WorldWideScience

Sample records for atomic resolution crystal

  1. The crystal structure of samarosporin I at atomic resolution.

    Science.gov (United States)

    Gessmann, Renate; Axford, Danny; Evans, Gwyndaf; Brückner, Hans; Petratos, Kyriacos

    2012-11-01

    The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.

  2. X-ray crystal structure of anhydrous chitosan at atomic resolution.

    Science.gov (United States)

    Naito, Philip-Kunio; Ogawa, Yu; Sawada, Daisuke; Nishiyama, Yoshiharu; Iwata, Tadahisa; Wada, Masahisa

    2016-07-01

    We determined the crystal structure of anhydrous chitosan at atomic resolution, using X-ray fiber diffraction data extending to 1.17 Å resolution. The unit cell [a = 8.129(7) Å, b = 8.347(6) Å, c = 10.311(7) Å, space group P21 21 21 ] of anhydrous chitosan contains two chains having one glucosamine residue in the asymmetric unit with the primary hydroxyl group in the gt conformation, that could be directly located in the Fourier omit map. The molecular arrangement of chitosan is very similar to the corner chains of cellulose II implying similar intermolecular hydrogen bonding between O6 and the amine nitrogen atom, and an intramolecular bifurcated hydrogen bond from O3 to O5 and O6. In addition to the classical hydrogen bonds, all the aliphatic hydrogens were involved in one or two weak hydrogen bonds, mostly helping to stabilize cohesion between antiparallel chains. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 361-368, 2016. PMID:26930586

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

    Science.gov (United States)

    Horrell, Sam; Antonyuk, Svetlana V; Eady, Robert R; Hasnain, S Samar; Hough, Michael A; Strange, Richard W

    2016-07-01

    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.

  4. 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.

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

    Science.gov (United States)

    Horrell, Sam; Antonyuk, Svetlana V; Eady, Robert R; Hasnain, S Samar; Hough, Michael A; Strange, Richard W

    2016-07-01

    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. PMID:27437114

  6. A high resolution X-ray crystal spectrometer to study electron and heavy-ion impact atomic collisions

    Indian Academy of Sciences (India)

    Ajay Kumar; D Misra; A H Kelkar; U R Kadhane; K V Thulasiram; Lokesh C Tribedi

    2007-06-01

    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 been used to give precise and controlled movement to the crystal and for data acquisition. The performance was tested by detecting the K diagram and satellite lines of several elements. The K satellite lines of Al have been studied in collision with 3–12 keV electrons and 40 MeV C4+ ions. In ion collisions as large as four L-vacancies are created simultaneously with the K-vacancy, compared to two satellites in case of the e-impact. In addition, we have measured the X-rays from H-, He- and Li-like Si ions which arise due to the electron loss/capture process in highly charged 80 MeV Si7+ ions in collision with thin carbon foil. Approximate charge state distribution has been obtained using this new technique.

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

    Science.gov (United States)

    Banerjee, Sanchari; Coussens, Nathan P; Gallat, François-Xavier; Sathyanarayanan, Nitish; Srikanth, Jandhyam; Yagi, Koichiro J; Gray, James S S; Tobe, Stephen S; Stay, Barbara; Chavas, Leonard M G; Ramaswamy, Subramanian

    2016-07-01

    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. PMID:27437115

  8. Achieving atomic resolution

    Directory of Open Access Journals (Sweden)

    John Spence

    2002-04-01

    Full Text Available The discovery of the nanotube in 19915 by high resolution electron microscopy (HREM, following closely on the discovery of fullerenes, has initiated a new field of science known as nanoscience. (In fact the fullerene buckyball itself was first observed in 1980, by HREM1. While nanoscience now spans many disciplines, from molecular biology to quantum computing, for all of them, the HREM technique has become the indispensable tool for analyzing the atomic structure of individual bulk nanostructural elements. However this method has long been the technique of choice whenever questions of microstructural characterization arise in materials science.

  9. Three complete turns of a 3(10)-helix at atomic resolution: the crystal structure of Z-(Aib)11-OtBu.

    Science.gov (United States)

    Gessmann, Renate; Brückner, Hans; Petratos, Kyriacos

    2003-01-01

    The crystal structure of the synthetic protected oligopeptide Z-(Aib)11-OtBu was determined by x-ray crystallography. The undecapeptide folds in a regular 3(10)-helix with nine consecutive 4 --> 1 hydrogen bonds. At present, this is the largest available structure of a homopeptide (including homopeptides consisting of standard amino acids) and also the longest observed regular 3(10)-helix at atomic resolution. Z-(Aib)11-OtBu crystallizes readily from hot ethanol-water mixture and is one of the crystals in which no solvent molecule is co-crystallized. In the crystal head-to-tail hydrogen bonded columns are formed in the [1 0 1] direction. Each helical column is surrounded by six others, whereby two are packed in parallel and four in antiparallel fashion. Helical columns are packed via apolar crystal contacts. The crystal structure of Z-(Aib)11-OtBu is compared with the crystal structures of Z-(Aib)10-OtBu and Z-(Aib)9-OtBu. The similarities and differences are analysed.

  10. Four complete turns of a curved 3₁₀-helix at atomic resolution: the crystal structure of the peptaibol trichovirin I-4A in a polar environment suggests a transition to α-helix for membrane function.

    Science.gov (United States)

    Gessmann, Renate; Axford, Danny; Owen, Robin L; Brückner, Hans; Petratos, Kyriacos

    2012-02-01

    The first crystal structure of a member of peptaibol antibiotic subfamily 4, trichovirin I-4A (14 residues), has been determined by direct methods and refined at atomic resolution. The monoclinic unit cell has two molecules in the asymmetric unit. Both molecules assume a 3₁₀ right-handed helical conformation and are significantly bent. The molecules pack loosely along the crystallographic twofold axis, forming two large tunnels between symmetry-related molecules in which no ordered solvent could be located. Carbonyl O atoms which are not involved in intramolecular hydrogen bonding participate in close van der Waals interactions with apolar groups. The necessary amphipathicity for biological activity of peptaibols is not realised in the crystal structure. Hence, a structural change of trichovirin to an α-helical conformation is proposed for membrane integration and efficient water/ion transportation across the lipid bilayer.

  11. Magnetic measurements with atomic-plane resolution

    Science.gov (United States)

    Rusz, Ján; Muto, Shunsuke; Spiegelberg, Jakob; Adam, Roman; Tatsumi, Kazuyoshi; Bürgler, Daniel E.; Oppeneer, Peter M.; Schneider, Claus M.

    2016-01-01

    Rapid development of magnetic nanotechnologies calls for experimental techniques capable of providing magnetic information with subnanometre spatial resolution. Available probes of magnetism either detect only surface properties, such as spin-polarized scanning tunnelling microscopy, magnetic force microscopy or spin-polarized low-energy electron microscopy, or they are bulk probes with limited spatial resolution or quantitativeness, such as X-ray magnetic circular dichroism or classical electron magnetic circular dichroism (EMCD). Atomic resolution EMCD methods have been proposed, although not yet experimentally realized. Here, we demonstrate an EMCD technique with an atomic size electron probe utilizing a probe-corrected scanning transmission electron microscope in its standard operation mode. The crucial element of the method is a ramp in the phase of the electron beam wavefunction, introduced by a controlled beam displacement. We detect EMCD signals with atomic-plane resolution, thereby bringing near-atomic resolution magnetic circular dichroism spectroscopy to hundreds of laboratories worldwide. PMID:27578421

  12. Magnetic measurements with atomic-plane resolution.

    Science.gov (United States)

    Rusz, Ján; Muto, Shunsuke; Spiegelberg, Jakob; Adam, Roman; Tatsumi, Kazuyoshi; Bürgler, Daniel E; Oppeneer, Peter M; Schneider, Claus M

    2016-01-01

    Rapid development of magnetic nanotechnologies calls for experimental techniques capable of providing magnetic information with subnanometre spatial resolution. Available probes of magnetism either detect only surface properties, such as spin-polarized scanning tunnelling microscopy, magnetic force microscopy or spin-polarized low-energy electron microscopy, or they are bulk probes with limited spatial resolution or quantitativeness, such as X-ray magnetic circular dichroism or classical electron magnetic circular dichroism (EMCD). Atomic resolution EMCD methods have been proposed, although not yet experimentally realized. Here, we demonstrate an EMCD technique with an atomic size electron probe utilizing a probe-corrected scanning transmission electron microscope in its standard operation mode. The crucial element of the method is a ramp in the phase of the electron beam wavefunction, introduced by a controlled beam displacement. We detect EMCD signals with atomic-plane resolution, thereby bringing near-atomic resolution magnetic circular dichroism spectroscopy to hundreds of laboratories worldwide. PMID:27578421

  13. Versatile compact atomic source for high resolution dual atom interferometry

    CERN Document Server

    Müller, T; Gilowski, M; Jentsch, C; Rasel, E M; Ertmer, W

    2007-01-01

    We present a compact $^{87}$Rb atomic source for high precision dual atom interferometers. The source is based on a double-stage magneto-optical trap (MOT) design, consisting of a 2-dimensional (2D)-MOT for efficient loading of a 3D-MOT. The accumulated atoms are precisely launched in a horizontal moving molasses. Our setup generates a high atomic flux ($>10^{10}$ atoms/s) with precise and flexibly tunable atomic trajectories as required for high resolution Sagnac atom interferometry. We characterize the performance of the source with respect to the relevant parameters of the launched atoms, i.e. temperature, absolute velocity and pointing, by utilizing time-of-flight techniques and velocity selective Raman transitions.

  14. 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.

  15. Spatial resolution in atom probe tomography

    CERN Document Server

    Gault, Baptiste; de Geuser, Frederic; La Fontaine, Alex; Stephenson, Leigh T; Haley, Daniel; Ringer, Simon P

    2015-01-01

    This article addresses gaps in definitions and a lack of standard measurement techniques to assess the spatial resolution in atom probe tomography. This resolution is known to be anisotropic, being better in the depth than laterally. Generally the presence of atomic planes in the tomographic reconstruction is considered as being a sufficient proof of the quality of the spatial resolution of the instrument. Based on advanced spatial distribution maps, an analysis methodology that interrogates the local neighborhood of the atoms within the tomographic reconstruction, it is shown how both the in-depth and the lateral resolution can be quantified. The influences of the crystallography and the temperature are investigated, and models are proposed to explain the observed results. We demonstrate that the absolute value of resolution is specimenspecific.

  16. Volcano structure in atomic resolution core-loss images

    Energy Technology Data Exchange (ETDEWEB)

    D' Alfonso, A.J.; Findlay, S.D. [School of Physics, University of Melbourne, Victoria, 3010 (Australia); Oxley, M.P. [Materials Science and Technology Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 (United States); Allen, L.J. [School of Physics, University of Melbourne, Victoria, 3010 (Australia)], E-mail: lja@physics.unimelb.edu.au

    2008-06-15

    A feature commonly present in simulations of atomic resolution electron energy loss spectroscopy images in the scanning transmission electron microscope is the volcano or donut structure. In the past this has been understood in terms of a geometrical perspective using a dipole approximation. It is shown that the dipole approximation for core-loss spectroscopy begins to break down as the probe forming aperture semi-angle increases, necessitating the inclusion of higher order terms for a quantitative understanding of volcano formation. Using such simulations we further investigate the mechanisms behind the formation of such structures in the single atom case and extend this to the case of crystals. The cubic SrTiO{sub 3} crystal is used as a test case to show the effects of nonlocality, probe channelling and absorption in producing the volcano structure in crystal images.

  17. Semiconductor crystal high resolution imager

    Science.gov (United States)

    Levin, Craig S. (Inventor); Matteson, James (Inventor)

    2011-01-01

    A radiation imaging device (10). The radiation image device (10) comprises a subject radiation station (12) producing photon emissions (14), and at least one semiconductor crystal detector (16) arranged in an edge-on orientation with respect to the emitted photons (14) to directly receive the emitted photons (14) and produce a signal. The semiconductor crystal detector (16) comprises at least one anode and at least one cathode that produces the signal in response to the emitted photons (14).

  18. 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...

  19. Imaging Genetic Molecules At Atomic Resolution

    Science.gov (United States)

    Coles, L. Stephen

    1993-01-01

    Proposed method of imaging informational polymeric biological molecules at atomic resolution enables determination of sequences of component monomers about 10 to the 3rd power to 10 to the 4th power times as fast as conventional methods do. Accelerates research on genetic structures of animals and plants. Also contributes significantly to imaging processes like scanning electron microscopy (SEM), atomic-force microscopy (AFM), and scanning tunneling microscopy (STM) in cases in which necessary to locate or identify small specimens on relatively large backgrounds and subtract background images to obtain images of specimens in isolation. V-grooves on silicon wafer laid out in square pattern, intersections of which marked to identify coordinates. Specimen molecules held in grooves for reproducible positioning and scanning by AFM or STM.

  20. Spontaneous Crystallization of Light and Ultracold Atoms

    Science.gov (United States)

    Ostermann, S.; Piazza, F.; Ritsch, H.

    2016-04-01

    Coherent scattering of light from ultracold atoms involves an exchange of energy and momentum introducing a wealth of nonlinear dynamical phenomena. As a prominent example, particles can spontaneously form stationary periodic configurations that simultaneously maximize the light scattering and minimize the atomic potential energy in the emerging optical lattice. Such self-ordering effects resulting in periodic lattices via bimodal symmetry breaking have been experimentally observed with cold gases and Bose-Einstein condensates (BECs) inside an optical resonator. Here, we study a new regime of periodic pattern formation for an atomic BEC in free space, driven by far off-resonant counterpropagating and noninterfering lasers of orthogonal polarization. In contrast to previous works, no spatial light modes are preselected by any boundary conditions and the transition from homogeneous to periodic order amounts to a crystallization of both light and ultracold atoms breaking a continuous translational symmetry. In the crystallized state the BEC acquires a phase similar to a supersolid with an emergent intrinsic length scale whereas the light field forms an optical lattice allowing phononic excitations via collective backscattering, which are gapped due to the infinte-range interactions. The system we study constitutes a novel configuration allowing the simulation of synthetic solid-state systems with ultracold atoms including long-range phonon dynamics.

  1. Time amplifying techniques towards atomic time resolution

    Institute of Scientific and Technical Information of China (English)

    LI JingZhen

    2009-01-01

    High speed imaging technology has opened applications in many fields,such as collision,detonating,high voltage discharge,disintegration and transfer of phonon and exciton in solid,photosynthesis primitive reaction,and electron dynamics inside atom shell.In principle,all of the transient processes need to be explained theoretically and,st the same time,the time amplifying technique is required for observations of these processes.The present review concerns the atomic time amplifying mechanism of optical information and the extremely-high speed imaging methods,which are expressed in terms of the short time amplifying techniques.It is well-known that for extremely-high speed imaging with the converter tube,the temporal resolution is in the order of sub-picosecond of the streak imaging,and the imaging frequency is 6×10~8-5×10~9 fps(frame per second)of the frame imaging.On the other hand,for the tubeless extremely-high speed imaging,the imaging frequency is 10~7-10~(14) fps,and its mechanism of forming high speed and framing could involve a lot of factors of the light under investigation,for instance,light speed,light parallelism,the parameters of light wave such as amplitude,phase,polarization and wavelength,and even quantum properties of photon.In the cascaded system of electromagnetic wave and particle wave,it is possible to simultaneously realize extremely-high resolution in time and space,which is higher than a kite resolution.Then it would be possible to break the limit of the Heisenberg uncertainty relation of the optical frequency band.

  2. Time amplifying techniques towards atomic time resolution

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    High speed imaging technology has opened applications in many fields,such as collision,detonating, high voltage discharge,disintegration and transfer of phonon and exciton in solid,photosynthesis primitive reaction,and electron dynamics inside atom shell.In principle,all of the transient processes need to be explained theoretically and,at the same time,the time amplifying technique is required for observations of these processes.The present review concerns the atomic time amplifying mechanism of optical information and the extremely-high speed imaging methods,which are expressed in terms of the short time amplifying techniques.It is well-known that for extremely-high speed imaging with the converter tube,the temporal resolution is in the order of sub-picosecond of the streak imaging,and the imaging frequency is 6×10 8 ―5×10 9 fps(frame per second)of the frame imaging.On the other hand,for the tubeless extremely-high speed imaging,the imaging frequency is 10 7 ―10 14 fps,and its mechanism of forming high speed and framing could involve a lot of factors of the light under investigation,for instance,light speed,light parallelism,the parameters of light wave such as amplitude,phase,polari- zation and wavelength,and even quantum properties of photon.In the cascaded system of electro- magnetic wave and particle wave,it is possible to simultaneously realize extremely-high resolution in time and space,which is higher than a kite resolution.Then it would be possible to break the limit of the Heisenberg uncertainty relation of the optical frequency band.

  3. High resolution crystal calorimetry at LHC

    International Nuclear Information System (INIS)

    The search for Higgs bosons above Lep200 reach could be one of the main tasks of the future pp and ee colliders. In the intermediate mass region, and in particular in the range 80-140 GeV/c2, only the 2-photon decay mode of a Higgs produced inclusively or in association with a W, gives a good chance of observation. A 'dedicated' very high resolution calorimeter with photon angle reconstruction and pion identification capability should detect a Higgs signal with high probability. A crystal calorimeter can be considered as a conservative approach to such a detector, since a large design and operation experience already exists. The extensive R and D needed for finding a dense, fast and radiation hard crystal, is under way. Guide-lines for designing an optimum calorimeter for LHC are discussed and preliminary configurations are given. (author) 7 refs., 3 figs., 2 tabs

  4. A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.

    Science.gov (United States)

    Nosrati, Meisam; Berbasova, Tetyana; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H

    2016-07-20

    The members of the rhodopsin family of proteins are involved in many essential light-dependent processes in biology. Specific photoisomerization of the protein-bound retinylidene PSB at a specified wavelength range of light is at the heart of all of these systems. Nonetheless, it has been difficult to reproduce in an engineered system. We have developed rhodopsin mimics, using intracellular lipid binding protein family members as scaffolds, to study fundamental aspects of protein/chromophore interactions. Herein we describe a system that specifically isomerizes the retinylidene protonated Schiff base both thermally and photochemically. This isomerization has been characterized at atomic resolution by quantitatively interconverting the isomers in the crystal both thermally and photochemically. This event is accompanied by a large pKa change of the imine similar to the pKa changes observed in bacteriorhodopsin and visual opsins during isomerization. PMID:27310917

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

    International Nuclear Information System (INIS)

    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

  6. 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.

  7. 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.

  8. High resolution field imaging with atomic vapor cells

    OpenAIRE

    Horsley, Andrew

    2015-01-01

    In this thesis, I report on the development of imaging techniques in atomic vapor cells. This is a relatively unexplored area, despite the ubiquitous use of imaging in experiments with ultracold atoms. Our main focus is in high resolution imaging of microwave near fields, for which there is currently no satisfactory established technique. We detect microwave fields through Rabi oscillations driven by the microwave on atomic hyperfine transitions. The technique can be easily modified to also i...

  9. High resolution neutron powder diffraction studies of the crystal structure of CsDSO4

    International Nuclear Information System (INIS)

    High resolution neutron powder diffraction data were used to determine the crystal structure of the superionic conductor CsDSO4 at 300 K (low conductivity phase) and at 448 K (superionic phase). A full structural analysis was performed using the Rietriveld method to obtain previously unknown atomic positions, site occupancies and temperature factors for the light atoms. The mechanism for deuterium diffusion is discussed. 18 refs.; 5 figs.; 5 tabs

  10. Can the Low-Resolution Structures of Photointermediates of Bacteriorhodopsin Explain Their Crystal Structures?

    OpenAIRE

    Kamikubo, Hironari; Kataoka, Mikio

    2004-01-01

    To understand the molecular mechanism of light-driven proton pumps, the structures of the photointermediates of bacteriorhodopsin have been intensively investigated. Low-resolution diffraction techniques have demonstrated substantial conformational changes at the helix level in the M and N intermediates, between which there are noticeable differences. The intermediate structures at atomic resolution have also been solved by x-ray crystallography. Although the crystal structures have demonstra...

  11. Super-resolution microscopy of single atoms in optical lattices

    CERN Document Server

    Alberti, Andrea; Alt, Wolfgang; Brakhane, Stefan; Karski, Michał; Reimann, René; Widera, Artur; Meschede, Dieter

    2015-01-01

    We report on image processing techniques and experimental procedures to determine the lattice-site positions of single atoms in an optical lattice with high reliability, even for limited acquisition time or optical resolution. Determining the positions of atoms beyond the diffraction limit relies on parametric deconvolution in close analogy to methods employed in super-resolution microscopy. We develop a deconvolution method that makes effective use of the prior knowledge of the optical transfer function, noise properties, and discreteness of the optical lattice. We show that accurate knowledge of the image formation process enables a dramatic improvement on the localization reliability. This is especially relevant for closely packed ensembles of atoms where the separation between particles cannot be directly optically resolved. Furthermore, we demonstrate experimental methods to precisely reconstruct the point spread function with sub-pixel resolution from fluorescence images of single atoms, and we give a m...

  12. 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.

  13. Atom column indexing: atomic resolution image analysis through a matrix representation.

    Science.gov (United States)

    Sang, Xiahan; Oni, Adedapo A; LeBeau, James M

    2014-12-01

    Here, we report the development of an approach to map atomic resolution images into a convenient matrix representation. Through the combination of two-dimensional Gaussian fitting and the projective standard deviation, atom column locations are projected onto two noncollinear reference lattice vectors that are used to assign each a unique (i, j) matrix index. By doing so, straightforward atomic resolution image analysis becomes possible. Using practical examples, we demonstrate that the matrix representation greatly simplifies categorizing atom columns to different sublattices. This enables a myriad of direct analyses, such as mapping atom column properties and correlating long-range atom column pairs. MATLAB source code can be downloaded from https://github.com/subangstrom/aci.

  14. Nonlinear optical response of a two-dimensional atomic crystal.

    Science.gov (United States)

    Merano, Michele

    2016-01-01

    The theory of Bloembergen and Pershan for the light waves at the boundary of nonlinear media is extended to a nonlinear two-dimensional (2D) atomic crystal, i.e., a single planar atomic lattice, placed between linear bulk media. The crystal is treated as a zero-thickness interface, a real 2D system. Harmonic waves emanate from it. Generalization of the laws of reflection and refraction give the direction and the intensity of the harmonic waves. As a particular case that contains all the essential physical features, second-order harmonic generation is considered. The theory, due to its simplicity that stems from the special character of a single planar atomic lattice, is able to elucidate and explain the rich experimental details of harmonic generation from a 2D atomic crystal.

  15. ATOMIC-FORCE MICROSCOPY AND REAL ATOMIC-RESOLUTION - SIMPLE COMPUTER-SIMULATIONS

    NARCIS (Netherlands)

    KOUTSOS, [No Value; MANIAS, E; TENBRINKE, G; 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 regis

  16. Atomic structure and crystallization processes of amorphous (Co,Ni)–P metallic alloy

    Energy Technology Data Exchange (ETDEWEB)

    Modin, Evgeny B., E-mail: modin.eb@dvfu.ru [Far Eastern Federal University, Shukhanova 8, Vladivostok 690950 (Russian Federation); Pustovalov, Evgeny V.; Fedorets, Aleksander N.; Dubinets, Aleksander V.; Grudin, Boris N.; Plotnikov, Vladimir S. [Far Eastern Federal University, Shukhanova 8, Vladivostok 690950 (Russian Federation); Grabchikov, Sergey S. [Scientific and Practical Centre of Material Science, Belarus National Academy of Sciences, P. Brovki 19, Minsk 220072 (Belarus)

    2015-08-25

    Highlights: • The CoP–CoNiP amorphous alloys were studied by the Cs-corrected high resolution transmission electron microscopy. • In situ heating experiments showed that crystallization starts at 200–250 °C on the network frame and cell boundaries. • Crystal growth occurs at the free surface, then the remaining material in the volume is crystallized. • Adding nickel to the CoP alloy leads to higher thermal stability. • At the beginning of crystallization there are high diffusion coefficients, 1.2–2.4 ∗ 10{sup −18} m{sup 2}/s at 250 °C. - Abstract: This work concerns the in situ investigation of the atomic structure of (Co,Ni)–P alloys during relaxation and crystallization by high resolution transmission electron microscopy. The CoP–CoNiP alloys, in the initial state, have a hierarchical network-like disordered structure. Crystallization starts at 200–250 °C on the network frame and cell boundaries. In the early stages, crystal growth occurs at the free surface, then the remaining material in the volume is crystallized. The diffusion coefficient at the start of crystallization is 1.2–2.4 × 10{sup −18} m{sup 2}/s at 250 °C and we assume that the high diffusion speed is due to surface diffusion.

  17. Super-resolution microscopy of single atoms in optical lattices

    Science.gov (United States)

    Alberti, Andrea; Robens, Carsten; Alt, Wolfgang; Brakhane, Stefan; Karski, Michał; Reimann, René; Widera, Artur; Meschede, Dieter

    2016-05-01

    We report on image processing techniques and experimental procedures to determine the lattice-site positions of single atoms in an optical lattice with high reliability, even for limited acquisition time or optical resolution. Determining the positions of atoms beyond the diffraction limit relies on parametric deconvolution in close analogy to methods employed in super-resolution microscopy. We develop a deconvolution method that makes effective use of the prior knowledge of the optical transfer function, noise properties, and discreteness of the optical lattice. We show that accurate knowledge of the image formation process enables a dramatic improvement on the localization reliability. This allows us to demonstrate super-resolution of the atoms’ position in closely packed ensembles where the separation between particles cannot be directly optically resolved. Furthermore, we demonstrate experimental methods to precisely reconstruct the point spread function with sub-pixel resolution from fluorescence images of single atoms, and we give a mathematical foundation thereof. We also discuss discretized image sampling in pixel detectors and provide a quantitative model of noise sources in electron multiplying CCD cameras. The techniques developed here are not only beneficial to neutral atom experiments, but could also be employed to improve the localization precision of trapped ions for ultra precise force sensing.

  18. 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.

  19. 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

    International Nuclear Information System (INIS)

    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

  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. CO tip functionalization in subatomic resolution atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Minjung [Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States); Chelikowsky, James R. [Center for Computational Materials, Institute for Computational Engineering and Sciences, and Departments of Physics and Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States)

    2015-10-19

    Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

  2. Atomic resolution in noncontact AFM by probing cantilever frequency shifts

    Institute of Scientific and Technical Information of China (English)

    Hong Yong Xie

    2007-01-01

    Rutile TiO2(001) quantum dots (or nano-marks) in different shapes were used to imitate uncleaved material surfaces or materials with rough surfaces. By numerical integration of the equation of motion of cantilever for silicon tip scanning along the [110] direction over the rutile TiO2 (001) quantum dots in ultra high vacuum (UHV), scanning routes were explored to achieve atomic resolution from frequency shift image. The tip-surface interaction forces were calculated from Lennard-Jones (12-6) potential by the Hamaker summation method. The calculated results showed that atomic resolution could be achieved by frequency shift image for TiO2 (001) surfaces of rhombohedral quantum dot scanning in a vertical route, and spherical cap quantum dot scanning in a superposition route.

  3. On atom–atom `short contact' bonding interactions in crystals

    OpenAIRE

    Claude Lecomte; Enrique Espinosa; Cherif F. Matta

    2015-01-01

    Professor Dunitz questions the usefulness of ascribing crystalline structural stability to individual atom–atom intermolecular interactions viewed as bonding (hence stabilizing) whenever linked by a bond path. An alternative view is expressed in the present essay that articulates the validity and usefulness of the bond path concept in a crystallographic and crystal engineering context.

  4. Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

    Science.gov (United States)

    Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

    2015-03-17

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

  5. Shear-accelerated crystallization in a supercooled atomic liquid.

    Science.gov (United States)

    Shao, Zhen; Singer, Jonathan P; Liu, Yanhui; Liu, Ze; Li, Huiping; Gopinadhan, Manesh; O'Hern, Corey S; Schroers, Jan; Osuji, Chinedum O

    2015-02-01

    A bulk metallic glass forming alloy is subjected to shear flow in its supercooled state by compression of a short rod to produce a flat disk. The resulting material exhibits enhanced crystallization kinetics during isothermal annealing as reflected in the decrease of the crystallization time relative to the nondeformed case. The transition from quiescent to shear-accelerated crystallization is linked to strain accumulated during shear flow above a critical shear rate γ̇(c)≈0.3 s(-1) which corresponds to Péclet number, Pe∼O(1). The observation of shear-accelerated crystallization in an atomic system at modest shear rates is uncommon. It is made possible here by the substantial viscosity of the supercooled liquid which increases strongly with temperature in the approach to the glass transition. We may therefore anticipate the encounter of nontrivial shear-related effects during thermoplastic deformation of similar systems.

  6. High-resolution crystal structures of the solubilized domain of porcine cytochrome b{sub 5}

    Energy Technology Data Exchange (ETDEWEB)

    Hirano, Yu [Quantum Beam Science Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195 (Japan); Kimura, Shigenobu [Faculty of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511 (Japan); Tamada, Taro, E-mail: tamada.taro@jaea.go.jp [Quantum Beam Science Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195 (Japan)

    2015-06-30

    Crystal structures of the solubilized domain of cytochrome b{sub 5} from porcine liver were determined at sub-angstrom resolution in two crystal forms for both the oxidized and reduced states. The high-resolution structures provided information about the factors that are important for regulating the electronic properties of the haem group of cytochrome b{sub 5}. Mammalian microsomal cytochrome b{sub 5} has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochrome b{sub 5} from porcine liver were determined at sub-angstrom resolution (0.76–0.95 Å) in two crystal forms for both the oxidized and reduced states. The high-resolution structures clearly displayed the electron density of H atoms in some amino-acid residues. Unrestrained refinement of bond lengths revealed that the protonation states of the haem propionate group may be involved in regulation of the haem redox properties. The haem Fe coordination geometry did not show significant differences between the oxidized and reduced structures. However, structural differences between the oxidized and reduced states were observed in the hydrogen-bond network around the axial ligand His68. The hydrogen-bond network could be involved in regulating the redox states of the haem group.

  7. High resolution atomic force microscopy of double-stranded RNA

    Science.gov (United States)

    Ares, Pablo; Fuentes-Perez, Maria Eugenia; Herrero-Galán, Elías; Valpuesta, José M.; Gil, Adriana; Gomez-Herrero, Julio; Moreno-Herrero, Fernando

    2016-06-01

    Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to

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

    Science.gov (United States)

    Blakeley, Matthew P; Hasnain, Samar S; Antonyuk, Svetlana V

    2015-07-01

    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-mm(3) 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. Neutron

  9. 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

  10. Simulation studies of atomic resolution X-ray holography

    Indian Academy of Sciences (India)

    Yogesh Kashyap; P S Sarkar; Amar Sinha; B K Godwal

    2004-02-01

    X-ray holography is a new method of structure determination based on measurement of interference of a known reference wave with an unknown object wave (containing information on atomic sites scattering the reference wave) so that phase information is preserved. Unlike X-ray diffraction, it does not demand for translational periodicity in the material. It is based on the idea similar to that of optical holography and has been tested on crystals, quasicrystals, thin films and doped semiconductors for their structure determination. In order to analyse potentials and limitations of this technique, we have carried out theoretical simulation studies on simple structures. In this paper we describe the basic algorithm of hologram generation and reconstruction of atomic positions from generated data. We illustrate this technique using Fe (bcc) single crystal as sample case to demonstrate its capabilities and limitations. Simulations were carried out on the Cu (fcc) structure and on complex structure such as the Al–Pd–Mn quasicrystal. Technical issues such as low signal to noise ratio, twin image problem etc have been discussed briefly to emphasize the need for high intensity X-ray source such as synchrotron for experiments and proper reconstruction algorithm. Finally the scope and potential of this technique have been discussed.

  11. High viscosity environments: an unexpected route to obtain true atomic resolution with atomic force microscopy

    International Nuclear Information System (INIS)

    Atomic force microscopy (AFM) is widely used in liquid environments, where true atomic resolution at the solid–liquid interface can now be routinely achieved. It is generally expected that AFM operation in more viscous environments results in an increased noise contribution from the thermal motion of the cantilever, thereby reducing the signal-to-noise ratio (SNR). Thus, viscous fluids such as ionic and organic liquids have been generally avoided for high-resolution AFM studies despite their relevance to, e.g. energy applications. Here, we investigate the thermal noise limitations of dynamic AFM operation in both low and high viscosity environments theoretically, deriving expressions for the amplitude, phase and frequency noise resulting from the thermal motion of the cantilever, thereby defining the performance limits of amplitude modulation, phase modulation and frequency modulation AFM. We show that the assumption of a reduced SNR in viscous environments is not inherent to the technique and demonstrate that SNR values comparable to ultra-high vacuum systems can be obtained in high viscosity environments under certain conditions. Finally, we have obtained true atomic resolution images of highly ordered pyrolytic graphite and mica surfaces, thus revealing the potential of high-resolution imaging in high viscosity environments. (paper)

  12. Atomic hydrogen doping in single-crystal vanadium dioxide

    Science.gov (United States)

    Ji, Heng; Hardy, Will; Wei, Jiang; Lin, Jian; Paik, Hanjong; Schlom, Darrell; Natelson, Douglas

    2014-03-01

    Vanadium dioxide is a strongly correlated material with a bulk metal-to-insulator transition (MIT) near 340 K. Previous experiments in single-crystal nanowires (J. Wei et al., Nature Nano. 7, 357-362 (2012)) have shown that catalytic doping with atomic hydrogen can stabilize the high temperature metallic state. In this experiment, we used a hot filament source to split hydrogen molecules and directly dope atomic hydrogen into VO2 material, including epitaxial films and nanowires, without any catalyst. From observations of the wire samples, we infer the relative diffusion rates of H in the monoclinic and rutile crystal structures. Transport measurements of the doped film samples show no temperature-driven transition, but rather a conducting state down to 2K. We present Hall and magnetoresistance measurements on macroscale and mesoscale devices fabricated from the doped films.

  13. Structural investigation of ionic liquid/rubrene single crystal interfaces by using frequency-modulation atomic force microscopy.

    Science.gov (United States)

    Yokota, Yasuyuki; Hara, Hisaya; Harada, Tomohiro; Imanishi, Akihito; Uemura, Takafumi; Takeya, Jun; Fukui, Ken-ichi

    2013-11-21

    Frequency-modulation atomic force microscopy (FM-AFM) was employed to reveal the structural properties of a rubrene single crystal immersed in an ionic liquid. We found large vacancies formed by the anisotropic dissolution of rubrene molecules. Molecular resolution imaging revealed that structures of FM-AFM images deviated from the bulk-terminated structure. PMID:24091742

  14. Suppressing unstable deformation of nanocolloidal crystals with atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Di [Department of Mechanical Engineering, Villanova University, Villanova, PA 19085 (United States); Zhang, Lei; Lee, Daeyeon [Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104 (United States); Cheng, Xuemei [Department of Physics, Bryn Mawr College, Bryn Mawr, PA 19010 (United States); Feng, Gang, E-mail: gang.feng@villanova.edu [Department of Mechanical Engineering, Villanova University, Villanova, PA 19085 (United States)

    2015-07-15

    Despite their useful photonic properties, poor mechanical robustness hinders the application of nanocolloidal crystals (NCCs). Understanding the mechanical behavior of NCCs is critical to propose effective reinforcement techniques. We find that as-assembled NCCs exhibit unstable deformation, manifested as pop-ins upon nanoindentation. By deepening indentation, the unstable deformation mode transitions from NC dislodging to shear band (SB) formation. We find that alumina atomic layer deposition (ALD) significantly suppresses NC dislodging and SB formations in NCCs by increasing interparticle bonding.

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

    Science.gov (United States)

    Pavlov, V. V.

    2008-02-01

    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.

  16. Design for a focusing high-resolution neutron crystal diffractometer

    CERN Document Server

    Ionita, I; Popovici, M; Popa, N C

    1999-01-01

    A new concept of high-resolution focusing configuration begins to be accepted as an alternative solution to the existing conventional configurations. Among the earliest work performed in this direction is that performed at the Institute for Nuclear Research, Pitesti. These results are presented below. The experimentally determined resolution properties for two focusing configurations obtained at TRIGA reactor Pitesti and at VVRS reactor Bucharest are given in order to be compared with those obtained for the conventional ones. The principles to get focusing in crystal neutron diffractometry are presented. The main characteristics for a focusing instrument are given. (author)

  17. 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.

    2016-09-01

    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±ikxxE(x)∝e±ikxx outside the bandgap to localized fields E(x)∝e-κx|x|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 D1D1 line of atomic cesium for N¯=3.0±0.5N¯=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.

  18. Clean surface processing of rubrene single crystal immersed in ionic liquid by using frequency modulation atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Yokota, Yasuyuki; Hara, Hisaya; Morino, Yusuke; Bando, Ken-ichi; Imanishi, Akihito; Fukui, Ken-ichi, E-mail: kfukui@chem.es.osaka-u.ac.jp [Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 (Japan); Uemura, Takafumi; Takeya, Jun, E-mail: takeya@k.u-tokyo.ac.jp [Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwa, Chiba 277-8561 (Japan); The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047 (Japan)

    2014-06-30

    Surface processing of a rubrene single crystal immersed in ionic liquids is valuable for further development of low voltage transistors operated by an electric double layer. We performed a precise and clean surface processing based on the tip-induced dissolution of rubrene molecules at the ionic liquid/rubrene single crystal interfaces by using frequency modulation atomic force microscopy. Molecular resolution imaging revealed that the tip-induced dissolution proceeded via metastable low density states derived from the anisotropic intermolecular interactions within the crystal structure.

  19. Clean surface processing of rubrene single crystal immersed in ionic liquid by using frequency modulation atomic force microscopy

    Science.gov (United States)

    Yokota, Yasuyuki; Hara, Hisaya; Morino, Yusuke; Bando, Ken-ichi; Imanishi, Akihito; Uemura, Takafumi; Takeya, Jun; Fukui, Ken-ichi

    2014-06-01

    Surface processing of a rubrene single crystal immersed in ionic liquids is valuable for further development of low voltage transistors operated by an electric double layer. We performed a precise and clean surface processing based on the tip-induced dissolution of rubrene molecules at the ionic liquid/rubrene single crystal interfaces by using frequency modulation atomic force microscopy. Molecular resolution imaging revealed that the tip-induced dissolution proceeded via metastable low density states derived from the anisotropic intermolecular interactions within the crystal structure.

  20. Atomic resolution structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A2

    International Nuclear Information System (INIS)

    The atomic resolution crystal structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A2 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

  1. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo [Yale University

    2014-12-10

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

  3. Rydberg atoms in hollow-core photonic crystal fibres

    CERN Document Server

    Epple, G; Euser, T G; Joly, N Y; Pfau, T; Russell, P St J; Löw, R

    2014-01-01

    The exceptionally large polarisability of highly excited Rydberg atoms (six orders of magnitude higher than ground-state atoms) makes them of great interest in fields such as quantum optics, quantum computing, quantum simulation and metrology. If however they are to be used routinely in applications, a major requirement is their integration into technically feasible, miniaturised devices. Here we show that a Rydberg medium based on room temperature caesium vapour can be confined in broadband-guiding kagome-style hollow-core photonic crystal fibres. Three-photon spectroscopy performed on a caesium-filled fibre detects Rydberg states up to a principal quantum number of n = 40. Besides small energy level shifts we observe narrow lines confirming the coherence of the Rydberg excitation. Using different Rydberg states and core diameters we study the influence of confinement within the fibre core after different exposure times. Understanding these effects is essential for the successful future development of novel ...

  4. ALCHEMI: a new technique for locating atoms in small crystals

    International Nuclear Information System (INIS)

    Atom Location by Channelling Enhanced Microanalysis (ALCHEMI) is a quantitative technique for identifying the crystallographic sites, distribution and types of substitutional impurities in many crystals. The method involves no adjustable parameters, can be applied to areas as small as a few hundred Angstroms and to impurity concentrations down to about 0.1 atomic per cent. It is capable of distinguishing neighbours in the periodic table. The method uses the incident electron beam orientation dependence of characteristic X-ray emission and uses an energy dispersive X-ray microanalyser fitted to a transmission electron microscope. The method does not require the specimen thickness or precise orientation to be known, and makes few assumptions about the form of the dynamical electron wavefunction, which need not be calculated or predicted. The classical problems of cation ordering in spinels, feldspars and olivine have now been studied by this method. (author)

  5. 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...

  6. Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Liqing, E-mail: chenlq@uah.edu; Wang, Yujun [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Wells, David; Toh, Diana; Harold, Hunt [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Zhou, Jing [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); DiGiammarino, Enrico [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Meehan, Edward J. [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States)

    2006-09-01

    The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.

  7. Tuning friction atom-by-atom in an ion-crystal simulator

    CERN Document Server

    Bylinskii, Alexei; Vuletic, Vladan

    2014-01-01

    Friction between ordered, atomically smooth surfaces at the nanoscale (nanofriction) is often governed by stick-slip processes. To test long-standing atomistic models of such processes, we implement a synthetic nanofriction interface between a laser-cooled Coulomb crystal of ions as the moving object, and a periodic light-field potential as the substrate, enabling us to directly observe and control individual atoms at a frictional interface. We show that stick-slip friction can be tuned from maximal to nearly frictionless via arrangement of the ions relative to the substrate. By varying the ion number, we also show that this strong dependence of friction on the structural mismatch, as predicted by many-particle models, already emerges at the level of two or three atoms. This model system enables a microscopic and systematic investigation of friction, potentially even into the quantum many-body regime.

  8. 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

    2014-06-01

    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.

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

    CERN Document Server

    Okaba, Shoichi; 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 miniaturisation. Here we report a novel platform for precision spectroscopy. Ultracold strontium atoms inside a kKagome-lattice hollow-core photonic crystal fibre (HC-PCF) 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 $^1 S_0-{}^3P_1$ (m=0) transition. Atoms singly trapped in a magic lattice in hollow-core photonic crystal fibresHC-PCFs improve the optical depth while preserving atomic coherence time.

  10. Hot atom chemistry of mixed crystals. 35 years of research

    International Nuclear Information System (INIS)

    When this contribution was prepared, the author decided to present the more personal aspects of his work and the concepts that directed him. Since the time when the author interested in solid state hot atom chemistry more than 30 years ago, still now the generally accepted theory has not been existed. The irradiation test by using the BEPO pile in Harwell is reported. The use of glass fiber paper instead of cellulose paper was investigated. The real problem of the different models of primary retention should be solved. The idea of mixed crystal systems was the result of an experimental accident. The attempt of preparing mixed crystals, the papers that the author has written, the procedures of the experiment such as electrophoresis, the results of the electrophoretic separation are discussed. The next step was obviously the investigation of the ligand recoil. The production of the transient ligand vacancy complexes and their final fate resulted in mixed hexachlorobromometallate species is shown for the system K2OsCl6-K2OsBr6(n,γ)38Cl. The reaction of the 38Cl, the information about recoil atom reactions which increased with the complexity of target substances, and the resulted informations are reported. (K.I.)71 refs

  11. Observing gas-catalyst dynamics at atomic resolution and single-atom sensitivity.

    Science.gov (United States)

    Helveg, S; Kisielowski, C F; Jinschek, J R; Specht, P; Yuan, G; Frei, H

    2015-01-01

    Transmission electron microscopy (TEM) has become an indispensable technique for studying heterogeneous catalysts. In particular, advancements of aberration-corrected electron optics and data acquisition schemes have made TEM capable of delivering images of catalysts with sub-Ångström resolution and single-atom sensitivity. Parallel developments of differentially pumped electron microscopes and of gas cells enable in situ observations of catalysts during the exposure to reactive gas environments at pressures of up to atmospheric levels and temperatures of up to several hundred centigrade. Here, we outline how to take advantage of the emerging state-of-the-art instrumentation and methodologies to study surface structures and dynamics to improve the understanding of structure-sensitive catalytic functionality. The concept of using low electron dose-rates in TEM in conjunction with in-line holography and aberration-correction at low voltage (80 kV) is introduced to allow maintaining atomic resolution and sensitivity during in situ observations of catalysts. Benefits are illustrated by exit wave reconstructions of TEM images of a nanocrystalline Co3O4 catalyst material acquired in situ during their exposure to either a reducing or oxidizing gas environment. PMID:25245867

  12. Gate-induced superconductivity in two-dimensional atomic crystals

    Science.gov (United States)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-09-01

    Two-dimensional (2D) crystals are attracting growing interest in condensed matter physics, since these systems exhibit not only rich electronic and photonic properties but also exotic electronic phase transitions including superconductivity and charge density wave. Moreover, owing to the recent development of transfer methods after exfoliation and electric-double-layer transistors, superconducting 2D atomic crystals, the thicknesses of which are below 1-2 nm, have been successfully obtained. Here, we present a topical review on the recent discoveries of 2D crystalline superconductors by ionic-liquid gating and a series of their novel properties. In particular, we highlight two topics; quantum metallic states (or possible metallic ground states) and superconductivity robust against in-plane magnetic fields. These phenomena can be discussed with the effects of weakened disorder and/or broken spacial inversion symmetry leading to valley-dependent spin-momentum locking (spin-valley locking). These examples suggest the superconducting 2D crystals are new platforms for investigating the intrinsic quantum phases as well as exotic nature in 2D superconductors.

  13. Gate-induced superconductivity in two-dimensional atomic crystals

    Science.gov (United States)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-09-01

    Two-dimensional (2D) crystals are attracting growing interest in condensed matter physics, since these systems exhibit not only rich electronic and photonic properties but also exotic electronic phase transitions including superconductivity and charge density wave. Moreover, owing to the recent development of transfer methods after exfoliation and electric-double-layer transistors, superconducting 2D atomic crystals, the thicknesses of which are below 1–2 nm, have been successfully obtained. Here, we present a topical review on the recent discoveries of 2D crystalline superconductors by ionic-liquid gating and a series of their novel properties. In particular, we highlight two topics; quantum metallic states (or possible metallic ground states) and superconductivity robust against in-plane magnetic fields. These phenomena can be discussed with the effects of weakened disorder and/or broken spacial inversion symmetry leading to valley-dependent spin-momentum locking (spin-valley locking). These examples suggest the superconducting 2D crystals are new platforms for investigating the intrinsic quantum phases as well as exotic nature in 2D superconductors.

  14. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    Science.gov (United States)

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous-crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  15. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    Science.gov (United States)

    Colvin, Michael T; Silvers, Robert; Ni, Qing Zhe; Can, Thach V; Sergeyev, Ivan; Rosay, Melanie; Donovan, Kevin J; Michael, Brian; Wall, Joseph; Linse, Sara; Griffin, Robert G

    2016-08-01

    Amyloid-β (Aβ) is a 39-42 residue protein produced by the cleavage of the amyloid precursor protein (APP), which subsequently aggregates to form cross-β amyloid fibrils that are a hallmark of Alzheimer's disease (AD). The most prominent forms of Aβ are Aβ1-40 and Aβ1-42, which differ by two amino acids (I and A) at the C-terminus. However, Aβ42 is more neurotoxic and essential to the etiology of AD. Here, we present an atomic resolution structure of a monomorphic form of AβM01-42 amyloid fibrils derived from over 500 (13)C-(13)C, (13)C-(15)N distance and backbone angle structural constraints obtained from high field magic angle spinning NMR spectra. The structure (PDB ID: 5KK3 ) shows that the fibril core consists of a dimer of Aβ42 molecules, each containing four β-strands in a S-shaped amyloid fold, and arranged in a manner that generates two hydrophobic cores that are capped at the end of the chain by a salt bridge. The outer surface of the monomers presents hydrophilic side chains to the solvent. The interface between the monomers of the dimer shows clear contacts between M35 of one molecule and L17 and Q15 of the second. Intermolecular (13)C-(15)N constraints demonstrate that the amyloid fibrils are parallel in register. The RMSD of the backbone structure (Q15-A42) is 0.71 ± 0.12 Å and of all heavy atoms is 1.07 ± 0.08 Å. The structure provides a point of departure for the design of drugs that bind to the fibril surface and therefore interfere with secondary nucleation and for other therapeutic approaches to mitigate Aβ42 aggregation. PMID:27355699

  16. Modeling molecular crystals formed by spin-active metal complexes by atom-atom potentials

    CERN Document Server

    Sinitskiy, Anton V; Tokmachev, Andrei M; Dronskowski, Richard

    2009-01-01

    We apply the atom-atom potentials to molecular crystals of iron (II) complexes with bulky organic ligands. The crystals under study are formed by low-spin or high-spin molecules of Fe(phen)$_{2}$(NCS)$_{2}$ (phen = 1,10-phenanthroline), Fe(btz)$_{2}$(NCS)$_{2}$ (btz = 5,5$^{\\prime }$,6,6$^{\\prime}$-tetrahydro-4\\textit{H},4$^{\\prime}$\\textit{H}-2,2$^{\\prime }$-bi-1,3-thiazine), and Fe(bpz)$_{2}$(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2$^{\\prime}$-bipyridine). All molecular geometries are taken from the X-ray experimental data and assumed to be frozen. The unit cell dimensions and angles, positions of the centers of masses of molecules, and the orientations of molecules corresponding to the minimum energy at 1 atm and 1 GPa are calculated. The optimized crystal structures are in a good agreement with the experimental data. Sources of the residual discrepancies between the calculated and experimental structures are discussed. The intermolecular contributions to the enthalpy of the spin transiti...

  17. 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

  18. Atomic-Resolution Structure of an N(5) Flavin Adduct in D-Arginine Dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Guoxing; Yuan, Hongling; Wang, Siming; Gadda, Giovanni; Weber, Irene T. (GSU)

    2011-09-06

    D-Arginine dehydrogenase (DADH) catalyzes the flavin-dependent oxidative deamination of D-arginine and other D-amino acids to the corresponding imino acids. The 1.07 {angstrom} atomic-resolution structure of DADH crystallized with D-leucine unexpectedly revealed a covalent N(5) flavin adduct, instead of the expected iminoleucine product in the active site. This acyl adduct has been successfully reproduced by photoreduction of DADH in the presence of 4-methyl-2-oxopentanoic acid (ketoleucine). The iminoleucine may be released readily because of weak interactions in the binding site, in contrast to iminoarginine, converted to ketoleucine, which reacts with activated FAD to form the covalently linked acyl adduct.

  19. Atomic-resolution structure of an N5 flavin adduct in D-arginine dehydrogenase.

    Science.gov (United States)

    Fu, Guoxing; Yuan, Hongling; Wang, Siming; Gadda, Giovanni; Weber, Irene T

    2011-07-26

    D-Arginine dehydrogenase (DADH) catalyzes the flavin-dependent oxidative deamination of D-arginine and other D-amino acids to the corresponding imino acids. The 1.07 Å atomic-resolution structure of DADH crystallized with D-leucine unexpectedly revealed a covalent N(5) flavin adduct, instead of the expected iminoleucine product in the active site. This acyl adduct has been successfully reproduced by photoreduction of DADH in the presence of 4-methyl-2-oxopentanoic acid (ketoleucine). The iminoleucine may be released readily because of weak interactions in the binding site, in contrast to iminoarginine, converted to ketoleucine, which reacts with activated FAD to form the covalently linked acyl adduct. PMID:21707047

  20. 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.

  1. The Atomic-scale Growth of Large-Area Monolayer Graphene on Single-Crystal Copper Substrates

    OpenAIRE

    Zhao, L; Rim, K. T.; Zhou, H.; He, R.; Heinz, T. F.; Pinczuk, A.; Flynn, G. W.; Pasupathy, A. N.

    2010-01-01

    We study the growth and microscopic structure of large-area graphene monolayers, grown on copper single crystals by chemical vapor deposition (CVD) in ultra-high vacuum (UHV). Using atomic-resolution scanning tunneling microscopy (STM), we find that graphene grows primarily in registry with the underlying copper lattice for both Cu(111) and Cu(100). The graphene has a hexagonal superstructure on Cu(111) with a significant electronic component, whereas it has a linear superstructure on Cu(100)...

  2. From atoms to steps: The microscopic origins of crystal evolution

    Science.gov (United States)

    Patrone, Paul N.; Einstein, T. L.; Margetis, Dionisios

    2014-07-01

    The Burton-Cabrera-Frank (BCF) theory of crystal growth has been successful in describing a wide range of phenomena in surface physics. Typical crystal surfaces are slightly misoriented with respect to a facet plane; thus, the BCF theory views such systems as composed of staircase-like structures of steps separating terraces. Adsorbed atoms (adatoms), which are represented by a continuous density, diffuse on terraces, and steps move by absorbing or emitting these adatoms. Here we shed light on the microscopic origins of the BCF theory by deriving a simple, one-dimensional (1D) version of the theory from an atomistic, kinetic restricted solid-on-solid (KRSOS) model without external material deposition. We define the time-dependent adatom density and step position as appropriate ensemble averages in the KRSOS model, thereby exposing the non-equilibrium statistical mechanics origins of the BCF theory. Our analysis reveals that the BCF theory is valid in a low adatom-density regime, much in the same way that an ideal gas approximation applies to dilute gasses. We find conditions under which the surface remains in a low-density regime and discuss the microscopic origin of corrections to the BCF model.

  3. A High Resolution Monolithic Crystal, DOI, MR Compatible, PET Detector

    Energy Technology Data Exchange (ETDEWEB)

    Robert S Miyaoka

    2012-03-06

    The principle objective of this proposal is to develop a positron emission tomography (PET) detector with depth-of-interaction (DOI) positioning capability that will achieve state of the art spatial resolution and sensitivity performance for small animal PET imaging. When arranged in a ring or box detector geometry, the proposed detector module will support <1 mm3 image resolution and >15% absolute detection efficiency. The detector will also be compatible with operation in a MR scanner to support simultaneous multi-modality imaging. The detector design will utilize a thick, monolithic crystal scintillator readout by a two-dimensional array of silicon photomultiplier (SiPM) devices using a novel sensor on the entrance surface (SES) design. Our hypothesis is that our single-ended readout SES design will provide an effective DOI positioning performance equivalent to more expensive dual-ended readout techniques and at a significantly lower cost. Our monolithic crystal design will also lead to a significantly lower cost system. It is our goal to design a detector with state of the art performance but at a price point that is affordable so the technology can be disseminated to many laboratories. A second hypothesis is that using SiPM arrays, the detector will be able to operate in a MR scanner without any degradation in performance to support simultaneous PET/MR imaging. Having a co-registered MR image will assist in radiotracer localization and may also be used for partial volume corrections to improve radiotracer uptake quantitation. The far reaching goal of this research is to develop technology for medical research that will lead to improvements in human health care.

  4. 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.

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

    International Nuclear Information System (INIS)

    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

  6. High-resolution adaptive imaging of a single atom

    Science.gov (United States)

    Wong-Campos, J. D.; Johnson, K. G.; Neyenhuis, B.; Mizrahi, J.; Monroe, C.

    2016-09-01

    Optical imaging systems are used extensively in the life and physical sciences because of their ability to non-invasively capture details on the microscopic and nanoscopic scales. Such systems are often limited by source or detector noise, image distortions and human operator misjudgement. Here, we report a general, quantitative method to analyse and correct these errors. We use this method to identify and correct optical aberrations in an imaging system for single atoms and realize an atomic position sensitivity of ˜0.5 nm Hz-1/2 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 three-dimensional particle tracking, imaging of atoms in three-dimensional optical lattices or sensing forces at the yoctonewton (10-24 N) scale.

  7. Electron emission from a two-dimensional crystal with atomic thickness

    OpenAIRE

    Xianlong Wei; Qing Chen; Lianmao Peng

    2013-01-01

    Electron emission from a two-dimensional (2D) crystal with atomic thickness is theoretically studied with all the features associated with the low dimensionality and the atomic thickness being well considered. It is shown that, the atomic thickness results in quantum confinement of electrons in the crystal along thickness direction, and consequently two different ways of electron emission from it without and with quantum confinement of electrons normal to emission boundary: edge emission and ...

  8. Radiation damage free two-color X-ray ghost diffraction with atomic resolution

    CERN Document Server

    Li, Zheng; Chapman, Henry; Shih, Yanhua

    2015-01-01

    The X-ray free electron lasers (XFEL) can enable diffractive structural determination of protein crystals or single molecules that are too small and radiation-sensitive for conventional X-ray analysis. However the electronic form factor could have been 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, to minimize radiation damage effect is of major concern to ensure faithful reconstruction of the structure. Here we show that a radiation damage free diffraction can be achieved with an atomic spatial resolution, by using X-ray parametric down-conversion (PDC), and two-color biphoton ghost imaging. We illustrate that formation of the diffractive patterns satisfies a condition analogous to the Bragg equation, with a resolution that could be as fine as the lattice length scale of several Angstrom. Because the samples are illuminated by the optical photons of low energy, they can be free of radiation damage...

  9. Draft crystal structure of the vault shell at 9-A resolution.

    Directory of Open Access Journals (Sweden)

    Daniel H Anderson

    2007-11-01

    Full Text Available Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMVP vaults, diffracting to about 9-A resolution. The asymmetric unit contains a half vault of molecular mass 4.65 MDa. X-ray phasing was initiated by molecular replacement, using density from cryo-electron microscopy (cryo-EM. Phases were improved by density modification, including concentric 24- and 48-fold rotational symmetry averaging. From this, the continuous cryo-EM electron density separated into domain-like blocks. A draft atomic model of cpMVP was fit to this improved density from 15 domain models. Three domains were adapted from a nuclear magnetic resonance substructure. Nine domain models originated in ab initio tertiary structure prediction. Three C-terminal domains were built by fitting poly-alanine to the electron density. Locations of loops in this model provide sites to test vault functions and to exploit vaults as nanocapsules.

  10. Draft crystal structure of the vault shell at 9-A resolution.

    Science.gov (United States)

    Anderson, Daniel H; Kickhoefer, Valerie A; Sievers, Stuart A; Rome, Leonard H; Eisenberg, David

    2007-11-01

    Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMVP vaults), diffracting to about 9-A resolution. The asymmetric unit contains a half vault of molecular mass 4.65 MDa. X-ray phasing was initiated by molecular replacement, using density from cryo-electron microscopy (cryo-EM). Phases were improved by density modification, including concentric 24- and 48-fold rotational symmetry averaging. From this, the continuous cryo-EM electron density separated into domain-like blocks. A draft atomic model of cpMVP was fit to this improved density from 15 domain models. Three domains were adapted from a nuclear magnetic resonance substructure. Nine domain models originated in ab initio tertiary structure prediction. Three C-terminal domains were built by fitting poly-alanine to the electron density. Locations of loops in this model provide sites to test vault functions and to exploit vaults as nanocapsules.

  11. Atomic resolution of nitrogen-doped graphene on Cu foils

    Science.gov (United States)

    Wang, Chundong; Schouteden, Koen; Wu, Qi-Hui; Li, Zhe; Jiang, Jianjun; Van Haesendonck, Chris

    2016-09-01

    Atomic-level substitutional doping can significantly tune the electronic properties of graphene. Using low-temperature scanning tunneling microscopy and spectroscopy, the atomic-scale crystalline structure of graphene grown on polycrystalline Cu, the distribution of nitrogen dopants and their effect on the electronic properties of graphene were investigated. Both the graphene sheet growth and nitrogen doping were performed using microwave plasma-enhanced chemical vapor deposition. The results indicated that the nitrogen dopants preferentially sit at the grain boundaries of the graphene sheets and confirmed that plasma treatment is a potential method to incorporate foreign atoms into the graphene lattice to tailor the graphene’s electronic properties.

  12. Reflection high resolution analytical electron microscopy: a technique for studying crystal surfaces

    International Nuclear Information System (INIS)

    Reflection electron microscopy (REM), reflection high energy electron diffraction (RHEED), reflection electron energy-loss spectroscopy (REELS), and energy dispersion x-ray spectroscopy (EDX) have been comprehensively used as a technique, termed reflection high resolution analytical electron microscopy (RHRAEM), for studying the structures of the bulk crystal GaAs (110) surfaces by transmission electron microscopy (TEM). The simultaneous observations of surface topography imaging, the surface diffraction mechanism with RHEED, surface atomic inner-shell excitations with REELS, and surface chemical compositions with EDX provide a systematic description of the atomic structure and chemical structure of the surface. The surface channelling effect has been observed in GaAs (110) with REELS, which may provide a basis for localizing surface foreign atoms with ALCHEMI. The theoretically predicted surface-resonance wave has been observed directly in the RHEED pattern; the surface-captured Bragg reflection wave have been identified. It is shown that surface chemical compositions can be determined by analyzing the EDX spectra obtained in the REM case. Finally, the surface monolayer resonance characteristic of the RHRAEM has been confirmed by calculations with dynamical RHEED theory

  13. High resolution detectors based on continuous crystals and SiPMs for small animal PET

    Energy Technology Data Exchange (ETDEWEB)

    Cabello, J. [Instituto de Física Corpuscular, Universitat de València/CSIC, Valencia (Spain); Barrillon, P. [Laboratoire de L' Accélérateur Linéaire (LAL), Orsay (France); Barrio, J. [Instituto de Física Corpuscular, Universitat de València/CSIC, Valencia (Spain); Bisogni, M.G.; Del Guerra, A. [Dipartimento di Fisica “E. Fermi“, Università di Pisa and INFN Pisa, Pisa (Italy); Lacasta, C. [Instituto de Física Corpuscular, Universitat de València/CSIC, Valencia (Spain); Rafecas, M. [Instituto de Física Corpuscular, Universitat de València/CSIC, Valencia (Spain); Departamento de Física Atómica, Nuclear y Molecular, Universitat de València, Valencia (Spain); Saikouk, H. [Laboratoire de Physique Nucléaire, Faculté des Sciences, Université Mohammed V-Agdal, Rabat (Morocco); Solaz, C.; Solevi, P. [Instituto de Física Corpuscular, Universitat de València/CSIC, Valencia (Spain); La Taille, C. de [Laboratoire de L' Accélérateur Linéaire (LAL), Orsay (France); Llosá, G., E-mail: gabriela.llosa@ific.uv.es [Instituto de Física Corpuscular, Universitat de València/CSIC, Valencia (Spain)

    2013-08-01

    Sensitivity and spatial resolution are the two main factors to maximize in emission imaging. The improvement of one factor deteriorates the other with pixelated crystals. In this work we combine SiPM matrices with monolithic crystals, using an accurate γ-ray interaction position determination algorithm that provides depth of interaction. Continuous crystals provide higher sensitivity than pixelated crystals, while an accurate interaction position determination does not degrade the spatial resolution. Monte Carlo simulations and experimental data show good agreement both demonstrating sub-millimetre intrinsic spatial resolution. A system consisting in two rotating detectors in coincidence is currently under operation already producing tomographic images.

  14. Design of a high-resolution high-stability positioning mechanism for crystal optics

    Energy Technology Data Exchange (ETDEWEB)

    Shu, D.; Toellner, T. S.; Alp, E. E.

    1999-10-11

    The authors present a novel miniature multi-axis driving structure that will allow positioning of two crystals with better than 50-nrad angular resolution and nanometer linear driving sensitivity.The precision and stability of this structure allow the user to align or adjust an assembly of crystals to achieve the same performance as does a single channel-cut crystal, so they call it an artificial channel-cut crystal. In this paper, the particular designs and specifications, as well as the test results,for a two-axis driving structure for a high-energy-resolution artificial channel-cut crystal monochromator are presented

  15. Study of BCC and FCC crystal atomic structure under instant plastic deformation

    International Nuclear Information System (INIS)

    Evolution of atomic structure of BCC and FCC crystals under conditions of pulsed external loads and great plastic deformations on the basis of computerized experiments is studied. Deformation of crystals was carried out stage-by-stage up to 32%. The results of computerized experiments showed that by instantaneous external loads plastic deformation, depending on its stage, may proceed either on the account of partial dislocations motion, or on account of twinning , or by means of atomic planes turn and shift. Regularities of the system potential energy turn angle of atomic planes change in dependence on the value of the crystal plastic deformation are determined

  16. Atomic-resolution incoherent high-angle annular dark field STEM images of Si(011)

    Science.gov (United States)

    Watanabe, K.; Yamazaki, T.; Kikuchi, Y.; Kotaka, Y.; Kawasaki, M.; Hashimoto, I.; Shiojiri, M.

    2001-02-01

    Characteristic atomic-resolution incoherent high-angle annular dark field (HAADF) scanning transmission electron microscope (STEM) images of [011]-orientated Si have been experimentally obtained by a through-focal series. Artificial bright spots appear at positions where no atomic columns exist along the electron beam, in some experimental images. Image simulation, based on the Bloch wave description by the Bethe method, reproduces the through-focal experimental images. It is shown that atomic-resolution HAADF STEM images, which are greatly influenced by the Bloch wave field depending on the incident electron beam probe, cannot always be interpreted intuitively as the projected atomic images. It is also found that the atomic-resolution HAADF STEM images can be simply explained using the relations to the probe functions without the need for complex dynamical simulations.

  17. Crystal structure of lactoperoxidase at 2.4 A resolution.

    Science.gov (United States)

    Singh, Amit Kumar; Singh, Nagendra; Sharma, Sujata; Singh, S Baskar; Kaur, Punit; Bhushan, A; Srinivasan, A; Singh, Tej P

    2008-02-29

    Lactoperoxidase (LPO) is a member of the mammalian peroxidase superfamily. It catalyzes the oxidation of thiocyanate and halides. Freshly isolated and purified samples of caprine LPO were saturated with ammonium iodide and crystallized using 20% polyethylene glycol 3350 in a hanging drop vapor diffusion setup. The structure has been determined using X-ray crystallographic method and refined to R(cryst) and R(free) factors of 0.196 and 0.203, respectively. The structure determination revealed an unexpected phosphorylation of Ser198 in LPO, which is also confirmed by anti-phosphoserine antibody binding studies. The structure is also notable for observing densities for glycan chains at all the four potential glycosylation sites. Caprine LPO consists of a single polypeptide chain of 595 amino acid residues and folds into an oval-shaped structure. The structure contains 20 well-defined alpha-helices of varying lengths including a helix, H(2a), unique to LPO, and two short antiparallel beta-strands. The structure confirms that the heme group is covalently linked to the protein through two ester linkages involving carboxylic groups of Glu258 and Asp108 and modified methyl groups of pyrrole rings A and C, respectively. The heme moiety is slightly distorted from planarity, but pyrrole ring B is distorted considerably. However, an iron atom is displaced only by 0.1 A from the plane of the heme group toward the proximal site. The substrate diffusing channel in LPO is cylindrical in shape with a diameter of approximately 6 A. Two histidine residues and six buried water molecules are connected through a hydrogen-bonded chain from the distal heme cavity to the surface of protein molecule and seemingly form the basis of proton relay for catalytic action. Ten iodide ions have been observed in the structure. Out of these, only one iodide ion is located in the distal heme cavity and is hydrogen bonded to the water molecule W1. W1 is also hydrogen bonded to the heme iron as well as

  18. Atomic resolution imaging at 2.5 GHz using near-field microwave microscopy

    OpenAIRE

    Lee, Jonghee; Long, Christian J.; Yang, Haitao; Xiang, Xiao-Dong; Takeuchi, Ichiro

    2010-01-01

    Atomic resolution imaging is demonstrated using a hybrid scanning tunneling/near-field microwave microscope (microwave-STM). The microwave channels of the microscope correspond to the resonant frequency and quality factor of a coaxial microwave resonator, which is built in to the STM scan head and coupled to the probe tip. We find that when the tip-sample distance is within the tunneling regime, we obtain atomic resolution images using the microwave channels of the microwave-STM. We attribute...

  19. Fluorine in shark teeth: its direct atomic-resolution imaging and strengthening function.

    Science.gov (United States)

    Chen, Chunlin; Wang, Zhongchang; Saito, Mitsuhiro; Tohei, Tetsuya; Takano, Yoshiro; Ikuhara, Yuichi

    2014-02-01

    Atomic-resolution imaging of beam-sensitive biominerals is extremely challenging, owing to their fairly complex structures and the damage caused by electron irradiation. Herein, we overcome these difficulties by performing aberration-corrected electron microscopy with low-dose imaging techniques, and report the successful direct atomic-resolution imaging of every individual atomic column in the complex fluorapatite structure of shark tooth enameloid, which can be of paramount importance for teeth in general. We demonstrate that every individual atomic column in shark tooth enameloid can be spatially resolved, and has a complex fluorapatite structure. Furthermore, ab initio calculations show that fluorine atoms can be covalently bound to the surrounding calcium atoms, which improves understanding of their caries-reducing effects in shark teeth.

  20. Submolecular Resolution Imaging of molecules by Atomic Force Microscopy:The influence of the Electrostatic Force

    NARCIS (Netherlands)

    van der Lit, J.; Cicco, F.; Hapala, P.; Jelinek, P.; Swart, Ingmar

    2016-01-01

    The forces governing the contrast in submolecular resolution imaging of molecules with atomic force microscopy (AFM) have recently become a topic of intense debate. Here, we show that the electrostatic force is essential to understand the contrast in atomically resolved AFM images of polar molecules

  1. Crystal growth rates and optical resolution of DL-methionine hydrochloride by preferential crystallization from aqueous solution

    Science.gov (United States)

    Srimahaprom, Watcharakarn; Flood, Adrian E.

    2013-01-01

    Optical resolution of DL-methionine hydrochloride (DL-met·HCl) by preferential crystallization was studied for the purification of L-met·HCl (the desired enantiomer) from supersaturated solutions of DL-met·HCl. The nucleation thresholds (NT) of DL-met·HCl affect the maximum resolution time suitable for preferential crystallization and also the percentage purity of the product crystals. Crystal growth rates of L-met·HCl single crystals both in supersaturated solutions of DL-met·HCl and in supersaturated solutions of pure L-met·HCl were measured in order to model the preferential crystallization more effectively. Results showed that the growth rate depends strongly on the relative supersaturation (especially from pure L-met·HCl solutions), that there is a wide crystal growth rate distribution in growth from both types of solution, and that the growth is faster from pure L-met·HCl solutions, as expected. A batch crystallizer seeded with L-met·HCl crystals was used to study the preferential crystallization, and to study the behavior of purity decrease of the product crystals during the crystallization process. The purity of the L-met·HCl product decreased to the equilibrium value over time, with almost no plateau at 100% purity (as is hoped for in preferential crystallizations). This is explainable by the very short induction times for nucleation in these solutions, and also that the L-met·HCl seed crystals may act as a template for the nucleation of the counter-enantiomer.

  2. Ultrafast Electron Diffraction with Spatiotemporal Resolution of Atomic Motion

    Institute of Scientific and Technical Information of China (English)

    LIANG Wen-Xi; ZHU Peng-Fei; WANG Xuan; NIE Shou-Hua; ZHANG Zhong-Chao; Clinite Rick; CAO Jian-Ming; SHENG Zheng-Ming; ZHANG Jie

    2009-01-01

    Ultrafast electron diffraction (UED) is a rapidly advancing technique capable of recording the atomic-detail structural dynamics in real time. We report the establishment of the first UED system in China. Employing this UED apparatus, both the coherent and the concurrent thermal lattice motions in an aluminium thin-film, trigged by ultrafast laser heating, have been observed. These results demonstrate its ability to directly measure a sub-milli-angstrom lattice spacing change on a sub-picosecond time scale.

  3. 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.

  4. Rydberg atoms inside hollow-core photonic crystal fibres

    Science.gov (United States)

    Löw, Robert; Epple, Georg; Kleinbach, Kathrin; Euser, Tijmen; Joly, Nicolas; Pfau, Tilman; Russell, Philip

    2014-05-01

    Rydberg atoms have peculiar properties as enhanced sensitivities to AC/DC electric fields or exaggerated strong interactions between them, leading to optical non-linearities on the single photon level. These properties are mostly studied with spectroscopic methods often limited by the free space diffraction limit. This can be avoided by confining Rydberg atoms inside hollow core fibres offering a perfect match of guided light modes with the atomic gas in terms of atom-light coupling. Additionally we choose Kagome type fibres due to their extremely thin structures, promising a reduced atom wall coupling. With coherent three photon spectroscopy we can show that Rydberg atoms can be excited within these fibres up to states of n = 46 without severe perturbations by the fibre environment.

  5. Atomic torsional modal analysis for high-resolution proteins

    Science.gov (United States)

    Tirion, Monique M.; ben-Avraham, Daniel

    2015-03-01

    We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier one-parameter formulation [M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996), 10.1103/PhysRevLett.77.1905] that characterized the slow modes associated with protein data bank structures. Here we develop that empirical potential function that is minimized at the outset to include two features essential to reproduce the eigenspectra and associated density of states in the 0 to 300 cm-1 frequency range, not merely the slow modes. First, introduction of preferred dihedral-angle configurations via use of torsional stiffness constants eliminates anomalous dispersion characteristics due to insufficiently bound surface side chains and helps fix the spectrum thin tail frequencies (100-300 cm-1 ). Second, we take into account the atomic identities and the distance of separation of all pairwise interactions, improving the spectrum distribution in the 20 to 300 cm-1 range. With these modifications, not only does the spectrum reproduce that of full atomic potentials, but we obtain stable reliable eigenmodes for the slow modes and over a wide range of frequencies.

  6. Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities.

    Science.gov (United States)

    Neumann, Piotr; Tittmann, Kai

    2014-12-01

    Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing.

  7. 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...

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

    NARCIS (Netherlands)

    van Oosten, D.; 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 shi

  9. Crystallization, phase evolution and corrosion of Fe-based metallic glasses: An atomic-scale structural and chemical characterization study

    International Nuclear Information System (INIS)

    Understanding phase changes, including their formation and evolution, is critical for the performance of functional as well as structural materials. We analyze in detail microstructural and chemical transformations of the amorphous steel Fe50Cr15Mo14C15B6 during isothermal treatments at temperatures ranging from 550 to 800 °C. By combining high-resolution transmission electron microscopy and Rietveld analyses of X-ray diffraction patterns together with the local chemical data obtained by atom probe tomography, this research provides relevant information at the atomic scale about the mechanisms of crystallization and the subsequent phases evolution. During the initial stages of crystallization a stable (Fe,Cr)23(C,B)6 precipitates as well as two metastable intermediates of M3(C,B) and the intermetallic χ-phase. When full crystallization is reached, only a percolated nano-scale Cr-rich (Fe,Cr)23(C,B)6 and Mo-rich η-Fe3Mo3C structure is detected, with no evidence to suggest that other phases appear at any subsequent time. Finally, the corrosion behavior of the developed phases is discussed from considerations of the obtained atomic information

  10. Spontaneous Emission from a Driven Atom Embedded in a Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    XIE Shuang-Yuan; YANG Ya-Ping; CHENG Hong; ZHU Shi-Yao; WU Xiang

    2000-01-01

    The properties of the spontaneous emission from a three-level atom with an external driving field in a photonic crystal are studied. The population in the two upper levels displays complete decay or oscillatory behavior,depending on the initial atomic state and the relative position of the two upper levels from the forbidden gap.The intensity and the phase of the external field can also affect spontaneous emission from the atom.

  11. ATMAN: Atomic Torsional Modal Analysis for high-resolution proteins

    CERN Document Server

    Tirion, Monique M

    2014-01-01

    We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation \\cite{tirion96} that characterized the slow modes associated with protein data bank structures. Here we develop that empirical potential function which is minimized at the outset to include two features essential to reproduce the eigenspectra and associated density of states over all frequencies, not merely the slow ones. First, introduction of preferred dihedral-angle configurations via use of torsional stiffness constants eliminates anomalous dispersion characteristics due to insufficiently bound surface sidechains. Second, we take into account the atomic identities and the distance of separation of all pairwise interactions. With these modifications we obtain stable, reliable eigenmodes over a wide range of frequencies.

  12. Mechanisms of protein and virus crystal growth: An atomic force microscopy study of canavalin and STMV crystallization

    Energy Technology Data Exchange (ETDEWEB)

    Land, T.A.; De Yoreo, J.J. [Lawrence Livermore National Lab., CA (United States). Dept. of Chemistry and Materials Science; Malkin, A.J.; Kutznesov, Yu.G.; McPherson, A. [Univ. of California, Riverside, CA (United States). Dept. of Biochemistry

    1996-05-01

    The evolution of surface morphology and step dynamics during growth of rhombohedral crystals of the protein canavalin and crystals of the cubic satellite tobacco mosaic virus (STMV) have been investigated for the first time by in situ atomic force microscopy. These two crystals were observed to grow by very different mechanisms. Growth of canavalin occurs on complex vicinal hillocks formed by multiple, independently acting screw dislocations. Small clusters were observed on the terraces. STMV on the other hand, was observed to grow by 2D nucleation of islands. No dislocations were found on the crystal. The results are used to determine the growth mechanisms and estimate the fundamental materials parameters. The images also illustrate the important mechanism of defect incorporation and provide insight to the processes that limit the growth rate and uniformity of these crystals.

  13. Observation of antisite domain boundaries in Cu2ZnSnS4 by atomic-resolution transmission electron microscopy

    Science.gov (United States)

    Kattan, N. A.; Griffiths, I. J.; Cherns, D.; Fermín, D. J.

    2016-07-01

    Atomic resolution transmission electron microscopy has been used to examine antisite defects in Cu2ZnSnS4 (CZTS) kesterite crystals grown by a hot injection method. High angle annular dark field (HAADF) imaging at sub-0.1 nm resolution, and lower magnification dark field imaging using reflections sensitive to cation ordering, are used to reveal antisite domain boundaries (ADBs). These boundaries, typically 5-20 nm apart, and extending distances of 100 nm or more into the crystals, lie on a variety of planes and have displacements of the type ½[110] or ¼[201], which translate Sn, Cu and Zn cations into antisite positions. It is shown that some ADBs describe a change in the local stoichiometry by removing planes of S and either Cu or Zn atoms, implying that these boundaries can be electrically charged. The observations also showed a marked increase in cation disorder in regions within 1-2 nm of the grain surfaces suggesting that growth of the ordered crystal takes place at the interface with a disordered shell. It is estimated that the ADBs contribute on average ~0.1 antisite defect pairs per unit cell. Although this is up to an order of magnitude less than the highest antisite defect densities reported, the presence of high densities of ADBs that may be charged suggests these defects may have a significant influence on the efficiency of CZTS solar cells.Atomic resolution transmission electron microscopy has been used to examine antisite defects in Cu2ZnSnS4 (CZTS) kesterite crystals grown by a hot injection method. High angle annular dark field (HAADF) imaging at sub-0.1 nm resolution, and lower magnification dark field imaging using reflections sensitive to cation ordering, are used to reveal antisite domain boundaries (ADBs). These boundaries, typically 5-20 nm apart, and extending distances of 100 nm or more into the crystals, lie on a variety of planes and have displacements of the type ½[110] or ¼[201], which translate Sn, Cu and Zn cations into antisite

  14. Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

    Science.gov (United States)

    Teschke, Omar; Soares, David Mendez

    2016-03-29

    Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

  15. Chemically modified STM tips for atomic-resolution imaging of ultrathin NaCI films

    Institute of Scientific and Technical Information of China (English)

    Zhe Li[1; Koen Schouteden[1; Violeta lancu[1; Ewald Janssens[1; Peter Lievens[1; Chris Van Haesendonck[1; Jorge I. Cerda[2

    2015-01-01

    Cl-functionalized scanning tunneling microscopy (STM) tips are fabricated by modifying a tungsten STM tip in situ on islands of ultrathin NaCI(100) films on Au(111) surfaces. The functionalized tips are used to achieve clear atomic- resolution imaging of NaCI(100) islands. In comparison with bare metal tips, the chemically modified tips yield drastically enhanced spatial resolution as well as contrast reversal in STM topographs, implying that Na atoms, rather than C1 atoms, are imaged as protrusions. STM simulations based on a Green's function formalism reveal that the experimentally observed contrast reversal in the STM topographs is due to the highly localized character of the Cl-pz states at the tip apex. An additional remarkable characteristic of the modified tips is that in dI/dV maps, a Na atom appears as a ring with a diameter that depends crucially on the tip-sample distance.

  16. Traceable atomic force microscopy of high-quality solvent-free crystals of [6,6]-phenyl-C{sub 61}-butyric acid methyl ester

    Energy Technology Data Exchange (ETDEWEB)

    Lazzerini, Giovanni Mattia; Yacoot, Andrew [National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Paternò, Giuseppe Maria; Tregnago, Giulia; Cacialli, Franco [Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT (United Kingdom); Treat, Neil; Stingelin, Natalie [Department of Materials Science, Imperial College London, London SW7 2AZ (United Kingdom)

    2016-02-01

    We report high-resolution, traceable atomic force microscopy measurements of high-quality, solvent-free single crystals of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). These were grown by drop-casting PCBM solutions onto the spectrosil substrates and by removing the residual solvent in a vacuum. A home-built atomic force microscope featuring a plane mirror differential optical interferometer, fiber-fed from a frequency-stabilized laser (emitting at 632.8 nm), was used to measure the crystals' height. The optical interferometer together with the stabilized laser provides traceability (via the laser wavelength) of the vertical measurements made with the atomic force microscope. We find that the crystals can conform to the surface topography, thanks to their height being significantly smaller compared to their lateral dimensions (namely, heights between about 50 nm and 140 nm, for the crystals analysed, vs. several tens of microns lateral dimensions). The vast majority of the crystals are flat, but an isolated, non-flat crystal provides insights into the growth mechanism and allows identification of “molecular terraces” whose height corresponds to one of the lattice constants of the single PCBM crystal (1.4 nm) as measured with X-ray diffraction.

  17. Traceable atomic force microscopy of high-quality solvent-free crystals of [6,6]-phenyl-C61-butyric acid methyl ester

    Science.gov (United States)

    Lazzerini, Giovanni Mattia; Paternò, Giuseppe Maria; Tregnago, Giulia; Treat, Neil; Stingelin, Natalie; Yacoot, Andrew; Cacialli, Franco

    2016-02-01

    We report high-resolution, traceable atomic force microscopy measurements of high-quality, solvent-free single crystals of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). These were grown by drop-casting PCBM solutions onto the spectrosil substrates and by removing the residual solvent in a vacuum. A home-built atomic force microscope featuring a plane mirror differential optical interferometer, fiber-fed from a frequency-stabilized laser (emitting at 632.8 nm), was used to measure the crystals' height. The optical interferometer together with the stabilized laser provides traceability (via the laser wavelength) of the vertical measurements made with the atomic force microscope. We find that the crystals can conform to the surface topography, thanks to their height being significantly smaller compared to their lateral dimensions (namely, heights between about 50 nm and 140 nm, for the crystals analysed, vs. several tens of microns lateral dimensions). The vast majority of the crystals are flat, but an isolated, non-flat crystal provides insights into the growth mechanism and allows identification of "molecular terraces" whose height corresponds to one of the lattice constants of the single PCBM crystal (1.4 nm) as measured with X-ray diffraction.

  18. Submolecular Resolution Imaging of Molecules by Atomic Force Microscopy: The Influence of the Electrostatic Force

    Science.gov (United States)

    van der Lit, Joost; Di Cicco, Francesca; Hapala, Prokop; Jelinek, Pavel; Swart, Ingmar

    2016-03-01

    The forces governing the contrast in submolecular resolution imaging of molecules with atomic force microscopy (AFM) have recently become a topic of intense debate. Here, we show that the electrostatic force is essential to understand the contrast in atomically resolved AFM images of polar molecules. Specifically, we image strongly polarized molecules with negatively and positively charged tips. A contrast inversion is observed above the polar groups. By taking into account the electrostatic forces between tip and molecule, the observed contrast differences can be reproduced using a molecular mechanics model. In addition, we analyze the height dependence of the various force components contributing to the high-resolution AFM contrast.

  19. Transmission electron microscopy studies of atomic ordering and crystal size determination on the nanometer scale

    International Nuclear Information System (INIS)

    Atomic ordering and site determination have been studied em areas of progressively smaller scale. In paper I we studied how AI and Si arc ordered in a π-AlFeMgSi matrix. Single crystal investigations were carried out using CBED for site-symmetry and refinement of atomic positions. Electron channelling was used to determine how Al and Si were arranged on atomic sites within the crystal. In paper III and IV, we studied MnO2 crystallites. The crystallites were of' nanometer size and therefore, in contrast to paper I and II, single crystal analysis could not be carried out. Instead, SAD was used to determine the arrangement of Mn atoms on the octahedral sites between oxygen hcp layers and also used to obtain information on how crystal and unit cell sizes vary within the film. The small size of nanocrystals generally limits the use of single crystal analysis techniques. However, electron channelling (or ALCHEMI) can be used to study the site arrangement of atoms in nanometer sized thin films if the film and substrate are coherent and if studied in plane view. This is explored m paper V. (Author)

  20. Hardness of materials: studies at levels from atoms to crystals

    Institute of Scientific and Technical Information of China (English)

    LI KeYan; XUE DongFeng

    2009-01-01

    Based on the electron-holding energy per unit volume, we extend the concept of hardness to atomic stiffness, ionic stiffness and bond hardness, investigating the nature of material hardness at these three levels. We find that the stiffness of isolated atoms or ions has no direct connection with the hardness of materials, whereas material hardness is directly related to bond hardness, which is es-sentially determined by the electron-holding energy of its constituent chemical bonds per unit volume. We establish a model for identifying the hardness of materials on the basis of bond hardness. This work offers a deeper understanding of the nature of material hardness at the atomic level, and provides a practical guide in the search for new superhard materials.

  1. Optimal experimental design for nano-particle atom-counting from high-resolution STEM images

    Energy Technology Data Exchange (ETDEWEB)

    De Backer, A.; De wael, A.; Gonnissen, J.; Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be

    2015-04-15

    In the present paper, the principles of detection theory are used to quantify the probability of error for atom-counting from high resolution scanning transmission electron microscopy (HR STEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom-counting using the expression for the probability of error. We show that for very thin objects LAADF is optimal and that for thicker objects the optimal inner detector angle increases.

  2. 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.

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

    International Nuclear Information System (INIS)

    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. (paper)

  4. 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.

  5. The development of high-resolution spectroscopic methods and their use in atomic structure studies

    International Nuclear Information System (INIS)

    This thesis discusses work performed during the last nine years in the field of atomic spectroscopy. Several high-resolution techniques, ranging from quantum beats, level crossings, rf-laser double resonances to nonlinear field atom interactions, have been employed. In particular, these methods have been adopted and developed to deal with fast accelerated atomic or ionic beams, allowing studies of problems in atomic-structure theory. Fine- and hyperfine-structure determinations in the He I and Li I isoelectronic sequences, in 51V I, and in 235U I, II have permitted a detailed comparison with ab initio calculations, demonstrating the change in problems when going towards heavier elements or higher ionization stage. The last part of the thesis is concerned with the fundamental question of obtaining very high optical resolution in the interaction between a fast accelerated atom or ion beam and a laser field, this problem being the core in the continuing development of atomic spectroscopy necessary to challenge the more precise and sophisticated theories advanced. (Auth.)

  6. Study of atomic jumps in quasi-crystals

    International Nuclear Information System (INIS)

    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)

  7. Photoluminescence and photoelectric properties of CdTe crystals doped with Er atoms

    International Nuclear Information System (INIS)

    The low-temperature photoluminescence (PL) and photodiffusion spectra of CdTe crystals doped with Er atoms were measured. The most intensive and narrow line in the PL spectrum is A°X-line which is caused by the emission of an exciton bound to a neutral center associated with Na residual impurity. The presence of Na atoms in CdTe:Er crystals is supported by observation of recombination between electrons of the conduction band and acceptor levels associated with these impurity atoms. Other PL bands caused by optical transition with participation of donor–acceptor pairs (DAP) are also observed. It is shown that in this case P acceptor centers and donors caused by the presence of Al atoms situated in the Cd sites take part in the recombination process. The PL bands associated with recombination of DAP which include the complex acceptor centers do not appear in the PL spectra. Our findings indicate a high optical quality of the crystals. Thus, they provide a way to improve structural properties of CdTe crystals using the ability of rare earth (RE) elements to react with residual impurities in semiconductor materials. This is a result of the manifestation of so-called “cleaning” process of the semiconductor materials by their doping with RE elements. - Highlights: • The photoluminescence (PL) and photoelectric properties of CdTe:Er crystals were studied. • The PL exciton (A°X)-line and exciton reflection band is very narrow (about 1 meV). • The broad PL bands are due to the recombination of DAPs and (e,A) transitions. • The nature and energy levels of donor and acceptor levels in CdTe:Er were found. • It was shown that Na and P atoms are the residual impurities in the investigated crystals. • The results provide a way to improve the optical properties of CdTe by RE doping

  8. High Resolution Imaging by Atomic Force Microscopy: Contribution of short-range force to the imaging

    Science.gov (United States)

    Eguchi, Toyoaki; Kotone, Akiyama; Masanori, Ono; Toshio, Sakurai; Yukio, Hasegawa

    2003-03-01

    Recent developments in force detection technique have made us possible to obtain atomically resolved images of the Si(111)-(7x7) surface by AFM. Compared with STM, however, its spatial resolution remains limited. In this presentation, we demonstrate that with careful pretreatment and appropriate experimental parameters, the structure of the rest-atom layer can be imaged using AFM by detecting the short-range force due to the single chemical bonding. The detection of the short-range force is verified by analysis of the frequency-shift versus distance curve (force curve). This unprecedented high resolution is achieved by reducing background forces due to the long-range interactions with small oscillation amplitude of the cantilever and an atomically sharp tip. The high temperature annealing of the cantilever assists in obtaining a bare silicon tip on the cantilever without unwanted tip-blunting, and improving the Q-factor of the cantilever. This study implies that characterization of the AFM tip in nanometer scale, not only on the apex atoms but also its shape near the apex, is important and critical for AFM high resolution imaging.

  9. Atomic Resolution Transmission Electron Microscopy of Defects in Hexagonal Boron Nitride and Graphene

    Science.gov (United States)

    Gibb, Ashley; Alem, Nasim; Song, Chengyu; Ciston, Jim; Zettl, Alex

    2014-03-01

    Monolayer sheets of sp2-bonded materials such as graphene and hexagonal boron nitride (h-BN) have been studied extensively due to their properties including high mechanical strength, thermal conductivity, stability, interesting electronic properties, and potential for integration into novel devices. Understanding the atomic scale structure of defects in these materials is important because defects can significantly affect the physical properties in these materials. In particular, understanding the dynamics of these defects explains much about the material's stability. We have synthesized h-BN and graphene using low pressure chemical vapor deposition and imaged defects using atomic resolution aberration corrected transmission electron microscopy.

  10. 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.

  11. Atomically resolved images of I(h) ice single crystals in the solid phase.

    Science.gov (United States)

    Kobayashi, Keita; Koshino, Masanori; Suenaga, Kazu

    2011-05-20

    The morphology and crystal structure of nanoparticles of ice were examined by high-resolution transmission electron microscopy. Two different crystal structures were found and unambiguously assigned to hexagonal (I(h)) and cubic (I(c)) ice crystals. Direct observation of oxygen columns clearly revealed the hexagonal packing of water molecules. Electron energy-loss spectroscopy was used to monitor the electronic excitation in ice, suggesting possible dissociation of water molecules. Dynamic process of phase transition between I(h) and I(c) phases of individual ice nanoparticles under electron beam irradiation was also monitored by in situ transmission electron diffractometry.

  12. Scattering of atomic and molecular ions from single crystal surfaces of Cu, Ag and Fe

    International Nuclear Information System (INIS)

    This thesis deals with analysis of crystal surfaces of Cu, Ag and Fe with Low Energy Ion scattering Spectroscopy (LEIS). Different atomic and molecular ions with fixed energies below 7 keV are scattered by a metal single crystal (with adsorbates). The energy and direction of the scattered particles are analysed for different selected charge states. In that way information can be obtained concerning the composition and atomic and electronic structure of the single crystal surface. Energy spectra contain information on the composition of the surface, while structural atomic information is obtained by direction measurements (photograms). In Ch.1 a description is given of the experimental equipment, in Ch.2 a characterization of the LEIS method. Ch.3 deals with the neutralization of keV-ions in surface scattering. Two different ways of data interpretation are presented. First a model is treated in which the observed directional dependence of neutralization action of the first atom layer of the surface is presented by a laterally varying thickness of the neutralizing layer. Secondly it is shown that the data can be reproduced by a more realistic, physical model based on atomic transition matrix elements. In Ch.4 the low energy hydrogen scattering is described. The study of the dissociation of H2+ at an Ag surface r0230ted in a model based on electronic dissociation, initialized by electron capture into a repulsive (molecular) state. In Ch.5 finally the method is applied to the investigation of the surface structure of oxidized Fe. (Auth.)

  13. 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.

  14. LiF crystals as high spatial resolution neutron imaging detectors

    Energy Technology Data Exchange (ETDEWEB)

    Matsubayashi, M., E-mail: matsubayashi.masahito@jaea.go.jp [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Shirane 2-4, Shirakata, Tokai, Ibaraki 319-1195 (Japan); Faenov, A.; Pikuz, T. [Joint Institute for High Temperatures of Russian Academy of Sciences, Izhorskaja Street 13/19, Moscow (Russian Federation); Fukuda, Y. [Kansai Photon Science Institute, Japan Atomic Energy Agency, Kizugawa, Kyoto 619-0215 (Japan); Kato, Y. [The Graduate School for the Creation of New Photonics Industries, Hamamatsu, Shizuoka 431-1202 (Japan); Yasuda, R.; Iikura, H.; Nojima, T.; Sakai, T. [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Shirane 2-4, Shirakata, Tokai, Ibaraki 319-1195 (Japan)

    2011-09-21

    Neutron imaging by color center formation in LiF crystals was applied to a sensitivity indicator (SI) as a standard samples for neutron radiography. The SI was exposed to a 5 mm pinhole-collimated thermal neutron beam with an LiF crystal and a neutron imaging plate (NIP) for 120 min in the JRR-3M thermal neutron radiography facility. The image in the LiF crystal was read out using a laser confocal microscope. All gaps were clearly observed in images for both the LiF crystal and the NIP. The experimental results showed that LiF crystals have excellent characteristics as neutron imaging detectors in areas such as high spatial resolution.

  15. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis

    Science.gov (United States)

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-01-01

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts. PMID:27650485

  16. Strain-engineered diffusive atomic switching in two-dimensional crystals

    Science.gov (United States)

    Kalikka, Janne; Zhou, Xilin; Dilcher, Eric; Wall, Simon; Li, Ju; Simpson, Robert E.

    2016-06-01

    Strain engineering is an emerging route for tuning the bandgap, carrier mobility, chemical reactivity and diffusivity of materials. Here we show how strain can be used to control atomic diffusion in van der Waals heterostructures of two-dimensional (2D) crystals. We use strain to increase the diffusivity of Ge and Te atoms that are confined to 5 Å thick 2D planes within an Sb2Te3-GeTe van der Waals superlattice. The number of quintuple Sb2Te3 2D crystal layers dictates the strain in the GeTe layers and consequently its diffusive atomic disordering. By identifying four critical rules for the superlattice configuration we lay the foundation for a generalizable approach to the design of switchable van der Waals heterostructures. As Sb2Te3-GeTe is a topological insulator, we envision these rules enabling methods to control spin and topological properties of materials in reversible and energy efficient ways.

  17. Rydberg atoms in hollow-core photonic crystal fibres

    Science.gov (United States)

    Epple, G.; Kleinbach, K. S.; Euser, T. G.; Joly, N. Y.; Pfau, T.; Russell, P. St. J.; Löw, R.

    2014-06-01

    The exceptionally large polarizability of highly excited Rydberg atoms—six orders of magnitude higher than ground-state atoms—makes them of great interest in fields such as quantum optics, quantum computing, quantum simulation and metrology. However, if they are to be used routinely in applications, a major requirement is their integration into technically feasible, miniaturized devices. Here we show that a Rydberg medium based on room temperature caesium vapour can be confined in broadband-guiding kagome-style hollow-core photonic crystal fibres. Three-photon spectroscopy performed on a caesium-filled fibre detects Rydberg states up to a principal quantum number of n=40. Besides small energy-level shifts we observe narrow lines confirming the coherence of the Rydberg excitation. Using different Rydberg states and core diameters we study the influence of confinement within the fibre core after different exposure times. Understanding these effects is essential for the successful future development of novel applications based on integrated room temperature Rydberg systems.

  18. 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...

  19. Torque and atomic forces for Cartesian tensor atomic multipoles with an application to crystal unit cell optimization.

    Science.gov (United States)

    Elking, Dennis M

    2016-08-15

    New equations for torque and atomic force are derived for use in flexible molecule force fields with atomic multipoles. The expressions are based on Cartesian tensors with arbitrary multipole rank. The standard method for rotating Cartesian tensor multipoles and calculating torque is to first represent the tensor with n indexes and 3(n) redundant components. In this work, new expressions for directly rotating the unique (n + 1)(n + 2)/2 Cartesian tensor multipole components Θpqr are given by introducing Cartesian tensor rotation matrix elements X(R). A polynomial expression and a recursion relation for X(R) are derived. For comparison, the analogous rotation matrix for spherical tensor multipoles are the Wigner functions D(R). The expressions for X(R) are used to derive simple equations for torque and atomic force. The torque and atomic force equations are applied to the geometry optimization of small molecule crystal unit cells. In addition, a discussion of computational efficiency as a function of increasing multipole rank is given for Cartesian tensors. © 2016 Wiley Periodicals, Inc. PMID:27349179

  20. State of the art in atomic resolution off-axis electron holography

    Energy Technology Data Exchange (ETDEWEB)

    Linck, Martin, E-mail: mlinck@lbl.gov [Triebenberg Laboratory, Institute of Structure Physics, Technische Universitaet Dresden, Zum Triebenberg 50, 01328 Dresden (Germany); Freitag, Bert; Kujawa, Stephan [FEI Company, Eindhoven, Building AAE, Achtseweg Noord 5, P.O. Box 80066, 5600 KA Eindhoven (Netherlands); Lehmann, Michael; Niermann, Tore [Institut fuer Optik und Atomare Physik, Technische Universitaet Berlin, Strasse des 17. Juni 135, 10623 Berlin (Germany)

    2012-05-15

    As proposed by Hannes Lichte, to resolve structure-property relations not only the question 'Which atom is where?' but also the question 'Which fields are around?' has to be answered. High-resolution off-axis electron holography opens up an access to these key questions in that it allows accessing the complete exit-wave of the object provided within the information limit of the microscope, i.e. amplitude and phase including atomic details such as position and species, and moreover, information about large area electric potentials and magnetic fields, which a conventional transmission electron microscope is blind for-also when using a Cs-corrector. For an excellent object exit-wave reconstruction, special care has to be taken on the hologram quality, i.e. interference fringe contrast and electron dose. Severe restrictions are given to signal resolution by the limited brightness of the electron source. Utilizing a new high-brightness Schottky field electron emitter in a state-of-the-art transmission electron microscope operated at 300 kV, the phase signal resolution at atomic resolution can significantly be enhanced. An improvement by at least a factor of 2.88 compared to the most recently reported single hologram at atomic resolution is found. To proof the applicability of this setup to real materials science problems, a grain boundary of gold has been investigated holographically. -- Highlights: Black-Right-Pointing-Pointer Impact of the brightness on the reconstructed signal in electron holography. Black-Right-Pointing-Pointer Factor 2.8 gain in signal quality by setup with a high brightness electron gun. Black-Right-Pointing-Pointer Investigation of a grain boundary in gold with a state-of-the-art holography setup. Black-Right-Pointing-Pointer A-posteriori aberration fine-tuning for true one Angstrom resolution in the object wave. Black-Right-Pointing-Pointer Mistilt analysis on the atomic scale by numerical wave optics.

  1. Atomic force microscopy: a powerful tool for high-resolution imaging of spermatozoa

    OpenAIRE

    Sen Prasenjit; Chaudhury Koel; Kumar Sunil; Guha Sujoy K

    2005-01-01

    Abstract Atomic force microscopy (AFM) has emerged as the only technique capable of real-time imaging of the surface of a living cell at nano-resolution. Since AFM provides the advantage of directly observing living biological cells in their native environment, this technique has found many applications in pharmacology, biotechnology, microbiology, structural and molecular biology, genetics and other biology-related fields. AFM has also proved to be a valuable tool for reproductive biologists...

  2. 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.

  3. 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.

  4. Lattice site specific diffusion properties for substitutional and interstitial impurity atoms in ZnO crystals

    Science.gov (United States)

    Yaqoob, Faisal; Huang, Mengbing

    2016-09-01

    Fundamental understanding of impurity diffusion in crystals remains a challenge due to lack of experimental capabilities for measuring the diffusion properties of atoms according to their substitutional and interstitial lattice locations. With examples of indium and silver in ZnO crystals, we demonstrate an ion beam based method to experimentally determine the energetics and entropy changes in diffusion of substitutional and interstitial impurity atoms. While the interstitial Ag diffuses much faster than the substitutional Ag, as normally expected, the interstitial In migrates slower than the substitutional In, which is attributed to a large negative entropy change (˜-10 kB), possibly caused by the large atomic size of In. The activation energy and the diffusivity pre-exponential factor for the interstitial Ag are significantly enhanced, being more than a factor of two and ˜13 orders of magnitude, respectively, relative to the case for the interstitial In. This implies two different diffusion mechanisms between these two types of interstitial atoms in ZnO crystals: the direct interstitial diffusion mechanism for the interstitial In and the kick-out diffusion mechanism for the interstitial Ag. In addition, the activation energies and the diffusivity prefactors follow the Meyer-Neldel relationship with an excitation energy of ˜92 meV.

  5. Cryogenic microcalorimeter energy resolution measurements for multi-keV atoms and molecules

    International Nuclear Information System (INIS)

    We have experimentally investigated the kinetic energy resolution of an ∝ 10 mK magnetic microcalorimeter (MMC) detector for 12-150 keV atomic and molecular ion beams. The ion masses were varied from 1 amu (H+) to 58 amu (C3H6O+). The resulting FWHM energy resolutions were atomic ions and resolutions were similar for the neutral particles of the corresponding ions. The high resolving power in energy, the charge independence, and the optional position sensitivity all demonstrate the expected versatility of the MMC detectors for use in various mass spectrometry techniques. As a next step we implement the MMC detector for mass and position resolved fragment counting in the Cryogenic Storage Ring (CSR) at the Max Planck Institute for Nuclear Physics in Heidelberg. The storage energies of ∝ 300 keV will allow 1 amu mass resolution for stored ions of up to ∝ 150 amu (assuming a separation of 2 FWHMs between peaks).

  6. Cryogenic microcalorimeter energy resolution measurements for multi-keV atoms and molecules

    Energy Technology Data Exchange (ETDEWEB)

    Novotny, Oldrich; Savin, Daniel W. [Columbia Astrophysics Laboratory, New York (United States); Allgeier, Steffen; Gamer, Lisa; Hengstler, Daniel; Kempf, Sebastian; Pabinger, Andreas; Pies, Christian; Enss, Christian; Fleischmann, Andreas [Kirchhoff Institute for Physics, Heidelberg (Germany); Krantz, Claude; Wolf, Andreas [Max Planck Institute for Nuclear Physics, Heidelberg (Germany); Schwalm, Dirk [Max Planck Institute for Nuclear Physics, Heidelberg (Germany); Weizmann Institute of Science, Rehovot (Israel)

    2014-07-01

    We have experimentally investigated the kinetic energy resolution of an ∝ 10 mK magnetic microcalorimeter (MMC) detector for 12-150 keV atomic and molecular ion beams. The ion masses were varied from 1 amu (H{sup +}) to 58 amu (C{sub 3}H{sub 6}O{sup +}). The resulting FWHM energy resolutions were atomic ions and resolutions were similar for the neutral particles of the corresponding ions. The high resolving power in energy, the charge independence, and the optional position sensitivity all demonstrate the expected versatility of the MMC detectors for use in various mass spectrometry techniques. As a next step we implement the MMC detector for mass and position resolved fragment counting in the Cryogenic Storage Ring (CSR) at the Max Planck Institute for Nuclear Physics in Heidelberg. The storage energies of ∝ 300 keV will allow 1 amu mass resolution for stored ions of up to ∝ 150 amu (assuming a separation of 2 FWHMs between peaks).

  7. Atomic resolution (0.97 Å) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2

    International Nuclear Information System (INIS)

    The crystal structure of a triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 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 A2 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 A2 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% (Rfree = 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

  8. The nonlinear optical response of a two-dimensional atomic crystal

    CERN Document Server

    Merano, Michele

    2015-01-01

    The theory of Bloembergen and Persham for the light waves at the boundary of nonlinear media is applied to a nonlinear two-dimensional atomic crystal placed in between linear bulk media. The crystal is treated as a zero-thickness interface, a real two-dimensional system. Harmonic waves emanate from it. Generalization of the laws of reflection and refraction give the direction and the intensity of the harmonic waves. The nonlinear polarization of these special materials is very sensitive to the substrate on which they are deposited. Experiments on second harmonic generation of a $\\rm MoS_{2}$ monolayer are discussed to elucidate this point.

  9. Atomic simulation of amorphization and crystallization of Ag50 Au50 alloy during rapid solidification

    Institute of Scientific and Technical Information of China (English)

    王丽; 杨华; 张均艳; 边秀房; 衣粟

    2002-01-01

    By means of constant temperature and constant pressure molecular dynamic simulation technique, a series of simulations of the glass transition and crystallization processes of Ag50Au50 were performed. The atoms interact via EAM potential function. Pair correlation functions of liquid Ag50Au50 during different cooling rates and temperatures were simulated to reveal the structural features of liquid, super-cooled liquid, glass state and crystal. The thermodynamics and kinetics of structure transition of Ag50Au50 during cooling processes were performed.

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

    Science.gov (United States)

    Litinskaya, Marina; Tignone, Edoardo; Pupillo, Guido

    2016-05-01

    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.

  11. An accurate determination of the Avogadro constant by counting the atoms in a 28Si crystal

    CERN Document Server

    Andreas, B; Bartl, G; Becker, P; Bettin, H; Borys, M; Busch, I; Gray, M; Fuchs, P; Fujii, K; Fujimoto, H; Kessler, E; Krumrey, M; Kuetgens, U; Kuramoto, N; Mana, G; Manson, P; Massa, E; Mizushima, S; Nicolaus, A; Picard, A; Pramann, A; Rienitz, O; Schiel, D; Valkiers, S; Waseda, A

    2010-01-01

    The Avogadro constant links the atomic and the macroscopic properties of matter. Since the molar Planck constant is well known via the measurement of the Rydberg constant, it is also closely related to the Planck constant. In addition, its accurate determination is of paramount importance for a definition of the kilogram in terms of a fundamental constant. We describe a new approach for its determination by "counting" the atoms in 1 kg single-crystal spheres, which are highly enriched with the 28Si isotope. It enabled isotope dilution mass spectroscopy to determine the molar mass of the silicon crystal with unprecedented accuracy. The value obtained, 6.02214084(18) x 10^23 mol^-1, is the most accurate input datum for a new definition of the kilogram.

  12. Characterization of the surface charge distribution on kaolinite particles using high resolution atomic force microscopy

    Science.gov (United States)

    Kumar, Naveen; Zhao, Cunlu; Klaassen, Aram; van den Ende, Dirk; Mugele, Frieder; Siretanu, Igor

    2016-02-01

    Most solid surfaces, in particular clay minerals and rock surfaces, acquire a surface charge upon exposure to an aqueous environment due to adsorption and/or desorption of ionic species. Macroscopic techniques such as titration and electrokinetic measurements are commonly used to determine the surface charge and ζ -potential of these surfaces. However, because of the macroscopic averaging character these techniques cannot do justice to the role of local heterogeneities on the surfaces. In this work, we use dynamic atomic force microscopy (AFM) to determine the distribution of surface charge on the two (gibbsite-like and silica-like) basal planes of kaolinite nanoparticles immersed in aqueous electrolyte with a lateral resolution of approximately 30 nm. The surface charge density is extracted from force-distance curves using DLVO theory in combination with surface complexation modeling. While the gibbsite-like and the silica-like facet display on average positive and negative surface charge values as expected, our measurements reveal lateral variations of more than a factor of two on seemingly atomically smooth terraces, even if high resolution AFM images clearly reveal the atomic lattice on the surface. These results suggest that simple surface complexation models of clays that attribute a unique surface chemistry and hence homogeneous surface charge densities to basal planes may miss important aspects of real clay surfaces.

  13. A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

    International Nuclear Information System (INIS)

    A script was created to allow SHELXL to use the new CDL v.1.2 stereochemical library which defines the target values for main-chain bond lengths and angles as a function of the residue’s ϕ/ψ angles. Test refinements using this script show that the refinement behavior of structures at resolutions even better than 1 Å is substantially enhanced by the use of the new conformation-dependent ideal geometry paradigm. To utilize a new conformation-dependent backbone-geometry library (CDL) in protein refinements at atomic resolution, a script was written that creates a restraint file for the SHELXL refinement program. It was found that the use of this library allows models to be created that have a substantially better fit to main-chain bond angles and lengths without degrading their fit to the X-ray data even at resolutions near 1 Å. For models at much higher resolution (∼0.7 Å), the refined model for parts adopting single well occupied positions is largely independent of the restraints used, but these structures still showed much smaller r.m.s.d. residuals when assessed with the CDL. Examination of the refinement tests across a wide resolution range from 2.4 to 0.65 Å revealed consistent behavior supporting the use of the CDL as a next-generation restraint library to improve refinement. CDL restraints can be generated using the service at http://pgd.science.oregonstate.edu/cdl_shelxl/

  14. Epitaxial growth of single-crystal C sub 60 on mica by helium-atom scattering

    Energy Technology Data Exchange (ETDEWEB)

    Schmicker, D.; Schmidt, S. (Max-Planck-Institut fuer Stroemungsforschung, Bunsenstrasse 10, W-3400 Goettingen (Germany)); Skofronick, J.G. (Department of Physics, Florida State University, Tallahassee, Florida 32306 (United States)); Toennies, J.P.; Vollmer, R. (Max-Planck-Institut fuer Stroemungsforschung, Bunsenstrasse 10, W-3400 Goettingen (Germany))

    1991-11-15

    We report on a helium-atom-scattering study of the growth, structure, and surface dynamics of a very thin film of C{sub 60} sublimed in ultrahigh vacuum onto a freshly cleaved mica substrate. The resulting diffraction pattern showed that the C{sub 60} forms a hexagonal crystal layer that is in registry with the mica substrate and at a spacing of 10.4 A. The dispersion results showed two Einstein modes.

  15. Transient Emission of Three-Level Atoms in a Photonic Crystal with a Pseudogap

    Institute of Scientific and Technical Information of China (English)

    XU Xing-Sheng; CHEN Hong-Da

    2006-01-01

    @@ We study the transient behaviour of an external field induced transient emission of three-level atomic systems embedded in a photonic crystal with a pseudogap. The expressions for fluorescence spectra and emission dynamics for luminescent materials in the pseudogap are obtained. The properties of the transient gain in the pseudogap are discussed. It shows that the transient emission in the pseudogap can be effectively controlled.

  16. Preparation of 2D crystals of membrane proteins for high-resolution electron crystallography data collection.

    Science.gov (United States)

    Abeyrathne, Priyanka D; Chami, Mohamed; Pantelic, Radosav S; Goldie, Kenneth N; Stahlberg, Henning

    2010-01-01

    Electron crystallography is a powerful technique for the structure determination of membrane proteins as well as soluble proteins. Sample preparation for 2D membrane protein crystals is a crucial step, as proteins have to be prepared for electron microscopy at close to native conditions. In this review, we discuss the factors of sample preparation that are key to elucidating the atomic structure of membrane proteins using electron crystallography.

  17. Atomic force microscopy studies on phase transitions and surface morphology transformation of CMTC crystals

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, X.N.; Xu, D.; Yuan, D.R.; Sun, D.L.; Lu, M.K.; Jiang, M.H. [State Key Laboratory of Crystal Materials, Institute of Crystal Materials, Shandong University, Jinan (China)

    2002-11-01

    Atomic force microscopy (AFM) has been used to investigate the phase transitions and surface morphology transformation of cadmium mercury thiocyanate (CMTC) crystals, which are highly efficient nonlinear optical (NLO) materials for generating blue-violet light by laser frequency doubling. Amorphous aggregates at the crystalline steps become greatly contracted and much more crystalloid after the crystal was kept for one day. Elimination of dangling bonds, which lower the surface free energy at the crystal surface, and structural adjustment inside the crystal are assumed to cause this phase transition. Surface morphology transformations were also observed in CMTC crystals during and after multiple scanning by AFM tips. We have visualized the continuous translation process from two-dimensional nuclei to trigonal microcrystals with almost equal sizes during multiple scanning. In other cases, however, the surface morphology did not change at all during scanning, but became greatly altered hours after scanning. These experimental results suggest that reconstruction is a characteristic growth phenomenon on CMTC crystal surfaces. Reconstruction probably results from the formation of intervening metastable phases that have the potential to arrive at more stable stages; however, multiple scanning of AFM tips greatly affects this translation process. (orig.)

  18. Ionization of Atoms and the Thomas-Fermi Model for the Electric Field in Crystal Planar Channels

    Institute of Scientific and Technical Information of China (English)

    LIU Ying-Tai; ZHANG Qi-Ren; GAO Chun-Yuan

    2002-01-01

    The electric field in the crystal planar channels is studied by the Thomas Fermi method. The Thomas-Fermi equation and the corresponding boundary conditions are derived for the crystal planar channels. The numericalsolution for the electric field in the channels between (110) planes of the single crystal silicon and the critical angles ofchannelling protons in them are shown. Reasonable agreements with the experimental data are obtained. The resultsshow that the Thomas-Fermi method for the crystal works well in this study, and a microscopic research of the channelelectric field with the contribution of all atoms and the atomic ionization being taken into account is practical.

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

    International Nuclear Information System (INIS)

    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.

  20. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    Science.gov (United States)

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  1. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    Science.gov (United States)

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

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

    Energy Technology Data Exchange (ETDEWEB)

    Gundacker, S., E-mail: stefan.gundacker@cern.ch; Knapitsch, A.; Auffray, E.; Jarron, P.; Meyer, T.; Lecoq, P.

    2014-02-11

    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 mm{sup 3} LSO:Ce codoped 0.4%Ca crystals coupled to commercially available SiPMs (Hamamatsu S10931-050P MPPC) we achieve a CTR of 108±5 ps FWHM at an energy of 511 keV. Under the same experimental conditions an increase in crystal length to 5 mm deteriorates the CTR to 123±7 ps FWHM, 10 mm to 143±7 ps FWHM and 20 mm to 176±7 ps FWHM. This degradation in CTR is caused by the light transfer efficiency (LTE) and light transfer time spread (LTTS) in the crystal. To quantitatively understand the measured values, we developed a Monte Carlo simulation tool in MATLAB incorporating the timing properties of the photodetector and electronics, the scintillation properties of the crystal and the light transfer within the crystal simulated by SLITRANI. In this work, we show that the predictions of the simulation are in good agreement with the experimental data. We conclude that for longer crystals the deterioration in CTR is mainly caused by the LTE, i.e. the ratio of photons reaching the photodetector to the total amount of photons

  3. High-Resolution Photoassociation Spectroscopy of Ultracold Ytterbium Atoms by Using the Intercombination Transition

    International Nuclear Information System (INIS)

    We observed high-resolution photoassociation spectra of laser-cooled ytterbium (Yb) atoms in the spin-forbidden 1S0-3P1 intercombination line. The rovibrational levels in the 0u+ state were measured for red detunings of the photoassociation laser ranging from 2.9 MHz to 1.97 GHz with respect to the atomic resonance. The rotational splitting of the vibrational levels near the dissociation limit were fully resolved due to the sub-MHz linewidth of the spectra in contrast to previous measurements using the spin-allowed singlet transition. In addition, from a comparison between the spectra of 174Yb and those of 176Yb, a d-wave shape resonance for 174Yb is strongly suggested

  4. High-resolution photoassociation spectroscopy of ultracold ytterbium atoms by using the intercombination transition.

    Science.gov (United States)

    Tojo, Satoshi; Kitagawa, Masaaki; Enomoto, Katsunari; Kato, Yutaka; Takasu, Yosuke; Kumakura, Mitsutaka; Takahashi, Yoshiro

    2006-04-21

    We observed high-resolution photoassociation spectra of laser-cooled ytterbium (Yb) atoms in the spin-forbidden 1S0 - 3P1 intercombination line. The rovibrational levels in the 0u+ state were measured for red detunings of the photoassociation laser ranging from 2.9 MHz to 1.97 GHz with respect to the atomic resonance. The rotational splitting of the vibrational levels near the dissociation limit were fully resolved due to the sub-MHz linewidth of the spectra in contrast to previous measurements using the spin-allowed singlet transition. In addition, from a comparison between the spectra of 174Yb and those of 176Yb, a d-wave shape resonance for 174Yb is strongly suggested. PMID:16712155

  5. Sample preparation for atomic-resolution STEM at low voltages by FIB

    Energy Technology Data Exchange (ETDEWEB)

    Schaffer, Miroslava, E-mail: mschaffer@SuperSTEM.org [SuperSTEM, STFC Daresbury Laboratories, Keckwick Lane, Warrington WA4 4AD (United Kingdom); Department of Engineering, George Holt Building, Ashton Street, Liverpool L69 3BX (United Kingdom); Schaffer, Bernhard [SuperSTEM, STFC Daresbury Laboratories, Keckwick Lane, Warrington WA4 4AD (United Kingdom); Kelvin Nanocharacterisation Centre, SUPA School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Ramasse, Quentin [SuperSTEM, STFC Daresbury Laboratories, Keckwick Lane, Warrington WA4 4AD (United Kingdom); Department of Engineering, George Holt Building, Ashton Street, Liverpool L69 3BX (United Kingdom)

    2012-03-15

    While FIB sample preparation for transmission electron microscopy is a well established technique, few examples exist of samples of sufficient quality for atomic resolution imaging by aberration corrected (scanning) transmission electron microscopy (STEM). In this work we demonstrate the successful preparation of such samples from five different materials and present the refined lift-out preparation technique, which was applied here. Samples with parallel surfaces and a general thickness between 20 and 40 nm over a range of several {mu}m were repeatedly prepared and analyzed by Cs-corrected STEM at 60 and 100 kV. Here, a novel 'wedge pre-milling' step helps to keep the protective surface layers intact during the whole milling process, allowing features close to or at the sample surface to be analyzed without preparation damage. Another example shows the cross-sectional preparation of a working thin film solar cell device to a final thickness of 10 to 20 nm over {mu}m sized areas in the region of interest, enabling atomic resolution imaging and elemental mapping across general grain boundaries without projection artefacts. All sample preparation has been carried out in modern Dual-Beam FIB microscopes capable of low-kV Ga{sup +} ion milling, but without additional preparation steps after the FIB lift-out procedure. -- Highlights: Black-Right-Pointing-Pointer Suitability of stand-alone FIB preparation for atomic resolution STEM is shown. Black-Right-Pointing-Pointer Reproducible preparation of 10-40 nm thick samples from 5 different materials. Black-Right-Pointing-Pointer Low-kV milling and adjusted procedure for crystalline, homogeneously thin specimen. Black-Right-Pointing-Pointer Wedge pre-milling to protect surface-near features.

  6. Gate-induced superconductivity in atomically thin MoS2 crystals

    Science.gov (United States)

    Costanzo, Davide; Jo, Sanghyun; Berger, Helmuth; Morpurgo, Alberto F.

    2016-04-01

    When thinned down to the atomic scale, many layered van der Waals materials exhibit an interesting evolution of their electronic properties, whose main aspects can be accounted for by changes in the single-particle bandstructure. Phenomena driven by interactions are also observed, but identifying experimentally systematic trends in their thickness dependence is challenging. Here, we explore the evolution of gate-induced superconductivity in exfoliated MoS2 multilayers ranging from bulk-like to individual monolayers. We observe a clear transition for all thicknesses down to the ultimate atomic limit, providing the first demonstration of gate-induced superconductivity in atomically thin exfoliated crystals. Additionally, we characterize the superconducting state by measuring the critical temperature TC and magnetic field BC in a large number of multilayer devices while decreasing their thickness. We find that the superconducting properties exhibit a pronounced reduction in TC and BC when going from bilayers to monolayers, for which we discuss possible microscopic mechanisms.

  7. High-resolution bent-crystal spectrometer for the ultra-soft x-ray region

    International Nuclear Information System (INIS)

    A multichannel vacuum Brag-crystal spectrometer has been developed for high-resolution measurements of the line emission from tokamak plasmas in the wavelength region between 4 and 25 /angstrom/. The spectrometer employs a bent crystal in Johann geometry and a microchannel-plate intensified photodiode array. The instrument is capable of measuring high-resolution spectra (λ/Δλ ∼ 3000) with fast time resolution (4 msec per spectrum) and good spatial resolution (3 cm). The spectral bandwidth is Δλ/λ0 = 8/angstrom/. A simple tilt mechanism allows access to different wavelength intervals. In order to illustrate the utility of the new spectrometer, time- and space-resolved measurements of the n = 3 to n = 2 spectrum of selenium from the Princeton Large Torus tokamak plasmas are presented. The data are used to determine the plasma transport parameters and to infer the radial distribution of fluorinelike, neonlike, and sodiumlike ions of selenium in the plasma. The new ultra-soft x-ray spectrometer has thus enabled us to demonstrate the utility of high-resolution L-shell spectroscopy of neonlike ions as a fusion diagnostic. 43 refs., 23 figs

  8. High-resolution Bent-crystal Spectrometer for the Ultra-soft X-ray Region

    Science.gov (United States)

    Beiersdorfer, P.; von Goeler, S.; Bitter, M.; Hill, K. W.; Hulse, R. A.; Walling, R. S.

    1988-10-01

    A multichannel vacuum Brag-crystal spectrometer has been developed for high-resolution measurements of the line emission from tokamak plasmas in the wavelength region between 4 and 25 angstrom. The spectrometer employs a bent crystal in Johann geometry and a microchannel-plate intensified photodiode array. The instrument is capable of measuring high-resolution spectra (lambda/..delta..lambda approx. 3000) with fast time resolution (4 msec per spectrum) and good spatial resolution (3 cm). The spectral bandwidth is ..delta..lambda/lambda{sub 0} = 8 angstrom. A simple tilt mechanism allows access to different wavelength intervals. In order to illustrate the utility of the new spectrometer, time- and space-resolved measurements of the n = 3 to n = 2 spectrum of selenium from the Princeton Large Torus tokamak plasmas are presented. The data are used to determine the plasma transport parameters and to infer the radial distribution of fluorinelike, neonlike, and sodiumlike ions of selenium in the plasma. The new ultra-soft x-ray spectrometer has thus enabled us to demonstrate the utility of high-resolution L-shell spectroscopy of neonlike ions as a fusion diagnostic.

  9. Atomic-resolution scanning transmission electron microscopy through 50-nm-thick silicon nitride membranes

    OpenAIRE

    Ramachandra, Ranjan; Demers, Hendrix; de Jonge, Niels

    2011-01-01

    Silicon nitride membranes can be used for windows of environmental chambers for in situ electron microscopy. We report that aberration corrected scanning transmission electron microscopy (STEM) achieved atomic resolution on gold nanoparticles placed on both sides of a 50-nm-thick silicon nitride membrane at 200 keV electron beam energy. Spatial frequencies of 1∕1.2 Å were visible for a beam semi-angle of 26.5 mrad. Imaging though a 100-nm-thick membrane was also tested. The achieved imaging c...

  10. Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers.

    Science.gov (United States)

    Stern, S; Holmegaard, L; Filsinger, F; Rouzée, A; Rudenko, A; Johnsson, P; Martin, A V; Barty, A; Bostedt, C; Bozek, J; Coffee, R; Epp, S; Erk, B; Foucar, L; Hartmann, R; Kimmel, N; Kühnel, K-U; Maurer, J; Messerschmidt, M; Rudek, B; Starodub, D; Thøgersen, J; Weidenspointner, G; White, T A; Stapelfeldt, H; Rolles, D; Chapman, H N; Küpper, J

    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 Coherent 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. PMID:25415561

  11. Kilohertz-resolution spectroscopy of cold atoms with an optical frequency comb

    CERN Document Server

    Fortier, T M; Stalnaker, J E; Ortega, D; Diddams, S A; Oates, C W; Hollberg, L

    2006-01-01

    We have performed sub-Doppler spectroscopy on the narrow intercombination line of cold calcium atoms using the amplified output of a femtosecond laser frequency comb. Injection locking of a 657-nm diode laser with a femtosecond comb allows for two regimes of amplification, one in which many lines of the comb are amplified, and one where a single line is predominantly amplified. The output of the laser in both regimes was used to perform kilohertz-level spectroscopy. This experiment demonstrates the potential for high-resolution absolute-frequency spectroscopy over the entire spectrum of the frequency comb output using a single high-finesse optical reference cavity.

  12. Kilohertz-resolution spectroscopy of cold atoms with an optical frequency comb.

    Science.gov (United States)

    Fortier, T M; Coq, Y Le; Stalnaker, J E; Ortega, D; Diddams, S A; Oates, C W; Hollberg, L

    2006-10-20

    We have performed sub-Doppler spectroscopy on the narrow intercombination line of cold calcium atoms using the amplified output of a femtosecond laser frequency comb. Injection locking of a 657-nm diode laser with a femtosecond comb allows for two regimes of amplification, one in which many lines of the comb are amplified, and one where a single line is predominantly amplified. The output of the laser in both regimes was used to perform kilohertz-level spectroscopy. This experiment demonstrates the potential for high-resolution absolute-frequency spectroscopy over the entire spectrum of the frequency comb output using a single high-finesse optical reference cavity. PMID:17155398

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

    CERN Document Server

    Stern, Stephan; Filsinger, Frank; Rouzée, Arnaud; Rudenko, Artem; Johnsson, Per; Martin, Andrew V; Barty, Anton; Bostedt, Christoph; Bozek, John D; Coffee, Ryan N; Epp, Sascha; Erk, Benjamin; Foucar, Lutz; Hartmann, Robert; Kimmel, Nils; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Rudek, Benedikt; Starodub, Dmitri G; Thøgersen, Jan; Weidenspointner, Georg; White, Thomas A; Stapelfeldt, Henrik; Rolles, Daniel; Chapman, Henry N; Küpper, Jochen

    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 Coherent 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.

  14. Characterization of microfabricated probes for combined atomic force and high-resolution scanning electrochemical microscopy.

    Science.gov (United States)

    Gullo, Maurizio R; Frederix, Patrick L T M; Akiyama, Terunobu; Engel, Andreas; deRooij, Nico F; Staufer, Urs

    2006-08-01

    A combined atomic force and scanning electrochemical microscope probe is presented. The probe is electrically insulated except at the very apex of the tip, which has a radius of curvature in the range of 10-15 nm. Steady-state cyclic voltammetry measurements for the reduction of Ru(NH3)6Cl3 and feedback experiments showed a distinct and reproducible response of the electrode. These experimental results agreed with finite element simulations for the corresponding diffusion process. Sequentially topographical and electrochemical studies of Pt lines deposited onto Si3N4 and spaced 100 nm apart (edge to edge) showed a lateral electrochemical resolution of 10 nm. PMID:16878880

  15. Investigating protein conformational energy landscapes and atomic resolution dynamics from NMR dipolar couplings: a review.

    Science.gov (United States)

    Salmon, Loïc; Blackledge, Martin

    2015-12-01

    Nuclear magnetic resonance spectroscopy is exquisitely sensitive to protein dynamics. In particular inter-nuclear dipolar couplings, that become measurable in solution when the protein is dissolved in a dilute liquid crystalline solution, report on all conformations sampled up to millisecond timescales. As such they provide the opportunity to describe the Boltzmann distribution present in solution at atomic resolution, and thereby to map the conformational energy landscape in unprecedented detail. The development of analytical methods and approaches based on numerical simulation and their application to numerous biologically important systems is presented. PMID:26517337

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

    Science.gov (United States)

    Smither, Robert K.

    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.

  17. Measurement of transient atomic displacements in thin films with picosecond and femtometer resolution

    Directory of Open Access Journals (Sweden)

    M. Kozina

    2014-05-01

    Full Text Available We report measurements of the transient structural response of weakly photo-excited thin films of BiFeO3, Pb(Zr,TiO3, and Bi and time-scales for interfacial thermal transport. Utilizing picosecond x-ray diffraction at a 1.28 MHz repetition rate with time resolution extending down to 15 ps, transient changes in the diffraction angle are recorded. These changes are associated with photo-induced lattice strains within nanolayer thin films, resolved at the part-per-million level, corresponding to a shift in the scattering angle three orders of magnitude smaller than the rocking curve width and changes in the interlayer lattice spacing of fractions of a femtometer. The combination of high brightness, repetition rate, and stability of the synchrotron, in conjunction with high time resolution, represents a novel means to probe atomic-scale, near-equilibrium dynamics.

  18. Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy

    Science.gov (United States)

    Kim, Minjung; Chelikowsky, James R.

    2015-03-01

    Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

  19. Measurement of transient atomic displacements in thin films with picosecond and femtometer resolution.

    Science.gov (United States)

    Kozina, M; Hu, T; Wittenberg, J S; Szilagyi, E; Trigo, M; Miller, T A; Uher, C; Damodaran, A; Martin, L; Mehta, A; Corbett, J; Safranek, J; Reis, D A; Lindenberg, A M

    2014-05-01

    We report measurements of the transient structural response of weakly photo-excited thin films of BiFeO3, Pb(Zr,Ti)O3, and Bi and time-scales for interfacial thermal transport. Utilizing picosecond x-ray diffraction at a 1.28 MHz repetition rate with time resolution extending down to 15 ps, transient changes in the diffraction angle are recorded. These changes are associated with photo-induced lattice strains within nanolayer thin films, resolved at the part-per-million level, corresponding to a shift in the scattering angle three orders of magnitude smaller than the rocking curve width and changes in the interlayer lattice spacing of fractions of a femtometer. The combination of high brightness, repetition rate, and stability of the synchrotron, in conjunction with high time resolution, represents a novel means to probe atomic-scale, near-equilibrium dynamics. PMID:26798776

  20. Properties of single crystal para-terphenyl as medium for high resolution TOF detector

    Science.gov (United States)

    De Gerone, M.; Biasotti, M.; Ceriale, V.; Corsini, D.; Gatti, F.; Orlando, A.; Pizzigoni, G.

    2016-07-01

    In the last years organic scintillators have been largely investigated in order to achieve high light yield together with good time response. Pure organic compound with high quality crystalline structure can achieve both this goals. Among a large type of organic compound, para-terphenyl (C18H14) have proven to have practical applications as detector medium for particle physics. In this work, the characterization of different sizes high quality mono-crystal p-terphenyl samples is presented. The optical and scintillation properties (emission spectrum, light yield, attenuation length, and decay time) are investigated. Coupling a Silicon PhotoMultiplier-based readout system to the crystal, a small prototype for a high resolution TOF detector was built; the preliminary results, obtained on a 20×30×3 mm3 sample, with dual-side read-out (Hamamatsu S10931-050P SiPMs) and irradiated with 90Sr source, show a time resolution of 35 ps.

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

    International Nuclear Information System (INIS)

    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

  2. Crystal structure determination of thymoquinone by high-resolution X-ray powder diffraction

    OpenAIRE

    Pagola, S.; Benavente, A; Raschi, A.; Romano, E; Molina, M. A. A.; Stephens, P.W.

    2004-01-01

    The crystal structure of 2-isopropyl-5-methyl-1,4-benzoquinone (thymoquinone) and its thermal behavior—as necessary physical and chemical properties—were determined in order to enhance the current understanding of thymoquinone chemical action by using high resolution x-ray powder diffraction, Fourier transform infrared spectroscopy (FTIR), and 3 thermo-analytical techniques thermogravimetric analysis (TGA), differential thermal analysis (DTA), and differential scanning calorimetry (DSC). The ...

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

    International Nuclear Information System (INIS)

    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

  4. 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.

  5. High resolution X-ray spherically bent crystal spectrometer for laser-produced plasma diagnostics

    Institute of Scientific and Technical Information of China (English)

    Shali Xiao; Hongjian Wang; Jun Shi; Changhuan Tang; Shenye Liu

    2009-01-01

    A new high spectral resolution crystal spectrometer is designed to measure very low emissive X-ray spectra of laser-produced plasma in 0.5 - 0.9 nm range. A large open aperture (30 x 20 (mm)) mica (002) spherically bent crystal with curvature radius R = 380 mm is used as dispersive and focusing element. The imaging plate is employed to obtain high spectral resolution with effective area of 30 x 80 (mm). The long designed path of the X-ray spectrometer beam is 980 mm from the source to the detector via the crystal. Experiment is carried out at a 20-J laser facility. X-ray spectra in an absolute intensity scale is obtained from Al laser produced plasmas created by laser energy of 6.78 J. Samples of spectra obtained with spectral resolution of up to E/鈻矱 ~ 1500 are presented. The results clearly show that the device is good to diagnose laser high-density plasmas.

  6. 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...

  7. High-resolution Fourier spectroscopy as a tool for studying quality of rare-earth-doped crystals

    Institute of Scientific and Technical Information of China (English)

    Marina N. Popova

    2014-01-01

    Three examples were considered of the use of high resolution Fourier-transform optical spectroscopy for studying quality of rare-earth-doped crystals. The first example was connected with defects present in crystals grown by flux techniques. The second example dealt with detection of stresses and deformations in rare-earth-containing crystals, by registering splitting of spectral lines. The third example showed that a very small amount (at the level of ppm) of different RE ions present in a crystal could be determined using high-resolution spectroscopy. This work was carried out by the author’s group in collaboration with several institutions in Rus-sia and abroad.

  8. Spontaneous emission spectrum of a three-level atom embedded in photonic crystal

    Institute of Scientific and Technical Information of China (English)

    刘国强; 王健; 张汉壮

    2005-01-01

    The two models of three-level (one upper level and two lower levels, or two upper levels and one lower level) atom embedded in a double-band photonic crystal are adopted. The atomic transitions from the upper levels to the lower levels are assumed to be coupled by the same reservoir which are respectively the isotropic photonic band gap (PBG)modes, the anisotropic PBG modes and the free vacuum modes. The effects of the fine structure of the atomic ground state levels in the model with one upper level and two lower levels, and the quantum interferences in the model with two upper levels and one lower level on the spontaneous emission spectrum of an atom are investigated in detail. Most interestingly, it is shown that new spontaneous emission lines are produced from the fine splitting of atomic ground state levels in the isotropic PBG case. The quantum interferences induce additional narrow spontaneous lines near the transition from the empty upper level to the lower level.

  9. 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

    In development of 12%Cr high temperature steels used for fossil fired power plants, the precipitation of large Z-phase particles, CrMN, has been identified as a major problem since they replace small and finely distributed MN particles. This causes a premature breakdown in the longterm creep...... 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...... contrast between heavy Ta atoms and light Cr atoms, the ordering of the Cr layers inside the TaN particles can clearly be observed....

  10. Development of new methods of measurement in atomic resolution holography and the influence of the crystalline sample structure on the holographic reconstruction

    International Nuclear Information System (INIS)

    Atomic resolution holography is a model-free method to reconstruct the neighborhood of an atom. In recent years it has been successfully applied to surface analysis using low-energy electrons. Due to their larger penetration depth, X-rays are used to determine the bulk properties of the sample. This work examines the possibility to use high-energy electrons to holographically probe bulk properties. This would reduce the experimental effort tremendously. However, it appears that the strong interaction of the high-energy electrons with matter prevents a holographic analysis of the measured data. Due to the small (10-4) signal-to-background ratio in X-ray holography, the statistics of the measured data should be as high as possible. New detection approaches to make this possible are shown: First, the fluorescence radiation of the sample is focused on the detector using an analyzer crystal. Second, all Auger electrons emitted from the sample are detected by a new measurement cell. Both methods produce data with statistics better than all previous measurements. Nevertheless, the quality of the holographic reconstructions of these data appears to be only marginally better than that of the previous measurements. It is shown that this is due to the influence of the distant neighbor atoms of the examined atom. It is not possible to remove these from the holographic data without producing artifacts in the reconstruction. The long-range order in crystalline samples leads to the formation of Kossel lines. It is shown than these patterns alone are sufficient to produce artifacts at true atomic positions in the reconstruction. Therefore, it is not possible to use atomic-resolution X-rays holography with crystalline samples. This makes the results of most of the previous published works questionable. (orig.)

  11. Mapping hydrophobicity on the protein molecular surface at atom-level resolution.

    Directory of Open Access Journals (Sweden)

    Dan V Nicolau

    Full Text Available 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

  12. High resolution X-ray diffraction studies on unirradiated and irradiated strontium hexaferrite crystals

    Indian Academy of Sciences (India)

    Balwinder Kaur; Monita Bhat; F Licci; Ravi Kumar; K K Bamzai; P N Kotru

    2012-04-01

    High-resolution X-ray diffraction technique, employing a three-crystal monochromator–collimator combination is used to study the irradiation induced defects in flux grown Sr-hexaferrite crystals irradiated with 50 MeV Li3+ ion beams at room temperature with a fluence value of 1 × 1014 ions/cm2. The diffraction curves of the irradiated crystals suggest the possibility of creation of low angle grain boundaries and other point/clusters of defects causing amorphization in the irradiated crystals. The perfection of the irradiated and unirradiated (0001) cleaved surfaces of the crystals is studied using the bulk method of X-ray topography. The topographs supplement the findings suggestive of modifications in the crystalline quality of SrFe12O19 on irradiation with SHI of Li3+. Etching of the (0001) cleaved surfaces in H3PO4 at 120°C suggests that the dissolution characteristics of the surfaces get affected on irradiation with SHI of Li3+, besides supporting the findings of HRXRD and X-ray topography regarding modifications in the perfection of SrFe12O19 on irradiation.

  13. Development of single-crystal diamond scanning probes with nitrogen-vacancy centers for cryogenic magnetometry with nanoscale spatial resolution

    Science.gov (United States)

    Jenkins, Alec; Pelliccione, Matthew; Ovartchaiyapong, Preeti; Reetz, Christopher; Bleszynski Jayich, Ania

    Scanning probes based on the nitrogen-vacancy (NV) defect center in diamond are powerful tools for imaging magnetic phenomena at the nanoscale. In particular, extending the operation of these probes to cryogenic temperatures opens up a wide range of condensed matter systems that can be studied. In this talk, we demonstrate a variable temperature NV scanning magnetometer consisting of an atomic-force microscope housed in a closed-cycle cryostat integrated with custom confocal optics. With this microscope we have observed 6-nm spatial resolution and 3 μT /√{Hz} sensitivity at T = 6 K. The single-crystal diamond scanning probes that contain shallow and coherent NV centers are critical to the performance of the microscope. The probes are designed with the aim of reducing the NV-sample separation and increasing collection of NV fluorescence, both while maintaining the spin coherence properties of the defects. We describe the fabrication of these probes as well as ongoing efforts to improve their sensitivity and spatial resolution.

  14. Strain-engineered diffusive atomic switching in two-dimensional crystals

    Science.gov (United States)

    Kalikka, Janne; Zhou, Xilin; Dilcher, Eric; Wall, Simon; Li, Ju; Simpson, Robert E.

    2016-01-01

    Strain engineering is an emerging route for tuning the bandgap, carrier mobility, chemical reactivity and diffusivity of materials. Here we show how strain can be used to control atomic diffusion in van der Waals heterostructures of two-dimensional (2D) crystals. We use strain to increase the diffusivity of Ge and Te atoms that are confined to 5 Å thick 2D planes within an Sb2Te3–GeTe van der Waals superlattice. The number of quintuple Sb2Te3 2D crystal layers dictates the strain in the GeTe layers and consequently its diffusive atomic disordering. By identifying four critical rules for the superlattice configuration we lay the foundation for a generalizable approach to the design of switchable van der Waals heterostructures. As Sb2Te3–GeTe is a topological insulator, we envision these rules enabling methods to control spin and topological properties of materials in reversible and energy efficient ways. PMID:27329563

  15. Effects of heat treatment on diffusion of Cu atoms into CdTe single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Soo, Y. L. [Department of Physics, State University of New York at Buffalo, Amherst, New York 14260 (United States); Huang, S. [Department of Physics, State University of New York at Buffalo, Amherst, New York 14260 (United States); Kim, S. [Department of Physics, State University of New York at Buffalo, Amherst, New York 14260 (United States); Kioseoglou, G. [Department of Physics, State University of New York at Buffalo, Amherst, New York 14260 (United States); Kao, Y. H. [Department of Physics, State University of New York at Buffalo, Amherst, New York 14260 (United States); Compaan, A. D. [Department of Physics and Astronomy, University of Toledo, Toledo, Ohio 43606 (United States); Grecu, D. [Department of Physics and Astronomy, University of Toledo, Toledo, Ohio 43606 (United States); Albin, D. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States)

    2000-06-19

    Angular dependence of x-ray fluorescence and x-ray absorption fine structure techniques have been used to study the diffusion of Cu atoms into the photovoltaic material CdTe. Depth profile, effective valency, and local structure of Cu atoms in a Cu-doped single crystal of CdTe were investigated before and after a second heat treatment. Enhanced Cu diffusion into the CdTe single crystal was observed as a result of heating at a moderate temperature around 200 degree sign C, resulting in a redistribution of the Cu impurities through a broader depth profile. Some of the Cu atoms are believed either to form small complexes with Te or occupy interstitial sites in the host but accompanied by a large local lattice distortion while others substitute for Cd on the cation sites. The results thus demonstrate that these nondestructive x-ray characterization methods are useful for probing microstructural changes in CdTe photovoltaic materials/devices in which some Cu-containing compounds are used as back contacts. (c) 2000 American Institute of Physics.

  16. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Campbellova, Anna; Klapetek, Petr [Czech Metrology Institute, OkruznI 31, 638 00, Brno (Czech Republic); Ondracek, Martin; JelInek, Pavel [Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnicka 10, 162 00 Prague (Czech Republic); Pou, Pablo; Perez, Ruben, E-mail: jelinekp@fzu.cz [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, 28049 Madrid (Spain)

    2011-07-22

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

  18. Localizing chemical groups while imaging single native proteins by high-resolution atomic force microscopy.

    Science.gov (United States)

    Pfreundschuh, Moritz; Alsteens, David; Hilbert, Manuel; Steinmetz, Michel O; Müller, Daniel J

    2014-05-14

    Simultaneous high-resolution imaging and localization of chemical interaction sites on single native proteins is a pertinent biophysical, biochemical, and nanotechnological challenge. Such structural mapping and characterization of binding sites is of importance in understanding how proteins interact with their environment and in manipulating such interactions in a plethora of biotechnological applications. Thus far, this challenge remains to be tackled. Here, we introduce force-distance curve-based atomic force microscopy (FD-based AFM) for the high-resolution imaging of SAS-6, a protein that self-assembles into cartwheel-like structures. Using functionalized AFM tips bearing Ni(2+)-N-nitrilotriacetate groups, we locate specific interaction sites on SAS-6 at nanometer resolution and quantify the binding strength of the Ni(2+)-NTA groups to histidine residues. The FD-based AFM approach can readily be applied to image any other native protein and to locate and structurally map histidine residues. Moreover, the surface chemistry used to functionalize the AFM tip can be modified to map other chemical interaction sites. PMID:24766578

  19. The crystal structure of Z-(Aib)10-OH at 0.65 Å resolution: three complete turns of 310-helix.

    Science.gov (United States)

    Gessmann, Renate; Brückner, Hans; Petratos, Kyriacos

    2016-02-01

    The synthetic peptide Z-(Aib)10-OH was crystallized from hot methanol by slow evaporation. The crystal used for data collection reflected synchrotron radiation to sub-atomic resolution, where the bonding electron density becomes visible between the non-hydrogen atoms. Crystals belong to the centrosymmetric space group P1. Both molecules in the asymmetric unit form regular 310 -helices. All residues in each molecule possess the same handedness, which is in contrast to all other crystal structure determined to date of longer Aib-homopeptides. These other peptides are C-terminal protected by OtBu or OMe. In these cases, because of the missing ability of the C-terminal protection group to form a hydrogen bond to the residue i-3, the sense of the helix is reversed in the last residue. Here, the C-terminal OH-groups form hydrogen bonds to the residues i-3, in part mediated by water molecules. This makes Z-(Aib)10-OH an Aib-homopeptide with three complete 310-helical turns in spite of the shorter length it has compared with Z-(Aib)11-OtBu, the only homopeptide to date with three complete turns.

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Katskov, Dmitri, E-mail: katskovda@tut.ac.za

    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 D{sub 2} 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

  2. Photonic Bandgap Properties of Atom-lattice Photonic Crystals in Polymer

    Institute of Scientific and Technical Information of China (English)

    REN Lin; WANG Dian; SUN Gui-ting; NIU Li-gang; YANG Han; SONG Jun-feng

    2011-01-01

    The present paper covers the various photonic crystals(PhCs) structures mimicking real atom-lattice structures in electronic crystals by using the femtosecond laser-induced two-photon photopolymerization of SU-8 resin. The bandgap properties were investigated by varying the crystal orientations in <111>, <110> and <100> of diamond-lattice PhCs. lhe photonic stop gaps were present at λ=3.88 μm in <111> direction, λ=4.01 μtm in <110> direction and λ=5.30 μm in <100> direction, respectively. In addition, defects were introduced in graphite-lattice PhCs and the strong localization of photons in this structure with defects at λ=5 μm was achieved. All the above work shows the powerful capability of femtosecond laser fabrication in manufacturing various complicated threedimensional photonic crystals and of controlling photons by inducing defects in the PhCs samples.

  3. Direct Identification of Atomic-Like Electronic Levels in InAs Nano crystal Quantum Dots

    International Nuclear Information System (INIS)

    The size dependent level structure of InAs nano crystals in the range 2-7 nm in diameter is investigated using both tunneling and optical spectroscopies. The tunneling measurements are performed using a cryogenic scanning tunneling microscope on individual nano crystals that, are attached to a gold substrate via dithiol molecules. The tunneling I-V characteristics manifest an interplay between single electron charging and quantum size effects. We are able to directly identify quantum confined states of isolated InAs nano crystals having s and p symmetries. These states are observed in the I-V curves as two and six-fold single electron charging multiplets. Excellent agreement is found between the strongly allowed optical transitions [1] and the spacing of levels detected in the tunneling experiment. This correlation provides new information on the quantum-dot level structure, from which we conclude that the top-most valence band state has both s and p characteristics. The interplay between level structure singles electron charging of the nano crystals obeys an atomic-like Aufbau sequential electron level occupation

  4. Atomic mercury vapor inside a hollow-core photonic crystal fiber

    CERN Document Server

    Vogl, Ulrich; Joly, Nicolas Y; Russell, Philip St J; Marquardt, Christoph; Leuchs, Gerd

    2014-01-01

    We demonstrate high atomic mercury vapor pressure in a kagom\\'e-style hollow-core photonic crystal fiber at room temperature. After a few days of exposure to mercury vapor the fiber is homogeneously filled and the optical depth achieved remains constant. With incoherent optical pumping from the ground state we achieve an optical depth of 114 at the $6^3P_2 - 6^3D_3$ transition, corresponding to an atomic mercury number density of $6 \\times 10^{10}$ cm$^{-3}$. The use of mercury vapor in quasi one-dimensional confinement may be advantageous compared to chemically more active alkali vapor, while offering strong optical nonlinearities in the ultraviolet region of the optical spectrum.

  5. High resolution nuclear magnetic resonance study of molecular motion in solids and liquid crystals

    International Nuclear Information System (INIS)

    Application of high resolution NMR techniques to study the molecular motion in solids and liquid crystals has been presented. A theory of NMR spectra and a theory of relaxation have been developed for rapidly-rotated solids whose spectra are narrowed by internal motion. The effect of molecular motion on resolution of the multipulse NMR technique has been calculated in the case of /1 3 2; 1 3 tilde 2/ /1 2 3; 1 2 tilde 3/ sequence. It has been shown, that in both techniques the molecular motion is an important factor limiting the resolution. It has been also found, that rotating frame relaxation T sub(1rhoR) for the spinning sample may extend the information of the conventional Tsub(1rho) about the slow molecular motion. Multipulse NMR techniques have been used to investigate the molecular motion in the lamellar mesophase of some lyotropic liquid crystals. A new method of direct measurement of the order parameter S has been developed, based on the analysis of the multipulse spectra. Chemical shift tensors have been also measured for the CF2 and CF3 groups in CsPFO molecule. (author)

  6. Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.

    Science.gov (United States)

    Sun, Siyang; Xiang, Ye; Akahata, Wataru; Holdaway, Heather; Pal, Pankaj; Zhang, Xinzheng; Diamond, Michael S; Nabel, Gary J; Rossmann, Michael G

    2013-04-02

    A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment. DOI:http://dx.doi.org/10.7554/eLife.00435.001.

  7. 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.

  8. Sub-nanometer resolution of an organic semiconductor crystal surface using friction force microscopy in water.

    Science.gov (United States)

    Pimentel, Carlos; Varghese, Shinto; Yoon, Seong-Jun; Park, Soo Young; Gierschner, Johannes; Gnecco, Enrico; Pina, Carlos M

    2016-04-01

    Organic semiconductors (OSC) are attracting much interest for (opto)electronic applications, such as photovoltaics, LEDs, sensors or solid state lasers. In particular, crystals formed by small π-conjugated molecules have shown to be suitable for constructing OSC devices. However, the (opto)electronic properties are complex since they depend strongly on both the mutual orientation of molecules as well as the perfection of bulk crystal surfaces. Hence, there is an urgent need to control nano-topographic OSC features in real space. Here we show that friction force microscopy in water is a very suitable technique to image the free surface morphology of an OSC single crystal (TDDCS) with sub-nanometer resolution. We demonstrate the power of the method by direct correlation to the structural information extracted from combined single crystal (SC-) and specular (s-) XRD studies, which allows us to identify the pinning centers encountered in the stick-slip motion of the probing tip with the topmost methyl groups on the TDDCS surface. PMID:26931487

  9. Atomic-resolution STM structure of DNA and localization of the retinoic acid binding site

    International Nuclear Information System (INIS)

    Single-molecule imaging by scanning tunnelling microscopy (STM) yields the atomic-resolution (0.6 A) structure of individual B-type DNA molecules. The strong correlation between these STM structures and those predicted from the known base sequence indicates that sequencing of single DNA molecules using STM may be feasible. There is excellent agreement between the STM and X-ray structures, but subtle differences exist due to radial distortions. We show that the interactions of other molecules with DNA, their binding configurations, and the structure of these complexes can be studied at the single-molecule level. The anti-cancer drug retinoic acid (RA) binds selectively to the minor groove of DNA with up to 6 RA molecules per DNA turn and with the plane of the RA molecule approximately parallel to the DNA symmetry axis. Similar studies for other drug molecules will be valuable in the a priori evaluation of the effectiveness of anti-cancer drugs

  10. 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.

  11. Spatial Resolution of Combined Wavelength Modulation Spectroscopy with Integrated Cavity Output Spectroscopy for Atomic Oxygen Detection

    Science.gov (United States)

    Matsui, Makoto; Nakajima, Daisuke

    2015-09-01

    For developments of thermal protection system, atomic oxygen plays important role. However, its measurement method has not been established because the pressure in front of TPS test materials is as high as a few kPa. Our group proposed combined wavelength modulation and integrated output spectroscopies based on the forbidden transition at OI 636 nm to measure the ground-state number densities. In this study, WM-ICOS system is developed and applied to a microwave oxygen plasma to evaluate measurable region. As a result, the estimated number density by ICOS could be measured as low as 1021 m21. For the condition, WM-ICOS was applied. The signal to noise ratio of the 2f signal was 40.4. Then, the sensitivity was improved about 26. This result corresponding to the measurement limit of the partial atomic oxygen pressure of 250 Pa. The sensitivity of WM-ICOS was found to enough to diagnose the shock layer in high enthalpy flows. However, the spatial resolution was as large as 8 mm. The size of the beam pattern depends on the cavity length, robust ness of the cavity and accuracy of the cavity alignment. In this presentation, the relationship among these parameters will be discussed.

  12. Atomic resolution holography using advanced reconstruction techniques for two-dimensional detectors

    Energy Technology Data Exchange (ETDEWEB)

    Marko, M; Szakal, A; Cser, L [Neutron Spectroscopy Department, Research Institute for Solid State Physics and Optics, PO Box 49, H-1525 Budapest (Hungary); Krexner, G [Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna (Austria); Schefer, J, E-mail: marko@szfki.h [Laboratory for Neutron Scattering (LNS), Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland)

    2010-06-15

    Atomic resolution holography is based on two concepts. Either the emitter of the radiation used is embedded in the sample (internal source concept) or, on account of the optical reciprocity law, the detector forms part of the sample (internal detector concept). In many cases, holographic objects (atoms and nuclei) simultaneously adopt the roles of both source and detector. Thus, the recorded image contains a mixture of both inside source and inside detector holograms. When reconstructing one type of hologram, the presence of the other hologram causes serious distortions. In the present work, we propose a new method, the so-called double reconstruction (DR), which not only suppresses the mutual distortions but also exploits the information content of the measured hologram more effectively. This novel approach also decreases the level of distortion arising from diffraction and statistical noise. The efficiency of the DR technique is significantly enhanced by employing two-dimensional (2D) area detectors. The power of the method is illustrated here by applying it to a real measurement on a palladium-hydrogen sample.

  13. High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K.

    Science.gov (United States)

    Chatake, Toshiyuki; Ishikawa, Takuya; Yanagisawa, Yasuhide; Yamada, Taro; Tanaka, Ichiro; Fujiwara, Satoru; Morimoro, Yukio

    2011-11-01

    Deuteration of macromolecules is an important technique in neutron protein crystallography. Solvent deuteration of protein crystals is carried out by replacing water (H(2)O) with heavy water (D(2)O) prior to neutron diffraction experiments in order to diminish background noise. The effects of solvent deuteration on the crystallization of proteinase K (PK) with polyethylene glycol as a precipitant were investigated using high-resolution X-ray crystallography. In previous studies, eight NO(3)(-) anions were included in the PK crystal unit cell grown in NaNO(3) solution. In this study, however, the PK crystal structure did not contain NO(3)(-) anions; consequently, distortions of amino acids arising from the presence of NO(3)(-) anions were avoided in the present crystal structures. High-resolution (1.1 Å) X-ray diffraction studies showed that the degradation of PK crystals induced by solvent deuteration was so small that this degradation would be negligible for the purpose of neutron protein crystallography experiments at medium resolution. Comparison of the nonhydrogen structures of nondeuterated and deuterated crystal structures demonstrated very small structural differences. Moreover, a positive correlation between the root-mean-squared differences and B factors indicated that no systematic difference existed.

  14. Strong light-matter coupling in two-dimensional atomic crystals

    CERN Document Server

    Liu, Xiaoze; Sun, Zheng; Xia, Fengnian; Lin, Erh-chen; Lee, Yi-Hsien; Kéna-Cohen, Stéphane; Menon, Vinod M

    2014-01-01

    Two dimensional (2D) atomic crystals of graphene, and transition metal dichalcogenides have emerged as a class of materials that show strong light-matter interaction. This interaction can be further controlled by embedding such materials into optical microcavities. When the interaction is engineered to be stronger than the dissipation of light and matter entities, one approaches the strong coupling regime resulting in the formation of half-light half-matter bosonic quasiparticles called microcavity polaritons. Here we report the evidence of strong light-matter coupling and formation of microcavity polaritons in a two dimensional atomic crystal of molybdenum disulphide (MoS2) embedded inside a dielectric microcavity at room temperature. A Rabi splitting of 46 meV and highly directional emission is observed from the MoS2 microcavity owing to the coupling between the 2D excitons and the cavity photons. Realizing strong coupling effects at room temperature in a disorder free potential landscape is central to the ...

  15. Near-atomic resolution structural model of the yeast 26S proteasome.

    Science.gov (United States)

    Beck, Florian; Unverdorben, Pia; Bohn, Stefan; Schweitzer, Andreas; Pfeifer, Günter; Sakata, Eri; Nickell, Stephan; Plitzko, Jürgen M; Villa, Elizabeth; Baumeister, Wolfgang; Förster, Friedrich

    2012-09-11

    The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits.

  16. High-resolution atomic force microscopy of duplex and triplex DNA molecules

    International Nuclear Information System (INIS)

    Double-stranded poly(dG)-poly(dC) and triple-stranded poly(dG)-poly(dG)-poly(dC) DNA were deposited on the modified surface of highly oriented pyrolitic graphite (HOPG) and visualized using atomic force microscopy with high-resolution (radius of ∼1 nm) tips. The high resolution attained by this technique enabled us to detect single-stranded regions in double-stranded poly(dG)-poly(dC) and double-stranded and single-stranded regions in poly(dG)-poly(dG)-poly(dC) triplexes, as well as to resolve the helical pitch of the triplex molecules. We could also follow the reaction of G-strand extension in poly(dG)-poly(dC) by the Klenow exo- fragment of DNA polymerase I. This approach to molecular visualization could serve as a useful tool for the investigation of irregular structures in canonical DNA and other biopolymers, as well as studies of the molecular mechanisms of DNA replication and transcription

  17. High-resolution atomic force microscopy of duplex and triplex DNA molecules

    Energy Technology Data Exchange (ETDEWEB)

    Klinov, Dmitry [Laboratory of Physics of Nanostructures, Ecole Polytechnique Federale de Lausanne (EPFL), Station 3, CH-1015 Lausanne (Switzerland); Dwir, Benjamin [Laboratory of Physics of Nanostructures, Ecole Polytechnique Federale de Lausanne (EPFL), Station 3, CH-1015 Lausanne (Switzerland); Kapon, Eli [Laboratory of Physics of Nanostructures, Ecole Polytechnique Federale de Lausanne (EPFL), Station 3, CH-1015 Lausanne (Switzerland); Borovok, Natalia [Department of Biochemistry, George S Wise Faculty of Life Sciences, Tel-Aviv University (Israel); Molotsky, Tatiana [Department of Biochemistry, George S Wise Faculty of Life Sciences, Tel-Aviv University (Israel); Kotlyar, Alexander [Department of Biochemistry, George S Wise Faculty of Life Sciences, Tel-Aviv University (Israel)

    2007-06-06

    Double-stranded poly(dG)-poly(dC) and triple-stranded poly(dG)-poly(dG)-poly(dC) DNA were deposited on the modified surface of highly oriented pyrolitic graphite (HOPG) and visualized using atomic force microscopy with high-resolution (radius of {approx}1 nm) tips. The high resolution attained by this technique enabled us to detect single-stranded regions in double-stranded poly(dG)-poly(dC) and double-stranded and single-stranded regions in poly(dG)-poly(dG)-poly(dC) triplexes, as well as to resolve the helical pitch of the triplex molecules. We could also follow the reaction of G-strand extension in poly(dG)-poly(dC) by the Klenow exo{sup -} fragment of DNA polymerase I. This approach to molecular visualization could serve as a useful tool for the investigation of irregular structures in canonical DNA and other biopolymers, as well as studies of the molecular mechanisms of DNA replication and transcription.

  18. High-resolution atomic force microscopy of duplex and triplex DNA molecules

    Science.gov (United States)

    Klinov, Dmitry; Dwir, Benjamin; Kapon, Eli; Borovok, Natalia; Molotsky, Tatiana; Kotlyar, Alexander

    2007-06-01

    Double-stranded poly(dG)-poly(dC) and triple-stranded poly(dG)-poly(dG)-poly(dC) DNA were deposited on the modified surface of highly oriented pyrolitic graphite (HOPG) and visualized using atomic force microscopy with high-resolution (radius of ~1 nm) tips. The high resolution attained by this technique enabled us to detect single-stranded regions in double-stranded poly(dG)-poly(dC) and double-stranded and single-stranded regions in poly(dG)-poly(dG)-poly(dC) triplexes, as well as to resolve the helical pitch of the triplex molecules. We could also follow the reaction of G-strand extension in poly(dG)-poly(dC) by the Klenow exo- fragment of DNA polymerase I. This approach to molecular visualization could serve as a useful tool for the investigation of irregular structures in canonical DNA and other biopolymers, as well as studies of the molecular mechanisms of DNA replication and transcription.

  19. Probing atomic-scale friction on reconstructed surfaces of single-crystal semiconductors

    Science.gov (United States)

    Goryl, M.; Budzioch, J.; Krok, F.; Wojtaszek, M.; Kolmer, M.; Walczak, L.; Konior, J.; Gnecco, E.; Szymonski, M.

    2012-02-01

    Friction force microscopy (FFM) investigations have been performed on reconstructed (001) surfaces of InSb and Ge in an ultrahigh vacuum. On the c(8×2) reconstruction of InSb(001) atomic resolution is achieved under superlubric conditions, and the features observed in the lateral force images are precisely reproduced by numerical simulations, taking into account possible decorations of the probing tip. On the simultaneously acquired (1×3) reconstruction a significant disorder of the surface atoms is observed. If the loading force increases, friction becomes much larger on this reconstruction compared to the c(8×2) one. In FFM images acquired on the Ge(001)(2×1) characteristic substructures are resolved within the unit cells. In such a case, a strong dependence of the friction pattern on the scan direction is observed.

  20. Determination of eight trace elements in doped crystal ALN by inductively coupled plasma atomic emission spectrometry

    International Nuclear Information System (INIS)

    Complete text of publication follows. In this paper, an accurate and simple method has been developed for the determination of trace Cr, Co, Cu, Fe, Mg, Mn ,Ni and Zn in doped AlN crystal using inductively coupled plasma atomic emission spectrometry (ICP-AES). AlN crystal becomes ideal substrate for the epitaxial growth of GaN, AlGaN with high Al ingredient and AlN which are used to fabricate ultraviolet LEDs, blue- ultraviolet solid state LDs, lasers, ultraviolet detectors. At present, It is a very important aspect for scientific workers to promote in the transition metals elements doped AlN showing ferromagne. Owing its low detection limits and multi-element capability, ICP-AES has been used in many fields.The optimum instrument working conditions are selected .AlN crystal was fused with KOH and the fusion product was dissolved in dilute aqua regia. Matrix effect from KOH and interference to the spectral lines of the elements to be determined were investigated and corrected by matrix matching and background correction method. Detection limits of elements were 0.01% to 0.0002% The recoveries for elements were 98% to 104%. The relative standard deviation was 0.5% to 4.0%.

  1. Characterization of a single LSO crystal layer High Resolution Research Tomograph

    International Nuclear Information System (INIS)

    The purpose of this study was to determine the performance of a single lutetium oxy-orthosilicate (LSO) crystal layer High Resolution Research Tomograph (HRRT) positron emission tomography (PET) scanner. The HRRT is a high resolution PET scanner designed for human brain and small animal imaging. The scanner consists of eight panel detectors, which have one layer of 2.1x2.1x7.5 mm thick LSO crystals. Several phantom studies were performed to determine scanner characteristics, such as resolution, scatter fraction, count rate and noise equivalent count rates (NECR). NECR curves were measured according to both NEMA NU2-1994 and NU2-2001 for three different energy windows, i.e. lower level discriminators (lld) of 350, 400 and 450 keV and an upper level discriminator (uld) of 650 keV. Accuracy of scatter and single photon attenuation corrections was evaluated according to NU2-1994. Data were acquired using a ring difference of 67 and a span of 9. Reconstructions were performed using FORE + 2D FBP or OSEM. Transaxial resolution varied from 2.7 to 2.9 mm FWHM between 1 and 10 cm off centre locations, and axial resolution varied from 3.2 to 4.4 mm FWHM. Scatter fractions (NU2-1994) equalled 0.31, 0.42 and 0.54 for lld of 450, 400 and 350 keV, respectively. NECR data were highest for an lld of 400 keV and showed a maximum of 46 kcps at 38 kBq cm-3. Lower NECR values were observed according to NU2-2001, but were still optimal for an lld of 400 keV. After scatter and attenuation corrections, pixel values within water, air and teflon inserts of the NU2-1994 phantom were 14, 4 and 35% of the background activity, respectively. The single layer LSO HRRT scanner shows excellent spatial resolution, making it suitable for small animal studies. The low count rate performance, due to the small amount of LSO, prohibits studies of the human brain, but is sufficient for studies in small laboratory animals

  2. Lineshape spectroscopy with a very high resolution, very high signal-to-noise crystal spectrometer

    Science.gov (United States)

    Beiersdorfer, P.; Magee, E. W.; Brown, G. V.; Chen, H.; Emig, J.; Hell, N.; Bitter, M.; Hill, K. W.; Allan, P.; Brown, C. R. D.; Hill, M. P.; Hoarty, D. J.; Hobbs, L. M. R.; James, S. F.

    2016-06-01

    We have developed a high-resolution x-ray spectrometer for measuring the shapes of spectral lines produced from laser-irradiated targets on the Orion laser facility. The instrument utilizes a spherically bent crystal geometry to spatially focus and spectrally analyze photons from foil or microdot targets. The high photon collection efficiency resulting from its imaging properties allows the instrument to be mounted outside the Orion chamber, where it is far less sensitive to particles, hard x-rays, or electromagnetic pulses than instruments housed close to the target chamber center in ten-inch manipulators. Moreover, Bragg angles above 50° are possible, which provide greatly improved spectral resolution compared to radially viewing, near grazing-incidence crystal spectrometers. These properties make the new instrument an ideal lineshape diagnostic for determining plasma temperature and density. We describe its calibration on the Livermore electron beam ion trap facility and present spectral data of the K-shell emission from highly charged sulfur produced by long-pulse as well as short-pulse beams on the Orion laser in the United Kingdom.

  3. 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.

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

    International Nuclear Information System (INIS)

    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. 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. 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

  5. Ionization of Atoms and the Thomas-Fermi Model for the Electric Field in Crystal Planar Channels

    Institute of Scientific and Technical Information of China (English)

    LIUYing-Tai; ZHANGQi-Ren; 等

    2002-01-01

    The electric field in the crystal planar channels is studied by the Thomas-Fermi method.The ThomasFermi equation and the corresponding boundary conditions are derived for the crystal palanar channels,The numerical solution for the elctric field in the channels between(110) Planes of the single crystal silicaon and the critical angles of channelling protons in them are shown.Reasonable agreements with the experimental data are obtained.The results show that the Thomas-Fermi method for the crystal works well in this study,and a microscopic research of the channel electric field with the contribution of all atoms and the atomic ionization being taken into account is practical.

  6. High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

    Science.gov (United States)

    Chiu, Thang K.; Kubelka, Jan; Herbst-Irmer, Regine; Eaton, William A.; Hofrichter, James; Davies, David R.

    2005-01-01

    The 35-residue subdomain of the villin headpiece (HP35) is a small ultrafast folding protein that is being intensely studied by experiments, theory, and simulations. We have solved the x-ray structures of HP35 and its fastest folding mutant [K24 norleucine (nL)] to atomic resolution and compared their experimentally measured folding kinetics by using laser temperature jump. The structures, which are in different space groups, are almost identical to each other but differ significantly from previously solved NMR structures. Hence, the differences between the x-ray and NMR structures are probably not caused by lattice contacts or crystal/solution differences, but reflect the higher accuracy of the x-ray structures. The x-ray structures reveal important details of packing of the hydrophobic core and some additional features, such as cross-helical H bonds. Comparison of the x-ray structures indicates that the nL substitution produces only local perturbations. Consequently, the finding that the small stabilization by the mutation is completely reflected in an increased folding rate suggests that this region of the protein is as structured in the transition state as in the folded structure. It is therefore a target for engineering to increase the folding rate of the subdomain from ≈0.5 μs–1 for the nL mutant to the estimated theoretical speed limit of ≈3 μs–1. PMID:15894611

  7. Atoms

    Institute of Scientific and Technical Information of China (English)

    刘洪毓

    2007-01-01

    Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what

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

    International Nuclear Information System (INIS)

    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. Atomic resolution strain analysis in highly textured FePt thin films

    Science.gov (United States)

    Wicht, S.; Wee, S. H.; Hellwig, O.; Mehta, V.; Jain, S.; Weller, D.; Rellinghaus, B.

    2016-03-01

    In this work, we present a detailed investigation of FePt-substrate interfaces and their influence towards the microstructural and magnetic configurations of the resulting metallic films. Discontinuous FePt films of roughly 15 nm thickness are deposited at 750 °C on MgO, MgAl2O4, SrTiO3, and (La,Sr)(Al,Ta)O3 single-crystalline substrates. All of these films mainly show out-of-plane textured FePt islands; however, fractions of L12 and in-plane oriented crystals are observed for the films on substrates with reduced lattice mismatch. Reduced easy axis coercivities and enhanced hard axis remanence values affirm this observation. Moreover, quantitative high-resolution transmission electron microscope analysis reveals that the reduced lattice mismatch results in a decreased density of dislocations, especially misfit dislocations, at the FePt-substrate interface. To further extend the research, carbon-doped FePt+32%C films are deposited on single-crystalline and sputtered MgO at 750 °C and 650 °C, respectively, to characterize the influence of a segregating media and reduced grain size. A comparison to the pure FePt sample reveals that the presence of seed layer grain boundaries leads to an increased fraction of in-plane oriented material, while the density of misfit dislocations solely depends on the degree of lattice mismatch.

  10. Design and implementation of an integral wall-mounted quartz crystal microbalance for atomic layer deposition.

    Science.gov (United States)

    Riha, Shannon C; Libera, Joseph A; Elam, Jeffrey W; Martinson, Alex B F

    2012-09-01

    Quartz crystal microbalance (QCM) measurements have played a vital role in understanding and expediting new atomic layer deposition (ALD) processes; however, significant barriers remain to their routine use and accurate execution. In order to turn this exclusively in situ technique into a routine characterization method, an integral QCM fixture was developed. This new design is easily implemented on a variety of chemical vapor deposition (CVD) tools, allows rapid sample exchange, prevents backside deposition, and minimizes both the footprint and flow disturbance. Unlike previous QCM designs, the fast thermal equilibration enables tasks such as temperature-dependent studies and ex situ sample exchange, further highlighting the utility of this QCM design for day-to-day use. Finally, the in situ mapping of thin film growth rates across the ALD reactor was demonstrated in a popular commercial tool operating in both continuous and quasi-static ALD modes. PMID:23020393

  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...... is approximated by a spherical one, which is dependent on the initial conditions of the individual scattering problem. For the spherical symmetrical potential, scattering angles and related quantities have been tabulated, but simple analytical approximations can be used too. As a result, one obtains...... 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...

  12. Quantum anomalous Hall effect in atomic crystal layers from in-plane magnetization

    Science.gov (United States)

    Ren, Yafei; Zeng, Junjie; Deng, Xinzhou; Yang, Fei; Pan, Hui; Qiao, Zhenhua

    2016-08-01

    We theoretically demonstrate that with in-plane magnetization, the quantum anomalous Hall effect (QAHE) can be realized in two-dimensional atomic crystal layers with preserved inversion symmetry but broken out-of-plane mirror reflection symmetry. By taking the honeycomb lattice system as an example, we find that the low-buckled structure satisfying the symmetry criteria is crucial to induce QAHE. The topologically nontrivial bulk gap carrying a Chern number of C =±1 opens in the vicinity of the saddle points M , where the band dispersion exhibits strong anisotropy. We further show that the QAHE with electrically tunable Chern number can be achieved in Bernal-stacked multilayer systems, and the applied interlayer potential differences can dramatically decrease the critical magnetization to make the QAHE experimentally feasible.

  13. Crystal structure of (L-Arg)-BO bovine insulin at 0.21 nm resolution

    Institute of Scientific and Technical Information of China (English)

    叶升; 万柱礼; 刘成国; 常文瑞; 梁栋材

    1996-01-01

    The crystal structure of (L-Arg)-B0 bovine insulin has been determined, using data to 0.21 nm and atomic parameters of 2Zn porcine insulin as a starting model, by the difference Fourier method, the restrained least square method and X-PLOR package, interspersed with careful review of the electron density, to a final R-factor of 0.182 and r.m.s. deviation of 0.002 2nm for the bond lengths and 4.3° for the bond angles. The electron densities of additional (L-Arg)-B0 residues to B-chain N-terminus of two monomers in each asymmetric unit are very dear. The crystallographic micro-environment of the N-terminus of the B-chain is different from that of rhombohedral 2-zinc insulin.

  14. High-resolution imaging of interfacial water by noncontact atomic force microscopy

    Science.gov (United States)

    Peng, Jinbo; Guo, Jing; Hapala, Prokop; Cao, Duanyun; Jelínek, Pavel; Xu, Limei; Wang, Enge; Jiang, Ying; Collaborative Innovation Center of Quantum Matter Collaboration

    Resolving the hydrogen-bonding configuration of water on the solid surfaces with atomic-scale precision is crucial in water science yet it remains challenging. Recently we have shown the possibility of attacking this problem by STM based on the submolecular orbital imaging of water. However, STM mainly probes the spatial distribution of the density of states near the Fermi level, thus is not sensitive to the chemical structure of molecules. Here we report the ultrahigh resolution imaging of water molecules on a NaCl film by NC-AFM, which enables us to determine the topology of hydrogen-bonding network in unprecedented details. Comparison with the theoretical simulations reveals that the sharp features in the AFM images result from the relaxation of the tip apex mainly due to the electrostatic force between the tip and the water molecules. Our results shed new light on the underlying mechanism of the ultrahigh imaging with NC-AFM and highlight the importance of electrostatics in the imaging of polar molecules such as water. This work was supported by the National Basic Research Programs of China.

  15. Slow light enhanced atomic frequency comb quantum memories in photonic crystal waveguides

    Science.gov (United States)

    Yuan, Chenzhi; Zhang, Wei; Huang, Yidong; Peng, Jiangde

    2016-09-01

    In this paper, we propose a slow light-enhanced quantum memory with high efficiency based on atomic frequency comb (AFC) in ion-doped photonic crystal waveguide (PCW). The performance of the quantum memory is investigated theoretically, considering the impact of the signal bandwidth. Both the forward and backward retrieval schemes are analyzed. In the forward retrieval scheme, the analysis shows that a moderate slow light effect can improve the retrieval efficiency to above 50% with very high fidelity, even when the intrinsic optical depth is very low and the signal bandwidth is comparable with the AFC bandwidth. In the backward retrieval scheme, retrieval efficiency larger than 90% can be obtained and fidelity can remain above 90% for signal with bandwidth much narrower than AFC bandwidth, when moderate slow light is introduced into waveguide with low intrinsic optical depth. Although the phase mismatching effect limits the slow light enhancement on retrieval efficiency and decreases the fidelity for signal with bandwidth approaching AFC bandwidth, we design a modified atomic frequency comb structure (MAFC) based on which a moderate slow light can make the retrieval efficiency larger than 85% and keep the fidelity above 80%. Our calculations show that the proposed scheme provides a promising way to realize high efficiency on-chip quantum memory.

  16. Near-atomic resolution analysis of BipD, a component of the type III secretion system of Burkholderia pseudomallei

    International Nuclear Information System (INIS)

    The type III secretion system needle-tip protein BipD has been crystallized in a form that diffracts X-rays to 1.5 Å resolution and the structure has been refined to an R factor of 16.1% and an Rfree of 19.8% at this resolution. The putative antiparallel dimer interface that was observed in earlier structures is conserved. Burkholderia pseudomallei, the causative agent of melioidosis, possesses a type III protein secretion apparatus that is similar to those found in Salmonella and Shigella. A major function of these secretion systems is to inject virulence-associated proteins into target cells of the host organism. The bipD gene of B. pseudomallei encodes a secreted virulence factor that is similar in sequence and is most likely to be functionally analogous to IpaD from Shigella and SipD from Salmonella. Proteins in this family are thought to act as extracellular chaperones at the tip of the secretion needle to help the hydrophobic translocator proteins enter the target cell membrane, where they form a pore and may also link the translocon pore with the secretion needle. BipD has been crystallized in a monoclinic crystal form that diffracted X-rays to 1.5 Å resolution and the structure was refined to an R factor of 16.1% and an Rfree of 19.8% at this resolution. The putative dimer interface that was observed in previous crystal structures was retained and a larger surface area was buried in the new crystal form

  17. Nuclear magnetic resonance parameters of atomic xenon dissolved in Gay-Berne model liquid crystal.

    Science.gov (United States)

    Lintuvuori, Juho; Straka, Michal; Vaara, Juha

    2007-03-01

    We present constant-pressure Monte Carlo simulations of nuclear magnetic resonance (NMR) spectral parameters, nuclear magnetic shielding relative to the free atom as well as nuclear quadrupole coupling, for atomic xenon dissolved in a model thermotropic liquid crystal. The solvent is described by Gay-Berne (GB) molecules with parametrization kappa=4.4, kappa{'}=20.0 , and mu=nu=1 . The reduced pressure of P{*}=2.0 is used. Previous simulations of a pure GB system with this parametrization have shown that upon lowering the temperature, the model exhibits isotropic, nematic, smectic- A , and smectic- B /molecular crystal phases. We introduce spherical xenon solutes and adjust the energy and length scales of the GB-Xe interaction to those of the GB-GB interaction. This is done through first principles quantum chemical calculations carried out for a dimer of model mesogens as well as the mesogen-xenon complex. We preparametrize quantum chemically the Xe nuclear shielding and quadrupole coupling tensors when interacting with the model mesogen, and use the parametrization in a pairwise additive fashion in the analysis of the simulation. We present the temperature evolution of {129/131}Xe shielding and 131Xe quadrupole coupling in the different phases of the GB model. From the simulations, separate isotropic and anisotropic contributions to the experimentally available total shielding can be obtained. At the experimentally relevant concentration, the presence of the xenon atoms does not significantly affect the phase behavior as compared to the pure GB model. The simulations reproduce many of the characteristic experimental features of Xe NMR in real thermotropic LCs: Discontinuity in the value or trends of the shielding and quadrupole coupling at the nematic-isotropic and smectic-A-nematic phase transitions, nonlinear shift evolution in the nematic phase reflecting the behavior of the orientational order parameter, and decreasing shift in the smectic-A phase. The last

  18. Crystal structure of a thiolase from Escherichia coli at 1.8 Å resolution.

    Science.gov (United States)

    Ithayaraja, M; Janardan, N; Wierenga, Rik K; Savithri, H S; Murthy, M R N

    2016-07-01

    Thiolases catalyze the Claisen condensation of two acetyl-CoA molecules to give acetoacetyl-CoA, as well as the reverse degradative reaction. Four genes coding for thiolases or thiolase-like proteins are found in the Escherichia coli genome. In this communication, the successful cloning, purification, crystallization and structure determination at 1.8 Å resolution of a homotetrameric E. coli thiolase are reported. The structure of E. coli thiolase co-crystallized with acetyl-CoA at 1.9 Å resolution is also reported. As observed in other tetrameric thiolases, the present E. coli thiolase is a dimer of two tight dimers and probably functions as a biodegradative enzyme. Comparison of the structure and biochemical properties of the E. coli enzyme with those of other well studied thiolases reveals certain novel features of this enzyme, such as the modification of a lysine in the dimeric interface, the possible oxidation of the catalytic Cys88 in the structure of the enzyme obtained in the presence of CoA and active-site hydration. The tetrameric enzyme also displays an interesting departure from exact 222 symmetry, which is probably related to the deformation of the tetramerization domain that stabilizes the oligomeric structure of the protein. The current study allows the identification of substrate-binding amino-acid residues and water networks at the active site and provides the structural framework required for understanding the biochemical properties as well as the physiological function of this E. coli thiolase. PMID:27380370

  19. 7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark; Zatsepin, Nadia A.; Barty, Anton; Benner, Henry; Boutet, Sebastien; Feld, Geoffrey K.; Hau-Riege, Stefan; Kirian, Rick; Kupitz, Christopher; Messerschmidt, Marc; Ogren, John I.; Pardini, Tommaso; Segelke, Brent; Williams, Garth J.; Spence , John C.; Abela, Rafael; Coleman, Matthew A.; Evans, James E.; Schertler, Gebhard; Frank, Matthias; Li, Xiao-Dan

    2014-06-09

    Membrane proteins arranged as two-dimensional (2D) crystals in the lipid en- vironment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. X-ray diffraction from individual 2D crystals did not represent a suitable investigation tool because of radiation damage. The recent availability of ultrashort pulses from X-ray Free Electron Lasers (X-FELs) has now provided a mean to outrun the damage. Here we report on measurements performed at the LCLS X-FEL on bacteriorhodopsin 2D crystals mounted on a solid support and kept at room temperature. By merg- ing data from about a dozen of single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 °A, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase of resolution. The presented results pave the way to further X-FEL studies on 2D crystals, which may include pump-probe experiments at subpicosecond time resolution.

  20. 7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source.

    Science.gov (United States)

    Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark S; Zatsepin, Nadia A; Barty, Anton; Benner, W Henry; Boutet, Sébastien; Feld, Geoffrey K; Hau-Riege, Stefan P; Kirian, Richard A; Kupitz, Christopher; Messerschmitt, Marc; Ogren, John I; Pardini, Tommaso; Segelke, Brent; Williams, Garth J; Spence, John C H; Abela, Rafael; Coleman, Matthew; Evans, James E; Schertler, Gebhard F X; Frank, Matthias; Li, Xiao-Dan

    2014-07-17

    Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump-probe experiments at subpicosecond time resolution. PMID:24914166

  1. Periodic order and defects in Ni-based inverse opal-like crystals on the mesoscopic and atomic scale

    NARCIS (Netherlands)

    Chumakova, A. V.; Valkovskiy, G. A.; Mistonov, A. A.; Dyadkin, V. A.; Grigoryeva, N. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Petukhov, Andrei V.; Grigoriev, S. V.

    2014-01-01

    The structure of inverse opal crystals based on nickel was probed on the mesoscopic and atomic levels by a set of complementary techniques such as scanning electron microscopy and synchrotron microradian and wide-angle diffraction. The microradian diffraction revealed the mesoscopic-scale face-cente

  2. 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. PMID:26907400

  3. Atomic-resolution studies of In2O3-ZnO compounds on aberration-corrected electron microscopes

    International Nuclear Information System (INIS)

    In this work, the characteristic inversion domain microstructures of In2O3(ZnO)m (m=30) compounds were investigated by TEM methods. At bright-atom contrast condition, atomically resolved HR-TEM images of In2O3(ZnO)30 were successfully acquired in [1 anti 100] zone axis of ZnO, with projected metal columns of ∝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 In2O3(ZnO)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 In2O3(ZnO)m compounds by using phase-contrast and Z-contrast imaging at atomic resolution, In3+ atoms are determined with trigonal bi-pyramidal co-ordination and are distributed at the pyramidal IDBs. (orig.)

  4. Fast timing study of a CeBr3 crystal: Time resolution below 120 ps at 60Co energies

    International Nuclear Information System (INIS)

    We report on the time response of a novel inorganic scintillator, CeBr3. The measurements were performed using a cylindrical crystal of 1-in. in height and 1-in. in diameter at 22Na and 60Co photon energies. The time response was measured against a fast reference BaF2 detector. Hamamatsu R9779 and Photonis XP20D0 fast photomultipliers (PMTs) were used. The PMT bias voltages and Constant Fraction Discriminator settings were optimized with respect to the timing resolution. The Full Width at Half Maximum (FWHM) time resolution for an individual CeBr3 crystal coupled to Hamamatsu PMT is found here to be as low as 119 ps at 60Co energies, which is comparable to the resolution of 107 ps reported for LaBr3(Ce). For 511 keV photons the measured FWHM time resolution for CeBr3 coupled to the Hamamatsu PMT is 164 ps.

  5. Calculating hyperfine couplings in large ionic crystals containing hundreds of QM atoms: subsystem DFT is the key.

    Science.gov (United States)

    Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele

    2013-11-14

    We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

  6. Atomic layer deposition of epitaxial layers of anatase on strontium titanate single crystals: Morphological and photoelectrochemical characterization

    Energy Technology Data Exchange (ETDEWEB)

    Kraus, Theodore J.; Nepomnyashchii, Alexander B.; Parkinson, B. A., E-mail: bparkin1@uwyo.edu [Department of Chemistry, School of Energy Resources, University of Wyoming, Laramie, Wyoming 82071 (United States)

    2015-01-15

    Atomic layer deposition was used to grow epitaxial layers of anatase (001) TiO{sub 2} on the surface of SrTiO{sub 3} (100) crystals with a 3% lattice mismatch. The epilayers grow as anatase (001) as confirmed by x-ray diffraction. Atomic force microscope images of deposited films showed epitaxial layer-by-layer growth up to about 10 nm, whereas thicker films, of up to 32 nm, revealed the formation of 2–5 nm anatase nanocrystallites oriented in the (001) direction. The anatase epilayers were used as substrates for dye sensitization. The as received strontium titanate crystal was not sensitized with a ruthenium-based dye (N3) or a thiacyanine dye (G15); however, photocurrent from excited state electron injection from these dyes was observed when adsorbed on the anatase epilayers. These results show that highly ordered anatase surfaces can be grown on an easily obtained substrate crystal.

  7. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits.

    Science.gov (United States)

    Passos, Dario Oliveira; Lyumkis, Dmitry

    2015-11-01

    A single-particle cryoEM reconstruction of the large ribosomal subunit from Saccharomyces cerevisiae was obtained from a dataset of ∼75,000 particles. The gold-standard and frequency-limited approaches to single-particle refinement were each independently used to determine orientation parameters for the final reconstruction. Both approaches showed similar resolution curves and nominal resolution values for the 60S dataset, estimated at 2.9 Å. The amount of over-fitting present during frequency-limited refinement was quantitatively analyzed using the high-resolution phase-randomization test, and the results showed no apparent over-fitting. The number of asymmetric subunits required to reach specific resolutions was subsequently analyzed by refining subsets of the data in an ab initio manner. With our data collection and processing strategies, sub-nanometer resolution was obtained with ∼200 asymmetric subunits (or, equivalently for the ribosomal subunit, particles). Resolutions of 5.6 Å, 4.5 Å, and 3.8 Å were reached with ∼1000, ∼1600, and ∼5000 asymmetric subunits, respectively. At these resolutions, one would expect to detect alpha-helical pitch, separation of beta-strands, and separation of Cα atoms, respectively. Using this map, together with strategies for ab initio model building and model refinement, we built a region of the ribosomal protein eL6, which was missing in previous models of the yeast ribosome. The relevance for more routine high-resolution structure determination is discussed.

  8. X-ray diffraction analysis of LiCu2O2 crystals with additives of silver atoms

    International Nuclear Information System (INIS)

    Silver-containing LiCu2O2 crystals up to 4 × 8 × 8 mm in size were grown by the crystallization of 80(1-x)CuO · 20xAgNO3 · 20Li2CO3 (0 ≤ x ≤ 0.5) mixture melt. According to the X-ray spectral and Rietveld X-ray diffraction data, the maximum amount of silver incorporated in the LiCu2O2 structure is about 4 at % relative to the copper content. It was established that silver atoms occupy statistically crystallographic positions of lithium atoms. The incorporation of silver atoms is accompanied by a noticeable increase in parameter c of the LiCu2O2 rhombic unit cell, a slight increase in parameter a, and a slight decrease in parameter b

  9. Crystal Structure of Bovine Mitochondrial Factor B at 0.96-Angstrom Resolution

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J.K.; Belogrudov, G.I.; Stroud, R.M.

    2009-05-20

    Coupling factor B (FB) is a mitochondrial inner membrane polypeptide that facilitates the energy-driven catalysis of ATP synthesis in animal mitochondria by blocking a proton leak across the membrane. Here, we report the crystal structure of the bovine mitochondrial FB mutant with Gly-3-Glu substitution determined at a resolution of 0.96 {angstrom} and that of the WT polypeptide at a resolution of 2.9 {angstrom}. The structure reveals an oblong, oval-shaped molecule with a unique globular N-terminal domain that is proposed to be the membrane anchor domain and the capping region to the C-terminal leucine-rich repeats domain. A short N-terminal {alpha}-helix, which extends away from the molecule's body, is suggestive of functioning as an anchor for FB to the matrix side of the mitochondrial inner membrane. Identification of a bound Mg{sup 2+} ion reveals that FB is a metalloprotein. We also report the cocrystal structures of FB bound with phenylarsine oxide and Cd{sup 2+}, two known inhibitors of the FB coupling activity.

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

    International Nuclear Information System (INIS)

    This progress report describes work carried out in the study of surface structure and dynamics of ionic insulators, the microscopic interactions controlling epitaxial growth and the formation of overlayers, and energy exchange in multiphonon surface scattering. The approach used is to employ high resolution helium atom scattering to study the geometry and structural features of the surfaces. Experiments have been carried out on the surface dynamics of RbCl and preliminary studies done on CoO and NiO. Epitaxial growth and overlayer dynamics experiments on the systems NaCl/NaCl(001), KBr/NaCl(001), NaCl/KBr(001) and KBr/RbCl(001) have been performed. They have collaborated with two theoretical groups to explore models of overlayer dynamics with which to compare and to interpret their experimental results. They have carried out extensive experiments on the multiphonon scattering of helium atoms from NaCl and, particularly, LiF. Work has begun on self-assembling organic films on gold and silver surfaces (alkyl thiols/Au(111) and Ag(111))

  11. 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

    2015-02-01

    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. PMID:25393218

  12. Low temperature interdiffusion in the HgCdTe/CdTe system, studied at near-atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Y.; Ourmazd, A.; Feldman, R.D. (AT T Bell Laboratories, Holmdel, New Jersey 07733 (US))

    1990-03-01

    By combining chemical lattice imaging and vector pattern recognition we determine, as a function of annealing temperature, the composition of individual atomic planes across each HgCdTe/CdTe interface of a multiquantum well stack. The resultant composition profiles, which directly reveal the chemical change across each interface at near atomic resolution, are analyzed in terms of linear and nonlinear diffusion theory, to deduce the interdiffusion coefficient and its activation energy. We find the interdiffusion coefficient to be nonlinear, and a sensitive function of the interface depth beneath the surface.

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

    International Nuclear Information System (INIS)

    Investigations have focused primarily on surface structure and dynamics of ionic insulators, epitaxial growth onto alkali halide crystals and multiphoton studies. The surface dynamics of RbCl has been re-examined. We have developed a simple force constant model which provides insight into the dynamics of KBr overlayers on NaCl(001), a system with a large lattice mismatch. The KBr/NaCl(001) results are compared to Na/Cu(001) and NaCl/Ge(001). We have completed epitaxial growth experiments for KBr onto RbCl(001). Slab dynamics calculations using a shell model for this system with very small lattice mismatch are being carried out in collaboration with Professor Manson of Clemson University and with Professor Schroeder in Regensburg, Germany. Extensive experiments on multiphoton scattering of helium atoms onto NaCl and, particularly, LiF have been carried out and the theory has been developed to a rather advanced stage by Professor Manson. This work will permit the extraction of more information from time-of-flight spectra. It is shown that the theoretical model provides a very good description of the multiphoton scattering from organic films. Work has started on self-assembling organic films on gold (alkyl thiols/Au(111)). We have begun to prepare and characterize the gold crystal; one of the group members has spent two weeks at the Oak Ridge National Laboratory learning the proper Au(111) preparation techniques. One of our students has carried out neutron scattering experiments on NiO, measuring both bulk phonon and magnon dispersion curves

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

    Science.gov (United States)

    Malinska, Maura; Dauter, Zbigniew

    2016-06-01

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

  15. 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 ...

  16. Methods to extract more light from minute scintillation crystals used in an ultra-high resolution positron emission tomography detector

    Energy Technology Data Exchange (ETDEWEB)

    Levin, Craig S. E-mail: clevin@stanford.edu; Habte, Frezghi; Foudray, Angela M

    2004-07-11

    Recently, there has been great interest in developing finely pixellated position-sensitive scintillation detectors for ultra-high-resolution Positron Emission Tomography (PET) systems designed for breast cancer detection, diagnosis, and staging and for imaging small laboratory animals. We are developing a different high-resolution PET detector design that promotes nearly complete scintillation light collection in {<=}1 mm wide, >10 mm thick lutetium oxyorthosilicate (LSO) crystals. The design requires the use of semiconductor photodetector arrays in novel configurations that significantly improve the light collection aspect ratio for minute crystals. To reduce design complexity and dead area we are investigating the use of 1 mm thick sheets of LSO in addition to discrete crystal rods, and the use of position-sensitive avalanche photodiodes (PSAPDs) which require only four readout channels per device, in addition to pixellated APD arrays. Using a 1 mm thick scintillation crystal sheet coupled to a finely pixellated APD array results in a pseudo-discrete response to flood irradiation: due to a very narrow light spread function in the thin sheet we observe sharp (<1 mm wide) peaks in sensitivity centered at the APD pixel locations in a very linear fashion all the way out to the crystal edge. We measured an energy resolution of 13.7% FWHM at 511 keV for a 1 mm LSO crystal coupled to two APD pixels. Using a 1 mm thick crystal sheet coupled to a PSAPD the response to flood and edge-on irradiation with a {sup 22}Na point source shows a compressed dynamic range compared to that observed with discrete crystals or direct X-ray irradiation. With a discrete LSO crystal array the flood response is peaked at the crystal location where light is focused onto one spot on the PSAPD. We observed strong pin-cushioning effects in all PSAPD measurements. All LSO-PSAPD configurations studied had high aspect ratio for light collection and achieved energy resolutions {<=}12% FWHM at 511 keV.

  17. Methods to extract more light from minute scintillation crystals used in an ultra-high resolution positron emission tomography detector

    Science.gov (United States)

    Levin, Craig S.; Habte, Frezghi; Foudray, Angela M.

    2004-07-01

    Recently, there has been great interest in developing finely pixellated position-sensitive scintillation detectors for ultra-high-resolution Positron Emission Tomography (PET) systems designed for breast cancer detection, diagnosis, and staging and for imaging small laboratory animals. We are developing a different high-resolution PET detector design that promotes nearly complete scintillation light collection in ⩽1 mm wide, >10 mm thick lutetium oxyorthosilicate (LSO) crystals. The design requires the use of semiconductor photodetector arrays in novel configurations that significantly improve the light collection aspect ratio for minute crystals. To reduce design complexity and dead area we are investigating the use of 1 mm thick sheets of LSO in addition to discrete crystal rods, and the use of position-sensitive avalanche photodiodes (PSAPDs) which require only four readout channels per device, in addition to pixellated APD arrays. Using a 1 mm thick scintillation crystal sheet coupled to a finely pixellated APD array results in a pseudo-discrete response to flood irradiation: due to a very narrow light spread function in the thin sheet we observe sharp (<1 mm wide) peaks in sensitivity centered at the APD pixel locations in a very linear fashion all the way out to the crystal edge. We measured an energy resolution of 13.7% FWHM at 511 keV for a 1 mm LSO crystal coupled to two APD pixels. Using a 1 mm thick crystal sheet coupled to a PSAPD the response to flood and edge-on irradiation with a 22Na point source shows a compressed dynamic range compared to that observed with discrete crystals or direct X-ray irradiation. With a discrete LSO crystal array the flood response is peaked at the crystal location where light is focused onto one spot on the PSAPD. We observed strong pin-cushioning effects in all PSAPD measurements. All LSO-PSAPD configurations studied had high aspect ratio for light collection and achieved energy resolutions ⩽12% FWHM at 511 keV.

  18. 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. PMID:27572730

  19. Understanding 2D atomic resolution imaging of the calcite surface in water by frequency modulation atomic force microscopy

    Science.gov (United States)

    Tracey, John; Miyazawa, Keisuke; Spijker, Peter; Miyata, Kazuki; Reischl, Bernhard; Federici Canova, Filippo; Rohl, Andrew L.; Fukuma, Takeshi; Foster, Adam S.

    2016-10-01

    Frequency modulation atomic force microscopy (FM-AFM) experiments were performed on the calcite (10\\bar{1}4) surface in pure water, and a detailed analysis was made of the 2D images at a variety of frequency setpoints. We observed eight different contrast patterns that reproducibly appeared in different experiments and with different measurement parameters. We then performed systematic free energy calculations of the same system using atomistic molecular dynamics to obtain an effective force field for the tip-surface interaction. By using this force field in a virtual AFM simulation we found that each experimental contrast could be reproduced in our simulations by changing the setpoint, regardless of the experimental parameters. This approach offers a generic method for understanding the wide variety of contrast patterns seen on the calcite surface in water, and is generally applicable to AFM imaging in liquids.

  20. Progress in hollow core photonic crystal fiber for atomic vapour based coherent optics

    Science.gov (United States)

    Bradley, T. D.; Wang, Y. Y.; Alharbi, M.; Fourcade Dutin, C.; Mangan, B. J.; Wheeler, N. V.; Benabid, F.

    2012-03-01

    We report on progress in different hollow core photonic crystal fiber (HC-PCF) design and fabrication for atomic vapor based applications. We have fabricated a Photonic bandgap (PBG) guiding HC-PCF with a record loss of 107dB/km at 785nm in this class of fiber. A double photonic bandgap (DPBG) guiding HC-PCF with guidance bands centred at 780nm and 1064nm is reported. A 7-cell 3-ring Kagome HC-PCF with hypocycloid core is reported, the optical loss at 780nm has been reduced to 70dB/km which to the best of our knowledge is the lowest optical loss reported at this wavelength using HC-PCF. Details on experimental loading of alkali metal vapours using a far off red detuned laser are reported. This optical loading has been shown to decrease the necessary loading time for Rb into the hollow core of a fiber. The quantity of Rb within the fiber core has been enhanced by a maximum of 14% through this loading procedure.

  1. Molecular self-assembly on two-dimensional atomic crystals: insights from molecular dynamics simulations.

    Science.gov (United States)

    Zhao, Yinghe; Wu, Qisheng; Chen, Qian; Wang, Jinlan

    2015-11-19

    van der Waals (vdW) epitaxy of ultrathin organic films on two-dimensional (2D) atomic crystals has become a sovereign area because of their unique advantages in organic electronic devices. However, the dynamic mechanism of the self-assembly remains elusive. Here, we visualize the nanoscale self-assembly of organic molecules on graphene and boron nitride monolayer from a disordered state to a 2D lattice via molecular dynamics simulation for the first time. It is revealed that the assembly toward 2D ordered structures is essentially the minimization of the molecule-molecule interaction, that is, the vdW interaction in nonpolar systems and the vdW and Coulomb interactions in polar systems that are the decisive factors for the formation of the 2D ordering. The role of the substrate is mainly governing the array orientation of the adsorbates. The mechanisms unveiled here are generally applicable to a broad class of organic thin films via vdW epitaxy. PMID:26523464

  2. Following Ostwald ripening in nanoalloys by high-resolution imaging with single-atom chemical sensitivity

    International Nuclear Information System (INIS)

    Several studies have shown that substantial compositional changes can occur during the coarsening of bimetallic nanoparticles (CoPt, AuPd). To explain this phenomenon that could dramatically impacts all the technologically relevant properties of nanoalloys, we have exploited the sensitivity of the latest generation of electron microscope to prove that during the beam-induced coarsening of CoPt nanoparticles, the dynamic of atom exchanges between the particles is different for Co and Pt. By distinguishing the chemical nature of individual atoms of Co and Pt, while they are diffusing on a carbon film, we have clearly shown that Co atoms have a higher mobility than Pt atoms because of their higher evaporation rate from the particles. These atomic-scale observations bring the experimental evidence on the origin of the compositional changes in nanoalloys induced by Ostwald ripening mechanisms.

  3. Following Ostwald ripening in nanoalloys by high-resolution imaging with single-atom chemical sensitivity

    Science.gov (United States)

    Alloyeau, D.; Oikawa, T.; Nelayah, J.; Wang, G.; Ricolleau, C.

    2012-09-01

    Several studies have shown that substantial compositional changes can occur during the coarsening of bimetallic nanoparticles (CoPt, AuPd). To explain this phenomenon that could dramatically impacts all the technologically relevant properties of nanoalloys, we have exploited the sensitivity of the latest generation of electron microscope to prove that during the beam-induced coarsening of CoPt nanoparticles, the dynamic of atom exchanges between the particles is different for Co and Pt. By distinguishing the chemical nature of individual atoms of Co and Pt, while they are diffusing on a carbon film, we have clearly shown that Co atoms have a higher mobility than Pt atoms because of their higher evaporation rate from the particles. These atomic-scale observations bring the experimental evidence on the origin of the compositional changes in nanoalloys induced by Ostwald ripening mechanisms.

  4. In-situ atomic layer deposition of tri-methylaluminum and water on pristine single-crystal (In)GaAs surfaces: electronic and electric structures

    Science.gov (United States)

    Pi, T. W.; Lin, Y. H.; Fanchiang, Y. T.; Chiang, T. H.; Wei, C. H.; Lin, Y. C.; Wertheim, G. K.; Kwo, J.; Hong, M.

    2015-04-01

    The electronic structure of single-crystal (In)GaAs deposited with tri-methylaluminum (TMA) and water via atomic layer deposition (ALD) is presented with high-resolution synchrotron radiation core-level photoemission and capacitance-voltage (CV) characteristics. The interaction of the precursor atoms with (In)GaAs is confined at the topmost surface layer. The Ga-vacant site on the GaAs(111)A-2 × 2 surface is filled with Al, thereby effectively passivating the As dangling bonds. The As-As dimers on the GaAs(001)-2 × 4 surface are entirely passivated by one cycle of TMA and water. The presumed layerwise deposition fails to happen in GaAs(001)-4 × 6. In In0.20Ga0.80As(001)-2 × 4, the edge row As atoms are partially bonded with the Al, and one released methyl then bonds with the In. It is suggested that the unpassivated surface and subsurface atoms cause large frequency dispersions in CV characteristics under the gate bias. We also found that the (In)GaAs surface is immune to water in ALD. However, the momentary exposure of it to air (less than one minute) introduces significant signals of native oxides. This indicates the necessity of in situ works of high κ/(In)GaAs-related experiments in order to know the precise interfacial atomic bonding and thus know the electronic characteristics. The electric CV measurements of the ALD-Al2O3 on these (In)GaAs surfaces are correlated with their electronic properties.

  5. Crystal structure determination of thymoquinone by high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Pagola, S; Benavente, A; Raschi, A; Romano, E; Molina, M A A; Stephens, P W

    2004-01-01

    The crystal structure of 2-isopropyl-5-methyl-1,4-benzoquinone (thymoquinone) and its thermal behavior--as necessary physical and chemical properties--were determined in order to enhance the current understanding of thymoquinone chemical action by using high resolution x-ray powder diffraction, Fourier transform infrared spectroscopy (FTIR), and 3 thermo-analytical techniques thermogravimetric analysis (TGA), differential thermal analysis (DTA), and differential scanning calorimetry (DSC). The findings obtained with high-resolution x-ray powder diffraction and molecular location methods based on a simulated annealing algorithm after Rietveld refinement showed that the triclinic unit cell was a = 6.73728(8) A, b = 6.91560(8) A, c = 10.4988(2) A, alpha = 88.864(2) degrees, beta = 82.449(1) degrees, gamma = 77.0299(9) degrees; cell volume = 472.52(1) A3, Z = 2, and space group P1. In addition, FTIR spectrum revealed absorption bands corresponding to the carbonyl and C-H stretching of aliphatic and vinylic groups characteristically observed in such p-benzoquinones. Also, a chemical decomposition process starting at 65 degrees C and ending at 213 degrees C was noted when TGA was used. DSC allowed for the determination of onset at 43.55 degrees C and a melting enthalpy value of DeltaH(m) = 110.6 J/g. The low value obtained for the fusion point displayed a van der Waals pattern for molecular binding, and the thermograms performed evidence that thymoquinone can only be found in crystalline triclinic form, as determined by DRX methods. PMID:15760086

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

    OpenAIRE

    Akihiko Nakatsuka; Kazumasa Sugiyama; Akira Yoneda; Keiko Fujiwara; Akira Yoshiasa

    2015-01-01

    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...

  7. High Resolution Imaging of Defect Structures in Polymer and Organic Molecular Crystals

    Science.gov (United States)

    Martin, David

    2003-03-01

    We have been developing techniques for the low dose High Resolution Electron Microscopy (HREM) imaging of defect structures in polymer and organic molecular crystals. We have examined a variety of technologically important materials systems including rigid-rod polymers, poly(imides), poly(diacetylenes), poly(bisthiazoles), poly(bisoxazoles), and aromatic polyamides such as poly(paraphenylene terephthalamide) (PPTA or Kevlar(R)) and poly(metaphenylene diisophthalamide) (MPDI or Nomex(R)). These studies have made it possible for us to image the molecular reorganization in the vicinity of dislocations, surfaces, and grain boundaries. We have also learned about the micromechanisms of lattice bending and twisting. Most recently we have been examining the microstructure of pentacene, a highly-crystalline conjugated organic small molecule that is of interest for making flexible electronic devices such as thin-film transistors. We have also been examing the utility of low voltage techniques using a table-top sized electron microscope that operates near 5 kV.

  8. Crystal structure of phosphoglucomutase from Leishmania major at 3.5 Å resolution.

    Science.gov (United States)

    Waugh, Barnali; Sen, Udayaditya; Banerjee, Rahul

    2016-02-01

    The crystal structure of phosphoglucomutase (LmPGM) from the parasite Leishmania major has been solved at 3.5 Å resolution. Although the active form of the enzyme is monomeric in solution, four molecules (A, B, C, D) were found in the asymmetric unit, of which the pairs (A,D) and (B,C) were of identical inter-subunit geometry. The parasitic enzyme constituted of four domains exhibited the canonical 'heart' shape of the protein, with domains I to III having a conserved α|β core, while the fourth (IV) domain being structurally distinct from the rest. Conformational variability of the IVth domain, postulated to be responsible for the catalytic function of the enzyme has been studied by normal mode analysis (NMA) and the conformational features responsible for domain movement in the 'hinge region' analyzed in detail. Although the active site of phosphoglucomutase is highly conserved from parasite to human, initial calculations show that a ligand binding pocket could exist near the hinge region, which is unique to the parasite. The enzymatic parameters of LmPGM have been determined and compared with other PGMs from orthologous species in addition to elucidating its mechanism of action by docking the substrate, intermediate onto the active site.

  9. Inhibition of lactoperoxidase by its own catalytic product: crystal structure of the hypothiocyanate-inhibited bovine lactoperoxidase at 2.3-A resolution.

    Science.gov (United States)

    Singh, A K; Singh, Nagendra; Sharma, Sujata; Shin, Kouichirou; Takase, Mitsunori; Kaur, Punit; Srinivasan, A; Singh, T P

    2009-01-01

    To the best of our knowledge, this is the first report on the structure of product-inhibited mammalian peroxidase. Lactoperoxidase is a heme containing an enzyme that catalyzes the inactivation of a wide range of microorganisms. In the presence of hydrogen peroxide, it preferentially converts thiocyanate ion into a toxic hypothiocyanate ion. Samples of bovine lactoperoxidase containing thiocyanate (SCN(-)) and hypothiocyanate (OSCN(-)) ions were purified and crystallized. The structure was determined at 2.3-A resolution and refined to R(cryst) and R(free) factors of 0.184 and 0.221, respectively. The determination of structure revealed the presence of an OSCN(-) ion at the distal heme cavity. The presence of OSCN(-) ions in crystal samples was also confirmed by chemical and spectroscopic analysis. The OSCN(-) ion interacts with the heme iron, Gln-105 N(epsilon1), His-109 N(epsilon2), and a water molecule W96. The sulfur atom of the OSCN(-) ion forms a hypervalent bond with a nitrogen atom of the pyrrole ring D of the heme moiety at an S-N distance of 2.8 A. The heme group is covalently bound to the protein through two ester linkages involving carboxylic groups of Glu-258 and Asp-108 and the modified methyl groups of pyrrole rings A and C, respectively. The heme moiety is significantly distorted from planarity, whereas pyrrole rings A, B, C, and D are essentially planar. The iron atom is displaced by approximately 0.2 A from the plane of the heme group toward the proximal site. The substrate channel resembles a long tunnel whose inner walls contain predominantly aromatic residues such as Phe-113, Phe-239, Phe-254, Phe-380, Phe-381, Phe-422, and Pro-424. A phosphorylated Ser-198 was evident at the surface, in the proximity of the calcium-binding channel.

  10. High-resolution neutron protein crystallography with radically small crystal volumes: Application of perdeuteration to human aldose reductase

    International Nuclear Information System (INIS)

    Neutron diffraction data have been collected to 2.2 (angstrom) resolution from a small (0.15 mm3) crystal of perdeuterated human aldose reductase (h-AR; MW = 36 kDa) in order to help to determine the protonation state of the enzyme. h-AR belongs to the aldo-keto reductase family and is implicated in diabetic complications. Its ternary complexes (h-AR-coenzyme NADPH-selected inhibitor) provide a good model to study both the enzymatic mechanism and inhibition. Here, the successful production of fully deuterated human aldose reductase (h-AR(D)), subsequent crystallization of the ternary complex h-AR(D)-NADPH-IDD594 and neutron Laue data collection at the LADI instrument at ILL using a crystal volume of just 0.15 mm3 are reported. Neutron data were recorded to 2 (angstrom) resolution, with subsequent data analysis using data to 2.2 (angstrom). This is the first fully deuterated enzyme of this size (36 kDa) to be solved by neutron diffraction and represents a milestone in the field, as the crystal volume is at least one order of magnitude smaller than those usually required for other high-resolution neutron structures determined to date. This illustrates the significant increase in the signal-to-noise ratio of data collected from perdeuterated crystals and demonstrates that good-quality neutron data can now be collected from more typical protein crystal volumes. Indeed, the signal-to-noise ratio is then dominated by other sources of instrument background, the nature of which is under investigation. This is important for the design of future instruments, which should take maximum advantage of the reduction in the intrinsic diffraction pattern background from fully deuterated samples.

  11. Atomic resolution structure of cucurmosin, a novel type 1 ribosome-inactivating protein from the sarcocarp of Cucurbita moschata.

    Science.gov (United States)

    Hou, Xiaomin; Meehan, Edward J; Xie, Jieming; Huang, Mingdong; Chen, Minghuang; Chen, Liqing

    2008-10-01

    A novel type 1 ribosome-inactivating protein (RIP) designated cucurmosin was isolated from the sarcocarp of Cucurbita moschata (pumpkin). Besides rRNA N-glycosidase activity, cucurmosin exhibits strong cytotoxicities to three cancer cell lines of both human and murine origins, but low toxicity to normal cells. Plant genomic DNA extracted from the tender leaves was amplified by PCR between primers based on the N-terminal sequence and X-ray sequence of the C-terminal. The complete mature protein sequence was obtained from N-terminal protein sequencing and partial DNA sequencing, confirmed by high resolution crystal structure analysis. The crystal structure of cucurmosin has been determined at 1.04A, a resolution that has never been achieved before for any RIP. The structure contains two domains: a large N-terminal domain composed of seven alpha-helices and eight beta-strands, and a smaller C-terminal domain consisting of three alpha-helices and two beta-strands. The high resolution structure established a glycosylation pattern of GlcNAc(2)Man(3)Xyl. Asn225 was identified as a glycosylation site. Residues Tyr70, Tyr109, Glu158 and Arg161 define the active site of cucurmosin as an RNA N-glycosidase. The structural basis of cytotoxicity difference between cucurmosin and trichosanthin is discussed.

  12. Atomic resolution structure of cucurmosin, a novel type 1 ribosome-inactivating protein from the sarcocarp of Cucurbita moschata

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Xiaomin; Meehan, Edward J.; Xie, Jieming; Huang, Mingdong; Chen, Minghuang; Chen, Liqing (UAH); (Fujian); (Chinese Aca. Sci.)

    2008-10-27

    A novel type 1 ribosome-inactivating protein (RIP) designated cucurmosin was isolated from the sarcocarp of Cucurbita moschata (pumpkin). Besides rRNA N-glycosidase activity, cucurmosin exhibits strong cytotoxicities to three cancer cell lines of both human and murine origins, but low toxicity to normal cells. Plant genomic DNA extracted from the tender leaves was amplified by PCR between primers based on the N-terminal sequence and X-ray sequence of the C-terminal. The complete mature protein sequence was obtained from N-terminal protein sequencing and partial DNA sequencing, confirmed by high resolution crystal structure analysis. The crystal structure of cucurmosin has been determined at 1.04 {angstrom}, a resolution that has never been achieved before for any RIP. The structure contains two domains: a large N-terminal domain composed of seven {alpha}-helices and eight {beta}-strands, and a smaller C-terminal domain consisting of three {alpha}-helices and two {beta}-strands. The high resolution structure established a glycosylation pattern of GlcNAc{sub 2}Man3Xyl. Asn225 was identified as a glycosylation site. Residues Tyr70, Tyr109, Glu158 and Arg161 define the active site of cucurmosin as an RNA N-glycosidase. The structural basis of cytotoxicity difference between cucurmosin and trichosanthin is discussed.

  13. Retrieval of Cloud Phase and Crystal Habit from Multiangle Imaging Spectroradiometer (MISR) and Moderate Resolution Imaging Spectroradiometer (MODIS) Data

    Energy Technology Data Exchange (ETDEWEB)

    McFarlane, Sally A.; Marchand, Roger T.; Ackerman, Thomas P.

    2005-07-22

    A method of retrieving cloud phase and the dominant ice crystal habit from radiances measured by the Multi-angle Imaging Spectro-Radiometer (MISR) and the Moderate Resolution Imaging Spectroradiometer (MODIS) has been developed. The retrieval method takes advantage of the differences in the phase function of various particle shapes as a function of scattering angle. Three case studies are presented which illustrate the retrieval method. A comparison with semi-coincident in situ observations for one case study indicates that the retrieved crystal habits are consistent with the observations.

  14. 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...

  15. Electron Scattering and Doping Mechanisms in Solid-Phase-Crystallized In2O3:H Prepared by Atomic Layer Deposition.

    Science.gov (United States)

    Macco, Bart; Knoops, Harm C M; Kessels, Wilhelmus M M

    2015-08-01

    Hydrogen-doped indium oxide (In2O3:H) has recently emerged as an enabling transparent conductive oxide for solar cells, in particular for silicon heterojunction solar cells because its high electron mobility (>100 cm(2)/(V s)) allows for a simultaneously high electrical conductivity and optical transparency. Here, we report on high-quality In2O3:H prepared by a low-temperature atomic layer deposition (ALD) process and present insights into the doping mechanism and the electron scattering processes that limit the carrier mobility in such films. The process consists of ALD of amorphous In2O3:H at 100 °C and subsequent solid-phase crystallization at 150-200 °C to obtain large-grained polycrystalline In2O3:H films. The changes in optoelectronic properties upon crystallization have been monitored both electrically by Hall measurements and optically by analysis of the Drude response. After crystallization, an excellent carrier mobility of 128 ± 4 cm(2)/(V s) can be obtained at a carrier density of 1.8 × 10(20) cm(-3), irrespective of the annealing temperature. Temperature-dependent Hall measurements have revealed that electron scattering is dominated by unavoidable phonon and ionized impurity scattering from singly charged H-donors. Extrinsic defect scattering related to material quality such as grain boundary and neutral impurity scattering was found to be negligible in crystallized films indicating that the carrier mobility is maximized. Furthermore, by comparison of the absolute H-concentration and the carrier density in crystallized films, it is deduced that <4% of the incorporated H is an active dopant in crystallized films. Therefore, it can be concluded that inactive H atoms do not (significantly) contribute to defect scattering, which potentially explains why In2O3:H films are capable of achieving a much higher carrier mobility than conventional In2O3:Sn (ITO). PMID:26168056

  16. Crystallization and semiconductor-metal switching behavior of thin VO2 layers grown by atomic layer deposition

    International Nuclear Information System (INIS)

    Crystalline vanadium dioxide (VO2) thin films were prepared by annealing amorphous VO2 films which were deposited by atomic layer deposition on a SiO2 substrate. A large influence of the oxygen partial pressure in the annealing ambient was observed by means of in-situ X-ray diffraction. In the range between 1 and 10 Pa of oxygen the interesting VO2(R) phase crystallized near 450 °C. Between 2 and 10 Pa of oxygen, metastable VO2(B) was observed as an intermediate crystalline phase before it transformed to VO2(R). Anneals in inert gas did not show any crystallization, while oxygen partial pressures above 10 Pa resulted in oxidation into the higher oxide phase V6O13. Film thickness did not have much effect on the crystallization behavior, but thinner films suffered more from agglomeration during the high-temperature crystallization on the SiO2 substrate. Nevertheless, continuous polycrystalline VO2(R) films were obtained with thicknesses down to 11 nm. In the case where VO2(R) was formed, the semiconductor–metal transition was observed by three complementary techniques. This transition near 68 °C was characterized by X-ray diffraction, showing the transformation of the crystal structure, by spectroscopic ellipsometry, mapping optical changes, and by sheet resistance measurements, showing resistance changes larger than 2 orders of magnitude between the low-temperature semiconducting state and the high-temperature metallic state. - Highlights: • Amorphous VO2 films were grown by atomic layer deposition. • Crystallization was studied by means of in-situ X-ray diffraction (XRD). • The optimal oxygen partial pressure during annealing was found to be around 1 Pa. • Continuous crystalline VO2 layers down to 11 nm thickness were obtained at 450 °C. • XRD, ellipsometry and sheet resistance showed the semiconductor–metal transition

  17. Electron Scattering and Doping Mechanisms in Solid-Phase-Crystallized In2O3:H Prepared by Atomic Layer Deposition.

    Science.gov (United States)

    Macco, Bart; Knoops, Harm C M; Kessels, Wilhelmus M M

    2015-08-01

    Hydrogen-doped indium oxide (In2O3:H) has recently emerged as an enabling transparent conductive oxide for solar cells, in particular for silicon heterojunction solar cells because its high electron mobility (>100 cm(2)/(V s)) allows for a simultaneously high electrical conductivity and optical transparency. Here, we report on high-quality In2O3:H prepared by a low-temperature atomic layer deposition (ALD) process and present insights into the doping mechanism and the electron scattering processes that limit the carrier mobility in such films. The process consists of ALD of amorphous In2O3:H at 100 °C and subsequent solid-phase crystallization at 150-200 °C to obtain large-grained polycrystalline In2O3:H films. The changes in optoelectronic properties upon crystallization have been monitored both electrically by Hall measurements and optically by analysis of the Drude response. After crystallization, an excellent carrier mobility of 128 ± 4 cm(2)/(V s) can be obtained at a carrier density of 1.8 × 10(20) cm(-3), irrespective of the annealing temperature. Temperature-dependent Hall measurements have revealed that electron scattering is dominated by unavoidable phonon and ionized impurity scattering from singly charged H-donors. Extrinsic defect scattering related to material quality such as grain boundary and neutral impurity scattering was found to be negligible in crystallized films indicating that the carrier mobility is maximized. Furthermore, by comparison of the absolute H-concentration and the carrier density in crystallized films, it is deduced that <4% of the incorporated H is an active dopant in crystallized films. Therefore, it can be concluded that inactive H atoms do not (significantly) contribute to defect scattering, which potentially explains why In2O3:H films are capable of achieving a much higher carrier mobility than conventional In2O3:Sn (ITO).

  18. Atom-Thin SnS2-xSex with Adjustable Compositions by Direct Liquid Exfoliation from Single Crystals.

    Science.gov (United States)

    Yang, Zhanhai; Liang, Hui; Wang, Xusheng; Ma, Xinlei; Zhang, Tao; Yang, Yanlian; Xie, Liming; Chen, Dong; Long, Yujia; Chen, Jitao; Chang, Yunjie; Yan, Chunhua; Zhang, Xinxiang; Zhang, Xueji; Ge, Binghui; Ren, Zhian; Xue, Mianqi; Chen, Genfu

    2016-01-26

    Two-dimensional (2D) chalcogenide materials are fundamentally and technologically fascinating for their suitable band gap energy and carrier type relevant to their adjustable composition, structure, and dimensionality. Here, we demonstrate the exfoliation of single-crystal SnS2-xSex (SSS) with S/Se vacancies into an atom-thin layer by simple sonication in ethanol without additive. The introduction of vacancies at the S/Se site, the conflicting atomic radius of sulfur in selenium layers, and easy incorporation with an ethanol molecule lead to high ion accessibility; therefore, atom-thin SSS flakes can be effectively prepared by exfoliating the single crystal via sonication. The in situ pyrolysis of such materials can further adjust their compositions, representing tunable activation energy, band gap, and also tunable response to analytes of such materials. As the most basic and crucial step of the 2D material field, the successful synthesis of an uncontaminated and atom-thin sample will further push ahead the large-scale applications of 2D materials, including, but not limited to, electronics, sensing, catalysis, and energy storage fields.

  19. Coke Formation in a Zeolite Crystal During the Methanol-to-Hydrocarbons Reaction as Studied with Atom Probe Tomography.

    Science.gov (United States)

    Schmidt, Joel E; Poplawsky, Jonathan D; Mazumder, Baishakhi; Attila, Özgün; Fu, Donglong; de Winter, D A Matthijs; Meirer, Florian; Bare, Simon R; Weckhuysen, Bert M

    2016-09-01

    Understanding the formation of carbon deposits in zeolites is vital to developing new, superior materials for various applications, including oil and gas conversion processes. Herein, atom probe tomography (APT) has been used to spatially resolve the 3D compositional changes at the sub-nm length scale in a single zeolite ZSM-5 crystal, which has been partially deactivated by the methanol-to-hydrocarbons reaction using (13) C-labeled methanol. The results reveal the formation of coke in agglomerates that span length scales from tens of nanometers to atomic clusters with a median size of 30-60 (13) C atoms. These clusters correlate with local increases in Brønsted acid site density, demonstrating that the formation of the first deactivating coke precursor molecules occurs in nanoscopic regions enriched in aluminum. This nanoscale correlation underscores the importance of carefully engineering materials to suppress detrimental coke formation.

  20. Coke Formation in a Zeolite Crystal During the Methanol-to-Hydrocarbons Reaction as Studied with Atom Probe Tomography.

    Science.gov (United States)

    Schmidt, Joel E; Poplawsky, Jonathan D; Mazumder, Baishakhi; Attila, Özgün; Fu, Donglong; de Winter, D A Matthijs; Meirer, Florian; Bare, Simon R; Weckhuysen, Bert M

    2016-09-01

    Understanding the formation of carbon deposits in zeolites is vital to developing new, superior materials for various applications, including oil and gas conversion processes. Herein, atom probe tomography (APT) has been used to spatially resolve the 3D compositional changes at the sub-nm length scale in a single zeolite ZSM-5 crystal, which has been partially deactivated by the methanol-to-hydrocarbons reaction using (13) C-labeled methanol. The results reveal the formation of coke in agglomerates that span length scales from tens of nanometers to atomic clusters with a median size of 30-60 (13) C atoms. These clusters correlate with local increases in Brønsted acid site density, demonstrating that the formation of the first deactivating coke precursor molecules occurs in nanoscopic regions enriched in aluminum. This nanoscale correlation underscores the importance of carefully engineering materials to suppress detrimental coke formation. PMID:27485276

  1. 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...

  2. 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.

  3. 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.

  4. Atomic resolution mapping of interfacial intermixing and segregation in InAs/GaSb superlattices: A correlative study

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Honggyu; Meng Yifei; Zuo Jianmin [Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801 (United States); Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801 (United States); Rouviere, Jean-Luc [CEA/INAC/SP2M/LEMMA, 19 rue des Martyrs, 38 054 Grenoble (France); Isheim, Dieter; Seidman, David N. [Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Northwestern University Center for Atom-Probe Tomography (NUCAPT), Northwestern University, Evanston, Illinois 60208 (United States)

    2013-03-14

    We combine quantitative analyses of Z-contrast images with composition analyses employing atom probe tomography (APT) correlatively to provide a quantitative measurement of atomic scale interfacial intermixing in an InAs/GaSb superlattice (SL). Contributions from GaSb and InAs in the Z-contrast images are separated using an improved image processing technique. Correlation with high resolution APT composition analyses permits an examination of interfacial segregation of both cations and anions and their incorporation in the short period InAs/GaSb SL. Results revealed short, intermediate, and long-range intermixing of In, Ga, and Sb during molecular beam epitaxial growth and their distribution in the SL.

  5. Study by atomistic theory and high-resolution electron microscopies of Cu atoms at an Al grain boundary

    Energy Technology Data Exchange (ETDEWEB)

    Plitzko, Jurgen M.; Campbell, Geoffrey H.; King, Wayne E.; Foiles, Stephen M.; Kisielowski, Christian; Duscher, Gerd

    2003-02-02

    New insight into the atomic segregation of copper to an aluminum grain boundary has been obtained using atomic resolution electron microscopy techniques coupled with ab-initio electronic structure calculations. We find the copper segregation to be site specific, changing the structure of the boundary by unexpectedly occupying interstitial sites. The calculated energy for segregation was found to be sufficient for essentially all of the interstitial sites to be filled. Minor elemental constituents in materials can have profound effects on their engineering performance, often through segregation to grain boundaries in the host material. One important example is the great resistance to electromigration damage in microelectronics imparted by small additions of copper to aluminum interconnects.

  6. Feasibility guidelines for kaonic-atom experiments with ultra-high-resolution X-ray spectrometry

    CERN Document Server

    Friedman, E

    2013-01-01

    Recent studies of strong interaction effects in kaonic atoms suggest that analysing so-called `lower' and `upper' levels in the same atom could separate one-nucleon absorption from multinucleon processes. The present work examines the feasibility of direct measurements of upper level widths in addition to lower level widths in future experiments, using superconducting microcalorimeter detectors. About ten elements are identified as possible candidates for such experiments, all of medium-weight and heavy nuclei. New experiments focused on achieving good accuracy for widths of such pairs of levels could contribute significantly to our knowledge of the $K^-$-nucleon interaction in the nuclear medium.

  7. High-resolution crystal structure of the recombinant diheme cytochrome c from Shewanella baltica (OS155).

    Science.gov (United States)

    De March, Matteo; Di Rocco, Giulia; Hickey, Neal; Geremia, Silvano

    2015-01-01

    Multiheme cytochromes c (cyts c) are c-type cyts characterized by non-standard structural and spectroscopic properties. The relative disposition of the heme cofactors in the core of these proteins is conserved and they can be classified from their geometry in two main groups. In one group the porphyrin planes are arranged in a perpendicular fashion, while in the other they are parallel. Orientation of the heme groups is a key factor that regulates the intramolecular electron transfer pathway. A 16.5 kDa diheme cyt c, isolated from the bacterium Shewanella baltica OS155 (Sb-DHC), was cloned and expressed in E. coli and its structure was investigated by X-ray crystallography. Using high-resolution data (1.14 Å) collected at ELETTRA (Trieste), the crystal structure, with an orthorhombic cell (a = 40.81, b = 42.97, c = 82.07 Å), was solved using the homologous diheme from Rhodobacter sphaeroides (Rs-DHC) as the initial model. The electron density map of the refined structure (Rfact of 13.8% and Rfree of 15.4%) shows a two domain structure connected by a central unstructured region (N72-G87). The Sb-DHC, like its homologue (Rs-DHC), folds into a new cyt c class: the N-terminal globular domain, with its three α-helices, belongs to class I of c-type cyts, while the C-terminal domain includes a rare π-helix. The metal centre of the c-type heme groups is axially coordinated by two His residues and it is covalently bound to the protein through two Cys bonds. PMID:24559494

  8. Crystallization-induced dynamic resolution R-epimer from 25-OCH3-PPD epimeric mixture.

    Science.gov (United States)

    Zhang, Sainan; Tang, Yun; Cao, Jiaqing; Zhao, Chen; Zhao, Yuqing

    2015-11-15

    25-OCH3-PPD is a promising antitumor dammarane sapogenin isolated from the total saponin-hydrolyzed extract of Panax ginseng berry and Panax notoginseng leaves. 20(R)-25-OCH3-PPD was more potent as an anti-cancer agent than 20(S)-25-OCH3-PPD and epimeric mixture of 25-OCH3-PPD. This paper describes the rapid separation process of the R-epimer of 25-OCH3-PPD from its epimeric mixture by crystallization-induced dynamic resolution (CIDR). The optimized CIDR process was based on single factor analysis and nine well-planned orthogonal design experiments (OA9 matrix). A rapid and sensitive reverse phase high-performance liquid chromatographic (HPLC) method with evaporative light-scattering detector (ELSD) was developed and validated for the quantitation of 25-OCH3-PPD epimeric mixture and crystalline product. Separation and quantitation were achieved with a silica column using a mobile phase consisting of methanol and water (87:13, v/v) at a flow rate of 1.0mL/min. The ELSD detection was performed at 50°C and 3L/min. Under conditions involving 3mL of 95% ethanol, 8% HCl, and a hermetically sealed environment for 72h, the maximum production of 25(R)-OCH3-PPD was achieved with a chemical purity of 97% and a total yield of 87% through the CIDR process. The 25(R)-OCH3-PPD was nearly completely separated from the 220mg 25-OCH3-PPD epimeric mixture. Overall, a simple and steady small-batch purification process for the large-scale production of 25(R)-OCH3-PPD from 25-OCH3-PPD epimeric mixture was developed.

  9. 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.

  10. Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

    Directory of Open Access Journals (Sweden)

    Gront Dominik

    2007-06-01

    Full Text Available Abstract Background Although experimental methods for determining protein structure are providing high resolution structures, they cannot keep the pace at which amino acid sequences are resolved on the scale of entire genomes. For a considerable fraction of proteins whose structures will not be determined experimentally, computational methods can provide valuable information. The value of structural models in biological research depends critically on their quality. Development of high-accuracy computational methods that reliably generate near-experimental quality structural models is an important, unsolved problem in the protein structure modeling. Results Large sets of structural decoys have been generated using reduced conformational space protein modeling tool CABS. Subsequently, the reduced models were subject to all-atom reconstruction. Then, the resulting detailed models were energy-minimized using state-of-the-art all-atom force field, assuming fixed positions of the alpha carbons. It has been shown that a very short minimization leads to the proper ranking of the quality of the models (distance from the native structure, when the all-atom energy is used as the ranking criterion. Additionally, we performed test on medium and low accuracy decoys built via classical methods of comparative modeling. The test placed our model evaluation procedure among the state-of-the-art protein model assessment methods. Conclusion These test computations show that a large scale high resolution protein structure prediction is possible, not only for small but also for large protein domains, and that it should be based on a hierarchical approach to the modeling protocol. We employed Molecular Mechanics with fixed alpha carbons to rank-order the all-atom models built on the scaffolds of the reduced models. Our tests show that a physic-based approach, usually considered computationally too demanding for large-scale applications, can be effectively used in such

  11. High-resolution X-ray study of the multiple ionization of Pd atoms by fast oxygen ions

    OpenAIRE

    Czarnota, M.; Banaś, D.; Berset, Michel; Chmielewska, D; Dousse, Jean-Claude; Hoszowska, Joanna; Maillard, Yves-Patrick; Mauron, Olivier; Pajek, M.; Polasik, M.; Raboud, Pierre-Alexandre; Rzadkiewicz, J.; Słabkowska, K.; Sujkowski, Z.

    2010-01-01

    The multiple ionization of the L- and M-shells of Pd by fast oxygen ions has been studied by measuring with high-resolution the satellite structures of the Lα1,2 X-ray transitions. Relativistic multi-configuration Dirac-Fock (MCDF) calculations were used to interpret the complex X-ray spectrum, allowing to derive the number of L- and M-shell spectator vacancies at the moment of the X-ray emission. After correcting these numbers for the atomic vacancy rearrangement processes that take place pr...

  12. 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...

  13. Measurement and models of bent KAP(001) crystal integrated reflectivity and resolution (invited)

    Science.gov (United States)

    Loisel, G. P.; Wu, M.; Stolte, W.; Kruschwitz, C.; Lake, P.; Dunham, G. S.; Bailey, J. E.; Rochau, G. A.

    2016-11-01

    The Advanced Light Source beamline-9.3.1 x-rays are used to calibrate the rocking curve of bent potassium acid phthalate (KAP) crystals in the 2.3-4.5 keV photon-energy range. Crystals are bent on a cylindrically convex substrate with a radius of curvature ranging from 2 to 9 in. and also including the flat case to observe the effect of bending on the KAP spectrometric properties. As the bending radius increases, the crystal reflectivity converges to the mosaic crystal response. The X-ray Oriented Programs (xop) multi-lamellar model of bent crystals is used to model the rocking curve of these crystals and the calibration data confirm that a single model is adequate to reproduce simultaneously all measured integrated reflectivities and rocking-curve FWHM for multiple radii of curvature in both 1st and 2nd order of diffraction.

  14. Draft Crystal Structure of the Vault Shell at 9-Å Resolution

    OpenAIRE

    Anderson, Daniel H; Kickhoefer, Valerie A.; Stuart A Sievers; Rome, Leonard H.; David Eisenberg

    2007-01-01

    Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMV...

  15. On the solid phase crystallization of In2O3:H transparent conductive oxide films prepared by atomic layer deposition

    Science.gov (United States)

    Macco, Bart; Verheijen, Marcel A.; Black, Lachlan E.; Barcones, Beatriz; Melskens, J.; Kessels, Wilhelmus M. M.

    2016-08-01

    Hydrogen-doped indium oxide (In2O3:H) has emerged as a highly transparent and conductive oxide, finding its application in a multitude of optoelectronic devices. Recently, we have reported on an atomic layer deposition (ALD) process to prepare high quality In2O3:H. This process consists of ALD of In2O3:H films at 100 °C, followed by a solid phase crystallization step at 150-200 °C. In this work, we report on a detailed electron microscopy study of this crystallization process which reveals new insights into the crucial aspects for achieving the large grain size and associated excellent properties of the material. The key finding is that the best optoelectronic properties are obtained by preparing the films at the lowest possible temperature prior to post-deposition annealing. Electron microscopy imaging shows that such films are mostly amorphous, but feature a very low density of embedded crystallites. Upon post-deposition annealing, crystallization proceeds merely from isotropic crystal grain growth of these embedded crystallites rather than by the formation of additional crystallites. The relatively high hydrogen content of 4.2 at. % in these films is thought to cause the absence of additional nucleation, thereby rendering the final grain size and optoelectronic properties solely dependent on the density of embedded crystallites. The temperature-dependent grain growth rate has been determined, from which an activation energy of (1.39 ± 0.04) eV has been extracted. Finally, on the basis of the observed crystallization mechanism, a simple model to fully describe the crystallization process has been developed. This model has been validated with a numerical implementation thereof, which accurately predicts the observed temperature-dependent crystallization behaviour.

  16. 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.

  17. Single-Crystal Y2O3 Epitaxially on GaAs(001 and (111 Using Atomic Layer Deposition

    Directory of Open Access Journals (Sweden)

    Y. H. Lin

    2015-10-01

    Full Text Available Single-crystal atomic-layer-deposited (ALD Y\\(_{\\mathrm{2}}\\O\\(_{\\mathrm{3}}\\ films 2 nm thick were epitaxially grown on molecular beam epitaxy (MBE GaAs(001-4 \\(\\times\\ 6 and GaAs(111A-2 \\(\\times\\ 2 reconstructed surfaces. The in-plane epitaxy between the ALD-oxide films and GaAs was observed using \\textit{in-situ} reflection high-energy electron diffraction in our uniquely designed MBE/ALD multi-chamber system. More detailed studies on the crystallography of the hetero-structures were carried out using high-resolution synchrotron radiation X-ray diffraction. When deposited on GaAs(001, the Y\\(_{\\mathrm{2}}\\O\\(_{\\mathrm{3}}\\ films are of a cubic phase and have (110 as the film normal, with the orientation relationship being determined: Y\\(_{\\mathrm{2}}\\O\\(_{\\mathrm{3}}\\(\\(110\\[\\(001\\][\\(\\overline{1}10\\]//GaAs(\\(001\\[\\(110\\][\\(1\\overline{1}0\\]. On GaAs(\\(111\\A, the Y\\(_{\\mathrm{2}}\\O\\(_{\\mathrm{3}}\\ films are also of a cubic phase with (\\(111\\ as the film normal, having the orientation relationship of Y\\(_{\\mathrm{2}}\\O\\(_{\\mathrm{3}}\\(\\(111\\[\\(2\\overline{1}\\overline{1}\\] [\\(01\\overline{1}\\]//GaAs (\\(111\\ [\\(\\overline{2}11\\][\\(0\\overline{1}1\\]. The relevant orientation for the present/future integrated circuit platform is (\\(001\\. The ALD-Y\\(_{\\mathrm{2}}\\O\\(_{\\mathrm{3}}\\/GaAs(\\(001\\-4 \\(\\times\\ 6 has shown excellent electrical properties. These include small frequency dispersion in the capacitance-voltage CV curves at accumulation of ~7% and ~14% for the respective p- and n-type samples with the measured frequencies of 1 MHz to 100 Hz. The interfacial trap density (Dit is low of ~10\\(^{12}\\ cm\\(^{−2}\\eV\\(^{−1}\\ as extracted from measured quasi-static CVs. The frequency dispersion at accumulation and the D\\(_{it}\\ are the lowest ever achieved among all the ALD-oxides on GaAs(\\(001\\.

  18. 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.

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

    Science.gov (United States)

    Nakatsuka, Akihiko; Sugiyama, Kazumasa; Yoneda, Akira; Fujiwara, Keiko; Yoshiasa, Akira

    2015-09-01

    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 octa-hedral layers and CaO8 hendeca-hedral layers along [010]. Chains formed by edge-sharing of IrO6 octa-hedra (point-group symmetry 2/m..) run along [100] and are inter-connected along [001] by sharing apical O atoms to build up the IrO6 octa-hedral layers. Chains formed by face-sharing of CaO8 hendeca-hedra (point-group symmetry m2m) run along [100] and are inter-connected along [001] by edge-sharing to build up the CaO8 hendeca-hedral layers. The IrO6 octa-hedral layers and CaO8 hendeca-hedral layers are inter-connected 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. PMID:26396860

  20. X-ray structure of bovine pancreatic phospholipase A(2) at atomic resolution

    NARCIS (Netherlands)

    Steiner, RA; Rozeboom, HJ; Kalk, KH; Murshudov, GN; Wilson, KS; Dijkstra, BW

    2001-01-01

    Using synchrotron radiation and a CCD camera, X-ray data have been collected from wild-type bovine pancreatic phospholipase A(2) at 100 K to 0.97 Angstrom resolution allowing full anisotropic refinement. The final model has a conventional R factor of 9.44% for all reflections, with a mean standard u

  1. 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.

  2. Crystallization and preliminary X-ray analysis of RsbS from Moorella thermoacetica at 2.5 Å resolution

    International Nuclear Information System (INIS)

    Crystallization and selenium substructure solution of RsbS from Moorella thermoacetica, the first ab initio phased crystal structure from Diamond. 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 σB. 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 P212121, with unit-cell parameters a = 51.07, b = 60.52, c = 89.28 Å, diffracted to 2.5 Å 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

  3. Investigations on atomic-vapor-filter high-spectral-resolution lidar for temperature measurements

    Science.gov (United States)

    Voss, E.; Weitkamp, C.

    1992-01-01

    The temperature measurement by the analysis of Rayleigh scattered laser radiation with atomic vapor filters is investigated in both theory and laboratory experiments. Synthetic air is irradiated with a cw dye laser at 283 nano-meters, and the backscattered spectrum is analyzed with two lead vapor cells in one oven. Temperature measurements are carried out, and the effect of different parameters on the accuracy is investigated. Important aspects for the realization of a lidar are given.

  4. Kilohertz-resolution spectroscopy of cold atoms with an optical frequency comb

    OpenAIRE

    Fortier, T. M.; Coq, Y Le; Stalnaker, J. E.; Ortega, D.; Diddams, S. A.; Oates, C. W.; Hollberg, L.

    2006-01-01

    We have performed sub-Doppler spectroscopy on the narrow intercombination line of cold calcium atoms using the amplified output of a femtosecond laser frequency comb. Injection locking of a 657-nm diode laser with a femtosecond comb allows for two regimes of amplification, one in which many lines of the comb are amplified, and one where a single line is predominantly amplified. The output of the laser in both regimes was used to perform kilohertz-level spectroscopy. This experiment demonstrat...

  5. Atomic layer deposition of TiO2 photonic crystal waveguide biosensors

    NARCIS (Netherlands)

    Jardinier, E.; Pandraud, G.; Pham, M.H.; French, P.J.; Sarro, P.M.

    2009-01-01

    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 TiO2. It is

  6. The role of impurities on the morphology of NaCl crystals : an atomic scale view

    NARCIS (Netherlands)

    Radenovic, N.

    2005-01-01

    It is well known that crystal growth and morphology are largely influenced by the presence of impurities in the growth solution. However, little is known about the actual process of impurity interaction with the growing crystal surface. In this thesis we study this influence in detail using the NaCl

  7. A new method in gamma-ray spectroscopy: A two crystal scintillation spectrometer with improved resolution

    NARCIS (Netherlands)

    Hoogenboom, A.M.

    1958-01-01

    A new method has been developed to measure the spectra of gamma radiation emitted in cascade disintegrations. Use is made of a two-crystal scintillation spectrometer and a gated multi-channel analysing device. The pulses produced by summing the outputs of the two crystal-photomultiplier combinations

  8. 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

  9. High-resolution continuum source electrothermal atomic absorption spectrometry: Linearization of the calibration curves within a broad concentration range

    Energy Technology Data Exchange (ETDEWEB)

    Katskov, Dmitri, E-mail: katskovda@tut.ac.za [Tshwane University of Technology, Chemistry Department, Pretoria 0001 (South Africa); Hlongwane, Miranda [Tshwane University of Technology, Chemistry Department, Pretoria 0001 (South Africa); Heitmann, Uwe [German Aerospace Center, Rose-Luxemburg Str. 2, 10178 Berlin (Germany); Florek, Stefan [ISAS-Leibniz-Institut fuer Analytische Wissenschaften e.V., Albert-Einstein-Str. 9,12489 Berlin (Germany)

    2012-05-15

    The calculation algorithm suggested provides linearization of the calibration curves in high-resolution continuum source electrothermal atomic absorption spectrometry. The algorithm is based on the modification of the function wavelength-integrated absorbance vs. concentration of analyte vapor in the absorption volume. According to the suggested approach, the absorption line is represented by a triangle for low and trapezium for high analyte vapor concentration in the absorption volume. The respective semi-empirical formulas include two linearization parameters, which depend on properties of the absorption line and characteristics of the atomizer and spectrometer. The parameters can be approximately evaluated from the theory and determined in practice from the original broad-range calibration curve. The parameters were found and the proposed calculation algorithm verified in the experiments on direct determination of Ag, Cd, Cu, Fe, Mn and Pb in the solutions within a concentration ranges from 0.15 to 625 {mu}g{center_dot}L{sup -1} using tube, platform tube and filter furnace atomizers. The use of various atomizers, lines, elements and atomization temperatures made possible the simulation of various practical analytical conditions. It was found that the algorithm and optimal linearization parameters made it possible to obtain for each line and atomizer linear approximations of the calibration curves within 3-4 orders of magnitude with correlation coefficients close to 0.999. The algorithm makes possible to employ a single line for the direct element determination over a broad concentration range. The sources of errors and the possibility of a priori theoretical evaluation of the linearization parameters are discussed. - Highlights: Black-Right-Pointing-Pointer New calculation algorithm for HR-CS ET AAS measurements was proposed and applied. Black-Right-Pointing-Pointer The suggested formulas include two parameters to be determined experimentally. Black

  10. Atomic Mineral Characteristics of Indonesian Osteoporosis by High-Resolution Inductively Coupled Plasma Mass Spectrometry

    OpenAIRE

    Zairin Noor; Sutiman Bambang Sumitro; Mohammad Hidayat; Agus Hadian Rahim; Akhmad Sabarudin; Tomonari Umemura

    2012-01-01

    Clinical research indicates that negative calcium balance is associated with low bone mass, rapid bone loss, and high fracture rates. However, some studies revealed that not only calcium is involved in bone strengthening as risk factor of fracture osteoporosis. Thus, in this report, the difference of metallic and nonmetallic elements in osteoporosis and normal bones was studied by high-resolution inductively coupled plasma mass spectrometry (HR-ICP-MS). The influence of these elements on bone...

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

    OpenAIRE

    Nakatsuka, Akihiko; Sugiyama, Kazumasa; Yoneda, Akira; Fujiwara, Keiko; Yoshiasa, Akira

    2015-01-01

    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 form...

  12. 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). PMID:27475560

  13. Set-up of a High-Resolution 300 mK Atomic Force Microscope in an Ultra-High Vacuum Compatible 3He/10T Cryostat

    CERN Document Server

    von Allwörden, Henning; Köhler, Arne; Eelbo, Thomas; Schwarz, Alexander; Wiesendanger, Roland

    2016-01-01

    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 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).

  14. 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).

  15. Atomic-scale configurations of synchroshear-induced deformation twins in the ionic MnS crystal

    Science.gov (United States)

    Zhou, Y. T.; Xue, Y. B.; Chen, D.; Wang, Y. J.; Zhang, B.; Ma, X. L.

    2014-01-01

    Deformation twinning was thought as impossible in ionic compounds with rock-salt structure due to the charge effect on {111} planes. Here we report the presence and formation mechanism of deformation {111} twins in the rock-salt manganese sulphide (MnS) inclusions embedded in a hot-rolled stainless steel. Based on the atomic-scale mapping under aberration-corrected scanning transmission electron microscopy, a dislocation-based mechanism involved two synchronized shear on adjacent atomic layers is proposed to describe the dislocation glide and consequently twinning formation. First-principles calculations of the energy barriers for twinning formation in MnS and comparing with that of PbS and MgO indicate the distinct dislocation glide scheme and deformation behaviors for the rock-salt compounds with different ionicities. This study may improve our understanding of the deformation mechanisms of rock-salt crystals and other ionic compounds. PMID:24874022

  16. 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.

  17. 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.

  18. 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.

  19. Exotic atoms and their electron shell

    Energy Technology Data Exchange (ETDEWEB)

    Simons, L.M.; Abbot, D.; Bach, B.; Bacher, R.; Badertscher, A.; Bluem, P.; DeCecco, P.; Eades, J.; Egger, J.; Elsener, K.; Gotta, D.; Hauser, P.; Heitlinger, K.; Horvath, D.; Kottmann, F.; Morenzoni, E.; Missimer, J.; Reidy, J.J.; Siegel, R.; Taqqu, D.; Viel, D. (Paul Scherrer Inst., Villigen (Switzerland) Coll. of William and Mary, Williamsburg, VA (United States) Kernforschungszentrum Karlsruhe GmbH, Inst. fuer Kernphysik, Karlsruhe (Germany) Inst. fuer Experimentelle Kernphysik, Univ. Karlsruhe (Germany) CERN, Geneva (Switzerland) Forschungszentrum Juelich GmbH, Inst. fuer Kernphysik (Germany) KFKI Research Inst. for Particle and Nuclear Physics, Budapest (Hungary) Univ. Pisa (Italy) INFN - Pisa (Italy) ETH Zuerich, Villigen (Switzerland) Physics Dept., Univ. of Mississippi, University, MS (United States))

    1994-04-01

    Progress in the field of exotic atoms seems to increase proportionally with the number of exotic atoms produced and the increase in energy resolution with which the transition energies are determined. Modern experiments use high resolution crystal spectrometers or even aim at laser spectroscopy. The accuracy of these methods is limited by the interaction of the exotic atoms with their surroundings. The most important source of errors is the energy shift caused by the not well known status of the atomic electron shell. A novel method to eliminate these sources of error is presented and the possibilities for further high precision experiments is outlined. (orig.)

  20. Exotic atoms and their electron shell

    Science.gov (United States)

    Simons, L. M.; Abbot, D.; Bach, B.; Bacher, R.; Badertscher, A.; Blüm, P.; DeCecco, P.; Eades, J.; Egger, J.; Elsener, K.; Gotta, D.; Hauser, P.; Heitlinger, K.; Horváth, D.; Kottmann, F.; Morenzoni, E.; Missimer, J.; Reidy, J. J.; Siegel, R.; Taqqu, D.; Viel, D.

    1994-04-01

    Progress in the field of exotic atoms seems to increase proportionally with the number of exotic atoms produced and the increase in energy resolution with which the transition energies are determined. Modern experiments use high resolution crystal spectrometers or even aim at laser spectroscopy. The accuracy of these methods is limited by the interaction of the exotic atoms with their surroundings. The most important source of errors is the energy shift caused by the not well known status of the atomic electron shell. A novel method to eliminate these sources of error is presented and the possibilities for further high precision experiments is outlined.

  1. 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.

  2. Electronic, mechanical and optical properties of atomically thin tow-dimensional crystals

    Directory of Open Access Journals (Sweden)

    A. Castellanos-Gómez

    2012-03-01

    Full Text Available This work is devoted to the study of electronic and mechanical properties of crystalline atomically thin two-dimensional sheets, such as graphene, MoS2, NbSe2 and mica by scanning probe microscopy.

  3. Estimating the activation energy of the displacement of Mg atoms in the channels of B25C4Mg1.42 crystals

    Science.gov (United States)

    Konovalikhin, S. V.; Ponomarev, V. I.

    2016-10-01

    The activation energy of displacement of Mg atoms through channels of B25C4Mg1.42 crystals is estimated using quantum chemical calculations (DFT (B3LYP potential), RHF, and UHF methods, 3-21G basis set) of the element of the structure modeling the channel and location of Mg atoms in it. The changes in the activation energy at the replacement of Mg atoms by Na and Li atoms were estimated. The greatest decreasing in the activation energy was detected for Li atoms. The obtained results can be regarded as a theoretical background for development of conducting systems based on B25C4Mg1.42 crystals.

  4. Elastic recoil atomic spectroscopy of light elements with sub-nanometer depth resolution

    International Nuclear Information System (INIS)

    In this thesis the QQDS magnetic spectrometer that is used for high resolution ion beam analysis (IBA) of light elements at the Helmholtz-Zentrum Dresden-Rossendorf is presented for the first time. In addition all parameters are investigated that influence the analysis. Methods and models are presented with which the effects can be minimised or calculated. There are five focal points of this thesis. The first point is the construction and commissioning of the QQDS magnetic spectrometer, the corresponding scattering chamber with all the peripherals and the detector, which is specially developed for high resolution elastic recoil detection. Both the reconstructed spectrometer and the detector were adapted to the specific experimental conditions needed for high-resolution Ion beam analysis of light elements and tested for routine practice. The detector consists of two components. At the back end of the detector a Bragg ionization chamber is mounted, which is used for the particle identification. At the front end, directly behind the entrance window a proportional counter is mounted. This proportional counter includes a highresistance anode. Thus, the position of the particles is determined in the detector. The following two points concern fundamental studies of ion-solid interaction. By using a magnetic spectrometer the charge state distribution of the particles scattered from the sample after a binary collision is both possible and necessary for the analysis. For this reason the charge states are measured and compared with existing models. In addition, a model is developed that takes into account the charge state dependent energy loss. It is shown that without the application of this model the depth profiles do not correspond with the quantitative measurements by conventional IBA methods and with the thickness obtained by transmission electron microscopy. The second fundamental ion-solid interaction is the damage and the modification of the sample that occurs during

  5. DIRECT DETERMINATION OF GOLD IN SUSPENSIONS OF ROCK AND ORE REFERENCE MATERIALS USING ELECTROTHERMAL HIGH RESOLUTION ATOMIC ABSORPTION SPECTROMETRY

    OpenAIRE

    Zakharov, Y. А.; Irisov, D. S.; Okunev, R. V.; Musin, R. Kh.; Haibullin, R. R.

    2014-01-01

    High resolution continuum source atomic absorption spectrometer ContrAA-700 with graphite furnace is used for direct gold determination in rocks and ores on the level 10-6-10-3 % mas. Russian standard reference materials of gold containing ore СЗР-4 (2.13 ± 0.05 g/ton), black slates of Sykhoy Log СЛг-1 (2.50 ± 0.03 g/ton) and СЧС-1 (0.10 ± 0.02 g/ton) in mass 1 mg was inserted into the furnace in the suspension form prepared on the mix of concentrated HNO3 and HCl (1:3) with following sevenfo...

  6. Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic-Resolution Electron Microscopy and Field Evaporation Simulation.

    Science.gov (United States)

    Devaraj, Arun; Colby, Robert; Vurpillot, François; Thevuthasan, Suntharampillai

    2014-04-17

    Oxide-supported metal nanoparticles are widely used in heterogeneous catalysis. The increasingly detailed design of such catalysts necessitates three-dimensional characterization with high spatial resolution and elemental selectivity. Laser-assisted atom probe tomography (APT) is uniquely suited to the task but faces challenges with the evaporation of metal/insulator systems. Correlation of APT with aberration-corrected scanning transmission electron microscopy (STEM), for Au nanoparticles embedded in MgO, reveals preferential evaporation of the MgO and an inaccurate assessment of nanoparticle composition. Finite element field evaporation modeling is used to illustrate the evolution of the evaporation front. Nanoparticle composition is most accurately predicted when the MgO is treated as having a locally variable evaporation field, indicating the importance of considering laser-oxide interactions and the evaporation of various molecular oxide ions. These results demonstrate the viability of APT for analysis of oxide-supported metal nanoparticles, highlighting the need for developing a theoretical framework for the evaporation of heterogeneous materials.

  7. Investigation of an alternating current plasma as an element selective atomic emission detector for high-resolution capillary gas chromatography and as a source for atomic absorption and atomic emission spectrometry

    Science.gov (United States)

    Ombaba, Jackson M.

    This thesis deals with the construction and evaluation of an alternating current plasma (ACP) as an element-selective detector for high resolution capillary gas chromatography (GC) and as an excitation source for atomic absorption spectrometry (AAS) and atomic emission spectrometry (AES). The plasma, constrained in a quartz discharge tube at atmospheric pressure, is generated between two copper electrodes and utilizes helium as the plasma supporting gas. The alternating current plasma power source consists of a step-up transformer with a secondary output voltage of 14,000 V at a current of 23 mA. The device exhibits a stable signal because the plasma is self-seeding and reignites itself every half cycle. A tesla coil is not required to commence generation of the plasma if the ac voltage applied is greater than the breakdown voltage of the plasma-supporting gas. The chromatographic applications studied included the following: (1) the separation and selective detection of the organotin species, tributyltin chloride (TBT) and tetrabutyltin (TEBT), in environmental matrices including mussels (Mvutilus edullus) and sediment from Boston Harbor, industrial waste water and industrial sludge, and (2) the detection of methylcyclopentadienyl manganesetricarbonyl (MMT) and similar compounds used as gasoline additives. An ultrasonic nebulizer (common room humidifier) was utilized as a sample introduction device for aqueous solutions when the ACP was employed as an atomization source for atomic absorption spectrometry and as an excitation source for atomic emission spectrometry. Plasma diagnostic parameters studied include spatial electron number density across the discharge tube, electronic, excitation and ionization temperatures. Interference studies both in absorption and emission modes were also considered. Figures of merits of selected elements both in absorption and emission modes are reported. The evaluation of a computer-aided optimization program, Drylab GC, using

  8. Atomic resolution imaging of the two-component Dirac-Landau levels in a gapped graphene monolayer

    Science.gov (United States)

    Wang, Wen-Xiao; Yin, Long-Jing; Qiao, Jia-Bin; Cai, Tuocheng; Li, Si-Yu; Dou, Rui-Fen; Nie, Jia-Cai; Wu, Xiaosong; He, Lin

    2015-10-01

    The wave function of Dirac fermions is a two-component spinor. In graphene, a one-atom-thick film showing two-dimensional Dirac-like electronic excitations, the two-component representation, reflects the amplitude of the electron wave function on the A and B sublattices. This unique property provides unprecedented opportunities to image the two components of Dirac fermions spatially. Here, we report atomic resolution imaging of two-component Dirac-Landau levels in gapped graphene monolayers by scanning tunneling microscopy and spectroscopy. A gap of about 20 meV, driven by inversion symmetry breaking by the substrate potential, is observed in the graphene sheets on both SiC and graphite substrates. Such a gap splits the n =0 Landau level (LL) into two levels, 0+ and 0-. We demonstrate that the amplitude of the wave function of the 0+ LL is mainly on the A sites and that of the 0- LL is mainly on the B sites of graphene, characterizing the internal structure of the spinor of the n =0 LL. This provides direct evidence of the two-component nature of Dirac fermions.

  9. Investigation of lead contents in lipsticks by solid sampling high resolution continuum source electrothermal atomic absorption spectrometry.

    Science.gov (United States)

    Gunduz, Sema; Akman, Suleyman

    2013-02-01

    In this study, the lead contents of different kinds of lipsticks were determined by solid sampling high resolution continuum source electrothermal atomic absorption spectrometry (SS-HR-CS ET AAS) and the results were compared with those obtained after microwave-assisted acid digestion of the samples. The experimental parameters for solid sampling such as the maximum amount of sample on the platforms of solid autosampler, graphite furnace program were optimized. Samples were directly loaded on the platforms of solid autosampler between 0.25 and 2.0mg and lead was determined applying 800 °C for pyrolysis and 2100 °C for atomization. Under optimized conditions, interference-free determination could be performed using aqueous standards. The LOD and the characteristic mass were 21.3 and 12.6 pg, respectively. The lead in the same lipstick samples was determined after microwave-assisted acid digestion and compared with those found by solid sampling. Mostly, there was no significant difference between the lead concentrations found by the two techniques. The lead in 25 lipstick samples with different properties were 0.11-4.48 ng mg(-1) which were not significantly different from those (<0.026-7.19 ng mg(-1)) reported by FDA for around 400 samples. PMID:23099440

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

    Directory of Open Access Journals (Sweden)

    M.Arulmani

    2014-06-01

    Full Text Available 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.

  11. In situ atomic force microscopy of layer-by-layer crystal growth and key growth concepts

    Science.gov (United States)

    Rashkovich, L. N.; de Yoreo, J. J.; Orme, C. A.; Chernov, A. A.

    2006-12-01

    Contradictions that have been found recently between the representations of classical theory and experiments on crystal growth from solutions are considered. Experimental data show that the density of kinks is low in many cases as a result of the low rate of their fluctuation generation, the Gibbs-Thomson law is not always applicable in these cases, and there is inconsistency with the Cabrera-Vermilyea model. The theory of growth of non-Kossel crystals, which is to be developed, is illustrated by the analysis of the experimental dependence of the growth rate on the solution stoichiometry.

  12. Stripping scattering of fast atoms on surfaces of metal-oxide crystals and ultrathin films

    International Nuclear Information System (INIS)

    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 SiO2/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.)

  13. Atomic resolution tomography reconstruction of tilt series based on a GPU accelerated hybrid input-output algorithm using polar Fourier transform.

    Science.gov (United States)

    Lu, Xiangwen; Gao, Wenpei; Zuo, Jian-Min; Yuan, Jiabin

    2015-02-01

    Advances in diffraction and transmission electron microscopy (TEM) have greatly improved the prospect of three-dimensional (3D) structure reconstruction from two-dimensional (2D) images or diffraction patterns recorded in a tilt series at atomic resolution. Here, we report a new graphics processing unit (GPU) accelerated iterative transformation algorithm (ITA) based on polar fast Fourier transform for reconstructing 3D structure from 2D diffraction patterns. The algorithm also applies to image tilt series by calculating diffraction patterns from the recorded images using the projection-slice theorem. A gold icosahedral nanoparticle of 309 atoms is used as the model to test the feasibility, performance and robustness of the developed algorithm using simulations. Atomic resolution in 3D is achieved for the 309 atoms Au nanoparticle using 75 diffraction patterns covering 150° rotation. The capability demonstrated here provides an opportunity to uncover the 3D structure of small objects of nanometers in size by electron diffraction.

  14. High-Resolution Distance Dependence Study of Surface-Enhanced Raman Scattering Enabled by Atomic Layer Deposition.

    Science.gov (United States)

    Masango, Sicelo S; Hackler, Ryan A; Large, Nicolas; Henry, Anne-Isabelle; McAnally, Michael O; Schatz, George C; Stair, Peter C; Van Duyne, Richard P

    2016-07-13

    We present a high-resolution distance dependence study of surface-enhanced Raman scattering (SERS) enabled by atomic layer deposition (ALD) at 55 and 100 °C. ALD is used to deposit monolayers of Al2O3 on bare silver film over nanospheres (AgFONs) and AgFONs functionalized with self-assembled monolayers. Operando SERS is used to measure the intensities of the Al-CH3 and C-H stretches from trimethylaluminum (TMA) as a function of distance from the AgFON surface. This study clearly demonstrates that SERS on AgFON substrates displays both a short- and long-range nanometer scale distance dependence. Excellent agreement is obtained between these experiments and theory that incorporates both short-range and long-range terms. This is a high-resolution operando SERS distance dependence study performed in one integrated experiment using ALD Al2O3 as the spacer layer and Raman label simultaneously. The long-range SERS distance dependence should make it possible to detect chemisorbed surface species located as far as ∼3 nm from the AgFON substrate and will provide new insight into the surface chemistry of ALD and catalytic reactions.

  15. Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR.

    Science.gov (United States)

    Surana, Parag; Das, Ranabir

    2016-08-01

    The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly-Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process. PMID:27111887

  16. 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

    , 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...

  17. Observation of atomic steps on CaCO3 crystal surface

    Institute of Scientific and Technical Information of China (English)

    SunJie-Lin; HuJun; 等

    1998-01-01

    By using scanning polarization force microscopy,the deliquescence process and the atomic steps on the cleavage surface of CaCO3 in air were studied in situ.Under an exposure to medium umidity(-57%),the sloiw step movement has been observed.

  18. Intermolecular atom–atom bonds in crystals – a chemical perspective1

    OpenAIRE

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

    2015-01-01

    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.

  19. A new high-resolution crystal structure of the Drosophila melanogaster angiotensin converting enzyme homologue, AnCE.

    Science.gov (United States)

    Harrison, Charlotte; Acharya, K Ravi

    2015-01-01

    Angiotensin converting enzyme (ACE) is a zinc-dependent dipeptidyl carboxypeptidase with an essential role in blood pressure homeostasis in mammals. ACE has long been targeted in the treatment of hypertension through ACE inhibitors, however current inhibitors are known to cause severe side effects. Therefore, there is a requirement for a new generation of ACE inhibitors and structural information will be invaluable in their development. ACE is a challenging enzyme to work with due to its extensive glycosylation. As such, the Drosophila melanogaster ACE homologue, AnCE, which shares ∼60% sequence similarity with human ACE, can be used as a model for studying inhibitor binding. The presence of ligands originating from the crystallisation condition at the AnCE active site has proved an obstacle to studying the binding of new inhibitor precursors. Here we present the crystal structure of AnCE (in a new crystal form) at 1.85 Å resolution, using crystals grown under different conditions. This new structure may be more suitable for studying the binding of new compounds, with the potential of developing a new generation of improved ACE inhibitors. PMID:26380810

  20. Investigations of atomic configurations of 60° basal dislocations in wurtzite GaN film by high-resolution transmission electron microscopy

    Science.gov (United States)

    Chang, Yunjie; Wang, Yumei; Deng, Zhen; Chen, Hong; Ge, Binghui

    2016-04-01

    GaN epitaxial films grown on Si (111) substrates were observed using a 200 kV high-resolution (HR) transmission electron microscope. Both perfect and dissociated 60° basal dislocations were found in ? HR images. By utilizing the image deconvolution method, the HR images were transformed into structure maps with an improved resolution, and then the atomic configurations of perfect and partial dislocations were determined. Afterwards, the possible dissociation schemes for the dissociated dislocations were derived.

  1. Atomic Physics with the Goddard High Resolution Spectrograph on the Hubble Space Telescope. V. Oscillator Strengths for Neutral Carbon Lines below 1200 Angstrom

    OpenAIRE

    Federman, S. R.; Zsargo, J.

    2001-01-01

    We analyzed high resolution spectra of interstellar neutral carbon absorption toward $\\lambda$ Ori, 1 Sco, and $\\delta$ Sco that were obtained with the Goddard High Resolution Spectrograph on the Hubble Space Telescope. Several multiplets were detected within the wavelength interval 1150 to 1200 A, where most neutral carbon lines have ill-defined oscillator strength; multiplets at longer wavelengths with well-defined atomic parameters were also seen. We extracted accurate column densities and...

  2. Set-up of a High-Resolution 300 mK Atomic Force Microscope in an Ultra-High Vacuum Compatible 3He/10T Cryostat

    OpenAIRE

    von Allwörden, Henning; Ruschmeier, Kai; Köhler, Arne; Eelbo, Thomas; Schwarz, Alexander; Wiesendanger, Roland

    2016-01-01

    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 tip and sample can be exchanged in-situ. Moreover, single atoms ...

  3. Ultrahigh resolution optical coherence tomography with femtosecond Ti:sapphire laser and photonic crystal fiber

    Institute of Scientific and Technical Information of China (English)

    XUE Ping; James G FUJIMOTO

    2008-01-01

    Optical coherence tomography (OCT) with ultrahigh axial resolution was achieved by the super-contin- uum generated by coupling femtosecond pulses from a commercial Ti :sapphire laser into an air-silica microstructure fiber. The visible spectrum of the super-continuum from 450 to 700 nm centered at 540 nm can be generated. A free-space axial OCT resolution of 0.64 IJm was achieved. The sensitivity of OCT system was 108 dB with incident light power 3 mW at sample, only 7dB below the theoretical limit. Subcellular OCT imaging was also demonstrated, showing great potential for biomedical application.

  4. How Modelling of Crystal Defects at the Atomic Scale can Provide Information on Seismic Anisotropy

    Science.gov (United States)

    Cordier, P.; Carrez, P.; Goryaeva, A.; Gouriet, K.; Hirel, P.; Kraych, A.; Ritterbex, S.

    2014-12-01

    Seismic anisotropy represents one of the few sources of information about flow in the mantle that takes place at timescales that are barely accessible at human timescales. Seismic waves travelling through rocks at the speed of sound can reveal flow lines frozen in rocks over hundreds of million years. The interpretation of seismic anisotropy also needs to bridge length-scales since crystal defects are responsible for the plastic anisotropy that align crystals in a deforming rock thus revealing elastic anisotropy at the macroscopic scale. Knowing the easiest slip systems for a given crystal structure is thus the fundamental information needed. To obtain it we propose the following approach based on multiscale numerical modeling. As a first approach, we calculate generalized stacking faults which inform us about the easiest shear paths imposed by the crystal chemistry. This leads to a short list of potential slip systems for which lattice friction will be calculated. A further selection will be done by modeling the core structures of screw dislocations. The tendency for core spreading of screw dislocations impose a selection on potential glide planes which is further validated by modeling corresponding edge dislocations and their respective mobilities. Finally, we model the mobility of these dislocations under the conjugate influence of stress and temperature using the kink-pair model which is based on the activation enthalpy of the critical configuration which allows a dislocation to glide from one stable position to the next. The output of this model is the so-called critical resolved shear stress which is the onset of plastic glide at a given temperature and strain rate. Comparison between slip systems provides constraints on the plastic anisotropy. Examples are presented among the major phases of the Earth's mantle.

  5. Early oriented isothermal crystallization of polyethylene studied by high-time-resolution SAXS/WAXS.

    Science.gov (United States)

    Stribeck, N; Almendarez Camarillo, A; Nöchel, U; Bösecke, P; Bayer, R K

    2007-01-01

    During cooling from the quiescent melt of a highly oriented polyethylene rod, highly oriented proto-lamellae are formed first, which are not crystalline. This is shown in scattering data which are recorded on two-dimensional detectors with a cycle time of 1 s and an exposure of 0.1 s. In the experiments small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS) are registered simultaneously during the first 3 min after quenching to a crystallization temperature. A non-uniform thickness between 20 and 100 nm is characteristic for the ensemble of proto-lamellae. During the first minute of isothermal treatment the number of proto-lamellae slowly increases without a change of the thickness distribution. As crystallization starts, the crystallites are not oriented in contrast to the proto-lamellae. During crystallization the layer thickness distribution narrows. The number of lamellae rapidly increases during the following 2 min of isothermal treatment (at 128 degrees C and 124 degrees C). The results are obtained by interpretation of the WAXS and of the multidimensional chord distribution function (CDF), a model-free real-space visualization of the nanostructure information contained in the SAXS data. PMID:17089099

  6. Raman spectroscopy of atomically thin two-dimensional magnetic iron phosphorus trisulfide (FePS3) crystals

    Science.gov (United States)

    Wang, Xingzhi; Du, Kezhao; Liu, Yu Yang Fredrik; Hu, Peng; Zhang, Jun; Zhang, Qing; Owen, Man Hon Samuel; Lu, Xin; Gan, Chee Kwan; Sengupta, Pinaki; Kloc, Christian; Xiong, Qihua

    2016-09-01

    Metal phosphorous trichalcogenide is an important group of layered two-dimensional (2D) materials with potentially diverse applications in low-dimensional magnetic and spintronic devices. Herein we present a comprehensive investigation on the lattice dynamics and spin-phonon interactions of mechanically exfoliated atomically thin 2D magnetic material—iron phosphorus trisulfide (FePS3) by Raman spectroscopy and first principle calculations. Layer-number and temperature dependent Raman spectroscopy suggests a magnetic persistence in FePS3 even down to monolayer regime through the spin-phonon coupling, while the Néel temperature decreases from 117 K in bulk to 104 K in monolayer sample. Our studies advocate the intriguing magnetic properties in 2D crystals and suggest that FePS3 is a promising candidate material for future magnetic applications.

  7. The interatomic vector's method, algorithms, and programs for the solution of atomic structure of nanoclusters in crystal

    International Nuclear Information System (INIS)

    A calculation technique and corresponding algorithms have been developed using the formalism of Fourier transform of finite functions. A software package for obtaining distributions of cluster interatomic vectors from diffuse X-ray scattering has been written and debugged. The programs were checked on a 30-atom cluster [CdTb3F26]. The attempts to obtain experimental data on a single crystal with nanoclusters using an Xcalibur S diffractometer (Oxford Diffraction) with a coordinate CCD detector were no success. The standard diffractometer software contains errors that lead to incorrect results upon the reconstruction of the distribution of diffuse scattering from different runs. These errors are of little importance when Bragg peaks are processed.

  8. Calculation of spontaneous emission from a V-type three-level atom in photonic crystals using fractional calculus

    International Nuclear Information System (INIS)

    Fractional time derivative, an abstract mathematical operator of fractional calculus, is used to describe the real optical system of a V-type three-level atom embedded in a photonic crystal. A fractional kinetic equation governing the dynamics of the spontaneous emission from this optical system is obtained as a fractional Langevin equation. Solving this fractional kinetic equation by fractional calculus leads to the analytical solutions expressed in terms of fractional exponential functions. The accuracy of the obtained solutions is verified through reducing the system into the special cases whose results are consistent with the experimental observation. With accurate physical results and avoiding the complex integration for solving this optical system, we propose fractional calculus with fractional time derivative as a better mathematical method to study spontaneous emission dynamics from the optical system with non-Markovian dynamics.

  9. Topological spin waves in the atomic-scale magnetic skyrmion crystal

    Science.gov (United States)

    Roldán-Molina, A.; Nunez, A. S.; Fernández-Rossier, J.

    2016-04-01

    We study the spin waves of the triangular skyrmion crystal that emerges in a two-dimensional spin lattice model as a result of the competition between Heisenberg exchange, Dzyalonshinkii–Moriya interactions, Zeeman coupling and uniaxial anisotropy. The calculated spin wave bands have a finite Berry curvature that, in some cases, leads to non-zero Chern numbers, making this system topologically distinct from conventional magnonic systems. We compute the edge spin-waves, expected from the bulk-boundary correspondence principle, and show that they are chiral, which makes them immune to elastic backscattering. Our results illustrate how topological phases can occur in self-generated emergent superlattices at the mesoscale.

  10. 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.

  11. Optimization of the nonuniformity in light collection of tapered PbWO{sub 4} crystals and its influence on the energy resolution of the PANDA barrel EMC

    Energy Technology Data Exchange (ETDEWEB)

    Diehl, Stefan; Drexler, Peter; Dormenev, Valery; Nazarenko, Svetlana; Kuske, Till; Novotny, Rainer W.; Rosenbaum, Christoph; Zaunick, Hans-Georg [II. Physics Institute, University Giessen (Germany); Kavatsyuk, Myroslav [KVI-CART Groningen (Netherlands); Rosier, Philippe [IPN, Orsay (France); Ryantsev, Andrej [IHEP Protvino (Russian Federation); Wieczorek, Peter; Wilms, Andrea [GSI Helmholtzzentrum fuer Schwerionenforschung, Darmstadt (Germany)

    2015-07-01

    The barrel part of the electromagnetic (EM) calorimeter of the PANDA detector at the future FAIR facility will consist of 11 crystal geometries with a different degree of tapering. Due to tapering the crystals show a nonuniformity (NUF) in light collection. For the most tapered crystals the light detected by the photosensor is enhanced by a factor 1.4, if the scintillation light is created in the front part of the crystal. Due to the spread and the fluctuations of the EM shower within the crystal, this effect causes a smearing of the response, resulting in a reduced energy resolution. Therefore one lateral side has been depolished for 9 crystals, decreasing the NUF down to <5%, with only a slighty reduced light yield. The contribution will compare the response of a 3 x 3 matrix of crystals with one depolished side, with an identical matrix of polished crystals using a tagged photon beam with energies <1 GeV and the results from GEANT4 simulations, which indicate a significant improvement of the energy resolution.

  12. High resolution phoswich gamma-ray imager utilizing monolithic MPPC arrays with submillimeter pixelized crystals

    Science.gov (United States)

    Kato, T.; Kataoka, J.; Nakamori, T.; Kishimoto, A.; Yamamoto, S.; Sato, K.; Ishikawa, Y.; Yamamura, K.; Kawabata, N.; Ikeda, H.; Kamada, K.

    2013-05-01

    We report the development of a high spatial resolution tweezers-type coincidence gamma-ray camera for medical imaging. This application consists of large-area monolithic Multi-Pixel Photon Counters (MPPCs) and submillimeter pixelized scintillator matrices. The MPPC array has 4 × 4 channels with a three-side buttable, very compact package. For typical operational gain of 7.5 × 105 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 brand-new scintillator, Ce-doped Gd3Al2Ga3O12 (Ce:GAGG) due to their high light yield and density. To improve the spatial resolution, these scintillators were fabricated into 15 × 15 matrices of 0.5 × 0.5 mm2 pixels. The Ce:LYSO and Ce:GAGG scintillator matrices were assembled into phosphor sandwich (phoswich) detectors, and then coupled to the MPPC array along with an acrylic light guide measuring 1 mm thick, and with summing operational amplifiers that compile the signals into four position-encoded analog outputs being used for signal readout. Spatial resolution of 1.1 mm was achieved with the coincidence imaging system using a 22Na point source. These results suggest that the gamma-ray imagers offer excellent potential for applications in high spatial medical imaging.

  13. Atomic structure of "vitreous" interfacial films in sialon

    OpenAIRE

    Thorel, A.; Laval, J; Broussaud, Daniel

    1988-01-01

    Atomic resolution imaging of siliceous interfacial films in a sialon has been achieved using transmission electron microscopy at 1000 KV. Although such films have always been reputed as vitreous, we show that they are at least partially crystallized. An atomic model is proposed and simulated. The stability of these films is discussed when special crystallographic relationships exist between the two adjacent grains.

  14. Atomic motion of resonantly vibrating quartz crystal visualized by time-resolved X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Aoyagi, Shinobu, E-mail: aoyagi@nsc.nagoya-cu.ac.jp [Department of Information and Basic Science, Nagoya City University, Nagoya 467-8501 (Japan); Osawa, Hitoshi; Sugimoto, Kunihisa; Fujiwara, Akihiko [SPring-8/JASRI, Sayo, Hyogo 679-5198 (Japan); Takeda, Shoichi; Moriyoshi, Chikako; Kuroiwa, Yoshihiro [Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima 739-8526 (Japan)

    2015-11-16

    Transient atomic displacements during a resonant thickness-shear vibration of AT-cut α-quartz are revealed by time-resolved X-ray diffraction under an alternating electric field. The lattice strain resonantly amplified by the alternating electric field is ∼10{sup 4} times larger than that induced by a static electric field. The resonantly amplified lattice strain is achieved by fast displacements of oxygen anions and collateral resilient deformation of Si−O−Si angles bridging rigid SiO{sub 4} tetrahedra, which efficiently transduce electric energy into elastic energy.

  15. Crystal and local atomic structure of Co-doped MgFeBO_4 warwickites

    OpenAIRE

    Kazak, N. V.; Platunov, M. S.; Knyazev, Yu. V.; Ivanova, N. B.; Zubavichus, Y. V.; Veligzhanin, A. A.; Vasiliev, A. D.; Bezmaternykh, L. N.; Bayukov, O. A.; Arauzo, A.; Bartolomé, J.; Lamonova, K. V.; Ovchinnikov, S. G.

    2014-01-01

    Single crystalline MgFeBO_4, Mg_0.5Co_0.5FeBO_4 and CoFeBO_4 have been grown by the flux method. The samples have been characterized by X-ray spectral analysis, X-ray diffraction and X-ray absorption spectroscopy. The X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectra have been measured at the Fe andCoK-edges over a wide temperature range (6.5 - 300 K). The composition, the charge state and local environment of both Fe and Co atoms have b...

  16. Atomic motion of resonantly vibrating quartz crystal visualized by time-resolved X-ray diffraction

    International Nuclear Information System (INIS)

    Transient atomic displacements during a resonant thickness-shear vibration of AT-cut α-quartz are revealed by time-resolved X-ray diffraction under an alternating electric field. The lattice strain resonantly amplified by the alternating electric field is ∼104 times larger than that induced by a static electric field. The resonantly amplified lattice strain is achieved by fast displacements of oxygen anions and collateral resilient deformation of Si−O−Si angles bridging rigid SiO4 tetrahedra, which efficiently transduce electric energy into elastic energy

  17. Atomic motion of resonantly vibrating quartz crystal visualized by time-resolved X-ray diffraction

    Science.gov (United States)

    Aoyagi, Shinobu; Osawa, Hitoshi; Sugimoto, Kunihisa; Fujiwara, Akihiko; Takeda, Shoichi; Moriyoshi, Chikako; Kuroiwa, Yoshihiro

    2015-11-01

    Transient atomic displacements during a resonant thickness-shear vibration of AT-cut α-quartz are revealed by time-resolved X-ray diffraction under an alternating electric field. The lattice strain resonantly amplified by the alternating electric field is ˜104 times larger than that induced by a static electric field. The resonantly amplified lattice strain is achieved by fast displacements of oxygen anions and collateral resilient deformation of Si-O-Si angles bridging rigid SiO4 tetrahedra, which efficiently transduce electric energy into elastic energy.

  18. 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.

  19. 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.

  20. Unusual calibration curves observed for iron using high-resolution continuum source graphite furnace atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Welz, Bernhard, E-mail: w.bernardo@terra.com.b [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis-SC (Brazil); Instituto Nacional de Ciencia e Tecnologia do CMPq-INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador-BA (Brazil); Santos, Lisia M.G. dos [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis-SC (Brazil); Instituto Nacional de Controle de Qualidade em Saude-INCQS-Fiocruz, 21040-900 Rio de Janeiro-RJ (Brazil); Araujo, Rennan G.O. [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis-SC (Brazil); Departamento de Quimica, Universidade Federal de Sergipe, 49100-000 Sao Cristovao-SE (Brazil); Jacob, Silvana do C. [Instituto Nacional de Controle de Qualidade em Saude-INCQS-Fiocruz, 21040-900 Rio de Janeiro-RJ (Brazil); Vale, Maria Goreti R. [Instituto Nacional de Ciencia e Tecnologia do CMPq-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); Okruss, Michael; Becker-Ross, Helmut [Leibniz-Institut fuer Analytische Wissenschaften-ISAS-Department Berlin, 12489 Berlin (Germany)

    2010-03-15

    The simultaneous determination of cadmium and iron in plant and soil samples has been investigated using high-resolution continuum source graphite furnace atomic absorption spectrometry. The primary cadmium resonance line at 228.802 nm and an adjacent secondary iron line at 228.726 nm, which is within the spectral interval covered by the charge-coupled device (CCD) array detector, have been used for the investigations. Due to the very high iron content in most of the soil samples the possibility has been investigated to reduce the sensitivity and extend the working range by using side pixels for measurement at the line wings instead of the line core. It has been found that the calibration curves measured at all the analytically useful pixels of this line consisted of two linear parts with distinctly different slopes. This effect has been independent of the positioning of the wavelength, i.e., if the Cd line or the Fe line was in the center of the CCD array. The most likely explanation for this unusual behavior is a significant difference between the instrument width DELTAlambda{sub Instr} and the absorption line width DELTAlambda{sub Abs}, which is quite pronounced in the case of Fe. Using both parts of the calibration curves and simultaneous measurement at the line center and at the wings made it possible to extend the working range for the iron determination to more than three orders of magnitude.

  1. Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures

    Science.gov (United States)

    Yang, H.; Rutte, R. N.; Jones, L.; Simson, M.; Sagawa, R.; Ryll, H.; Huth, M.; Pennycook, T. J.; Green, M.L.H.; Soltau, H.; Kondo, Y.; Davis, B. G.; Nellist, P. D.

    2016-01-01

    The aberration-corrected scanning transmission electron microscope (STEM) has emerged as a key tool for atomic resolution characterization of materials, allowing the use of imaging modes such as Z-contrast and spectroscopic mapping. The STEM has not been regarded as optimal for the phase-contrast imaging necessary for efficient imaging of light materials. Here, recent developments in fast electron detectors and data processing capability is shown to enable electron ptychography, to extend the capability of the STEM by allowing quantitative phase images to be formed simultaneously with incoherent signals. We demonstrate this capability as a practical tool for imaging complex structures containing light and heavy elements, and use it to solve the structure of a beam-sensitive carbon nanostructure. The contrast of the phase image contrast is maximized through the post-acquisition correction of lens aberrations. The compensation of defocus aberrations is also used for the measurement of three-dimensional sample information through post-acquisition optical sectioning. PMID:27561914

  2. Acoustic emission and magnification of atomic lines resolution for laser breakdown of salt water in ultrasound field

    International Nuclear Information System (INIS)

    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

  3. Modeling the crystal distribution of lead-sulfate in lead-acid batteries with 3D spatial resolution

    Science.gov (United States)

    Huck, Moritz; Badeda, Julia; Sauer, Dirk Uwe

    2015-04-01

    For the reliability of lead-acid batteries it is important to have an accurate prediction of its response to load profiles. A model for the lead-sulfate growth is presented, which is embedded in a physical-chemical model with 3D spatial resolution is presented which is used for analyzing the different mechanism influencing the cell response. One import factor is the chemical dissolution and precipitation of lead-sulfate, since its dissolution speed limits the charging reaction and the accumulation of indissolvable of lead-sulfate leads to capacity degradation. The cell performance/behavior is not only determined by the amount of the sulfate but also by the radii and distribution of the crystals. The presented model can be used to for an improved understanding of the interaction of the different mechanisms.

  4. Ultrafast probing of the x-ray-induced lattice and electron dynamics in graphite at atomic-resolution

    Energy Technology Data Exchange (ETDEWEB)

    Hau-Riege, S

    2010-10-07

    We used LCLS pulses to excite thin-film and bulk graphite with various different microstructures, and probed the ultrafast ion and electron dynamics through Bragg and x-ray Thomson scattering (XRTS). We pioneered XRTS at LCLS, making this technique viable for other users. We demonstrated for the first time that the LCLS can be used to characterize warm-dense-matter through Bragg and x-ray Thomson scattering. The warm-dense-matter conditions were created using the LCLS beam. Representative examples of the results are shown in the Figure above. In our experiment, we utilized simultaneously both Bragg and two Thomson spectrometers. The Bragg measurements as a function of x-ray fluence and pulse length allows us to characterize the onset of atomic motion at 2 keV with the highest resolution to date. The Bragg detector was positioned in back-reflection, providing us access to scattering data with large scattering vectors (nearly 4{pi}/{lambda}). We found a clear difference between the atomic dynamics for 70 and 300 fs pulses, and we are currently in the process of comparing these results to our models. The outcome of this comparison will have important consequences for ultrafast diffractive imaging, for which it is still not clear if atomic resolution can truly be achieved. The backward x-ray Thomson scattering data suggests that the average graphite temperature and ionization was 10 eV and 1.0, respectively, which agrees with our models. In the forward scattering data, we observed an inelastic feature in the Thomson spectrum that our models currently do not reproduce, so there is food for thought. We are in the process of writing these results up. Depending on if we can combine the Bragg and Thomson data or not, we plan to publish them in a single paper (e.g. Nature or Science) or as two separate papers (e.g. two Phys. Rev. Lett.). We will present the first analysis of the results at the APS Plasma Meeting in November 2010. We had a fantastic experience performing our

  5. Existence of Dirac cones in the Brillouin zone of diperiodic atomic crystals according to group theory

    Science.gov (United States)

    Damljanović, V.; Gajić, R.

    2016-03-01

    We have considered non-magnetic materials with weak spin-orbit coupling, that are periodic in two non-collinear directions, and finite in the third, orthogonal direction. In some cases, the combined time-reversal and crystal symmetry of such systems, allows the existence of Dirac cones at certain points in the reciprocal space. We have investigated in a systematic way, all points of the Brillouin zone of all 80 diperiodic groups and have found sufficient conditions for the existence of s  =  1/2 Dirac fermions, with symmetry-provided band touching at the vertex of the Dirac cones. Conversely, complete linear dispersion is forbidden for orbital wave functions belonging to two-dimensional (2D) irreducible representations (irreps) of little groups that do not satisfy certain group theoretical conditions given in this paper. Our results are illustrated by a tight-binding example.

  6. Layer- and frequency-dependent second harmonic generation in reflection from GaSe atomic crystals

    Science.gov (United States)

    Tang, Yanhao; Mandal, Krishna C.; McGuire, John A.; Lai, Chih Wei

    2016-09-01

    We report optical second-harmonic generation (SHG) in reflection from GaSe crystals of 1 to more than 100 layers using a fundamental picosecond pulsed pump at 1.58 eV and a supercontinuum white light pulsed laser with energies ranging from 0.85 to 1.4 eV. The measured reflected SHG signal is maximal in samples of ˜20 layers, decreasing in thicker samples as a result of interference. The thickness- and frequency-dependence of the SHG response of samples thicker than ˜7 layers can be reproduced by a second-order optical susceptibility that is the same as in bulk samples. For samples ≲7 layers, the second-order optical susceptibility is reduced compared to that in thicker samples, which is attributed to the expected band-gap increase in mono- and few-layer GaSe.

  7. Existence of Dirac cones in the Brillouin zone of diperiodic atomic crystals according to group theory.

    Science.gov (United States)

    Damljanović, V; Gajić, R

    2016-03-01

    We have considered non-magnetic materials with weak spin-orbit coupling, that are periodic in two non-collinear directions, and finite in the third, orthogonal direction. In some cases, the combined time-reversal and crystal symmetry of such systems, allows the existence of Dirac cones at certain points in the reciprocal space. We have investigated in a systematic way, all points of the Brillouin zone of all 80 diperiodic groups and have found sufficient conditions for the existence of s  =  1/2 Dirac fermions, with symmetry-provided band touching at the vertex of the Dirac cones. Conversely, complete linear dispersion is forbidden for orbital wave functions belonging to two-dimensional (2D) irreducible representations (irreps) of little groups that do not satisfy certain group theoretical conditions given in this paper. Our results are illustrated by a tight-binding example. PMID:26829015

  8. Quantum Interference in Spontaneous Emission from a V-Type Three-Level Atom in a Two-Band Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    YANG Ya-Ping; Chen Hong; ZHU Shi-Yao

    2000-01-01

    The spontaneous emission from a V-type three-level atom embedded in a two-band photonic crystal is studied.Due to the quantum interference between the two transitions and existence of two bands, the populations in the upper levels display some novel behavior: anti-trapping, population oscillation, and population inversion.

  9. 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.

  10. 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. PMID:23187595

  11. ZnS0.8Se0.2 film for high resolution liquid crystal light valve

    Institute of Scientific and Technical Information of China (English)

    SHEN Da-ke(沈大可); HAN Gao-rong(韩高荣); DU Pi-yi(杜丕一); QUE Duan-lin(阙端麟); SOU I.K.

    2004-01-01

    The structural characteristics and optical and electrical properties of molecular-beam-epitaxy (MBE) grown ZnS0.8Se0.2 thin films on indium-tin-oxide (ITO) glass substrates were investigated in this work. The X-ray diffraction (XRD)results indicated that high quality polycrystalline ZnS0.8Se0.2 thin film grown at the optimized temperature had a preferred orientation along the (111) planes. The transmission electron microscopy (TEM) cross-sectional micrograph of the sample showed a well defined columnar structure with lateral crystal dimension in the order ofa few hundred angstroms. Ultraviolet (UV) photoresponsivity as high as 0.01 A/W had been demonstrated and for wavelengths longer than 450 nm, the response was down from the peak response by more than 3 orders of magnitude. The thin ZnS0.8Se0.2 photosensor layer, with a wide energy gap and anisotropic electrical property, makes a transmission UV liquid crystal light valve ( LCLV) with high resolution feasible.

  12. ZnS0.8Se0.2 film for high resolution liquid crystal light valve

    Institute of Scientific and Technical Information of China (English)

    沈大可; 韩高荣; 杜丕一; 阙端麟; SOUI.K

    2004-01-01

    The structural characteristics and optical and electrical properties of molecular-beam-epitaxy (MBE) grown ZnS0.8Se0.2 thin films on indium-tin-oxide (ITO) glass substrates were investigated in this work. The X-ray diffraction (XRD) results indicated that high quality polycrystalline ZnS0.8Se0.2 thin film grown at the optimized temperature had a preferred orientation along the (111) planes. The transmission electron microscopy (TEM) cross-sectional micrograph of the sample showed a well defined columnar structure with lateral crystal dimension in the order of a few hundred angstroms. Ultraviolet(UV) photoresponsivity as high as 0.01 A/W had been demonstrated and for wavelengths longer than 450 nm, the response was down from the peak response by more than 3 orders of magnitude. The thin ZnS0.8Se0,2 photosensor layer, with a wide energy gap and anisotropic electrical property, makes a transmission UV liquid crystal light valve (LCLV) with high resolution feasible.

  13. High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein.

    Science.gov (United States)

    Klumpp, Klaus; Lam, Angela M; Lukacs, Christine; Vogel, Robert; Ren, Suping; Espiritu, Christine; Baydo, Ruth; Atkins, Kateri; Abendroth, Jan; Liao, Guochun; Efimov, Andrey; Hartman, George; Flores, Osvaldo A

    2015-12-01

    The hepatitis B virus (HBV) core protein is essential for HBV replication and an important target for antiviral drug discovery. We report the first, to our knowledge, high-resolution crystal structure of an antiviral compound bound to the HBV core protein. The compound NVR-010-001-E2 can induce assembly of the HBV core wild-type and Y132A mutant proteins and thermostabilize the proteins with a Tm increase of more than 10 °C. NVR-010-001-E2 binds at the dimer-dimer interface of the core proteins, forms a new interaction surface promoting protein-protein interaction, induces protein assembly, and increases stability. The impact of naturally occurring core protein mutations on antiviral activity correlates with NVR-010-001-E2 binding interactions determined by crystallography. The crystal structure provides understanding of a drug efficacy mechanism related to the induction and stabilization of protein-protein interactions and enables structure-guided design to improve antiviral potency and drug-like properties.

  14. Crystal structure of echicetin from Echis carinatus (Indian saw-scaled viper) at 2.4A resolution.

    Science.gov (United States)

    Jasti, Jayasankar; Paramasivam, M; Srinivasan, A; Singh, T P

    2004-01-01

    Echicetin is a heterodimeric protein from the venom of the Indian saw-scaled viper, Echis carinatus. It binds to platelet glycoprotein Ib (GPIb) and thus inhibits platelet aggregation. It has two subunits, alpha and beta, consisting of 131 and 123 amino acid residues, respectively. The two chains are linked with a disulphide bond. The level of amino acid sequence homology between two subunits is 50%. The protein was purified from the venom of E.carinatus and crystallized using ammonium sulphate as a precipitant. The crystal structure has been determined at 2.4A resolution and refined to an R-factor of 0.187. Overall dimensions of the heterodimer are approximately 80Ax35Ax35A. The backbone folds of the two subunits are similar. The central portions of the polypeptide chains of alpha and beta-subunits move into each other to form a tight dimeric association. The remaining portions of the chains of both subunits fold in a manner similar to those observed in the carbohydrate-binding domains of C-type lectins. In echicetin, the Ca(2+)-binding sites are not present, despite being topologically equivalent to other similar Ca(2+)-binding proteins of the superfamily. The residues Ser41, Glu43 and Glu47 in the calcium-binding proteins of the related family are conserved but the residues Glu126/120 are replaced by lysine at the corresponding sites in the alpha and beta-subunits. PMID:14659748

  15. Calibration of the OHREX high-resolution imaging crystal spectrometer at the Livermore electron beam ion traps

    Science.gov (United States)

    Hell, N.; Beiersdorfer, P.; Magee, E. W.; Brown, G. V.

    2016-11-01

    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.

  16. Velocity tuning of friction with two trapped atoms

    CERN Document Server

    Gangloff, Dorian; Counts, Ian; Jhe, Wonho; Vuletić, Vladan

    2015-01-01

    Friction is the basic, ubiquitous mechanical interaction between two surfaces that results in resistance to motion and energy dissipation. In spite of its technological and economic significance, our ability to control friction remains modest, and our understanding of the microscopic processes incomplete. At the atomic scale, mismatch between the two contacting crystal lattices can lead to a reduction of stick-slip friction (structural lubricity), while thermally activated atomic motion can give rise to a complex velocity dependence, and nearly vanishing friction at sufficiently low velocities (thermal lubricity). Atomic force microscopy has provided a wealth of experimental results, but limitations in the dynamic range, time resolution, and control at the single-atom level have hampered a full quantitative description from first principles. Here, using an ion-crystal friction emulator with single-atom, single substrate-site spatial resolution and single-slip temporal resolution, we measure the friction force...

  17. Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with NAD[superscript +] and Fluoroalcohols Define Strained Michaelis Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Plapp, Bryce V.; Ramaswamy, S. (inSTEM); (Iowa)

    2013-01-16

    Structures of horse liver alcohol dehydrogenase complexed with NAD{sup +} and unreactive substrate analogues, 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol, were determined at 100 K at 1.12 or 1.14 {angstrom} resolution, providing estimates of atomic positions with overall errors of 0.02 {angstrom}, the geometry of ligand binding, descriptions of alternative conformations of amino acid residues and waters, and evidence of a strained nicotinamide ring. The four independent subunits from the two homodimeric structures differ only slightly in the peptide backbone conformation. Alternative conformations for amino acid side chains were identified for 50 of the 748 residues in each complex, and Leu-57 and Leu-116 adopt different conformations to accommodate the different alcohols at the active site. Each fluoroalcohol occupies one position, and the fluorines of the alcohols are well-resolved. These structures closely resemble the expected Michaelis complexes with the pro-R hydrogens of the methylene carbons of the alcohols directed toward the re face of C4N of the nicotinamide rings with a C-C distance of 3.40 {angstrom}. The oxygens of the alcohols are ligated to the catalytic zinc at a distance expected for a zinc alkoxide (1.96 {angstrom}) and participate in a low-barrier hydrogen bond (2.52 {angstrom}) with the hydroxyl group of Ser-48 in a proton relay system. As determined by X-ray refinement with no restraints on bond distances and planarity, the nicotinamide rings in the two complexes are slightly puckered (quasi-boat conformation, with torsion angles of 5.9{sup o} for C4N and 4.8{sup o} for N1N relative to the plane of the other atoms) and have bond distances that are somewhat different compared to those found for NAD(P){sup +}. It appears that the nicotinamide ring is strained toward the transition state on the path to alcohol oxidation.

  18. The crystal structure of human dopamine β-hydroxylase at 2.9 Å resolution.

    Science.gov (United States)

    Vendelboe, Trine V; Harris, Pernille; Zhao, Yuguang; Walter, Thomas S; Harlos, Karl; El Omari, Kamel; Christensen, Hans E M

    2016-04-01

    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 other proteins, reveals a possible metal-binding site and a ligand-binding pocket. The catalytic core structure shows two different conformations: an open active site, as also seen in another member of this enzyme family [the peptidylglycine α-hydroxylating (and α-amidating) monooxygenase], and a closed active site structure, in which the two copper-binding sites are only 4 to 5 Å apart, in what might be a coupled binuclear copper site. The dimerization domain adopts a conformation that bears no resemblance to any other known protein structure. The structure provides new molecular insights into the numerous devastating disorders of both physiological and neurological origins associated with the dopamine system. PMID:27152332

  19. 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.

  20. Atomically thin epitaxial template for organic crystal growth using graphene with controlled surface wettability.

    Science.gov (United States)

    Nguyen, Nguyen Ngan; Jo, Sae Byeok; Lee, Seong Kyu; Sin, Dong Hun; Kang, Boseok; Kim, Hyun Ho; Lee, Hansol; Cho, Kilwon

    2015-04-01

    A two-dimensional epitaxial growth template for organic semiconductors was developed using a new method for transferring clean graphene sheets onto a substrate with controlled surface wettability. The introduction of a sacrificial graphene layer between a patterned polymeric supporting layer and a monolayer graphene sheet enabled the crack-free and residue-free transfer of free-standing monolayer graphene onto arbitrary substrates. The clean graphene template clearly induced the quasi-epitaxial growth of crystalline organic semiconductors with lying-down molecular orientation while maintaining the "wetting transparency", which allowed the transmission of the interaction between organic molecules and the underlying substrate. Consequently, the growth mode and corresponding morphology of the organic semiconductors on graphene templates exhibited distinctive dependence on the substrate hydrophobicity with clear transition from lateral to vertical growth mode on hydrophilic substrates, which originated from the high surface energy of the exposed crystallographic planes of the organic semiconductors on graphene. The optical properties of the pentacene layer, especially the diffusion of the exciton, also showed a strong dependency on the corresponding morphological evolution. Furthermore, the effect of pentacene-substrate interaction was systematically investigated by gradually increasing the number of graphene layers. These results suggested that the combination of a clean graphene surface and a suitable underlying substrate could serve as an atomically thin growth template to engineer the interaction between organic molecules and aromatic graphene network, thereby paving the way for effectively and conveniently tuning the semiconductor layer morphologies in devices prepared using graphene. PMID:25798655

  1. Morphology Change of C60 Islands on Organic Crystals Observed by Atomic Force Microscopy.

    Science.gov (United States)

    Freund, Sara; Hinaut, Antoine; Pawlak, Rémy; Liu, Shi-Xia; Decurtins, Silvio; Meyer, Ernst; Glatzel, Thilo

    2016-06-28

    Organic-organic heterojunctions are nowadays highly regarded materials for light-emitting diodes, field-effect transistors, and photovoltaic cells with the prospect of designing low-cost, flexible, and efficient electronic devices.1-3 However, the key parameter of optimized heterojunctions relies on the choice of the molecular compounds as well as on the morphology of the organic-organic interface,4 which thus requires fundamental studies. In this work, we investigated the deposition of C60 molecules at room temperature on an organic layer compound, the salt bis(benzylammonium)bis(oxalato)cupurate(II), by means of noncontact atomic force microscopy. Three-dimensional molecular islands of C60 having either triangular or hexagonal shapes are formed on the substrate following a "Volmer-Weber" type of growth. We demonstrate the dynamical reshaping of those C60 nanostructures under the local action of the AFM tip at room temperature. The dissipated energy is about 75 meV and can be interpreted as the activation energy required for this migration process.

  2. Inhibition of Crystal Growth during Plasma Enhanced Atomic Layer Deposition by Applying BIAS

    Directory of Open Access Journals (Sweden)

    Stephan Ratzsch

    2015-11-01

    Full Text Available In this study, the influence of direct current (DC biasing on the growth of titanium dioxide (TiO2 layers and their nucleation behavior has been investigated. Titania films were prepared by plasma enhanced atomic layer deposition (PEALD using Ti(OiPr4 as metal organic precursor. Oxygen plasma, provided by remote inductively coupled plasma, was used as an oxygen source. The TiO2 films were deposited with and without DC biasing. A strong dependence of the applied voltage on the formation of crystallites in the TiO2 layer is shown. These crystallites form spherical hillocks on the surface which causes high surface roughness. By applying a higher voltage than the plasma potential no hillock appears on the surface. Based on these results, it seems likely, that ions are responsible for the nucleation and hillock growth. Hence, the hillock formation can be controlled by controlling the ion energy and ion flux. The growth per cycle remains unchanged, whereas the refractive index slightly decreases in the absence of energetic oxygen ions.

  3. Dialysis purification of integrase-DNA complexes provides high-resolution atomic force microscopy images: dimeric recombinant HIV-1 integrase binding and specific looping on DNA.

    Directory of Open Access Journals (Sweden)

    Tatsuaki Tsuruyama

    Full Text Available It remains difficult to obtain high-resolution atomic force microscopy images of HIV-1 integrase bound to DNA in a dimeric or tetrameric fashion. We therefore constructed specific target DNAs to assess HIV-1 integrase binding and purified the complex by dialysis prior to analysis. Our resulting atomic force microscopy analyses indicated precise size of binding human immunodeficiency virus type 1 (HIV-1 recombinant integrase in a tetrameric manner, inducing formation of a loop-like or figure-eight-like secondary structure in the target DNA. Our findings regarding the target DNA secondary structure provide new insights into the intermediate states of retroviral integration.

  4. Dialysis purification of integrase-DNA complexes provides high-resolution atomic force microscopy images: dimeric recombinant HIV-1 integrase binding and specific looping on DNA.

    Science.gov (United States)

    Tsuruyama, Tatsuaki; Nakai, Tonau; Ohmori, Rei; Ozeki, Munetaka; Tamaki, Keiji; Yoshikawa, Kenichi

    2013-01-01

    It remains difficult to obtain high-resolution atomic force microscopy images of HIV-1 integrase bound to DNA in a dimeric or tetrameric fashion. We therefore constructed specific target DNAs to assess HIV-1 integrase binding and purified the complex by dialysis prior to analysis. Our resulting atomic force microscopy analyses indicated precise size of binding human immunodeficiency virus type 1 (HIV-1) recombinant integrase in a tetrameric manner, inducing formation of a loop-like or figure-eight-like secondary structure in the target DNA. Our findings regarding the target DNA secondary structure provide new insights into the intermediate states of retroviral integration.

  5. 光子晶体中Ξ型三能级原子的光场-原子束缚态%Photon-Atom Bound Dressed State of Three-Level Atom With Ξ Type in Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    焦志伟; 陈西园

    2001-01-01

    光子晶体中光子带隙的存在使得频率在带隙内的光无法通过光子晶体,镶嵌在光子晶体中的原子的自发辐射必然不同于在均匀介质中原子的自发辐射。关于二能级原子和V型三能级原子在光子晶体中的自发辐射已有文献报道,采用的方法是用拉普拉斯变换求解薛定鄂方程。用求系统本征值的方法讨论了光子晶体中单个三能级原子的自发辐射。讨论的模型为Ξ型三能级原子。由于光的局域化,两个上能级的粒子数布居取决于两个上能级之间跃迁频率相对于光子带隙边缘频率ωc的大小,当两个上能级之间跃迁频率位于带隙内时,两个上能级的粒子数布居出现了反转。这一性质区别于V型三能级原子在光子晶体中的自发辐射。%The band gap in the crystal for photons leads that the light with frequency in the band gap can not go through the photonic crystal. Spontaneous emission from atom in photonic crystal is different from that of atom in other medium. Spontaneous emission from a three-level atom embedded in the photonic crystal is studied with the solution for eigenvalue problem of atom-field trapped state. A model of Ξ type for three-level atom has been discussed. Because of the localization of light, the population of particles in the two upper levels depends on the transition frequency between the two upper levels. When the transition frequency between the two upper levels is within the forbidden band-gap, there is population inversion in the two upper levels, which differs from that of the two-level atom and other three-level atoms in a photonic crystal.

  6. 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...

  7. 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

    1993-01-01

    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 structu

  8. 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...

  9. 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

    2016-07-01

    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.

  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

    2016-07-01

    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. Migration of constituent atoms and interface morphology in a heterojunction between CdS and CuInSe{sub 2} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Soo, Y.L.; Huang, S.; Kao, Y.H. [Department of Physics, State University of New York at Buffalo, Amherst, New York, 14260 (United States); Deb, S.K.; Ramanathan, K. [National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, Colorado 80401 (United States); Takizawa, T. [Nihon University (Japan)

    1999-12-01

    Angular dependence of x-ray fluorescence (ADXRF), x-ray absorption fine structure (XAFS), and grazing incidence x-ray scattering measurements were carried out using synchrotron radiation for a study of the interface morphology and migration of constituent atoms in a heterojunction formed between CdS and CuInSe{sub 2} single crystals. The advantage of using a single crystal for this study is to avoid the usually complicated problems arising from multiple phases of the Cu{endash}In{endash}Se compounds. By a comparison of the results obtained with a bare CuInSe{sub 2} single crystal, the changes of interface microstructures in the CdS/CuInSe{sub 2} heterojunction system with {ital well-defined stoichiometry} can therefore be investigated. Prominent features in the ADXRF data clearly demonstrate that both Cu and Se atoms have migrated into the CdS layer in the heterojunction while In atoms remain intact in the CuInSe{sub 2} single crystal. The local structures around Cu in the system also show a significant change after the deposition of CdS, as manifested by the appearance of new Cd near neighbors in the XAFS spectra. {copyright} {ital 1999 American Institute of Physics.}

  12. High energy-resolution x-ray spectroscopy at ultra-high dilution with spherically bent crystal analyzers of 0.5 m radius

    CERN Document Server

    Rovezzi, Mauro; Manceau, Alain; Glatzel, Pieter; Verbeni, Roberto

    2016-01-01

    We present the development, manufacturing and performance of spherically bent crystal analyzers (SBCAs) of 100 mm diameter and 0.5 m bending radius. The elastic strain in the crystal wafer is partially released by a "strip-bent" method where the crystal wafer is cut in strips prior to the anodic bonding process. Compared to standard 1 m SBCAs, a gain in intensity is obtained without loss of energy resolution. The gain ranges between 2.5 and 7, depending on the experimental conditions and the width of the emission line measured. This reduces the acquisition times required to perform high energy-resolution x-ray absorption and emission spectroscopy on ultra-dilute species, accessing concentrations of the element of interest down to, or below, the ppm (ng/mg) level.

  13. Crystal structure of the disintegrin heterodimer from saw-scaled viper (Echis carinatus) at 1.9 A resolution.

    Science.gov (United States)

    Bilgrami, Sameeta; Yadav, Savita; Kaur, Punit; Sharma, Sujata; Perbandt, Markus; Betzel, Christian; Singh, Tej P

    2005-08-23

    Disintegrins constitute a family of potent polypeptide inhibitors of integrins. Integrins are transmembrane heterodimeric molecules involved in cell-cell and cell-extracellular matrix interactions. They are involved in many diseases such as cancer and thrombosis. Thus, disintegrins have a great potential as anticancer and antithrombotic agents. A novel heterodimeric disintegrin was isolated from the venom of saw-scaled viper (Echis carinatus) and was crystallized. The crystals diffracted to 1.9 A resolution and belonged to space group P4(3)2(1)2. The data indicated the presence of a pseudosymmetry. The structure was solved by applying origin shifts to the disintegrin homodimer schistatin solved in space group I4(1)22 with similar cell dimensions. The structure refined to the final R(cryst)/R(free) factors of 0.213/0.253. The notable differences are observed between the loops, (Gln39-Asp48) containing the important Arg42-Gly43-Asp44, of the present heterodimer and schistatin. These differences are presumably due to the presence of two glycines at positions 43 and 46 that allow the molecule to adopt variable conformations. A comparative analysis of the surface-charge distributions of various disintegrins showed that the charge distribution on monomeric disintegrins occurred uniformly over the whole surface of the molecule, while in the dimeric disintegrins, the charge is distributed only on one face. Such a feature may be important in the binding of two integrins to a single dimeric disintegrin. The phylogenetic analysis developed on the basis of amino acid sequence and three-dimensional structures indicates that the protein diversification and evolution presumably took place from the medium disintegrins and both the dimeric and short disintegrins evolved from them. PMID:16101289

  14. Accurate Treatment of Electrostatics during Molecular Adsorption in Nanoporous Crystals without Assigning Point Charges to Framework Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, T; Manz, TA; Sholl, DS

    2011-03-24

    Molecular simulations have become an important complement to experiments for studying gas adsorption and separation in crystalline nanoporous materials. Conventionally, these simulations use force fields that model adsorbate-pore interactions by assigning point charges to the atoms of the adsorbent. The assignment of framework charges always introduces ambiguity because there are many different choices for defining point charges, even when the true electron density of a material is known. We show how to completely avoid such ambiguity by using the electrostatic potential energy surface (EPES) calculated from plane wave density functional theory (DFT). We illustrate this approach by simulating CO(2) adsorption in four metal-organic frameworks (MOFs): IRMOF-1, ZIE-8, ZIE-90, and Zn(nicotinate)(2). The resulting CO(2) adsorption isotherms are insensitive to the exchange-correlation functional used in the DFT calculation of the EPES but are sensitive to changes in the crystal structure and lattice parameters. Isotherms computed from the DFT EPES are compared to those computed from several point charge models. This comparison makes possible, for the first time, an unbiased assessment of the accuracy of these point charge models for describing adsorption in MOFs. We find an unusually high Henry's constant (109 mmol/g.bar) and intermediate isosteric heat of adsorption (34.9 kJ/mol) for Zn(nicotinate)(2), which makes it a potentially attractive mateiial for CO(2) adsorption applications.

  15. Accurate Treatment of Electrostatics during Molecular Adsorption in Nanoporous Crystals without Assigning Point Charges to Framework Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Taku [Georgia Inst. of Technology, Atlanta, GA (United States); Manz, Thomas A. [Georgia Inst. of Technology, Atlanta, GA (United States); Sholl, David S. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2011-02-28

    Molecular simulations have become an important complement to experiments for studying gas adsorption and separation in crystalline nanoporous materials. Conventionally, these simulations use force fields that model adsorbate-pore interactions by assigning point charges to the atoms of the adsorbent. The assignment of framework charges always introduces ambiguity because there are many different choices for defining point charges, even when the true electron density of a material is known. We show how to completely avoid such ambiguity by using the electrostatic potential energy surface (EPES) calculated from plane wave density functional theory (DFT). We illustrate this approach by simulating CO2 adsorption in four metal-organic frameworks (MOFs): IRMOF-1, ZIF-8, ZIF-90, and Zn(nicotinate)2. The resulting CO2 adsorption isotherms are insensitive to the exchange-correlation functional used in the DFT calculation of the EPES but are sensitive to changes in the crystal structure and lattice parameters. Isotherms computed from the DFT EPES are compared to those computed from several point charge models. This comparison makes possible, for the first time, an unbiased assessment of the accuracy of these point charge models for describing adsorption in MOFs. We find an unusually high Henry’s constant (109 mmol/g·bar) and intermediate isosteric heat of adsorption (34.9 kJ/mol) for Zn(nicotinate)2, which makes it a potentially attractive material for CO2 adsorption applications.

  16. 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.

  17. High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-l-arabinofuranosidase activity

    International Nuclear Information System (INIS)

    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 Mn2+ 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 Mn2+ 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

  18. Detection of heterogeneities in single-crystal CaCu{sub 3}Ti{sub 4}O{sub 12} using conductive atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Fiorenza, Patrick; Lo Nigro, Raffaella; Raineri, Vito [Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche, Stradale Primosole 50, 95121 Catania (Italy); Krohns, Stephan; Lunkenheimer, Peter; Loidl, Alois [Experimental Physics V, Center for Electronic Correlations and Magnetism, University of Augsburg, 86135 Augsburg (Germany); Ebbinghaus, Stefan G [Solid State Chemistry, Martin-Luther University Halle-Wittemberg, 06120 Halle (Germany); Ferrarelli, Matthew C; Sinclair, Derek C; West, Anthony R, E-mail: patrick.fiorenza@imm.cnr.it [Department of Engineering Materials, Sir Robert Hadfield Building, University of Sheffield, Mappin Street, Sheffield, S1 3JD (United Kingdom)

    2010-02-15

    This paper reports on a conductive atomic force microscopy (C-AFM) investigation to provide local electrical characterization in a single crystal of CaCu{sub 3}Ti{sub 4}O{sub 12} (CCTO). The microstructure and dielectric properties were studied and provide evidence for an insulating secondary phase embedded within the semiconducting CCTO matrix. Such insulating electrical heterogeneities cannot be observed with macroscopic measurements such as conventional Impedance Spectroscopy and this study reveals C-AFM to be a powerful tool to assess the electrical homogeneity of semiconducting single crystals such as CCTO.

  19. Structure of gramicidin D-RbCl complex at atomic resolution from low-temperature synchrotron data: interactions of double-stranded gramicidin channel contents and cations with channel wall

    Energy Technology Data Exchange (ETDEWEB)

    Glówka, M.L.; Olczak, A.; Bojarska, J.; Szczesio, M.; Duax, W.L.; Burkhart, B.M.; Pangborn, W.A.; Langs, D.A.; Wawrzak, Z. (Poland); (NWU); (Hauptman)

    2010-03-05

    Gramicidin D (gD) is a naturally occurring ionophoric antibiotic that forms membrane channels specific for monovalent cations. The crystal structure of the RbCl complex of gD has been determined at 1.14 {angstrom} resolution from low-temperature (100 K) synchrotron-radiation data with a final R of 16%. The structure was refined with anisotropic temperature factors for all non-H atoms and with partial occupancies for many of them. The asymmetric unit in the crystal contains four crystallographically independent molecules that form two right-handed antiparallel double-stranded dimers. There are seven distinct rubidium-binding sites in each dimeric channel. The occupancy factors of Rb cations are between 0.11 and 0.35 and the total ion contents of the two crystallographically independent channels are 1.59 and 1.22 ions, respectively. Although each channel is 'chemically symmetrical', the side-chain conformations, the distributions of rubidium cations and their binding sites in the two independent channels are not. Cations are 'coordinated' by delocalized {pi}-electrons of three to five carbonyl groups that together with peptide backbone chains form the gramicidin channel walls. The water:cation ratio in the channel interior is four or five:one, and five or six waters separate Rb cations during their passage through the channel.

  20. 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.

  1. 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

  2. STUDIES ON PRIMARY CRYSTALLIZATION OF RAPIDLY QUENCHED Al-Ni-Cu-Nd METALLIC GLASS BY USING HIGH RESOLUTION TRASMISSION ELECTRON MICROSCOPY

    Institute of Scientific and Technical Information of China (English)

    Y.D. Xiao; W.X. Li; D. Jacovkis; N. Clavaguera; M.T. Clavaguera-Mora; J. Rodriguez- Viejo

    2003-01-01

    Rapidly solidified Al87Ni7Cu3Nd3 metallic glasses, prepared by using melt spinning,were treated under both isothermal and non-isothermal regime. The amorphous ribbon and the annealed samples were closely examined by means of differential scanning calorimetric, conventional X-ray diffraction and high resolution transmission electron microscopy with selected-area electron diffraction, with special interest in primary crystallization into α-Al nanocrystalline particles, in order to understand structural characteristics of Al-based amorphous/nanocrystalline alloys, and nucleation and grain growth mechanism on the nanometer scale during primary crystallization.The results show that, the as-prepared ribbons are fully amorphous and homogeneous in the micron scale, but contain high density of quenched-in clusters or crystallite embryos. Primary crystallization mainly leads to formation of two-phase mixture of α-Al crystal and residual amorphous phase. The annealed ribbons exposed isothermally at 110℃f or 5, 130 minutes and heated continuously up to less than 310℃ at 40℃/min consist of large amount of α-Al fcc crystal nanoparticles dispersed uniformly in an amorphous matrix. However, a very little amount of finer orthorhombie Al3Ni intermetalics particles exist in the annealed ribbons heated up to 310℃. During primary crystallization, the leading kinetic mechanics to impede growth of the α-Al crystal is soft impingement, instead of geometrie impingement.

  3. High-resolution spectroscopy of HoFe3(BO3)4 crystal: a study of phase transitions

    Science.gov (United States)

    Erofeev, D. A.; Chukalina, E. P.; Bezmaternykh, L. N.; Gudim, I. A.; Popova, M. N.

    2016-04-01

    The transmission spectra of HoFe3(BO3) multiferroic single crystals are studied by optical Fourier-transform spectroscopy at temperatures of 1.7-423 K in polarized light in the spectral range 500-10 000 cm-1 with a resolution up to 0.1 cm-1. A new first-order structural phase transition close to the second-order transition is recorded at T c = 360 K by the appearance of a new phonon mode at 976 cm-1. The reasons for considerable differences in T c for different samples of holmium ferroborate are discussed. By temperature variations in the spectra of the f-f transitions in the Ho3+ ion, we studied two magnetic phase transitions, namely, magnetic ordering into an easy-plane structure as a second-order phase transition at T N = 39 K and spin reorientation from the ab plane to the c axis as a first-order phase transition at T SR = 4.7 ± 0.2 K. It is shown that erbium impurity in a concentration of 1 at % decreases the spin-reorientation transition temperature to T SR = 4.0 K.

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

    Science.gov (United States)

    Lai, Xuelei; Soler-Lopez, Montserrat; Ismaya, Wangsa T; Wichers, Harry J; Dijkstra, Bauke W

    2016-03-01

    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 the truncated and cleaved MtaL present in the complex with tyrosinase directly isolated from mushroom shows that the general β-trefoil fold is conserved. However, differences are detected in the loop regions, particularly in the β2-β3 loop, which is intact and not cleaved in the recombinant MtaL. Furthermore, the N-terminal tail is rotated inwards, covering the tyrosinase-binding interface. Thus, MtaL must undergo conformational changes in order to bind mature mushroom tyrosinase. Very interestingly, the β-trefoil fold has been identified to be essential for carbohydrate interaction in other lectin-like proteins. Comparison of the structures of MtaL and a ricin-B-like lectin with a bound disaccharide shows that MtaL may have a similar carbohydrate-binding site that might be involved in glycoreceptor activity. PMID:26919530

  5. 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.

  6. A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

    International Nuclear Information System (INIS)

    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

  7. 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.

  8. Detection of high energy muons with sub-20 ps timing resolution using L(Y)SO crystals and SiPM readout

    Science.gov (United States)

    Benaglia, A.; Gundacker, S.; Lecoq, P.; Lucchini, M. T.; Para, A.; Pauwels, K.; Auffray, E.

    2016-09-01

    Precise timing capability will be a key aspect of particle detectors at future high energy colliders, as the time information can help in the reconstruction of physics events at the high collision rate expected there. Other than being used in detectors for PET, fast scintillating crystals coupled to compact Silicon Photomultipliers (SiPMs) constitute a versatile system that can be exploited to realize an ad-hoc timing device to be hosted in a larger high energy physics detector. In this paper, we present the timing performance of LYSO:Ce and LSO:Ce codoped 0.4% Ca crystals coupled to SiPMs, as measured with 150 GeV muons at the CERN SPS H2 extraction line. Small crystals, with lengths ranging from 5 mm up to 30 mm and transverse size of 2 × 2mm2 or 3 × 3mm2 , were exposed to a 150 GeV muon beam. SiPMs from two different companies (Hamamatsu and FBK) were used to detect the light produced in the crystals. The best coincidence time resolution value of (14.5 ± 0.5) ps , corresponding to a single-detector time resolution of about 10 ps, is demonstrated for 5 mm long LSO:Ce,Ca crystals coupled to FBK SiPMs, when time walk corrections are applied.

  9. Crystal structure of raw pure Mysore silk fibre based on (Ala-Gly)2-Ser-Gly peptide sequence using Linked-Atom-Least-Squares method

    Indian Academy of Sciences (India)

    Sangappa; S S Mahesh; R Somashekar

    2005-03-01

    We have carried out crystal structure analysis of raw pure Mysore silk fibers belonging to Bombyx mori on the basis of model parameters of Marsh et al using Linked-Atom-Least-Squares technique. The intensity of all the reflections were computed employing CCP13 software. We observe that the molecular modification is essentially same as -pleated structure with antipolar-antiparallel arrangements formed by hydrogen bonds. The essential differences observed in the structure are highlighted and discussed.

  10. Modulation of Calcium Oxalate Crystallization by Proteins and Small Molecules Investigated by In Situ Atomic Force Microscopy

    Science.gov (United States)

    Qiu, R.; Orme, C.; Cody, A. M.; Wierzbicki, A.; Hoyer, J.; Nancollas, G.; de Yoreo, J.

    2002-12-01

    Understanding the physical mechanisms by which biological inhibitors control nucleation and growth of inorganic crystals is a major focus of biomineral research. Calcium oxalate monohydrate (COM), which plays a functional role in plant physiology, is also a source of pathogenesis in humans where it causes kidney stone disease. Although a great deal of research has been carried out on the modulation COM by proteins and small molecules, the basic mechanism has not yet been understood. However, because the proteins that play a role in COM growth have been identified and sequenced, COM provides an excellent model system for research into biomineral growth. In this study, in situ atomic force microscopy (AFM) was used to monitor the COM surface under controlled growth conditions both from pure solutions and those doped with citrate and osteopontin (OPN) in order to determine their effects on surface morphology and growth dynamics at the molecular level. As with other solution-grown crystals such as calcite, COM grows on complex dislocation hillocks. In pure solution, while growth on the (010) face is isotropic, hillocks on the (-101) face exhibit anisotropic step kinetics. Steps of [-10-1] and orientation are clearly delineated with the [-10-1] being the fast growing direction. When citrate is added to the solution, both growth rate and morphology are drastically changed on (-101) face, especially along the [-10-1] direction. This results in isotropic disc-shaped hillocks a shape that is then reflected in the macroscopic growth habit. In contrast, no large growth changes were observed on the (010) facet. At the same time, molecular modeling predicts an excellent fit of the citrate ion into the (-101) plane and a poor fit to the (010) face. Here we propose a model that reconciles the step-specific interactions implied by the AFM results with the face-specific predictions of the calculations. Finally, we present the results of doping with aspartic acid as well as OPN, an

  11. 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.)

  12. Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca 2+ -calmodulin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jiusheng; van den Bedem, Henry; Brunger, Axel T.; Wilson, Mark A.

    2016-01-01

    Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca2+-CaM, but no assignment of these features has been made. In addition, Ca2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca2+-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.

  13. Phases and phase transitions of polymeric liquid crystals: A high resolution x ray diffraction and light scattering study

    Science.gov (United States)

    Nachaliel, Ehud

    1991-03-01

    Liquid crystal polymers (LCP) were compared with monomeric liquid crystals (MLC) by means of high-resolution x-ray (HIREX) and light scattering (LIS). Both HIREX and LIS were used to study the nematic-smectic(sub a) phase transition of P4.1 polysiloxane; the following critical exponents were determined: nu(sub parallel) = 0.77 +/-0.05; nu(sub normal) = 0.57 +/-0.08; gamma = 1.3 +/-0.10. The bare correlation lengths were found to be: xi(sup 0)(sub parallel) = 3.27 +/-0.08; xi(sup 0)(sub normal)q(sub 0) = 1.09 +/-0.14 which are unusually large in comparison with MLC. LIS experiments confirmed these values and indicated 'cross over' of nu(sub parallel) from 0.77 to 0.53. These results are typical of a system near to a tricritical point. HIREX was used to study the nematic-smectic(sub c) phase transition in C6-polysiloxane; the results were a good fit to Chen and Lubensky's mean field theory but the correlation lengths saturated near the transition to the nematic phase. A study of the smectic(sub a) phase of PA6 polyacrylate, near the transition to the nematic phase, showed that, except very close to the transition, the first and second harmonics of the x-ray structure factor were found to be consistent with the harmonic theory of de Gennes and Caille. This is thought to indicate the importance of anharmonic corrections near the phase transition. Fits to the experimental data yielded the compressibility constant, B and the splay elastic constant, K(sub s). B was found to obey a power law: B varies as t(sup phi) in which phi = 0.82 +/-0.08. In good agreement with theoretical predictions using exponents from the literature, but in disagreement with previous experimental results on MLC's. The splay elastic constant K(sub s) has roughly the same magnitude as in MLC's but tends to decrease by approximately 50% upon approaching the transition from below. This temperature dependence might give further evidence for the importance of anharmonicity in the system. Finally, the

  14. Investigation of Ge-Si Atomic Interdiffusion in Ge Nano-dots Multilayer Structure by Double Crystal X-ray Diffraction

    Institute of Scientific and Technical Information of China (English)

    Wenhua SHI; Lei ZHAO; Liping LUO; Qiming WANG

    2007-01-01

    The fluctuations of the strained layer in a superlattice or quantum well can broaden the width of satellite peaks in double crystal X-ray diffraction (DCXRD) pattern. It is found that the width of the 0th peak is directly proportional to the fluctuation of the strained layer if the other related facts are ignored. By this method, the Ge-Si atomic interdiffusion in Ge nano-dots and wetting layers has been investigated by DCXRD. It is found that thermal annealing can activate Ge-Si atomic interdiffusion and the interdiffusion in the nano-dots area is much stronger than that in the wetting layer area. Therefore the fluctuation of the Ge layer decreases and the distribution of Ge atoms becomes homogeneous in the horizontal Ge (GeSi actually) layer, which make the width of the 0th peak narrow after annealing.

  15. Crystal structure of silica-ZSM-12 by the combined use of high-resolution solid-state MAS NMR spectroscopy and synchrotron x-ray powder diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Fyfe, C.A.; Kokotailo, G.T. (Univ. of British Columbia, Vancouver (Canada)); Gies, H.; Marler, B. (Mineralogisches Institut der CAU, Kiel (West Germany)); Cox, D.E. (Brookhaven National Lab., Upton, NY (USA))

    1990-05-03

    The crystal structure of the synthetic zeolite silica-ZSM-12, 56 SiO{sub 2}, has been solved by the combined use of high-resolution solid-state MAS NMR spectroscopy and high-resolution synchrotron X-ray powder diffraction ZSM-12 crystallizes in the monoclinic space group C2/c with a{sub 0} = 24.863 {angstrom}, b{sub 0} = 5.012 {angstrom}, c{sub 0} = 24.328 {angstrom}, and {beta} = 107.7{degree}. The zeolite host structure is built from corner-linked SiO{sub 4} tetrahedra to give a three-dimensional 4-connected net. The pores of the structure are one-dimensional channels that do not intersect, with 12-membered ring pore openings of approximately 5.6 {times} 7.7 {angstrom}. The structure of ZSM-12 is frequently twinned with (100) as the twin plane, which indicates a new zeolite structure type.

  16. Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.

    Science.gov (United States)

    Zhang, H; Huang, K; Li, Z; Banerjei, L; Fisher, K E; Grishin, N V; Eisenstein, E; Herzberg, O

    2000-07-01

    Structural genomics of proteins of unknown function most straightforwardly assists with assignment of biochemical activity when the new structure resembles that of proteins whose functions are known. When a new fold is revealed, the universe of known folds is enriched, and once the function is determined by other means, novel structure-function relationships are established. The previously unannotated protein HI1434 from H. influenzae provides a hybrid example of these two paradigms. It is a member of a microbial protein family, labeled in SwissProt as YbaK and ebsC. The crystal structure at 1.8 A resolution reported here reveals a fold that is only remotely related to the C-lectin fold, in particular to endostatin, and thus is not sufficiently similar to imply that YbaK proteins are saccharide binding proteins. However, a crevice that may accommodate a small ligand is evident. The putative binding site contains only one invariant residue, Lys46, which carries a functional group that could play a role in catalysis, indicating that YbaK is probably not an enzyme. Detailed sequence analysis, including a number of newly sequenced microbial organisms, highlights sequence homology to an insertion domain in prolyl-tRNA synthetases (proRS) from prokaryote, a domain whose function is unknown. A HI1434-based model of the insertion domain shows that it should also contain the putative binding site. Being part of a tRNA synthetases, the insertion domain is likely to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. By analogy, YbaK may also play a role in nucleotide or oligonucleotide binding, the nature of which is yet to be determined.

  17. Phase-modulated electronic wave-packet interferometry reveals high resolution vibronic spectra of free Rb atoms and Rb*He molecules

    CERN Document Server

    Bruder, Lukas; Stienkemeier, Frank

    2015-01-01

    Phase-modulated wave-packet interferometry is combined with mass-resolved photoion detection to investigate rubidium atoms attached to helium nanodroplets in a molecular beam experiment. The spectra of atomic Rb electronic states show a vastly enhanced sensitivity and spectral resolution when compared to conventional pump-probe wave-packet interferometry. Furthermore, the formation of Rb*He exciplex molecules is probed and for the first time a fully resolved vibrational spectrum for transitions between the lowest excited $5\\Pi_{3/2}$ and the high-lying electronic states $2^2\\Pi$, $4^2\\Delta$, $6^2\\Sigma$ is obtained and compared to theory. The feasibility of applying coherent multidimensional spectroscopy to dilute cold gas phase samples is demonstrated in these experiments.

  18. High-resolution resonance Bragg-scattering spectroscopy of an atomic transition from a population difference grating in a vapour cell

    International Nuclear Information System (INIS)

    We present a novel high-resolution backward resonance Bragg-scattering (RBS) spectroscopy from a population difference grating (PDG). The PDG in thermal 87Rb vapour is formed by a standing-wave (SW) pump field, which periodically modulates the space population distributions of two levels in the 87Rb D1 line. A probe beam, having identical frequency and orthogonal polarization with the SW pump field, is Bragg-scattered by the PDG. The Bragg-scattered light is strongest at an atomic transition, and forms an RBS spectrum with a high signal-to-noise and sub-natural linewidth (60% of the natural linewidth). The observed RBS is a type of degenerate four-wave-mixing signal and can also be explained with the coherent superposition of the optical fields Rayleigh-scattered from the oscillating dipole moments of individual atoms on the PDG.

  19. High-resolution Resonance Bragg-scattering spectroscopy of an atomic transition from a population difference grating in a vapor cell

    CERN Document Server

    Wang*, Hai; Li, Shujing; Zhang, Chunhong; Xie, Changde; Peng, Kunchi

    2009-01-01

    The laser spectroscopy with a narrow linewidth and high signal to noise ratio (S/N) is very important in the precise measurement of optical frequencies. Here, we present a novel high-resolution backward resonance Bragg-scattering (RBS) spectroscopy from a population difference grating (PDG). The PDG is formed by a standing-wave (SW) pump field in thermal 87Rb vapor, which periodically modulates the space population distribution of two levels in the 87Rb D1 line. A probe beam, having the identical frequency and the orthogonal polarization with the SW pump field, is Bragg-scattered by the PDG. Such Bragg-scattered light becomes stronger at an atomic resonance transition, which forms the RBS spectrum with a high S/N and sub-natural linewidth. Using the scheme of the coherent superposition of the individual Rayleigh-scattered light emitted from the atomic dipole oscillators on the PDG, the experimentally observed RBS spectroscopy is theoretically explained.

  20. High-resolution resonance Bragg-scattering spectroscopy of an atomic transition from a population difference grating in a vapour cell

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hai; Yang, Xudong; Zhang, Ling; Li, Shujing; Zhang, Chunhong; Xie, Changde; Peng, Kunchi, E-mail: wanghai@sxu.edu.c [The State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Opto-Electronics, Shanxi University, Taiyuan 030006 (China)

    2010-07-14

    We present a novel high-resolution backward resonance Bragg-scattering (RBS) spectroscopy from a population difference grating (PDG). The PDG in thermal {sup 87}Rb vapour is formed by a standing-wave (SW) pump field, which periodically modulates the space population distributions of two levels in the {sup 87}Rb D1 line. A probe beam, having identical frequency and orthogonal polarization with the SW pump field, is Bragg-scattered by the PDG. The Bragg-scattered light is strongest at an atomic transition, and forms an RBS spectrum with a high signal-to-noise and sub-natural linewidth (60% of the natural linewidth). The observed RBS is a type of degenerate four-wave-mixing signal and can also be explained with the coherent superposition of the optical fields Rayleigh-scattered from the oscillating dipole moments of individual atoms on the PDG.

  1. IN-SITU AFM OF POLYMER CRYSTALLIZATION

    Institute of Scientific and Technical Information of China (English)

    J.K.Hobbs

    2003-01-01

    Atomic force microscopy images taken during the crystallization of polyethylene both from processed and quiescent melts are presented. Crystallization from processed melts provides further evidence of a region in front of a growing lamella that is influenced by the crystallization process, but extending only 40 nm into the melt. High-resolution images of the growing crystal tip, taken during crystallization, show no direct evidence of the existence of intermediate phases. The growing tip is shown to be slightly rounded. In-filling crystallization, occurring after the initial flush of growth,is imaged in polyethylene for the first time, and shown to continue to a temperature 8℃ below the initial crystallization temperature.

  2. 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.)

  3. Absolute configuration and crystal packing for three chiral drugs prone to spontaneous resolution: Guaifenesin, methocarbamol and mephenesin

    Science.gov (United States)

    Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Krivolapov, Dmitry B.; Pashagin, Alexander V.; Litvinov, Igor A.

    2009-02-01

    Popular chiral drugs, guaifenesin, methocarbamol, and mephenesin were investigated by single-crystal X-ray analysis both for enantiopure and racemic samples. The absolute configurations for all substances were established through Flack parameter method. The conglomerate-forming nature for the compounds was confirmed by equivalence of crystal characteristics of enantiopure and racemic samples. The molecular structures and crystal packing details were evaluated and compared with one another for all three investigated substances.

  4. Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

    Science.gov (United States)

    Croll, Tristan Ian; Andersen, Gregers Rom

    2016-09-01

    While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement.

  5. Theoretical and experimental study of the Stark effect in the ground state of alkali atoms in helium crystals

    OpenAIRE

    Ulzega, Simone; Weis, Antoine

    2007-01-01

    This thesis work describes a detailed study of the Stark interaction in the ground state of cesium atoms trapped in a solid helium matrix. The motivation for the investigation of electric field effects on alkali species implanted in solid helium is related to the original main goal of our experimental activities, i.e., the measurement of a permanent atomic electric dipole moment (EDM). The existence of an atomic EDM simultaneously violates the discrete symmetries of time reversal (T) and pari...

  6. Crack nucleation using combined crystal plasticity modelling, high-resolution digital image correlation and high-resolution electron backscatter diffraction in a superalloy containing non-metallic inclusions under fatigue

    Science.gov (United States)

    Zhang, Tiantian; Jiang, Jun; Britton, Ben; Shollock, Barbara; Dunne, Fionn

    2016-05-01

    A crystal plasticity finite-element model, which explicitly and directly represents the complex microstructures of a non-metallic agglomerate inclusion within polycrystal nickel alloy, has been developed to study the mechanistic basis of fatigue crack nucleation. The methodology is to use the crystal plasticity model in conjunction with direct measurement at the microscale using high (angular) resolution-electron backscatter diffraction (HR-EBSD) and high (spatial) resolution-digital image correlation (HR-DIC) strain measurement techniques. Experimentally, this sample has been subjected to heat treatment leading to the establishment of residual (elastic) strains local to the agglomerate and subsequently loaded under conditions of low cyclic fatigue. The full thermal and mechanical loading history was reproduced within the model. HR-EBSD and HR-DIC elastic and total strain measurements demonstrate qualitative and quantitative agreement with crystal plasticity results. Crack nucleation by interfacial decohesion at the nickel matrix/agglomerate inclusion boundaries is observed experimentally, and systematic modelling studies enable the mechanistic basis of the nucleation to be established. A number of fatigue crack nucleation indicators are also assessed against the experimental results. Decohesion was found to be driven by interface tensile normal stress alone, and the interfacial strength was determined to be in the range of 1270-1480 MPa.

  7. Crack nucleation using combined crystal plasticity modelling, high-resolution digital image correlation and high-resolution electron backscatter diffraction in a superalloy containing non-metallic inclusions under fatigue

    Science.gov (United States)

    Zhang, Tiantian; Britton, Ben; Shollock, Barbara; Dunne, Fionn

    2016-01-01

    A crystal plasticity finite-element model, which explicitly and directly represents the complex microstructures of a non-metallic agglomerate inclusion within polycrystal nickel alloy, has been developed to study the mechanistic basis of fatigue crack nucleation. The methodology is to use the crystal plasticity model in conjunction with direct measurement at the microscale using high (angular) resolution-electron backscatter diffraction (HR-EBSD) and high (spatial) resolution-digital image correlation (HR-DIC) strain measurement techniques. Experimentally, this sample has been subjected to heat treatment leading to the establishment of residual (elastic) strains local to the agglomerate and subsequently loaded under conditions of low cyclic fatigue. The full thermal and mechanical loading history was reproduced within the model. HR-EBSD and HR-DIC elastic and total strain measurements demonstrate qualitative and quantitative agreement with crystal plasticity results. Crack nucleation by interfacial decohesion at the nickel matrix/agglomerate inclusion boundaries is observed experimentally, and systematic modelling studies enable the mechanistic basis of the nucleation to be established. A number of fatigue crack nucleation indicators are also assessed against the experimental results. Decohesion was found to be driven by interface tensile normal stress alone, and the interfacial strength was determined to be in the range of 1270–1480 MPa. PMID:27279765

  8. 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.

  9. X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.

    Science.gov (United States)

    Peters, J W; Lanzilotta, W N; Lemon, B J; Seefeldt, L C

    1998-12-01

    A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by x-ray crystallography using multiwavelength anomalous dispersion (MAD) phasing. CpI, an enzyme that catalyzes the two-electron reduction of two protons to yield dihydrogen, was found to contain 20 gram atoms of iron per mole of protein, arranged into five distinct [Fe-S] clusters. The probable active-site cluster, previously termed the H-cluster, was found to be an unexpected arrangement of six iron atoms existing as a [4Fe-4S] cubane subcluster covalently bridged by a cysteinate thiol to a [2Fe] subcluster. The iron atoms of the [2Fe] subcluster both exist with an octahedral coordination geometry and are bridged to each other by three non-protein atoms, assigned as two sulfide atoms and one carbonyl or cyanide molecule. This structure provides insights into the mechanism of biological hydrogen activation and has broader implications for [Fe-S] cluster structure and function in biological systems.

  10. Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms

    OpenAIRE

    Ho, Bosco K.; Agard, David A.

    2008-01-01

    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 (

  11. Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms

    OpenAIRE

    Agard David A; Ho Bosco K

    2008-01-01

    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 (

  12. An analysis of the shape of a luminescence band induced by free electron-to-carbon atom transitions in semi-insulating undoped GaAs crystals

    CERN Document Server

    Glinchuk, K D; Prokhorovich, A V; Strilchuk, O N

    2001-01-01

    The shape of a photoluminescence (band observed due to recombination of free electrons on carbon atoms) in semi-insulating undoped GaAs crystals is analyzed at different temperatures (T=4.8 to 77 K). It is shown that at low temperatures the shape essentially differs from the theoretical one while at high temperatures is very close to it for radiative transitions of free electrons to isolated shallow acceptors. The observed difference of the experimental and theoretical shapes of the photoluminescence band is connected with the broadening of carbon-induced acceptor levels, resulting from the influence of electric fields of randomly distributed ionized acceptors and donors on isolated carbon atoms. Coincidence of the shapes is connected with a considerable in the energy of free carriers

  13. Atom probe tomography of secondary γ′ precipitation in a single crystal Ni-based superalloy after isothermal aging at 1100 °C

    Energy Technology Data Exchange (ETDEWEB)

    Tan, X.P., E-mail: xptan1985@gmail.com [IM 2NP, UMR 7334 CNRS, Université Aix-Marseille, 13397 Marseille Cedex 20 (France); Mangelinck, D.; Perrin-Pellegrino, C. [IM 2NP, UMR 7334 CNRS, Université Aix-Marseille, 13397 Marseille Cedex 20 (France); Rougier, L. [LSMX, MXG, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland); Gandin, Ch.-A. [CEMEF, UMR 7635 CNRS, MINES ParisTech, 06904 Sophia Antipolis (France); Jacot, A. [LSMX, MXG, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland); Ponsen, D.; Jaquet, V. [Snecma-SAFRAN Group, Service YQGC, 92702 Colombes (France)

    2014-10-25

    Highlights: • Bimodal size distribution of γ′ precipitates occurs after isothermal aging at 1100 °C. • Characterization of secondary γ′ by atom probe tomography. • It is proposed that the secondary γ′ occurs via a non-classical nucleation. • The coarsening of secondary γ′ precipitates well obeys the classical LSW theory. - Abstract: Secondary γ′ precipitation in a commercial single crystal Ni-based superalloy after the 1100 °C isothermal aging has been investigated by atom probe tomography. After the isothermal aging for 300 s, 1800 s and 3600 s, a bimodal size distribution of larger primary γ′ precipitates and numerous smaller secondary γ′ precipitates was obtained. It is proposed that the secondary γ′ precipitated via a non-classical nucleation mode. The coarsening of secondary γ′ precipitates well obeys the classical LSW theory.

  14. Growth morphology of {l_brace}1 1 0{r_brace} faces of manganese mercury thiocyanate crystals investigated by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Y.L. [State Key Laboratory of Crystal Materials, Institute of Crystal Materials, Shandong University, Jinan 250100 (China)]. E-mail: ylgeng@icm.sdu.edu.cn; Xu, D. [State Key Laboratory of Crystal Materials, Institute of Crystal Materials, Shandong University, Jinan 250100 (China)]. E-mail: xdoffice@sdu.edu.cn; Wang, X.Q. [State Key Laboratory of Crystal Materials, Institute of Crystal Materials, Shandong University, Jinan 250100 (China); Du, W. [State Key Laboratory of Crystal Materials, Institute of Crystal Materials, Shandong University, Jinan 250100 (China); Liu, H.Y. [State Key Laboratory of Crystal Materials, Institute of Crystal Materials, Shandong University, Jinan 250100 (China); Zhang, G.H. [State Key Laboratory of Crystal Materials, Institute of Crystal Materials, Shandong University, Jinan 250100 (China)

    2006-04-10

    Atomic force microscopy is employed to investigate the surface morphology of the {l_brace}1 1 0{r_brace} faces of MMTC crystals grown at 40 deg. C at a supersaturation of {sigma} = 0.5. Growth hillocks generated by dislocation sources often appear in groups, which leads to faster growth of the local area and forming layers with large height difference up to 30 nm. Growth centers operate nearly equally during the growth process. Serried and sparse monolayer steps dominate alternately on the surface, which is thought to be distinct phenomenon of the two-metal-centered complex compounds family.

  15. Preparation, crystallization and X-ray diffraction analysis to 1.5 Å resolution of rat cysteine dioxygenase, a mononuclear iron enzyme responsible for cysteine thiol oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Chad R. [Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001 (United States); Hao, Quan [MacCHESS at the Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853-8001 (United States); Stipanuk, Martha H., E-mail: mhs6@cornell.edu [Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001 (United States)

    2005-11-01

    Recombinant rat cysteine dioxygenase (CDO) has been expressed, purified and crystallized and X-ray diffraction data have been collected to 1.5 Å resolution. Cysteine dioxygenase (CDO; EC 1.13.11.20) is an ∼23 kDa non-heme iron metalloenzyme that is responsible for the oxidation of cysteine by O{sub 2}, yielding cysteinesulfinate. CDO catalyzes the first step in the conversion of cysteine to taurine, as well as the first step in the catabolism of cysteine to pyruvate plus sulfate. Recombinant rat CDO was heterologously expressed, purified and crystallized. The protein was expressed as a fusion protein bearing a polyhistidine tag to facilitate purification, a thioredoxin tag to improve solubility and a factor Xa cleavage site to permit removal of the entire N-terminus, leaving only the 200 amino acids inherent to the native protein. A multi-step purification scheme was used to achieve >95% purity of CDO. The optimal CDO crystals diffracted to 1.5 Å resolution and belonged to space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 57.55, c = 123.06 Å, α = β = γ = 90°. CDO shows little homology to any other proteins; therefore, the structure of the enzyme will be determined by ab initio phasing using a selenomethionyl derivative.

  16. 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.

  17. Two Keggin-type heteropolytungstates with transition metal as a central atom: Crystal structure and magnetic study with 2D-IR correlation spectroscopy

    International Nuclear Information System (INIS)

    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. 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

    This paper presents a new high-precision zircon U-Pb geochronological view on the crystallization and assembly process of one of the most important and intensely studied intrusive bodies on Earth the Skaergaard intrusion in East Greenland. With analytical uncertainties of a few tens of thousands...... of years, we were able to resolve several important events during cooling of this intrusion. Initial cooling of the shallowly intruded similar to 300 km(3) of tholeiitic basaltic magma from liquidus to zircon saturation at similar to 1000 degrees C is recorded by a precise zircon crystallization age of 55.......960 +/- 0.018 Ma of an intercumulus gabbroic pegmatite in the lower portion of the intrusion. Based on this zircon crystallization age and a published cooling model we estimate the ``true'' age of emplacement to be similar to 56.02 Ma. The last portions of Skaergaard appear to crystallize completely similar...

  19. High-resolution X-ray focusing concave (elliptical) curved crystal spectrograph for laser-produced plasma

    Institute of Scientific and Technical Information of China (English)

    Shali xiao(肖沙里); Yingjun Pan(潘英俊); Xianxin Zhong(钟先信); Xiancai Xiong(熊先才); Guohong Yang(杨国洪); Zongli Liu(刘宗礼); Yongkun Ding(丁永坤)

    2004-01-01

    The X-ray spectrum emitted from laser-produced plasma contains plentiful information.X-ray spectrometer is a powerful tool for plasma diagnosis and studying the information and evolution of the plasma.X-ray concave(elliptical)curved crystals analyzer was designed and manufactured to investigate the properties of laser-produced plasma.The experiment was carried out on Mianyang Xingguang-ⅡFacility and aimed at investigating the characteristics of a high density iron plasma.Experimental results using KAP,LIF,PET,and MICA curved crystal analyzers are described,and the spectra of Au,Ti laser-produced plasma are shown.The focusing crystal analyzer clearly gave an increase in sensitivity over a flat crystal.

  20. Model Catalysis – Single Crystal Surfaces and Graphene-Supported Metal Nanocluster Arrays Studied by In Situ High Resolution XPS

    OpenAIRE

    Gotterbarm, Karin

    2015-01-01

    Model catalysts with defined properties are necessary to understand heterogene-ous catalytic processes on the atomic level. One important aspect of catalytic acti-vity, namely poisoning with atomic sulfur and sulfur oxides, was investigated on the Pd(100) surface. On Pd(100), SO2 is reduced stepwise to atomic sulfur upon heating. However, in an oxygen-rich environment sulfur is removed effectively from the surface by oxidation. The oxidation proceeds stepwise to SO, SO2, SO3 and SO4, which fi...

  1. Chemical ordering of Co and Ni in a W-(AlCoNi) crystalline approximant related to Al-Co-Ni decagonal quasicrystals studied by atomic resolution energy-dispersive X-ray spectroscopy

    Science.gov (United States)

    Yasuhara, Akira; Hiraga, Kenji

    2015-01-01

    A W-(AlCoNi) crystalline approximant, which is closely related to Al-Co-Ni decagonal quasicrystals, in an Al72.5Co20Ni7.5 alloy has been studied by atomic resolution energy-dispersive X-ray spectroscopy (EDS), in an instrument attached to a spherical aberration (Cs)-corrected scanning transmission electron microscope. On high-resolution EDS maps of Co and Ni elements, obtained by integrating many sets of EDS data taken from undamaged areas, chemical ordering of Co and Ni is clearly detected. In the structure of the W-(AlCoNi) phase, consisting of arrangements of transition-metal (TM) atoms located at vertices of pentagonal tilings and pentagonal arrangements of mixed sites (MSs) of TM and Al atoms, Co atoms occupy the TM atom positions with the pentagonal tiling and Ni is enriched in part of the pentagonal arrangements of MSs.

  2. Preparation of the Crystal Complex of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis with Coenzyme A and Investigation of Its Three-Dimensional Structure at 2.1-A Resolution

    International Nuclear Information System (INIS)

    Recombinant phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPAT Mt), which was produced by a high-producing strain and purified to 99%, was used for the crystal growth of the complex of the enzyme with coenzyme A (CoA). Crystals suitable for X-ray diffraction study were obtained by cocrystallization. The crystals belong to sp. gr. R32 and have the unit-cell parameters a = b = 98.840 A, c = 112.880 A, α = β = 90.00o, and γ = 120.00o. The three-dimensional structure of the complex was determined based on X-ray diffraction data collected from the crystals to 2.1 A resolution and refined to Rf = 22.7% and Rfree = 25.93%. Active-site bound coenzyme A was found, and its nearest environment was described. The conformational changes of the enzyme due to ligand binding were revealed. The binding of CoA by tuberculosis phosphopantetheine adenylyltransferase was characterized by comparing the structures of the title complex to a similar complex of PPAT from E. coli (PPAT Ec).

  3. 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

    of kagome nets and its cavity packing is an analog to the packing scheme of atoms in the cubic Laves phase MgCu2. Dodecasil 1H has an arrangement of [512] cavities in an AA stacking of kagome nets and is analogous to the alloy structure type CaZn5. Edingtonite and natrolite are built from two types......, 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...

  4. Atomic resolution structure of Moloney murine leukemia virus matrix protein and its relationship to other retroviral matrix proteins.

    Science.gov (United States)

    Riffel, Nico; Harlos, Karl; Iourin, Oleg; Rao, Zihe; Kingsman, Alan; Stuart, David; Fry, Elizabeth

    2002-12-01

    Matrix proteins associated with the viral membrane are important in the formation of the viral particle and in virus maturation. The 1.0 A crystal structure of the ecotropic Gammaretrovirus Moloney murine leukemia virus (M-MuLV) matrix protein reveals the conserved topology of other retroviral matrix proteins, despite undetectable sequence similarity. The N terminus (normally myristylated) is exposed and adjacent to a basic surface patch, features likely to contribute to membrane binding. The four proteins in the asymmetric unit make varied contacts. The M-MuLV matrix structure is intermediate, between those of the lentiviruses and other retroviruses. The protein fold appears to be maintained, in part, by the conservation of side chain packing, which may provide a useful tool for searching for weak distant similarities in proteins. PMID:12467570

  5. Local symmetry breaking of a thin crystal structure of β-Si3N4 as revealed by spherical aberration corrected high-resolution transmission electron microscopy images.

    Science.gov (United States)

    Kim, Hwang Su; Zhang, Zaoli; Kaiser, Ute

    2012-06-01

    This report is an extension of the study for structural imaging of 5-6 nm thick β-Si(3)N(4) [0001] crystal with a spherical aberration corrected transmission electron microscope by Zhang and Kaiser [2009. Structure imaging of β-Si(3)N(4) by spherical aberration-corrected high-resolution transmission electron microscopy. Ultramicroscopy 109, 1114-1120]. In this work, a local symmetry breaking with an uneven resolution of dumbbells in the six-membered rings revealed in the reported images in the study of Zhang and Kaiser has been analyzed in detail. It is found that this local asymmetry in the image basically is not relevant to a slight mistilt of the specimen and/or a beam tilt (coma). Rather the certain variation of the tetrahedral bond length of Si-N(4) in the crystal structure is found to be responsible for the uneven resolution with a local structural variation from region to region. This characteristic of the variation is also supposed to give a distorted lattice of apparently 2°-2.5° deviations from the perfect hexagonal unit cell as observed in the reported image in the work of Zhang and Kaiser. It is discussed that this variation may prevail only in a thin specimen with a thickness ranging ~≤ 5-6 nm. At the same time, it is noted that the average of the bond length variation is close to the fixed length known in a bulk crystal of β-Si(3)N(4).

  6. New protein fold revealed by a 1.65 Å resolution crystal structure of Francisella tularensis pathogenicity island protein IglC

    Science.gov (United States)

    Sun, Ping; Austin, Brian P.; Schubot, Florian D.; Waugh, David S.

    2007-01-01

    Francisella tularensis is a highly infectious Gram-negative intracellular pathogen that causes the fulminating disease tularemia and is considered to be a potential bioweapon. F. tularensis pathogenicity island proteins play a key role in modulating phagosome biogenesis and subsequent bacterial escape into the cytoplasm of macrophages. The 23 kDa pathogenicity island protein IglC is essential for the survival and proliferation of F. tularensis in macrophages. Seeking to gain some insight into its function, we determined the crystal structure of IglC at 1.65 Å resolution. IglC adopts a β-sandwich conformation that exhibits no similarity with any known protein structure. PMID:17905833

  7. 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...... are filled by other ligand fragments. This novel binding mode shows that the acyl moiety can flip out of its classical binding pocket and bind elsewhere, suggesting a mechanism for the acyl-CoA transfer between ACBP and the active site of a target enzyme. This mechanism is of possible relevance...

  8. Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0.

    Science.gov (United States)

    Chiu, Po-Lin; Li, Xueming; Li, Zongli; Beckett, Brian; Brilot, Axel F; Grigorieff, Nikolaus; Agard, David A; Cheng, Yifan; Walz, Thomas

    2015-11-01

    The K2 Summit camera was initially the only commercially available direct electron detection camera that was optimized for high-speed counting of primary electrons and was also the only one that implemented centroiding so that the resolution of the camera can be extended beyond the Nyquist limit set by the physical pixel size. In this study, we used well-characterized two-dimensional crystals of the membrane protein aquaporin-0 to characterize the performance of the camera below and beyond the physical Nyquist limit and to measure the influence of electron dose rate on image amplitudes and phases.

  9. Deformable elastic network refinement for low-resolution macromolecular crystallography.

    Science.gov (United States)

    Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

    2014-09-01

    Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  10. Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy

    Science.gov (United States)

    Cartagena, Alexander; Hernando-Pérez, Mercedes; Carrascosa, José L.; de Pablo, Pedro J.; Raman, Arvind

    2013-05-01

    Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the study of structure-property-function relationships. We present an in vitro dynamic AFM technique operating in the intermittent contact regime which synthesizes anharmonic Lorentz-force excited AFM cantilevers to map quantitatively at nanometer resolution the local electro-mechanical force gradient, adhesion, and hydration layer viscosity within individual φ29 virions. Furthermore, the changes in material properties over the entire φ29 virion provoked by the local disruption of its shell are studied, providing evidence of bacteriophage depressurization. The technique significantly generalizes recent multi-harmonic theory (A. Raman, et al., Nat. Nanotechnol., 2011, 6, 809-814) and enables high-resolution in vitro quantitative mapping of multiple material properties within weakly bonded viruses and nanoparticles with complex structure that otherwise cannot be observed using standard AFM techniques.Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the

  11. 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.

  12. External Heavy-Atom Effect via Orbital Interactions Revealed by Single-Crystal X-ray Diffraction.

    Science.gov (United States)

    Sun, Xingxing; Zhang, Baicheng; Li, Xinyang; Trindle, Carl O; Zhang, Guoqing

    2016-07-28

    Enhanced spin-orbit coupling through external heavy-atom effect (EHE) has been routinely used to induce room-temperature phosphorescence (RTP) for purely organic molecular materials. Therefore, understanding the nature of EHE, i.e., the specific orbital interactions between the external heavy atom and the luminophore, is of essential importance in molecular design. For organic systems, halogens (e.g., Cl, Br, and I) are the most commonly seen heavy atoms serving to realize the EHE-related RTP. In this report, we conduct an investigation on how heavy-atom perturbers and aromatic luminophores interact on the basis of data obtained from crystallography. We synthesized two classes of molecular systems including N-haloalkyl-substituted carbazoles and quinolinium halides, where the luminescent molecules are considered as "base" or "acid" relative to the heavy-atom perturbers, respectively. We propose that electron donation from a π molecular orbital (MO) of the carbazole to the σ* MO of the C-X bond (π/σ*) and n electron donation to a π* MO of the quinolinium moiety (n/π*) are responsible for the EHE (RTP) in the solid state, respectively.

  13. External Heavy-Atom Effect via Orbital Interactions Revealed by Single-Crystal X-ray Diffraction.

    Science.gov (United States)

    Sun, Xingxing; Zhang, Baicheng; Li, Xinyang; Trindle, Carl O; Zhang, Guoqing

    2016-07-28

    Enhanced spin-orbit coupling through external heavy-atom effect (EHE) has been routinely used to induce room-temperature phosphorescence (RTP) for purely organic molecular materials. Therefore, understanding the nature of EHE, i.e., the specific orbital interactions between the external heavy atom and the luminophore, is of essential importance in molecular design. For organic systems, halogens (e.g., Cl, Br, and I) are the most commonly seen heavy atoms serving to realize the EHE-related RTP. In this report, we conduct an investigation on how heavy-atom perturbers and aromatic luminophores interact on the basis of data obtained from crystallography. We synthesized two classes of molecular systems including N-haloalkyl-substituted carbazoles and quinolinium halides, where the luminescent molecules are considered as "base" or "acid" relative to the heavy-atom perturbers, respectively. We propose that electron donation from a π molecular orbital (MO) of the carbazole to the σ* MO of the C-X bond (π/σ*) and n electron donation to a π* MO of the quinolinium moiety (n/π*) are responsible for the EHE (RTP) in the solid state, respectively. PMID:27319778

  14. Preparation and Loading Process of Single Crystalline Samples into a Gas Environmental Cell Holder for In Situ Atomic Resolution Scanning Transmission Electron Microscopic Observation.

    Science.gov (United States)

    Straubinger, Rainer; Beyer, Andreas; Volz, Kerstin

    2016-06-01

    A reproducible way to transfer a single crystalline sample into a gas environmental cell holder for in situ transmission electron microscopic (TEM) analysis is shown in this study. As in situ holders have only single-tilt capability, it is necessary to prepare the sample precisely along a specific zone axis. This can be achieved by a very accurate focused ion beam lift-out preparation. We show a step-by-step procedure to prepare the sample and transfer it into the gas environmental cell. The sample material is a GaP/Ga(NAsP)/GaP multi-quantum well structure on Si. Scanning TEM observations prove that it is possible to achieve atomic resolution at very high temperatures in a nitrogen environment of 100,000 Pa. PMID:27026281

  15. Atomic resolution view into the structure–function relationships of the human myelin peripheral membrane protein P2

    Energy Technology Data Exchange (ETDEWEB)

    Ruskamo, Salla [University of Oulu, Oulu (Finland); University of Oulu, Oulu (Finland); Yadav, Ravi P. [Banaras Hindu University, Varanasi (India); Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg (Germany); Sharma, Satyan; Lehtimäki, Mari [University of Oulu, Oulu (Finland); University of Oulu, Oulu (Finland); Laulumaa, Saara [University of Oulu, Oulu (Finland); University of Oulu, Oulu (Finland); Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg (Germany); Aggarwal, Shweta; Simons, Mikael [Max Planck Institute for Experimental Medicine, Göttingen (Germany); Bürck, Jochen; Ulrich, Anne S. [Karlsruhe Institute for Technology (KIT), Karlsruhe (Germany); Juffer, André H. [University of Oulu, Oulu (Finland); University of Oulu, Oulu (Finland); Kursula, Inari [University of Oulu, Oulu (Finland); Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg (Germany); Kursula, Petri, E-mail: petri.kursula@oulu.fi [University of Oulu, Oulu (Finland); University of Oulu, Oulu (Finland); Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg (Germany); University of Hamburg, Hamburg (Germany)

    2014-01-01

    The structure of the human myelin peripheral membrane protein P2 has been refined at 0.93 Å resolution. In combination with functional experiments in vitro, in vivo and in silico, the fine details of the structure–function relationships in P2 are emerging. P2 is a fatty acid-binding protein expressed in vertebrate peripheral nerve myelin, where it may function in bilayer stacking and lipid transport. P2 binds to phospholipid membranes through its positively charged surface and a hydrophobic tip, and accommodates fatty acids inside its barrel structure. The structure of human P2 refined at the ultrahigh resolution of 0.93 Å allows detailed structural analyses, including the full organization of an internal hydrogen-bonding network. The orientation of the bound fatty-acid carboxyl group is linked to the protonation states of two coordinating arginine residues. An anion-binding site in the portal region is suggested to be relevant for membrane interactions and conformational changes. When bound to membrane multilayers, P2 has a preferred orientation and is stabilized, and the repeat distance indicates a single layer of P2 between membranes. Simulations show the formation of a double bilayer in the presence of P2, and in cultured cells wild-type P2 induces membrane-domain formation. Here, the most accurate structural and functional view to date on P2, a major component of peripheral nerve myelin, is presented, showing how it can interact with two membranes simultaneously while going through conformational changes at its portal region enabling ligand transfer.

  16. High-sensitivity high-resolution refractometry with twin turn-around-point long-period gratings in a photonic crystal fiber

    Science.gov (United States)

    Kanka, Jiri

    2013-05-01

    We present the numerical design of a turn-around-point long-period grating in a photonic crystal fiber (TAP PCFLPG) for high-sensitivity, high-resolution refractometry of gases. High refractive-index sensitivity is achieved by operating LPGs in the vicinity of the dispersion turning point of the optimized PCF. Despite the resonant wavelength of the optimized PCF-LPG is highly sensitive to the refractive index of analytes, its large shifts could be monitored with a reduced resolution because the resonance dip in the TAP LPG transmission spectrum is broad. To provide also high refractive-index resolution, twin TAP-LPGs have been proposed to be used as 3 dB broadband mode converters in the interferometric scheme. The first LPG couples a portion of the light in the core mode to a forward propagating cladding mode and the second LPG couples the light back to the core mode. The resulting interference fringes within the envelope of LPG attenuation dip provide a means for higher resolution sensing. Instead of monitoring the wavelength shift as a result of a refractive index change, the transmission spectrum can also be analyzed in terms of the shift in phase suffered by the fringe pattern. This is a more accurate way of interpreting the interferometric sensor measurements, since the phase shift is a direct result of an analyte-induced change in optical path length.

  17. Comparison of observer performance on soft-copy reading of digital chest radiographs: High resolution liquid-crystal display monitors versus cathode-ray tube monitors

    International Nuclear Information System (INIS)

    The purpose of this study is to compare observer performance for detection of abnormalities on chest radiographs with 5-megapixel resolution liquid-crystal displays (LCD) and 5-megapixel resolution cathode-ray tube (CRT) monitors under bright and subdued ambient light conditions. Six radiologists reviewed a total of 254 digital chest radiographs under four different conditions with a combination of two types of monitors (a 5-megapixel resolution LCD and a 5-megapixel resolution CRT monitor) and with two types of ambient light (460 and 50 lux). The abnormalities analyzed were nodules, pneumothorax and interstitial lung disease. For each reader, the detection performance using 5-megapixel LCD and 5-megapixel CRT monitors under bright and subdued ambient light conditions were compared using multi-case and multi-modality ROC analysis. For each type of ambient light, the average detection performance with the two types of monitors was also compared. For each reader, the observer performance of 5-megapixel LCD and 5-megapixel CRT monitors, under both bright and subdued ambient light conditions, showed no significant statistical differences for detecting nodules, pneumothorax and interstitial lung disease. In addition, there was no significant statistical difference in the average performance when the two monitor displays, under both bright and subdued ambient light conditions, were compared

  18. Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

    Science.gov (United States)

    Croll, Tristan Ian; Andersen, Gregers Rom

    2016-09-01

    While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement. PMID

  19. Morphological stability of the atomically clean surface of silicon (100) crystals after microwave plasma-chemical processing

    International Nuclear Information System (INIS)

    The morphological stability of atomically clean silicon (100) surface after low-energy microwave plasma-chemical etching in various plasma-forming media is studied. It is found that relaxation changes in the surface density and atomic bump heights after plasma processing in inert and chemically active media are multidirectional in character. After processing in a freon-14 medium, the free energy is minimized due to a decrease in the surface density of microbumps and an increase in their height. After argon-plasma processing, an insignificant increase in the bump density with a simultaneous decrease in bump heights is observed. The physicochemical processes causing these changes are considered

  20. Morphological stability of the atomically clean surface of silicon (100) crystals after microwave plasma-chemical processing

    Energy Technology Data Exchange (ETDEWEB)

    Yafarov, R. K., E-mail: pirpc@yandex.ru; Shanygin, V. Ya. [Russian Academy of Sciences, Saratov Branch of the Kotel’nikov Institute of Radio Engineering and Electronics (Russian Federation)

    2016-01-15

    The morphological stability of atomically clean silicon (100) surface after low-energy microwave plasma-chemical etching in various plasma-forming media is studied. It is found that relaxation changes in the surface density and atomic bump heights after plasma processing in inert and chemically active media are multidirectional in character. After processing in a freon-14 medium, the free energy is minimized due to a decrease in the surface density of microbumps and an increase in their height. After argon-plasma processing, an insignificant increase in the bump density with a simultaneous decrease in bump heights is observed. The physicochemical processes causing these changes are considered.

  1. Neutron diffraction study of the atomic structure of cubic sodium-tungsten bronze (Na0.69WO3) single crystal

    International Nuclear Information System (INIS)

    The atomic structure of a single crystal of one of four Na0.69WO3 phases, which exist below 293 K, has been refined from neutron diffraction data (WWR-c reactor at the Karpov Institute of Physical Chemistry, Obninsk Branch; λ = 1.168 Å; λ/2 contribution −1). The Na0.69WO3 atomic structure has been refined (198 independent reflections) taking into account the anisotropy of thermal vibrations (Rw = 4.0%). The stoichiometric coefficient Na(0.69) is also refined. A structural distortion is revealed, which is characterized by the displacement of oxygen atoms (0, 0.2609(2), 0.2391(2)) from the ideal perovskite positions (0, 1/4, 1/4); this displacement doubles the ideal perovskite lattice period. The oxygen displacements can be described as rotations of oxygen octahedra by 3.58° around the [111] direction. The structure remains cubic because the octahedra rotations with respect to all three perovskite cubic axes are identical.

  2. Comparative high-resolution spectroscopy and emission dynamics of Nd-doped GSGG crystals and transparent ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Lupei, V. [Institute of Atomic Physics-INFLPR, 409 Atomistilor Street, 077125 Bucharest-Magurele (Romania)], E-mail: v.lupei@pluto.infim.ro; Lupei, A.; Gheorghe, C. [Institute of Atomic Physics-INFLPR, 409 Atomistilor Street, 077125 Bucharest-Magurele (Romania); Ikesue, A. [World-Laboratory Co. Ltd, Atsuta-ku, Nagoya 4656-8587 (Japan)

    2008-05-15

    The comparative spectroscopic and emission decay investigation of Nd:GSGG single crystals and transparent ceramics indicates that their properties are similar. The accurate characterization of the effect of energy transfer processes on emission decay enables a reliable calculation of the Nd concentration dependence of emission quantum efficiency.

  3. Comparative high-resolution spectroscopy and emission dynamics of Nd-doped GSGG crystals and transparent ceramics

    International Nuclear Information System (INIS)

    The comparative spectroscopic and emission decay investigation of Nd:GSGG single crystals and transparent ceramics indicates that their properties are similar. The accurate characterization of the effect of energy transfer processes on emission decay enables a reliable calculation of the Nd concentration dependence of emission quantum efficiency

  4. 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.

  5. Evaluation of solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry for direct determination of chromium in medicinal plants

    Science.gov (United States)

    Virgilio, Alex; Nóbrega, Joaquim A.; Rêgo, Jardes F.; Neto, José A. Gomes

    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 °C and 2400 °C, respectively. Slopes of calibration curves (50-750 pg Cr, R2 > 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 μg g- 1 Cr range. The highest RSD (n = 5) was 15.4% for the sample Melissa officinalis containing 13.9 ± 2.1 μg g- 1 Cr. The limit of detection was 3.3 ng g- 1 Cr.

  6. Solid sampling determination of lithium and sodium additives in microsamples of yttrium oxyorthosilicate by high-resolution continuum source graphite furnace atomic absorption spectrometry

    Science.gov (United States)

    Laczai, Nikoletta; Kovács, László; Péter, Ágnes; Bencs, László

    2016-03-01

    Solid sampling high resolution continuum source graphite furnace atomic absorption spectrometry (SS-HR-CS-GFAAS) methods were developed and studied for the fast and sensitive quantitation of Li and Na additives in microsamples of cerium-doped yttrium oxyorthosilicate (Y2SiO5:Ce) scintillator materials. The methods were optimized for solid samples by studying a set of GFAAS conditions (i.e., the sample mass, sensitivity of the analytical lines, and graphite furnace heating programs). Powdered samples in the mass range of 0.099-0.422 mg were dispensed onto graphite sample insertion boats, weighed and analyzed. Pyrolysis and atomization temperatures were optimized by the use of single-element standard solutions of Li and Na (acidified with 0.144 mol/L HNO3) at the Li I 610.353 nm and Na I 285.3013 nm analytical lines. For calibration purposes, the method of standard addition with Li and Na solutions was applied. The correlation coefficients (R values) of the calibration graphs were not worse than 0.9678. The limit of detection for oxyorthosilicate samples was 20 μg/g and 80 μg/g for Li and Na, respectively. The alkaline content of the solid samples were found to be in the range of 0.89 and 8.4 mg/g, respectively. The accuracy of the results was verified by means of analyzing certified reference samples, using methods of standard (solution) addition calibration.

  7. Simultaneous determination of iron and nickel in fluoropolymers by solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry.

    Science.gov (United States)

    Soares, Bruno M; Santos, Rafael F; Bolzan, Rodrigo C; Muller, Edson I; Primel, Ednei G; Duarte, Fabio A

    2016-11-01

    This paper reports the development of a method of simultaneous determination of iron and nickel in fluoropolymers by high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS GF AAS) with direct solid sampling. In order to carry out simultaneous measurements, both the main resonance line of nickel (232.003nm) and the adjacent secondary line of iron (232.036nm) were monitored in the same spectral window. The proposed method was optimized with a perfluoroalkoxy (PFA) sample and was applied to the determination of iron and nickel in fluorinated ethylene propylene (FEP) and modified polytetrafluoroethylene (PTFE-TFM) samples. Pyrolysis and atomization temperatures, as well as the use of Pd and H2 (during pyrolysis) as chemical modifiers, were carefully investigated. Compromise temperatures for pyrolysis and atomization of both analytes were achieved at 800 and 2300°C, respectively, using only 0.5Lmin(-1) H2 as chemical modifier during pyrolysis. Calibration curves were performed with aqueous standards by using a single solution which contained both analytes. Limits of detection were 221 and 9.6ngg(-1) for iron and nickel, respectively. Analyte concentrations in all samples ranged from 3.53 to 12.4µgg(-1) for iron and from 37 to 78ngg(-1) for nickel, with relative standard deviation less than 19%. Accuracy was evaluated by comparing these results with those obtained by inductively coupled plasma mass spectrometry after sample digestion by microwave-induced combustion and no significant statistical difference was observed. PMID:27591638

  8. Monitoring and Method development of Hg in Istanbul Airborne Particulates by Solid Sampling Continuum Source-High Resolution Electrothermal Atomic Absorption Spectromerty

    Directory of Open Access Journals (Sweden)

    Soydemir E.

    2014-07-01

    Full Text Available In this work, a method has been developed and monitoring for the determination of mercury in PM2.5 airborne particulates by solid sampling high-resolution continuum source electrothermal atomic absorption spectrometry. The PM2.5 airborne particulates were collected on quartz filters using high volume samplers (500 L/min in Istanbul (Turkey for 96 hours every month in one year. At first, experimental conditions as well as the validation tests were optimized using collected filter. For this purpose, the effects of atomization temperature, amount of sample intoduced in to the furnace, addition of acids and/or KMnO4 on the sample, covering of graphite tube and platform or using of Ag nanoparticulates, Au nanoparticulates, and Pd solutions on the accuracy and precision were investigated. After optimization of the experimental conditions, the mercury concentrations were determined in the collected filter. The filters with PM2.5 airborne particulates were dried, divided into small fine particles and then Hg concentrations were determined directly. In order to eliminate any error due to the sensitivity difference between aqueous standards and solid samples, the quantification was performed using solid calibrants. The limit of detection, based on three times the standard deviations for ten atomizations of an unused filter, was 30 ng/g. The Hg content was dependent on the sampling site, season etc, ranging from

  9. High energy resolution five-crystal spectrometer for high quality fluorescence and absorption measurements on an x-ray absorption spectroscopy beamline

    International Nuclear Information System (INIS)

    Fluorescence detection is classically achieved with a solid state detector (SSD) on x-ray absorption spectroscopy (XAS) beamlines. This kind of detection however presents some limitations related to the limited energy resolution and saturation. Crystal analyzer spectrometers (CAS) based on a Johann-type geometry have been developed to overcome these limitations. We have tested and installed such a system on the BM30B/CRG-FAME XAS beamline at the ESRF dedicated to the structural investigation of very dilute systems in environmental, material and biological sciences. The spectrometer has been designed to be a mobile device for easy integration in multi-purpose hard x-ray synchrotron beamlines or even with a laboratory x-ray source. The CAS allows to collect x-ray photons from a large solid angle with five spherically bent crystals. It will cover a large energy range allowing to probe fluorescence lines characteristic of all the elements from Ca (Z = 20) to U (Z = 92). It provides an energy resolution of 1–2 eV. XAS spectroscopy is the main application of this device even if other spectroscopic techniques (RIXS, XES, XRS, etc.) can be also achieved with it. The performances of the CAS are illustrated by two experiments that are difficult or impossible to perform with SSD and the complementarity of the CAS vs SSD detectors is discussed.

  10. Focusing bent perfect-crystal neutron monochromator a key to high-resolution stress/strain measurement studies of polycrystalline materials

    CERN Document Server

    Ono, M; Harjo, S; Saroun, J; Yoneda, K; Sawano, J; Sakurai, Y; Kobayashi, T

    2000-01-01

    A new neutron focusing device with bent Si-single crystal has been installed at high-resolution neutron diffractometer dedicated to strain/stress investigations in polycrystalline materials and introduced into routine operation as a neutron strain scanner using reactor neutrons from supermirror guider at Kyoto University Research Reactor (KUR). Properties of the diffractometer are described on the basis of experimental results when one slab or two slabs of curved Si single crystals are employed as monochromator:i.e. 1) the luminosity 2) the absolute value of monochromatic neutrons with the Au-foil activation method, 3) beam profiles with the imaging plate method, 4) characterization of the diffractometer with alpha Fe (211) peak and its comparison with the Bragg optical prediction. It is confirmed that the FWHM of the instrumental delta d/d-profile of the peak can be less than 3*10/sup -3/ at d=1.17 A and the resolution permits us to investigate both the macro- and microstrains with good luminosity. The lumin...

  11. 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.

  12. Layout And Results From The Initial Opeeration Of The High-resolution X-ray Imaging Crystal Spectrometer On The Large Helical Device

    Energy Technology Data Exchange (ETDEWEB)

    Pablant, N A; Delgado-Apricio, L; Goto, M; Hill, K W; Lzerson, S; Morita, S; Roquemore, A L; Gates, D; Monticello, D; Neilson, H; Reiman, A; Reinke, M; Rice, J E

    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.

  13. Efficient phase contrast imaging in STEM using a pixelated detector. Part 1: Experimental demonstration at atomic resolution

    International Nuclear Information System (INIS)

    We demonstrate a method to achieve high efficiency phase contrast imaging in aberration corrected scanning transmission electron microscopy (STEM) with a pixelated detector. The pixelated detector is used to record the Ronchigram as a function of probe position which is then analyzed with ptychography. Ptychography has previously been used to provide super-resolution beyond the diffraction limit of the optics, alongside numerically correcting for spherical aberration. Here we rely on a hardware aberration corrector to eliminate aberrations, but use the pixelated detector data set to utilize the largest possible volume of Fourier space to create high efficiency phase contrast images. The use of ptychography to diagnose the effects of chromatic aberration is also demonstrated. Finally, the four dimensional dataset is used to compare different bright field detector configurations from the same scan for a sample of bilayer graphene. Our method of high efficiency ptychography produces the clearest images, while annular bright field produces almost no contrast for an in-focus aberration-corrected probe. - Highlights: • Ptychographic high efficiency phase contrast imaging is demonstrated in STEM. • We rely on a hardware aberration corrector to eliminate aberrations. • High efficiency is achieved by collecting all the relevant interference. • Use of a pixelated detector allows comparison of bright field modes post acquisition. • Ptychography provides the clearest images among the STEM bright field modes tested

  14. Efficient phase contrast imaging in STEM using a pixelated detector. Part 1: Experimental demonstration at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Pennycook, Timothy J., E-mail: tpennycook@gmail.com [EPSRC SuperSTEM Facility, Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Lupini, Andrew R. [Oak Ridge National Laboratory, Materials Science and Technology Division, Oak Ridge, TN 37830 (United States); Yang, Hao [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Murfitt, Matthew F. [Nion Co., 1102 8th St., Kirkland, WA 98033 (United States); Jones, Lewys [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Nellist, Peter D. [EPSRC SuperSTEM Facility, Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom)

    2015-04-15

    We demonstrate a method to achieve high efficiency phase contrast imaging in aberration corrected scanning transmission electron microscopy (STEM) with a pixelated detector. The pixelated detector is used to record the Ronchigram as a function of probe position which is then analyzed with ptychography. Ptychography has previously been used to provide super-resolution beyond the diffraction limit of the optics, alongside numerically correcting for spherical aberration. Here we rely on a hardware aberration corrector to eliminate aberrations, but use the pixelated detector data set to utilize the largest possible volume of Fourier space to create high efficiency phase contrast images. The use of ptychography to diagnose the effects of chromatic aberration is also demonstrated. Finally, the four dimensional dataset is used to compare different bright field detector configurations from the same scan for a sample of bilayer graphene. Our method of high efficiency ptychography produces the clearest images, while annular bright field produces almost no contrast for an in-focus aberration-corrected probe. - Highlights: • Ptychographic high efficiency phase contrast imaging is demonstrated in STEM. • We rely on a hardware aberration corrector to eliminate aberrations. • High efficiency is achieved by collecting all the relevant interference. • Use of a pixelated detector allows comparison of bright field modes post acquisition. • Ptychography provides the clearest images among the STEM bright field modes tested.

  15. Atomic Physics with the Goddard High Resolution Spectrograph on the Hubble Space Telescope. III; Oscillator Strengths for Neutral Carbon

    Science.gov (United States)

    Zsargo, J.; Federman, S. R.; Cardelli, Jason A.

    1997-01-01

    High quality spectra of interstellar absorption from C I toward beta(sup 1) S(sub co), rho O(sub ph) A, and chi O(sub ph) were obtained with the Goddard High Resolution Spectrograph on HST. Many weak lines were detected within the observed wavelength intervals: 1150-1200 A for beta(sup 1) S(sub co) and 1250-1290 A for rho O(sub ph) A and chi O(sub ph). Curve-of-growth analyses were performed in order to extract accurate column densities and Doppler parameters from lines with precise laboratory-based f-values. These column densities and b-values were used to obtain a self-consistent set of f-values for all the observed C I lines. A particularly important constraint was the need to reproduce data for more than one line of sight. For about 50% of the lines, the derived f-values differ appreciably from the values quoted by Morton.

  16. Human monoclonal antiphospholipid antibodies disrupt the annexin A5 anticoagulant crystal shield on phospholipid bilayers: evidence from atomic force microscopy and functional assay.

    Science.gov (United States)

    Rand, Jacob H; Wu, Xiao-Xuan; Quinn, Anthony S; Chen, Pojen P; McCrae, Keith R; Bovill, Edwin G; Taatjes, Douglas J

    2003-09-01

    The antiphospholipid (aPL) syndrome is an autoimmune condition that is marked by recurrent pregnancy losses and/or systemic vascular thrombosis in patients who have antibodies against phospholipid/co-factor complexes. The mechanism(s) for pregnancy losses and thrombosis in this condition is (are) not known. Annexin A5 is a potent anticoagulant protein, expressed by placental trophoblasts and endothelial cells, that crystallizes over anionic phospholipids, shielding them from availability for coagulation reactions. We previously presented data supporting the hypothesis that aPL antibody-mediated disruption of the anticoagulant annexin A5 shield could be a thrombogenic mechanism in the aPL syndrome. However, this has remained a subject of controversy. We therefore used atomic force microscopy, a method previously used to study the crystallization of annexin A5, to image the effects of monoclonal human aPL antibodies on the crystal structure of the protein over phospholipid bilayers. In the presence of the aPL monoclonal antibodies (mAbs) and beta(2)-GPI, the major aPL co-factor, structures presumed to be aPL mAb-antigen complexes were associated with varying degrees of disruption to the annexin A5 crystallization pattern over the bilayer. In addition, measurements of prothrombinase activity on the phospholipid bilayers showed that the aPL mAbs reduced the anti-coagulant effect of annexin A5 and promoted thrombin generation. These data provide morphological evidence that support the hypothesis that aPL antibodies can disrupt annexin A5 binding to phospholipid membranes and permit increased generation of thrombin. The aPL antibody-mediated disruption of the annexin A5 anticoagulant shield may be an important prothrombotic mechanism in the aPL syndrome. PMID:12937161

  17. Determination of crystal growth rates during rapid solidification of polycrystalline aluminum by nano-scale spatio-temporal resolution in situ transmission electron microscopy

    Science.gov (United States)

    Zweiacker, K.; McKeown, J. T.; Liu, C.; LaGrange, T.; Reed, B. W.; Campbell, G. H.; Wiezorek, J. M. K.

    2016-08-01

    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-1 to ˜2.5 m s-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-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.

  18. Algebraic dependence of the structure factor and possible anharmonicity in a high-resolution x-ray study of a side-group polymeric liquid crystal

    Science.gov (United States)

    Nachaliel, E.; Keller, E. N.; Davidov, D.; Boeffel, C.

    1991-03-01

    We report on a high-resolution x-ray study of the smectic-A phase near the nematic-smectic-A transition of a side-group polymeric liquid crystal, polyacrylate. Except at the very near vicinity of the phase transition, the first- and the second-harmonic x-ray structure factors were found to be consistent with the harmonic theory of de Gennes and Caille. However, very close to the phase transition, the attempts to fit the two harmonics completely failed. We believe that this is evidence for the importance of anharmonic corrections near the phase transition. The fits to the experimental data yield the compressibility constant B and the splay elastic constant Ks. We found that B can be described by a power law B~tφ, where t=(Tc-T)/Tc, Tc being the phase-transition temperature. φ was found to be 0.82+/-0.08, in good agreement with theoretical predictions using exponents from the literature, but in disagreement with previous experimental results on monomeric liquid crystals. The splay elastic constant Ks has roughly the same magnitude as in monomeric liquid crystals but tends to decrease by approximately 50% upon approaching the transition from below. This temperature dependence is further evidence for the importance of anharmonicity in the system.

  19. Crystal Growth and Characterization of Ca3NbGa3Si2O14 Single Crystal

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Single crystals of Ca3NbGa3Si2O14 (CNGS) with ordered Ca3Ga2Ge4O14 (CGG) structure were successfully grown from stoichiometric melts by conventional Czochralski technique along the a-axis and two large (001) facets and two small (100) facets appear in every crystal. An arrangement of parallel steps and a clear height change were observed in (001) facet by atomic force microscopy (AFM). High-resolution X-ray diffraction (HRXRD) results indicate that CNGS crystals have good quality and free low-angle boundaries. The crystals also exhibit good optical quality and high optical transmittance in c-direction.

  20. 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.

  1. Extensive simulation studies on the reconstructed image resolution of a position sensitive detector based on pixelated CdTe crystals

    CERN Document Server

    Zachariadou, K; Kaissas, I; Seferlis, S; Lambropoulos, C; Loukas, D; Potiriadis, C

    2011-01-01

    We present results on the reconstructed image resolution of a position sensitive radiation instrument (COCAE) based on extensive simulation studies. The reconstructed image resolution has been investigated in a wide range of incident photon energies emitted by point-like sources located at different source-to-detector distances on and off the detector's symmetry axis. The ability of the detector to distinguish multiple radioactive sources observed simultaneously is investigating by simulating point-like sources of different energies located on and off the detector's symmetry axis and at different positions

  2. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution

    Energy Technology Data Exchange (ETDEWEB)

    Das, Debanu; Kozbial, Piotr; Axelrod, Herbert L.; Miller, Mitchell D.; McMullan, Daniel; Krishna, S. Sri; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Burra, Prasad; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Elias, Ylva; Elsliger, Marc-André; Ernst, Dustin; Farr, Carol; Feuerhelm, Julie; Grzechnik, Anna; Grzechnik, Slawomir K.; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Murphy, Kevin D.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Sudek, Sebastian; Tien, Henry; Trame, Christine; Trout, Christina V.; van den Bedem, Henry; Weekes, Dana; White, Aprilfawn; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.; (SLAC); (Scripps); (SSRL); (JCSG); (SSRl); (UCSD); (Burnham)

    2009-08-28

    ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.

  3. High-resolution EPMA X-ray images of mother liquid inclusions in a Pd2Ga single crystal

    International Nuclear Information System (INIS)

    During crystal growth from solution inclusions of different compositions were trapped at the rim of a Pd2Ga single crystal. Their fine-grained (< 5 μm) internal structure demands special requirements for electron microprobe analysis, realized by low-voltage (5 keV) element mapping applying a step size of 0.138 μm for each pixel. It can be shown, that these inclusions represent an isolated chemical system, and that crystallisation upon cooling follows the expected thermodynamic phase relations. Thus the final composition in the centre of the inclusion consists of a small-scale mixture of PdGa and Pd5Ga3 evolved out of a solid-solid decomposition of Pd5Ga4

  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. %) B20=±8

  5. Research on the optical band positions, spin-Hamiltonian parameters and atom-position parameter of Co{sup 2+} ion in CdSe crystal

    Energy Technology Data Exchange (ETDEWEB)

    Mei, Yang [School of Physics & Electronic Engineering, Mianyang Normal University, Mianyang 621000 (China); Research Center of Computational Physics, Mianyang Normal University, Mianyang 621000 (China); Zheng, Wen-Chen, E-mail: zhengwc1@163.com [Department of Material Science, Sichuan University, Chengdu 610064 (China); Peng, Ren-Ming; Wei, Cheng-Fu [School of Physics & Electronic Engineering, Mianyang Normal University, Mianyang 621000 (China)

    2015-10-01

    The optical band positions and EPR (or spin-Hamiltonian) parameters (g factors g{sub //}, g{sub ⊥} and zero-field splitting D) of Co{sup 2+} ion in the trigonally-distorted tetrahedral Cd{sup 2+} site of CdSe crystal are calculated simultaneously from the complete diagonalization (of energy matrix) method (CDM) based on the two-spin–orbit-parameter model. This model contains the contributions to the spectral data from both the spin–orbit parameters of central d{sup n} ion (i.e., one-spin–orbit-parameter model) in the conventional crystal-field theory and that of ligand ions via covalence effect. The calculated 12 optical band positions and three spin-Hamiltonian parameters using four adjustable parameters show reasonable agreement with the experimental values. The local atom-position parameter u{sub loc} (where the corresponding parameter u in the host CdSe crystal is unlikely) in the Co{sup 2+} center is also estimated from the calculations. The calculations of these spectral data from the CDM based on the conventional one-spin–orbit parameter model are also made for comparison. It is found that the calculated optical band positions are also close to the experimental values, but the calculated spin-Hamiltonian parameters are in poor agreement with the observed values. So, for the unified and reasonable calculations of optical and EPR data of d{sup n} ions in crystals (in particular, in the cases of ligand with large spin–orbit parameter), the CDM based on the two-spin–orbit-parameter model should be applied. - Highlights: • Fifteen optical and EPR data of Co{sup 2+} center in CdSe are calculated together. • Calculation is using the complete diagonalization (of energy matrix) method (CDM). • The CDM based on the two-spin–orbit-parameter model is more reasonable. • Local atom-position parameter in Co{sup 2+} center in CdSe is obtained from calculation.

  6. Spectral aspects of the determination of Si in organic and aqueous solutions using high-resolution continuum source or line source flame atomic absorption spectrometry

    Science.gov (United States)

    Kowalewska, Zofia; Pilarczyk, Janusz; Gościniak, Łukasz

    2016-06-01

    High-resolution continuum source flame atomic absorption spectrometry (HR-CS FAAS) was applied to reveal and investigate spectral interference in the determination of Si. An intensive structured background was observed in the analysis of both aqueous and xylene solutions containing S compounds. This background was attributed to absorption by the CS molecule formed in the N2O-C2H2 flame. The lines of the CS spectrum at least partially overlap all five of the most sensitive Si lines investigated. The 251.611 nm Si line was demonstrated to be the most advantageous. The intensity of the structured background caused by the CS molecule significantly depends on the chemical form of S in the solution and is the highest for the most-volatile CS2. The presence of O atoms in an initial S molecule can diminish the formation of CS. To overcome this S effect, various modes of baseline fitting and background correction were evaluated, including iterative background correction (IBC) and utilization of correction pixels (WRC). These modes were used either independently or in conjunction with least squares background correction (LSBC). The IBC + LSBC mode can correct the extremely strong interference caused by CS2 at an S concentration of 5% w:w in the investigated solution. However, the efficiency of this mode depends on the similarity of the processed spectra and the correction spectra in terms of intensity and in additional effects, such as a sloping baseline. In the vicinity of the Si line, three lines of V were recorded. These lines are well-separated in the HR-CS FAAS spectrum, but they could be a potential source of overcorrection when using line source flame atomic absorption spectrometry (LS FAAS). The expected signal for the 251.625 nm Fe line was not registered at 200 mg L- 1 Fe concentration in the solution, probably due to the diminished population of Fe atoms in the high-temperature flame used. The observations made using HR-CS FAAS helped to establish a "safe" level

  7. 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.

  8. Solid state parameters, structure elucidation, High Resolution X-Ray Diffraction (HRXRD), phase matching, thermal and impedance analysis on L-Proline trichloroacetate (L-PTCA) NLO single crystals.

    Science.gov (United States)

    Kalaiselvi, P; Raj, S Alfred Cecil; Jagannathan, K; Vijayan, N; Bhagavannarayana, G; Kalainathan, S

    2014-11-11

    Nonlinear optical single crystal of L-Proline trichloroacetate (L-PTCA) was successfully grown by Slow Evaporation Solution Technique (SEST). The grown crystals were subjected to single crystal X-ray diffraction analysis to confirm the structure. From the single crystal XRD data, solid state parameters were determined for the grown crystal. The crystalline perfection has been evaluated using high resolution X-ray diffractometer. The frequencies of various functional groups were identified from FTIR spectral analysis. The percentage of transmittance was obtained from UV Visible spectral analysis. TGA-DSC measurements indicate the thermal stability of the crystal. The dielectric constant, dielectric loss and ac conductivity were measured by the impedance analyzer. The DC conductivity was calculated by the cole-cole plot method.

  9. 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.

  10. Atomic force microscopy studies on growth mechanisms and defect formations on {l_brace}110{r_brace} faces of cadmium mercury thiocyanate crystals

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, X.N.; Xu, D.; Yuan, D.R.; Sun, D.L.; Lu, M.K.; Zhang, G.H.; Guo, S.Y. [Shandong Univ., Jinan, SD (China). Inst. of Crystal Materials

    2001-07-01

    Growth mechanisms and defect formations on {l_brace}110{r_brace} faces of cadmium mercury thiocyanate crystals grown at 30 C ({sigma} = 0.24) were investigated by using atomic force microscopy (AFM). It was found that, under this condition, spiral dislocation controlled mechanism and 2D nucleation mechanism operates simultaneously and equally during growth, which is completely different from the traditional 2D nucleation and dislocation source controlled mechanisms. A number of 2D nucleus are formed at the large step terraces generated by dislocation sources, leading to the unequal growth rates of the elementary steps and thereby ''step bunches'' are caused. Various defects are formed under this growth condition, which is assumed to result from the incongruence between the steps generated by different sources. A new kind of 2D defect, corresponding to one growth layer in height, was observed for the first time. (orig.)

  11. Determination of Iron in Layered Crystal Sodium Disilicate and Sodium Silicate by Flame Atomic Absorption Spectrometry with Boric Acid as a Matrix Modifier

    Institute of Scientific and Technical Information of China (English)

    Zhi Hua WANG; Min CAI; Shu Jun WANG

    2006-01-01

    The effects of matrix silicate and experimental conditions on the determination of iron in flame atomic absorption spectrometry (FAAS) were investigated. It was found that boric acid as a matrix modifier obviously eliminated silicate interference. Under the optimum operating conditions, the determination results of iron in layered crystal sodium disilicate and sodium silicate samples by FAAS were satisfactory. The linear range of calibration curve is 0-10.5 μg.mL-1, the relative standard deviation of method is 1.2%-2.2%, the recovery of added iron is 96.0%-101%, the of iron of the standard curve method, standard addition calibration and colorimetry method was the same, but the first has the merits of rapid sample preparation, reduced contamination risks and fast analysis.

  12. Interface Properties of Atomic-Layer-Deposited Al2O3 Thin Films on Ultraviolet/Ozone-Treated Multilayer MoS2 Crystals.

    Science.gov (United States)

    Park, Seonyoung; Kim, Seong Yeoul; Choi, Yura; Kim, Myungjun; Shin, Hyunjung; Kim, Jiyoung; Choi, Woong

    2016-05-11

    We report the interface properties of atomic-layer-deposited Al2O3 thin films on ultraviolet/ozone (UV/O3)-treated multilayer MoS2 crystals. The formation of S-O bonds on MoS2 after low-power UV/O3 treatment increased the surface energy, allowing the subsequent deposition of uniform Al2O3 thin films. The capacitance-voltage measurement of Au-Al2O3-MoS2 metal oxide semiconductor capacitors indicated n-type MoS2 with an electron density of ∼10(17) cm(-3) and a minimum interface trap density of ∼10(11) cm(-2) eV(-1). These results demonstrate the possibility of forming a high-quality Al2O3-MoS2 interface by proper UV/O3 treatment, providing important implications for their integration into field-effect transistors.

  13. On the lipid-bacterial protein interaction studied by quartz crystal microbalance with dissipation, transmission electron microscopy and atomic force microscopy

    CERN Document Server

    Delcea, Mihaela; Pum, Dietmar; Sleytr, Uwe Bernd; Toca-Herrera, Jose Luis

    2009-01-01

    The interaction between the bacterial S-protein SbpA on different types of lipid membranes has been studied using atomic force microscopy, transmission electron microscopy, and quartz crystal microbalance with dissipation. On one hand, It has been found that the bacterial forms two dimensional nanocrystals on zwitterionic DOPC bilayers and negatively charged DMPG vesicles adsorbed on mica, on zwitterionic DPPC and charged DPPC/DMPG (1:1) monolayers adsorbed on carbon grids. On the other hand, SbpA protein adsorption took place on zwitterionic DOPC bilayers and DOPC/DOPS (4:1) bilayers, previously adsorbed on silicon supports. SbpA adsorption also took place on DPPC/DOPS (1:1) monolayers adsorbed on carbon grids. Finally, neither SbpA adsorption, nor recrystallization was observed on zwitterionic DMPC vesicles (previously adsorbed on polyelectrolyte multilayers), and on DPPC vesicles supported on silicon.

  14. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un; Gruner, Sol M.

    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.

  15. 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 ...

  16. An Overview of Biological Macromolecule Crystallization

    Directory of Open Access Journals (Sweden)

    Irene Russo Krauss

    2013-05-01

    Full Text Available 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.

  17. 'Seeing' atoms: the crystallographic revolution.

    Science.gov (United States)

    Schwarzenbach, Dieter

    2014-01-01

    Laue's experiment in 1912 of the diffraction of X-rays by crystals led to one of the most influential discoveries in the history of science: the first determinations of crystal structures, NaCl and diamond in particular, by W. L. Bragg in 1913. For the first time, the visualisation of the structure of matter at the atomic level became possible. X-ray diffraction provided a sort of microscope with atomic resolution, atoms became observable physical objects and their relative positions in space could be seen. All branches of science concerned with matter, solid-state physics, chemistry, materials science, mineralogy and biology, could now be firmly anchored on the spatial arrangement of atoms. During the ensuing 100 years, structure determination by diffraction methods has matured into an indispensable method of chemical analysis. We trace the history of the development of 'small-structure' crystallography (excepting macromolecular structures) in Switzerland. Among the pioneers figure Peter Debye and Paul Scherrer with powder diffraction, and Paul Niggli and his Zurich School with space group symmetry and geometrical crystallography. Diffraction methods were applied early on by chemists at the Universities of Bern and Geneva. By the 1970s, X-ray crystallography was firmly established at most Swiss Universities, directed by full professors. Today, chemical analysis by structure determination is the task of service laboratories. However, the demand of diffraction methods to solve problems in all disciplines of science is still increasing and powerful radiation sources and detectors are being developed in Switzerland and worldwide. PMID:24801690

  18. Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate.

    Science.gov (United States)

    Andersson, I

    1996-05-31

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from spinach is a hexadecamer (L8S8, Mr = 550,000) consisting of eight large (L, 475 residues) and eight small subunits (S, 123 residues). High-resolution data collection on crystals with large unit cells is not a trivial task due to the effect of radiation damage and the large number of overlapping reflections when conventional data collection methods are used. In order to minimise these effects, data on rubisco were collected with a giant Weissenberg camera at long crystal to image-plate distances at the synchrotron of the Photon Factory, Japan. Relative to conventional data sets, this experimental arrangement allowed a 20 to 30-fold reduction of the X-ray dose/exposure time for data collection. This paper describes the refined 1.6 A crystal structure of activated rubisco complexed with a transition state analogue, 2-carboxyarabinitol-bisphosphate. The crystallographic asymmetric unit contains an L4S4 unit, representing half of the molecule. The structure presented here is currently the highest resolution structure for any protein of comparable size. Refinement of the model was carried out by restrained least squares techniques without non-crystallographic symmetry averaging. The results show that all L and S subunits have identical three-dimensional structures, and their arrangement within the hexadecamer has no intrinsic asymmetry. A detailed analysis of the high-resolution maps identified 30 differences in the sequence of the small subunit, indicating a larger than usual heterogeneity for this nuclear encoded protein in spinach. No such differences were found in the sequence of the chloroplast encoded large subunit. The transition state analogue is in the cis conformation at the active site suggesting a key role for the carbamate of Lys201 in catalysis. Analysis of the active site around the catalytically essential magnesium ion further indicates that residues in the second liganding sphere of the metal

  19. The crystal structure of deshexapeptide(B25-B30)insulin at 0.25 nm resolution

    Institute of Scientific and Technical Information of China (English)

    常文瑞; 江涛; 任重; 万柱礼; 徐英博; 梁栋材; 朱尚权; 张友尚

    1995-01-01

    The determination of deshexapeptide(B25-B30)insulin(DHI)was divided into two steps.At the first step,the rough structure model of DHI molecule was determined by using the molecularreplacement method associated with the molecular close-packing method at 0.30 nm resolution based on the re-flection data collected on four-cycle diffractometer.At the second step,the DHI model was adjusted and re-fined at 0.25nm resolution based on the data collected on Area Detector.40 water molecules were determinedduring the refinement,the final R-factor is 0.185 with R.M.S.deviation of 0.002nm for bond lengths and 1.9°for bond angles.The differences in conformation and function of DHI with other insulin analogues werecompared and discussed.

  20. 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.