30 mg kg{sup -1} level of V in crude oil.

  16. Structure of GES-1 at Atomic Resolution: Insights Into the Evolution of Carbapenamase Activity in the Class a Extended-Spectrum Beta-Lactamases

    Energy Technology Data Exchange (ETDEWEB)

    Smith, C.A.; /SLAC, SSRL; Caccamo, M.; /Notre Dame U.; Kantardjieff, K.A.; /Cal State, Fullerton; Vakulenko, S.; /Notre Dame U.

    2007-10-08

    The structure of the class A extended-spectrum {beta}-lactamase GES-1 from Klebsiella pneumoniae has been determined to 1.1 Angstrom resolution. GES-1 has the characteristic active-site disulfide bond of the carbapenemase family of {beta}-lactamases and has a structure that is very similar to those of other known carbapenemases, including NMC-A, SME-1 and KPC-2. Most residues implicated in the catalytic mechanism of this class of enzyme are present in the GES-1 active site, including Ser70, which forms a covalent bond with the carbonyl C atom of the {beta}-lactam ring of the substrate during the formation of an acyl-enzyme intermediate, Glu166, which is implicated as both the acylation and deacylation base, and Lys73, which is also implicated as the acylation base. A water molecule crucial to catalysis is observed in an identical location as in other class A {beta}-lactamases, interacting with the side chains of Ser70 and Glu166. One important residue, Asn170, also normally a ligand for the hydrolytic water, is missing from the GES-1 active site. This residue is a glycine in GES-1 and the enzyme is unable to hydrolyze imipenem. This points to this residue as being critically important in the hydrolysis of this class of {beta}-lactam substrate. This is further supported by flexible-docking studies of imipenem with in silico-generated Gly170Asn and Gly170Ser mutant GES-1 enzymes designed to mimic the active sites of imipenem-hydrolyzing point mutants GES-2 and GES-5.

  17. Fast sequential multi-element determination of major and minor elements in environmental samples and drinking waters by high-resolution continuum source flame atomic absorption spectrometry.

    Science.gov (United States)

    Gómez-Nieto, Beatriz; Gismera, Ma Jesús; Sevilla, Ma Teresa; Procopio, Jesús R

    2015-01-07

    The fast sequential multi-element determination of 11 elements present at different concentration levels in environmental samples and drinking waters has been investigated using high-resolution continuum source flame atomic absorption spectrometry. The main lines for Cu (324.754 nm), Zn (213.857 nm), Cd (228.802 nm), Ni (232.003 nm) and Pb (217.001 nm), main and secondary absorption lines for Mn (279.482 and 279.827 nm), Fe (248.327, 248.514 and 302.064 nm) and Ca (422.673 and 239.856 nm), secondary lines with different sensitivities for Na (589.592 and 330.237 nm) and K (769.897 and 404.414 nm) and a secondary line for Mg (202.582 nm) have been chosen to perform the analysis. A flow injection system has been used for sample introduction so sample consumption has been reduced up to less than 1 mL per element, measured in triplicate. Furthermore, the use of multiplets for Fe and the side pixel registration approach for Mg have been studied in order to reduce sensitivity and extend the linear working range. The figures of merit have been calculated and the proposed method was applied to determine these elements in a pine needles reference material (SRM 1575a), drinking and natural waters and soil extracts. Recoveries of analytes added at different concentration levels to water samples and extracts of soils were within 88-115% interval. In this way, the fast sequential multi-element determination of major and minor elements can be carried out, in triplicate, with successful results without requiring additional dilutions of samples or several different strategies for sample preparation using about 8-9 mL of sample. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Simultaneous determination of V, Ni and Fe in fuel fly ash using solid sampling high resolution continuum source graphite furnace atomic absorption spectrometry.

    Science.gov (United States)

    Cárdenas Valdivia, A; Vereda Alonso, E; López Guerrero, M M; Gonzalez-Rodriguez, J; Cano Pavón, J M; García de Torres, A

    2018-03-01

    A green and simple method has been proposed in this work for the simultaneous determination of V, Ni and Fe in fuel ash samples by solid sampling high resolution continuum source graphite furnace atomic absorption spectrometry (SS HR CS GFAAS). The application of fast programs in combination with direct solid sampling allows eliminating pretreatment steps, involving minimal manipulation of sample. Iridium treated platforms were applied throughout the present study, enabling the use of aqueous standards for calibration. Correlation coefficients for the calibration curves were typically better than 0.9931. The concentrations found in the fuel ash samples analysed ranged from 0.66% to 4.2% for V, 0.23-0.7% for Ni and 0.10-0.60% for Fe. Precision (%RSD) were 5.2%, 10.0% and 9.8% for V, Ni and Fe, respectively, obtained as the average of the %RSD of six replicates of each fuel ash sample. The optimum conditions established were applied to the determination of the target analytes in fuel ash samples. In order to test the accuracy and applicability of the proposed method in the analysis of samples, five ash samples from the combustion of fuel in power stations, were analysed. The method accuracy was evaluated by comparing the results obtained using the proposed method with the results obtained by ICP OES previous acid digestion. The results showed good agreement between them. The goal of this work has been to develop a fast and simple methodology that permits the use of aqueous standards for straightforward calibration and the simultaneous determination of V, Ni and Fe in fuel ash samples by direct SS HR CS GFAAS. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Determination of Pb (Lead), Cd (Cadmium), Cr (Chromium), Cu (Copper), and Ni (Nickel) in Chinese tea with high-resolution continuum source graphite furnace atomic absorption spectrometry.

    Science.gov (United States)

    Zhong, Wen-Si; Ren, Ting; Zhao, Li-Jiao

    2016-01-01

    The contents of lead, cadmium, chromium, copper, and nickel were determined in 25 tea samples from China, including green, yellow, white, oolong, black, Pu'er, and jasmine tea products, using high-resolution continuum source graphite furnace atomic absorption spectrometry. The methods used for sample preparation, digestion, and quantificational analysis were established, generating satisfactory analytical precisions (represented by relative standard deviations ranging from 0.6% to 2.5%) and recoveries (98.91-101.32%). The lead contents in tea leaves were 0.48-10.57 mg/kg, and 80% of these values were below the maximum values stated by the guidelines in China. The contents of cadmium and chromium ranged from 0.01 mg/kg to 0.39 mg/kg and from 0.27 mg/kg to 2.45 mg/kg, respectively, remaining in compliance with the limits stipulated by China's Ministry of Agriculture. The copper contents were 7.73-63.71 mg/kg; only 64% of these values complied with the standards stipulated by the Ministry of Agriculture. The nickel contents ranged from 2.70 mg/kg to 13.41 mg/kg. Consequently, more attention must be paid to the risks of heavy metal contamination in tea. The quantitative method established in this work lays a foundation for preventing heavy metal toxicity in human from drinking tea and will help establish regulations to control the contents of heavy metals in tea. Copyright © 2015. Published by Elsevier B.V.

  20. Determination of Pb (Lead, Cd (Cadmium, Cr (Chromium, Cu (Copper, and Ni (Nickel in Chinese tea with high-resolution continuum source graphite furnace atomic absorption spectrometry

    Directory of Open Access Journals (Sweden)

    Wen-Si Zhong

    2016-01-01

    Full Text Available The contents of lead, cadmium, chromium, copper, and nickel were determined in 25 tea samples from China, including green, yellow, white, oolong, black, Pu'er, and jasmine tea products, using high-resolution continuum source graphite furnace atomic absorption spectrometry. The methods used for sample preparation, digestion, and quantificational analysis were established, generating satisfactory analytical precisions (represented by relative standard deviations ranging from 0.6% to 2.5% and recoveries (98.91–101.32%. The lead contents in tea leaves were 0.48–10.57 mg/kg, and 80% of these values were below the maximum values stated by the guidelines in China. The contents of cadmium and chromium ranged from 0.01 mg/kg to 0.39 mg/kg and from 0.27 mg/kg to 2.45 mg/kg, respectively, remaining in compliance with the limits stipulated by China's Ministry of Agriculture. The copper contents were 7.73–63.71 mg/kg; only 64% of these values complied with the standards stipulated by the Ministry of Agriculture. The nickel contents ranged from 2.70 mg/kg to 13.41 mg/kg. Consequently, more attention must be paid to the risks of heavy metal contamination in tea. The quantitative method established in this work lays a foundation for preventing heavy metal toxicity in human from drinking tea and will help establish regulations to control the contents of heavy metals in tea.

  1. Application of Internal Standard Method for Several 3d-Transition Metallic Elements in Flame Atomic Absorption Spectrometry Using a Multi-wavelength High-resolution Spectrometer.

    Science.gov (United States)

    Toya, Yusuke; Itagaki, Toshiko; Wagatsuma, Kazuaki

    2017-01-01

    We investigated a simultaneous internal standard method in flame atomic absorption spectrometry (FAAS), in order to better the analytical precision of 3d-transition metals contained in steel materials. For this purpose, a new spectrometer system for FAAS, comprising a bright xenon lamp as the primary radiation source and a high-resolution Echelle monochromator, was employed to measure several absorption lines at a wavelength width of ca. 0.3 nm at the same time, which enables the absorbances of an analytical line and also an internal standard line to be estimated. In considering several criteria for selecting an internal standard element and the absorption line, it could be suggested that platinum-group elements: ruthenium, rhodium, or palladium, were suitable for an internal standard element to determine the 3d-transition metal elements, such as titanium, iron, and nickel, by measuring an appropriate pair of these absorption lines simultaneously. Several variances of the absorption signal, such as a variation in aspirated amounts of sample solution and a short-period drift of the primary light source, would be corrected and thus reduced, when the absorbance ratio of the analytical line to the internal standard line was measured. In Ti-Pd, Ni-Rh, and Fe-Ru systems chosen as typical test samples, the repeatability of the signal respnses was investigated with/without the internal standard method, resulting in better precision when the internal standard method was applied in the FAAS with a nitrous oxide-acetylene flame rather than an air-acetylene flame.

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

    Science.gov (United States)

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

    2009-12-15

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

  3. [Evaluation of image quality using the normalized-rank approach for primary class liquid-crystal display (LCD) monitors with different colors and resolution].

    Science.gov (United States)

    Kuroki, Hidefumi; Katayama, Reiji; Sakaguchi, Taro; Maeda, Takashi; Morishita, Junji; Hayabuchi, Naofumi

    2010-11-20

    The purposes of this study were to evaluate the image quality of five types of liquid-crystal display (LCD) monitors by utilizing the normalized-rank approach and to investigate the effect of LCD monitor specifications, such as display colors, luminance, and resolution, on the evaluators' ranking. The LCD monitors used in this study were 2, 3 and 5 mega-pixel monochrome LCD monitors, and 2 and 3 mega-pixel color LCD monitors (Eizo Nanao Corporation). All LCD monitors were calibrated to the grayscale standard display function (GSDF) with different maximum luminance (recommended luminance) settings. Also, four kinds of radiographs were used for observer study based on the normalized-rank approach: three adult chest radiographs, three pediatric chest radiographs, three ankle joint radiographs, and four double-contrasted upper gastrointestinal radiographs. Ten radiological technologists participated in the observer study. Monochrome LCD monitors exhibited superior ranking with statistically significant differences (pLCD monitors in all kinds of radiographs. The major difference between monochrome and color monitors was luminance. Therefore, it is considered that the luminance of LCD monitors affects observers' evaluations based on image quality. Moreover, in the case of radiographs that include high frequency image components, the monitor resolution also affects the evaluation. In clinical practice, it is necessary to optimize the luminance and choose appropriate LCD monitors for diagnostic images.

  4. Crystallization and preliminary X-ray analysis of the 12S central subunit of transcarboxylase from Propionibacterium shermanii.

    Science.gov (United States)

    Wang, Y F; Hyatt, D C; Rivera, R E; Carey, P R; Yee, V C

    2001-02-01

    The hexameric 12S central subunit of transcarboxylase has been crystallized in both free and substrate-bound forms. The apo crystals belong to the cubic space group P4(2)32, with unit-cell parameters a = b = c = 188.5 A, and diffract to 3.5 A resolution. Crystals of two substrate-bound complexes, 12S with methylmalonyl CoA and 12S with malonyl CoA, are isomorphous and belong to space group C2, with unit-cell parameters a = 115.5, b = 201.4, c = 146.9 A, beta = 102.7 degrees. These crystals diffract to 1.9 A resolution with synchrotron radiation. Two useful heavy-atom phasing derivatives of methylmalonyl CoA-bound crystals have been obtained by co-crystallization or crystal soaking.

  5. Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms

    Directory of Open Access Journals (Sweden)

    Agard David A

    2008-10-01

    Full Text Available Abstract Background An important element in homology modeling is the use of rotamers to parameterize the sidechain conformation. Despite the many libraries of sidechain rotamers that have been developed, a number of rotamers have been overlooked, due to the fact that they involve hydrogen atoms. Results We identify new, well-populated rotamers that involve the hydroxyl-hydrogen atoms of Ser, Thr and Tyr, and the sulfhydryl-hydrogen atom of Cys, using high-resolution crystal structures ( Conclusion Knowledge of these new rotamers will improve the evaluation of hydrogen-bonding networks in protein structures.

  6. High precision spectroscopy of pionic and antiprotonic atoms; Spectroscopie de precision des atomes pioniques et antiprotoniques

    Energy Technology Data Exchange (ETDEWEB)

    El-Khoury, P

    1998-04-15

    The study of exotic atoms, in which an orbiting electron of a normal atom is replaced by a negatively charged particle ({pi}{sup -}, {mu}{sup -}, p, {kappa}{sup -}, {sigma}{sup -},...) may provide information on the orbiting particle and the atomic nucleus, as well as on their interaction. In this work, we were interested in pionic atoms ({pi}{sup -14} N) on the one hand in order to determine the pion mass with high accuracy (4 ppm), and on the other hand in antiprotonic atoms (pp-bar) in order to study the strong nucleon-antinucleon interaction at threshold. In this respect, a high-resolution crystal spectrometer was coupled to a cyclotron trap which provides a high stop density for particles in gas targets at low pressure. Using curved crystals, an extended X-ray source could be imaged onto the detector. Charge-Coupled Devices were used as position sensitive detectors in order to measure the Bragg angle of the transition to a high precision. The use of gas targets resolved the ambiguity owing to the number of K electrons for the value of the pion mass, and, for the first time, strong interaction shift and broadening of the 2p level in antiprotonic hydrogen were measured directly. (author)

  7. Energy resolution of LaBr{sub 3}:Ce in a phoswich configuration with CsI:Na and NaI:Tl scintillator crystals

    Energy Technology Data Exchange (ETDEWEB)

    Hull, G., E-mail: hull@ipno.in2p3.fr [Institut de Physique Nucleaire d' Orsay, IN2P3-CNRS, Universite Paris-Sud, 91406 Orsay Cedex (France); Genolini, B.; Josselin, M.; Matea, I.; Peyre, J.; Pouthas, J.; Zerguerras, T. [Institut de Physique Nucleaire d' Orsay, IN2P3-CNRS, Universite Paris-Sud, 91406 Orsay Cedex (France)

    2012-12-11

    We studied the performances of the LaBr{sub 3}:Ce scintillator when optically coupled to NaI:Tl and CsI:Na in a Phoswich detector for the R and D phase of the gamma ray calorimeter PARIS (Photon Array for the studies with Radioactive Ion and Stable beams). This detector has the purpose to measure {gamma}-energies in a wide range (100 keV-40 MeV), and it will be used principally as a part of the SPIRAL2 instrumentation at GANIL. In this communication we report on the study of the light yield and energy resolution for gamma detection realized by coupling the phoswiches with various photomultiplier tubes, providing different characteristics. We were interested in investigating the possible degradation of the scintillation light produced by the LaBr{sub 3}:Ce due to the presence of NaI:Tl/CsI:Na crystals, before being detected on the photocathode. For this purpose we realized all the measurements employing a standard ADC and QDC read-out system leading the possibility to perform a gate-based event selection. In this study we measured an energy resolution of 4.6% with an uncollimated {sup 137}Cs source for a 50.8 Multiplication-Sign 50.8 Multiplication-Sign 50.8 mm{sup 3} LaBr{sub 3}:Ce coupled to a 50.8 Multiplication-Sign 50.8 Multiplication-Sign 152.4 mm{sup 3} NaI:Tl. This value is 30% bigger than the energy resolution measured for a 50.8 Multiplication-Sign 50.8 Multiplication-Sign 101.6 mm{sup 3} stand-alone LaBr{sub 3}:Ce but still in the specifications for the PARIS collaboration physics list.

  8. X-ray absorption spectroscopy investigation of structurally modified lithium niobate crystals

    Energy Technology Data Exchange (ETDEWEB)

    Vitova, Tonya

    2008-02-15

    The type and concentration of impurity centers in different valence states are crucial for tuning the photorefractive properties of doped Lithium Niobate (LN) crystals. X-ray Absorption Spectroscopy (XAS) is an appropriate tool for studying the local structure of impurity centers. XAS combined with absorption in UV/VIS/IR and High Resolution X-ray Emission Spectroscopy (HRXES) provide information about the valence state of the dopant ions in as-grown, reduced or oxidized doped LN crystals. Cu (Cu{sup 1+} and Cu{sup 2+}) and Fe (Fe{sup 2+} and Fe{sup 3+}) atoms are found in two different valence states, whereas there are indications for a third Mn valency, in addition to Mn{sup 2+} and Mn{sup 3+} in manganese-doped LN crystals. One of the charge compensation mechanisms during reduction of copper- doped LN crystals is outgassing of oxygen atoms. Cu ions in the reduced crystals have at least two different site symmetries: twofold (Cu{sup 1+}) and sixfold (Cu{sup 2+}) coordinated by O atoms. Fe and Mn atoms are coordinated by six O atoms. Cu and Fe ions are found to occupy only Li sites, whereas Mn ions are also incorporated into Li and Nb sites. The refractive index change in LN crystals irradiated with {sup 3}He{sup 2+} ions is caused by structurally disordered centers, where Nb atoms are displaced from normal crystallographic sites and Li or/and O vacancies are present. (orig.)

  9. Protein crystallization facilitated by molecularly imprinted polymers

    Science.gov (United States)

    Saridakis, Emmanuel; Khurshid, Sahir; Govada, Lata; Phan, Quan; Hawkins, Daniel; Crichlow, Gregg V.; Lolis, Elias; Reddy, Subrayal M.; Chayen, Naomi E.

    2011-01-01

    We present a previously undescribed initiative and its application, namely the design of molecularly imprinted polymers (MIPs) for producing protein crystals that are essential for determining high-resolution 3D structures of proteins. MIPs, also referred to as “smart materials,” are made to contain cavities capable of rebinding protein; thus the fingerprint of the protein created on the polymer allows it to serve as an ideal template for crystal formation. We have shown that six different MIPs induced crystallization of nine proteins, yielding crystals in conditions that do not give crystals otherwise. The incorporation of MIPs in screening experiments gave rise to crystalline hits in 8–10% of the trials for three target proteins. These hits would have been missed using other known nucleants. MIPs also facilitated the formation of large single crystals at metastable conditions for seven proteins. Moreover, the presence of MIPs has led to faster formation of crystals in all cases where crystals would appear eventually and to major improvement in diffraction in some cases. The MIPs were effective for their cognate proteins and also for other proteins, with size compatibility being a likely criterion for efficacy. Atomic force microscopy (AFM) measurements demonstrated specific affinity between the MIP cavities and a protein-functionalized AFM tip, corroborating our hypothesis that due to the recognition of proteins by the cavities, MIPs can act as nucleation-inducing substrates (nucleants) by harnessing the proteins themselves as templates. PMID:21690356

  10. Crystallization of Mitochondrial Respiratory Complex II fromChicken Heart: A Membrane-Protein Complex Diffracting to 2.0Angstrom

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Li-shar; Borders, Toni M.; Shen, John T.; Wang, Chung-Jen; Berry, Edward A.

    2004-12-17

    Procedure is presented for preparation of diffraction-quality crystals of a vertebrate mitochondrial respiratory Complex II. The crystals have the potential to diffract to at least 2.0 Angstrom with optimization of post-crystal-growth treatment and cryoprotection. This should allow determination of the structure of this important and medically relevant membrane protein complex at near-atomic resolution and provide great detail of the mode of binding of substrates and inhibitors at the two substrate-binding sites.

  11. Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate

    DEFF Research Database (Denmark)

    Venskutonyte, Raminta; Frydenvang, Karla; Gajhede, Michael

    2011-01-01

    present the first X-ray crystal structure of the ligand binding domain of GluK3 in complex with glutamate, determined to 1.6Å resolution. The structure reveals a conserved glutamate binding mode, characteristic for iGluRs, and a water molecule network in the glutamate binding site similar to that seen...

  12. Observations on structural features and characteristics of biological apatite crystals. 8. Observation on fusion of human enamel crystals.

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1993-12-01

    In a series of studies to investigate the basic structural features and characteristics of the biological apatite crystals, using a transmission electron microscope, we examined the ultrastructure of the human enamel, dentin, and bone crystals at near atomic resolution and showed the configuration of the hydroxyapatite structure through the cross and longitudinal sections of the crystals. Subsequently, based on the results of the observations by the authors of the ultrastructure of the tooth and bone, using the same approach, we have been able to directly examine the images of the lattice imperfections in the human tooth and bone crystals, such as the point defect structure, line defect, and face defect, in the crystals. In this report, we describe the images of the crystal fusion obtained by using the same approach from the sections of the human enamel crystals. The materials used for this study were the noncarious enamel from the freshly extracted human erupted lower first molars. The small cubes of the material were fixed in glutaraldehyde and osmium tetroxide and embedded in epoxy resin using the routine methods. The ultrathin sections were cut with a diamond knife without decalcification. The sections were examined with the HITACHI H-800 H and H-9000 type transmission electron microscopes operated at 200 kV and 300 kV. Each crystal was observed at an initial magnification of 300,000 times and at a final magnification of 10,000,000 times and over. We are, therefore, able to confirm that the fusion between the adjacent crystals can occur at some time during the life history of the human enamel. We sincerely believe that the electron micrographs shown in this report are the first to show the ultrastructures of the crystal fusion in the human enamel crystals at near atomic resolution.

  13. Visualization of drug-nucleic acid interactions at atomic resolution. VI. Structure of two drug/ dinucleoside monophosphate crystalline complexes, ellipticine: 5-iodocytidylyl(3'-5')guanosine and 3,5,6,8-tetramethyl-n-methyl phenanthrolinium: 5-iodocytidylyl(3'-5')guanosine

    Energy Technology Data Exchange (ETDEWEB)

    Jain, S.C.; Bhandary, K.K.; Sobell, H.M.

    1979-01-01

    Ellipticine and 3,5,6,8-tetramethyl-N-methyl phenanthrolinium (TMP) form complexes with the dinucleoside monophosphate, 5-iodocytidylyl(3'-5')guanosine (iodoCpG). These crystals are isomorphous: ellipticine-iodoCpG crystals are monoclinic, space group P2/sub 1/, with a = 13.88 A, b = 19.11 A, c = 21.42 A, ..beta.. = 105.4; TMP-iodoCpG crystals are monoclinic, space group P2/sub 1/, with a = 13.99 A, b = 19.12 A, c = 21.31 A, ..beta.. = 104.9. Both structures have been solved to atomic resolution by Patterson and Fourier methods, and refined by full matrix least squares. The asymmetric unit in the ellipticine-iodoCpG structure contains two ellipticine molecules, two iodoCpG molecules, 16 water molecules and 2 methanol molecules, a total of 140 atoms, whereas, in the tetramethyl-N-methyl phenanthrolinium-iodoCpG complex, the asymmetric unit contains two TMP molecules, two iodoCpG molecules, 17 water molecules and 2 methanol molecules, a total of 141 atoms. In both structures, the two iodoCpG molecules are hydrogen bonded together by guanine-cytosine Watson--Crick base-pairing. Adjacent base-pairs within this paired iodoCpG structure are separated by about 6.7 A; this separation results from intercalative binding by one ellipticine (of TMP) molecule and stacking by the other ellipticine (or TMP) molecule above or below the base-pairs. Base-pairs within the paired nucleotide units are related by a twist of 10 to 12/sup 0/. The stereochemistry observed in these model drug-nucleic acid intercalative complexes is almost identical to that observed in the ethidium-iodoUpA and iodoCpG complexesdetermined previously. This stereochemistry is also very similar to that observed in the 9-amino-acridine-iodoCpG and acridine orange-iodoCpG complexes.

  14. Absolute atomic oxygen and nitrogen densities in radio-frequency driven atmospheric pressure cold plasmas: Synchrotron vacuum ultra-violet high-resolution Fourier-transform absorption measurements

    Energy Technology Data Exchange (ETDEWEB)

    Niemi, K.; O' Connell, D.; Gans, T. [York Plasma Institute, Department of Physics, University of York, York YO10 5DD (United Kingdom); Oliveira, N. de; Joyeux, D.; Nahon, L. [Synchrotron Soleil, l' Orme des Merisiers, St. Aubin BP 48, 91192 Gif sur Yvette Cedex (France); Booth, J. P. [Laboratoire de Physique des Plasmas-CNRS, Ecole Polytechnique, 91128 Palaiseau (France)

    2013-07-15

    Reactive atomic species play a key role in emerging cold atmospheric pressure plasma applications, in particular, in plasma medicine. Absolute densities of atomic oxygen and atomic nitrogen were measured in a radio-frequency driven non-equilibrium plasma operated at atmospheric pressure using vacuum ultra-violet (VUV) absorption spectroscopy. The experiment was conducted on the DESIRS synchrotron beamline using a unique VUV Fourier-transform spectrometer. Measurements were carried out in plasmas operated in helium with air-like N{sub 2}/O{sub 2} (4:1) admixtures. A maximum in the O-atom concentration of (9.1 {+-} 0.7) Multiplication-Sign 10{sup 20} m{sup -3} was found at admixtures of 0.35 vol. %, while the N-atom concentration exhibits a maximum of (5.7 {+-} 0.4) Multiplication-Sign 10{sup 19} m{sup -3} at 0.1 vol. %.

  15. Structural changes in helium implanted Zr{sub 0.8}Y{sub 0.2}O{sub 1.9} single crystals characterized by atomic force microscopy and EXAFS spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kuri, G. [LWV, NES, Paul Scherrer Institute, CH-5232 Villigen PSI (Switzerland)], E-mail: goutam.kuri@psi.ch; Gavillet, D. [LWV, NES, Paul Scherrer Institute, CH-5232 Villigen PSI (Switzerland); Doebeli, M. [Ion Beam Physics, Paul Scherrer Institute and ETH Zurich, CH-8093 Zurich (Switzerland); Novikov, D. [HASYLAB at Deutsches Elektronen-Synchrotron DESY, D-22603 Hamburg (Germany)

    2008-04-15

    The present work is devoted to investigate the local atomic environment (of Zr, Y and O) as well as surface modifications associated with excess helium in the cubic phase of (1 0 0)-oriented Zr{sub 0.8}Y{sub 0.2}O{sub 1.9} single crystal substrates. Commercially available oxide crystals have been implanted at various fluences in the range 0.15-2.0 x 10{sup 16} He-atoms/cm{sup 2} using a 2.74 MeV He{sup +} ion beam passing through a 8.0 {mu}m Al foil. The microstructure and surface morphology of the irradiated surface are examined using atomic force microscopy (AFM). The local atomic environments of Zr, Y and O in the implanted layer are studied using synchrotron radiation and by extended X-ray absorption fine structure (EXAFS) measured at glancing angles to probe the implanted layer. From AFM studies it was observed that the surface roughness increases as fluence increases and above a critical fluence stage, small blister-like structures originating from helium bubbles are scattered on the irradiated surface. The radial distribution functions (RDFs), derived from EXAFS data at the Zr K-edge, have been found to evolve continuously as a function of ion fluence describing the atomic scale structural modifications in YSZ by helium implantation. From the pristine data, long range order (beyond the first- and second-shell) is apparent in the RDF spectrum. It shows several nearest neighbour peaks at about 2.1, 3.6, 4.3 and 5.4 A. In the implanted specimens, all these peaks are greatly reduced in magnitude and their average positions are changed, typical of damaged material. A simple model taking into account only the existence of lattice vacancies has been used for the interpretation of measured EXAFS spectra.

  16. Marine sediments monitoring studies for trace elements with the application of fast temperature programs and solid sampling high resolution continuum source atomic absorption spectrometry

    Science.gov (United States)

    Orani, Anna Maria; Han, Eunmi; Mandjukov, Petko; Vassileva, Emilia

    2015-01-01

    Analytical procedure for the determination of As, Cd, Cu, Ni, Co and Cr in marine sediment samples using high-resolution continuum source graphite furnace atomic absorption spectrometry (HR CS AAS) and direct solid sample analysis has been developed. The application of fast programs in combination with direct solid sampling allows to eliminate the drying and pretreatment steps, however makes impossible the use of liquid standards for calibration. Iridium treated platforms were applied throughout the present study. Calibration technique based on the use of solid certified reference materials (marine sediments) similar to the nature of the analyzed sample and statistics of regression analysis were applied to the real sediment samples. The instrumental parameters were optimized in order to obtain reproducible and interference free analytical signals. The ISO-17025 requirements and Eurachem guidelines were followed in the validation of the proposed analytical procedure. Accordingly, blanks, selectivity, calibration, linearity, working range, trueness, repeatability reproducibility, limits of detection and quantification and expanded uncertainty (k = 2) for all investigated elements were assessed. Two different approaches for the estimation of measurement uncertainty were applied and obtained results compared. The major contributors to the combined uncertainty of the analyte mass fraction were found to be the homogeneity of the samples and the microbalance precision. The influence of sample particle sizes on the total combined uncertainty was also evaluated. Traceability to SI system of units of the obtained by the proposed analytical procedure results was demonstrated. Additionally, validation of the methodology developed was effectuated by the comparison of the obtained results with independent method e.g. ICP-MS with external calibration. The use of solid sampling HR CS AAS for the determination of trace elements in marine sediment matrix gives significant advantages

  17. Crystal structure of the high-alkaline serine protease PB92 from Bacillus alcalophilus

    NARCIS (Netherlands)

    van der Laan, J.M.; Teplyakov, A.V.; Kelders, H.; Kalk, K.H.; Misset, O.; Mulleners, L.J.S.M.; Dijkstra, B.W.

    The crystal structure of a serine protease from the alkalophilic strain Bacillus alcalophilus PB92 has been determined by X-ray diffraction at 1.75 Å resolution. The structure has been solved by molecular replacement using the atomic model of subtilisin Carlsberg. The model of the PB92 protease has

  18. The effect orientation of features in reconstructed atom probe data on the resolution and measured composition of T1 plates in an A2198 aluminium alloy.

    Science.gov (United States)

    Mullin, Maria A; Araullo-Peters, Vicente J; Gault, Baptiste; Cairney, Julie M

    2015-12-01

    Artefacts in atom probe tomography can impact the compositional analysis of microstructure in atom probe studies. To determine the integrity of information obtained, it is essential to understand how the positioning of features influences compositional analysis. By investigating the influence of feature orientation within atom probe data on measured composition in microstructural features within an AA2198 Al alloy, this study shows differences in the composition of T1 (Al2CuLi) plates that indicates imperfections in atom probe reconstructions. The data fits a model of an exponentially-modified Gaussian that scales with the difference in evaporation field between solutes and matrix. This information provides a guide for obtaining the most accurate information possible. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Atomic imaging using secondary electrons in a scanning transmission electron microscope: Experimental observations and possible mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Inada, H. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Hitachi High Technologies Corp., Ibaraki (Japan); Su, D. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Egerton, R.F. [University of Alberta, Edmonton (Canada); Konno, M. [Hitachi High Technologies Corp., Ibaraki (Japan); Wu, L.; Ciston, J.; Wall, J. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Zhu, Y., E-mail: zhu@bnl.gov [Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2011-06-15

    We report detailed investigation of high-resolution imaging using secondary electrons (SE) with a sub-nanometer probe in an aberration-corrected transmission electron microscope, Hitachi HD2700C. This instrument also allows us to acquire the corresponding annular dark-field (ADF) images both simultaneously and separately. We demonstrate that atomic SE imaging is achievable for a wide range of elements, from uranium to carbon. Using the ADF images as a reference, we studied the SE image intensity and contrast as functions of applied bias, atomic number, crystal tilt, and thickness to shed light on the origin of the unexpected ultrahigh resolution in SE imaging. We have also demonstrated that the SE signal is sensitive to the terminating species at a crystal surface. A possible mechanism for atomic-scale SE imaging is proposed. The ability to image both the surface and bulk of a sample at atomic-scale is unprecedented, and can have important applications in the field of electron microscopy and materials characterization. -- Research highlights: {yields} Atomic imaging using secondary electrons in an aberration-corrected electron microscope. {yields} High-resolution secondary electron imaging mechanism. {yields} Image contrast quantification and as functions of imaging conditions. {yields} Simultaneous acquisition of atomic images from surface and bulk.

  20. Fabrication of Al2O3 coated 2D TiO2 nanoparticle photonic crystal layers by reverse nano-imprint lithography and plasma enhanced atomic layer deposition.

    Science.gov (United States)

    Kim, Ki-Kang; Ko, Ki-Young; Ahn, Jinho

    2013-10-01

    This paper reports simple process to enhance the extraction efficiency of photoluminescence (PL) from Eu-doped yttrium oxide (Y2O3:Eu3+) thin-film phosphor (TFP). Two-dimensional (2D) photonic crystal layer (PCL) was fabricated on Y2O3:Eu3+ phosphor films by reverse nano-imprint method using TiO2 nanoparticle solution as a nano-imprint resin and a 2D hole-patterned PDMS stamp. Atomic scale controlled Al2O3 deposition was performed onto this 2D nanoparticle PCL for the optimization of the photonic crystal pattern size and stabilization of TiO2 nanoparticle column structure. As a result, the light extraction efficiency of the Y2O3:Eu3+ phosphor film was improved by 2.0 times compared to the conventional Y2O3:Eu3+ phosphor film.

  1. Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.

    Science.gov (United States)

    Lawson, D M; Williams, C E; Mitchenall, L A; Pau, R N

    1998-12-15

    . Periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. Nevertheless, almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains. The ligand is bound at the bottom of a deep cleft, which lies at the interface between these two domains. The oxyanion-binding proteins are notable in that they can discriminate between very similar ligands. . Azotobacter vinelandii is unusual in that it possesses two periplasmic molybdate-binding proteins. The crystal structure of one of these with bound ligand has been determined at 1.2 A resolution. It superficially resembles the structure of sulphate-binding protein (SBP) from Salmonella typhimurium and uses a similar constellation of hydrogen-bonding interactions to bind its ligand. However, the detailed interactions are distinct from those of SBP and the more closely related molybdate-binding protein of Escherichia coli. . Despite differences in the residues involved in binding, the volumes of the binding pockets in the A. vinelandii and E. coli molybdate-binding proteins are similar and are significantly larger than that of SBP. We conclude that the discrimination between molybdate and sulphate shown by these binding proteins is largely dependent upon small differences in the sizes of these two oxyanions.

  2. Application of high-resolution continuum source flame atomic absorption spectrometry to reveal, evaluate and overcome certain spectral effects in Pb determination of unleaded gasoline

    Science.gov (United States)

    Kowalewska, Zofia; Laskowska, Hanna; Gzylewski, Michał

    2017-06-01

    High-resolution continuum source and line source flame atomic absorption spectrometry (HR-CS FAAS and LS FAAS, respectively) were applied for Pb determination in unleaded aviation or automotive gasoline that was dissolved in methyl-isobutyl ketone. When using HR-CS FAAS, a structured background (BG) was registered in the vicinity of both the 217.001 nm and 283.306 nm Pb lines. In the first case, the BG, which could be attributed to absorption by the OH molecule, directly overlaps with the 217 nm line, but it is of relatively low intensity. For the 283 nm line, the structured BG occurs due to uncompensated absorption by OH molecules present in the flame. BG lines of relatively high intensity are situated at a large distance from the 283 nm line, which enables accurate analysis, not only when using simple variants of HR-CS FAAS but also for LS FAAS with a bandpass of 0.1 nm. The lines of the structured spectrum at 283 nm can have ;absorption; (maxima) or ;emission; (minima) character. The intensity of the OH spectra can significantly depend on the flame character and composition of the investigated organic solution. The best detection limit for the analytical procedure, which was 0.01 mg L- 1 for Pb in the investigated solution, could be achieved using HR-CS FAAS with the 283 nm Pb line, 5 pixels for the analyte line measurement and iterative background correction (IBC). In this case, least squares background correction (LSBC) is not recommended. However, LSBC (available as the ;permanent structures; option) would be recommended when using the 217 nm Pb line. In LS FAAS, an additional phenomenon related to the nature of the organic matrix (for example, isooctane or toluene) can play an important role. The effect is of continuous character and probabl