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Sample records for atomic resolution crystal

  1. 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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Liebschner, Dorothee; Dauter, Miroslawa [Argonne National Laboratory, Argonne, IL 60439 (United States); Brzuszkiewicz, Anna [Argonne National Laboratory, Argonne, IL 60439 (United States); University of Wroclaw, 50-383 Wroclaw (Poland); Dauter, Zbigniew, E-mail: dauter@anl.gov [Argonne National Laboratory, Argonne, IL 60439 (United States)

    2013-08-01

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

  4. Expression, purification and crystallization of a human protein SH3BGRL at atomic resolution

    International Nuclear Information System (INIS)

    The protein SH3BGRL, containing both SH3-binding and Homer EVH1-binding motifs, has been crystallized using the hanging-drop vapour-diffusion method. The protein SH3BGRL, containing both SH3-binding and Homer EVH1-binding motifs, has been crystallized using the hanging-drop vapour-diffusion method. The crystals diffract to 0.88 Å resolution and belong to space group P212121, with unit-cell parameters a = 28.8886, b = 34.9676, c = 98.0016 Å. Preliminary analysis indicates that the asymmetric unit contains one molecule and has a solvent content of about 34%

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

    Czech Academy of Sciences Publication Activity Database

    Dostál, Jiří; Pecina, Adam; Hrušková-Heidingsfeldová, Olga; Marečková, L.; Pichová, Iva; Řezáčová, Pavlína; Lepšík, Martin; Brynda, Jiří

    2015-01-01

    Roč. 71, č. 12 (2015), s. 2494-2504. ISSN 1399-0047 R&D Projects: GA ČR(CZ) GA14-23022S Institutional support: RVO:61388963 ; RVO:68378050 Keywords : aspartic protease * Candida parapsilosis * Sapp2p * crystal structure * ultrahigh resolution * interaction energy * quantum mechanics Subject RIV: CE - Biochemistry; EB - Genetics ; Molecular Biology (UMG-J) Impact factor: 2.674, year: 2014

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

    International Nuclear Information System (INIS)

    Recent advancement in dynamic-mode atomic force microscopy (AFM) has enabled its operation in liquid with atomic-scale resolution. However, its imaging speed has often been too slow to visualize atomic-scale dynamic processes. Here, we propose a method for making a significant improvement in the operation speed of dynamic-mode AFM. In this method, we use a wideband and low-latency phase detector with an improved algorithm for the signal complexification. We demonstrate atomic-scale imaging of a calcite crystal growth process in water at one frame per second. The significant improvement in the imaging speed should enable various studies on unexplored atomic-scale interfacial processes

  7. 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

  8. 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.

  9. Achieving atomic resolution

    OpenAIRE

    John Spence

    2002-01-01

    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 nanostru...

  10. 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.

  11. Atomic resolution studies of carbonic anhydrase II

    International Nuclear Information System (INIS)

    The structure of human carbonic anhydrase II has been solved with a sulfonamide inhibitor at 0.9 Å resolution. Structural variation and flexibility is seen on the surface of the protein and is consistent with the anisotropic ADPs obtained from refinement. Comparison with 13 other atomic resolution carbonic anhydrase structures shows that surface variation exists even in these highly ordered isomorphous crystals. Carbonic anhydrase has been well studied structurally and functionally owing to its importance in respiration. A large number of X-ray crystallographic structures of carbonic anhydrase and its inhibitor complexes have been determined, some at atomic resolution. Structure determination of a sulfonamide-containing inhibitor complex has been carried out and the structure was refined at 0.9 Å resolution with anisotropic atomic displacement parameters to an R value of 0.141. The structure is similar to those of other carbonic anhydrase complexes, with the inhibitor providing a fourth nonprotein ligand to the active-site zinc. Comparison of this structure with 13 other atomic resolution (higher than 1.25 Å) isomorphous carbonic anhydrase structures provides a view of the structural similarity and variability in a series of crystal structures. At the center of the protein the structures superpose very well. The metal complexes superpose (with only two exceptions) with standard deviations of 0.01 Å in some zinc–protein and zinc–ligand bond lengths. In contrast, regions of structural variability are found on the protein surface, possibly owing to flexibility and disorder in the individual structures, differences in the chemical and crystalline environments or the different approaches used by different investigators to model weak or complicated electron-density maps. These findings suggest that care must be taken in interpreting structural details on protein surfaces on the basis of individual X-ray structures, even if atomic resolution data are available

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-05-23

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

  13. Purification, crystallization and preliminary X-ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus

    International Nuclear Information System (INIS)

    Dihydrodipicolinate synthase (DHDPS), an enzyme of the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the expression, purification, crystallization and preliminary diffraction analysis to 1.45 Å resolution of DHDPS from methicillin-resistant S. aureus is reported. In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. DHDPS is part of the diaminopimelate pathway leading to lysine, coupling (S)-aspartate-β-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from methicillin-resistant Staphylococcus aureus, an important bacterial pathogen, are reported. The enzyme was crystallized in a number of forms, predominantly from PEG precipitants, with the best crystal diffracting to beyond 1.45 Å resolution. The space group was P1 and the unit-cell parameters were a = 65.4, b = 67.6, c = 78.0 Å, α = 90.1, β = 68.9, γ = 72.3°. The crystal volume per protein weight (VM) was 2.34 Å3 Da−1, with an estimated solvent content of 47% for four monomers per asymmetric unit. The structure of the enzyme will help to guide the design of novel therapeutics against the methicillin-resistant S. aureus pathogen

  14. 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

  15. HRTEM Imaging of Atoms at Sub-Angstrom Resolution

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-04-06

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

  16. 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.

  17. 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.

  18. 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.

  19. Imaging Lithium Atoms at Sub-Angstrom Resolution

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-01-03

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

  20. Positronium atom coherent photoproduction in crystal

    International Nuclear Information System (INIS)

    Coherent production of relativistic positronium atom by a high energy photon under the axial orientation is considered. The consideration is based on the interactions with a separate axis, i.e. with the chain of N atoms. In this case the cross section positronium atom production is formed by summation of production amplitudes on N atoms, calculation of modulus square of complete amplitude and summation by all photon states of a crystal. It is shown that application of photon beams of accelerators can serve as an effective method for positronium atom generation

  1. High resolution electron microscopic study of tin dioxide crystals

    Science.gov (United States)

    Smith, David J.; Bursill, L. A.; Wood, G. J.

    1983-11-01

    Crystals of Sb-doped tin dioxide have been examined by high resolution electron microscopy (≤2.3 Å point-to-point resolution) in [100], [001], and [1 overline111] zone axes projections, and images of twin interfaces, inclined defects, and a possible crystallographic shear plane have been recorded. Image simulations confirmed that the metal atom rows have been clearly resolved in each of these three low-index projections for specific electron-optical conditions. Image observation and consideration of the possible atomic arrangements about a (011)-type twin interface suggested that this resulted from a glide operation given by {1}/{2} (011) and a very close match with an experimental through-focal series was obtained using computer image simulations. The structural determination of crystal defects by high resolution electron microscopy is briefly discussed.

  2. Wave impedance of an atomically thin crystal.

    Science.gov (United States)

    Merano, Michele

    2015-11-30

    I propose an expression for the electromagnetic wave impedance of a two-dimensional atomic crystal, and I deduce the Fresnel coefficients in terms of this quantity. It is widely known that a two-dimensional crystal can absorb light, if its conductivity is different from zero. It is less emphasized that they can also store a certain amount of electromagnetic energy. The concept of impedance is useful to quantify this point. PMID:26698783

  3. Atomic steps on single crystals

    International Nuclear Information System (INIS)

    So far, atomic steps constitute the only well investigated defect among possible structural surface defects. With Low Energy Electron Diffraction (LEED), step density, orientation, terrace width, step arrangements and other structural parameters may be measured. Steps are present on nearly all surfaces; special step configurations may be produced by proper treatment. The presence of steps affects many surface properties like surface states, work function, adsorption and catalytic activity. It is therefore important to know the existence and properties of steps on all investigated surfaces. (orig.)

  4. 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.

  5. 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 precip...... layer between the crystalline nitride and ferrite matrix. Usually precipitates are described as having (semi) coherent or incoherent interfaces, but in this case it is more energetically favourable to create an amorphous layer instead of the incoherent interface....

  6. Image simulation for atomic resolution secondary electron image

    International Nuclear Information System (INIS)

    It has been demonstrated recently that an atomic resolution secondary electron (SE) image can be achieved with a scanning transmission electron microscope (STEM) equipped with a probe-aberration corrector. Its high sensitivity to the surface structure provides a powerful tool to simultaneously study both surface and bulk structure in the STEM, in the combination with the annular dark field (ADF) image. To quantitatively explain the atomic resolution SE image and retrieve surface-structure information, an image simulation is required. Here, we develop a method to simultaneously calculate, for the first time, the atomic resolution SE and ADF-STEM images, based on the multislice method with a frozen-phonon approximation. An object function for secondary electrons, derived from the inelastic scattering, is used to calculate the intensity distribution of the secondary electrons emitted from each slice. The simulations show that the SE image contrast is sensitive to the surface structure and the electron inelastic mean free path, but insensitive to specimen thickness when the thickness is more than 5 nm. The simulated SE images for SrTiO3 crystal show good agreement with the experimental observations. -- Highlights: ► A method is proposed to simulate secondary electron images at atomic resolution. ► Multislice method is used for propagation of primary electrons. ► An object function is derived to calculate secondary electrons emitted from each slice. ► The calculations are compared with experiments. ► It is demonstrated that the secondary electron image is sensitive to the surface structure.

  7. Streptavidin and its biotin complex at atomic resolution

    International Nuclear Information System (INIS)

    Analysis of atomic resolution crystal structures of wild-type streptavidin (1.03 Å) and its biotin complex (0.95 Å) indicate the range of conformational states taken on by this protein in the solid state. Most of the structural variation is found in the polypeptide loops between the strands in this β-sandwich protein. Atomic resolution crystallographic studies of streptavidin and its biotin complex have been carried out at 1.03 and 0.95 Å, respectively. The wild-type protein crystallized with a tetramer in the asymmetric unit, while the crystals of the biotin complex contained two subunits in the asymmetric unit. Comparison of the six subunits shows the various ways in which the protein accommodates ligand binding and different crystal-packing environments. Conformational variation is found in each of the polypeptide loops connecting the eight strands in the β-sandwich subunit, but the largest differences are found in the flexible binding loop (residues 45–52). In three of the unliganded subunits the loop is in an ‘open’ conformation, while in the two subunits binding biotin, as well as in one of the unliganded subunits, this loop ‘closes’ over the biotin–binding site. The ‘closed’ loop contributes to the protein’s high affinity for biotin. Analysis of the anisotropic displacement parameters included in the crystallographic models is consistent with the variation found in the loop structures and the view that the dynamic nature of the protein structure contributes to the ability of the protein to bind biotin so tightly

  8. Atomic resolution imaging of ferroelectric domains

    International Nuclear Information System (INIS)

    Electron optical principles involved in obtaining atomic resolution images of ferroelectric domains are reviewed, including the methods available to obtain meaningful interpretation and analysis of the image detail in terms of the atomic structures. Recent work is concerned with establishing the relationship between the essentially static chemical nanodomains and the spatial and temporal fluctuations of the nanoscale polar domains present in the relaxor class of materials, including lead scandium tantalate (PST) and lead magnesium niobate (PMN). Correct interpretation of the images required use of Next Nearest Neighbour Ising model simulations for the chemical domain textures upon which we must superimpose the polar domain textures; an introduction to this work is presented. A thorough analysis of the atomic scale chemical inhomogeneities, based upon the HRTEM results, has lead to an improved formulation of the theory of the dielectric response of PMN and PST, which is capable to predict the observed temperature and frequency dependence. HRTEM may be combined with solid state and statistical physics principles to provide a deeper understanding of structure/property relationships. 15 refs., 6 figs

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. Resolution limit of a phononic crystal superlens

    Science.gov (United States)

    Robillard, J.-F.; Bucay, J.; Deymier, P. A.; Shelke, A.; Muralidharan, K.; Merheb, B.; Vasseur, J. O.; Sukhovich, A.; Page, J. H.

    2011-06-01

    We report on the subwavelength imaging capabilities of a phononic crystal (PC) flat lens consisting of a triangular array of steel cylinders in methanol, all surrounded by water. The image resolution of the PC flat lens beats the Rayleigh diffraction limit because bound modes in the lens can be excited by evanescent waves emitted by the source. These are modes that only propagate in the direction parallel to the water-lens interface. These modes resonantly amplify evanescent waves that contribute to the reconstruction of an image. By employing the finite difference time domain method and ultrasonic experiments, we also explore the effect on the image resolution and focal point on various structural and operational parameters, such as source frequency, geometry of the lens, source position, and time. The mechanisms by which these factors affect resolution are discussed in terms of the competition between the contribution of propagative modes to focusing and the ability of the source to excite bound modes of the PC lens.

  14. Alkali atoms, dimers, exciplexes and clusters in 4He crystals

    International Nuclear Information System (INIS)

    Full text: A closed-shell He atom and a single-electron alkali atom strongly repel each other because of the Pauli principle. As a consequence, an alkali atom immersed into condensed (superfluid or solid) 4He forms a spherical bubble state, in which the alkali repels the He quantum fluid/solid by imposing its own symmetry on the local He environment. For 15 years we have investigated such atomic bubbles in solid 4He using optical and magnetic resonance spectroscopy. In this talk I will first review our high resolution magnetic resonance studies performed on solid He matrix-isolated alkali atoms in the radio-frequency and microwave domains with special emphasis on their sensitive dependence on the crystalline structure (body-centered cubic, bcc, versus hexagonally close-packed, hcp) of the helium matrix. In recent years we have extended the purely atomic studies to larger bound complexes, such as exciplexes, dimers and clusters. I will present some of our intriguing recent results: in their respective ground states, alkali and He atoms are the worst enemies in the periodic table and strongly repel each other. Excited alkali atoms, however, attract He atoms and form bound states (so-called exciplexes), in which up to 7 He atoms can be attached to one alkali atom. Cs2 and Rb2 dimers in solid He can be excited via a large variety of absorption bands, and the deexcitation proceeds either by photodissociation or by emission of radiation. We made the strange observation that, irrespective of the excitation band, dimer fluorescence is only emitted on the (1)3Πu → X1Σg triplet-singlet transition which is forbidden in the free dimer. When the first excited P1/2 state of an alkali atom is populated by direct atomic excitation, it fluoresces at 879 nm (1.7 % blueshifted from the free atomic transition at 894 nm), a quantitatively well explained fact. However, when the same state is populated by photodissociation of the dimer, the emission wavelength is 885 nm. We attribute

  15. 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

  16. 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.

  17. 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.

  18. 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...

  19. 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

  20. 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...

  1. 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...

  2. High resolution adaptive imaging of a single atom

    CERN Document Server

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

    2015-01-01

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

  3. ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

    OpenAIRE

    Zhou, Z. Hong

    2011-01-01

    Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density m...

  4. 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.

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

    International Nuclear Information System (INIS)

    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 ∗ 10−18 m2/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 × 10−18 m2/s at 250 °C and we assume that the high diffusion speed is due to surface diffusion

  6. Visualizing Nanoparticle Mobility in Liquid at Atomic Resolution

    OpenAIRE

    Dukes, Madeline J.; Jacobs, Benjamin W.; Morgan, David G; Hegde, Harshad; Kelly, Deborah F.

    2013-01-01

    Gold nanorods are widely known for their photothermal properties to treat solid tumors. Our work demonstrates the unrealized capacity to image these reagents in liquid at high resolution using Transmission Electron Microscopy (TEM). Here we perform the first atomic measurements of functionalized nanorods in solution while visualizing their dynamic behaviour with TEM.

  7. Atomic resolution cryo electron microscopy of macromolecular complexes.

    Science.gov (United States)

    Zhou, Z Hong

    2011-01-01

    Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their "native," noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

  8. 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

  9. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-03-02

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

  11. The wave impedance of an atomically thin crystal

    CERN Document Server

    Merano, Michele

    2015-01-01

    I propose an expression for the electromagnetic wave impedance of a two-dimensional atomic crystal, and I deduce the Fresnel coefficients in terms of this quantity. It is widely known that a two-dimensional crystal can absorb light, if its conductivity is different from zero. It is less emphasized that they can also store a certain amount of electromagnetic energy. The concept of impedance is useful to quantify this point.

  12. Crystal structure solution from experimentally determined atomic pair distribution functions

    OpenAIRE

    Juhas, Pavol; Granlund, Luke; Gujarathi, Saurabh R.; Duxbury, Phillip M.; Billinge, Simon J. L.

    2010-01-01

    The paper describes an extension of the Liga algorithm for structure solution from atomic pair distribution function (PDF), to handle periodic crystal structures with multiple elements in the unit cell. The procedure is performed in 2 separate steps - at first the Liga algorithm is used to find unit cell sites consistent with pair distances extracted from the experimental PDF. In the second step the assignment of atom species over cell sites is solved by minimizing the overlap of their empiri...

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

    OpenAIRE

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

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These tor...

  14. CO tip functionalization in subatomic resolution atomic force microscopy

    International Nuclear Information System (INIS)

    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

  15. 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.

  16. 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.

  17. 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.

  18. The Fresnel coefficients of a two-dimensional atomic crystal

    CERN Document Server

    Merano, Michele

    2016-01-01

    I deduce the Fresnel coefficients valid for a generic two dimensional crystal. In general the optical properties of an atomically thin monolayer are interpreted by modelling it as a homogeneous medium with an effective thickness. The comparison with experimental results, published in literature, shows that the Fresnel coefficients are better suited to this end than the above mentioned model.

  19. 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.

  20. High-resolution crystal structures of the solubilized domain of porcine cytochrome b5

    International Nuclear Information System (INIS)

    Crystal structures of the solubilized domain of cytochrome b5 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 b5. Mammalian microsomal cytochrome b5 has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochrome b5 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

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

    Science.gov (United States)

    2014-01-01

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

  2. Structural and chemical characterization of complex nanomaterials at atomic resolution

    Science.gov (United States)

    Sanchez, Sergio I.

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

  3. 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

  4. 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.

  5. 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

  6. 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)

  7. Atomic layer deposition in porous structures: 3D photonic crystals

    International Nuclear Information System (INIS)

    This paper reports recent results from studies of atomic layer deposition for the infiltration of three-dimensional photonic crystals. Infiltration of ZnS:Mn and TiO2 are reported for SiO2-based opal templates. It has been demonstrated that high filling fractions can be achieved and that the infiltrated material can be of high crystalline quality as assessed by photoluminescence measurements. The highly conformal and uniform coatings obtained in these studies are shown to contribute significantly to the photonic band gap properties. These investigations show the advantages of atomic layer deposition (ALD) as a flexible and practical pathway for attaining high performance photonic crystal structures and optical microcavities

  8. Fresnel coefficients of a two-dimensional atomic crystal

    OpenAIRE

    Merano, Michele

    2015-01-01

    In general the experiments on the linear optical properties of a single-layer two-dimensional atomic crystal are interpreted by modeling it as a homogeneous slab with an effective thickness. Here I fit the most remarkable experiments in graphene optics by using the Fresnel coefficients, fixing both the surface susceptibility and the surface conductivity of graphene. It is shown that the Fresnel coefficients and the slab model are not equivalent. Experiments indicate that the Fresnel coefficie...

  9. Polarizable atomic multipole X-ray refinement: application to peptide crystals

    International Nuclear Information System (INIS)

    A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered Rfree by 20–40% relative to the original spherically symmetric scattering model

  10. Polarizable atomic multipole X-ray refinement: application to peptide crystals

    Energy Technology Data Exchange (ETDEWEB)

    Schnieders, Michael J. [Department of Chemistry, Stanford, CA 94305 (United States); Fenn, Timothy D. [Department of Molecular and Cellular Physiology, Stanford, CA 94305 (United States); Howard Hughes Medical Institute (United States); Pande, Vijay S., E-mail: pande@stanford.edu [Department of Chemistry, Stanford, CA 94305 (United States); Brunger, Axel T., E-mail: pande@stanford.edu [Department of Molecular and Cellular Physiology, Stanford, CA 94305 (United States); Howard Hughes Medical Institute (United States); Department of Chemistry, Stanford, CA 94305 (United States)

    2009-09-01

    A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ionita, I. E-mail: onu@cc.nuclear.ro; Stoica, A.D.; Popovici, M.; Popa, N.C

    1999-07-21

    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)

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

    Science.gov (United States)

    Ionita, I.; Stoica, A. D.; Popovici, M.; Popa, N. C.

    1999-07-01

    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.

  13. 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)

  14. Precision crystal alignment for high-resolution electron microscope imaging

    International Nuclear Information System (INIS)

    One of the more difficult tasks involved in obtaining quality high-resolution electron micrographs is the precise alignment of a specimen into the required zone. The current accepted procedure, which involves changing to diffraction mode and searching for symmetric point diffraction pattern, is insensitive to small amounts of misalignment and at best qualitative. On-line analysis of the fourier space representation of the image, both for determining and correcting crystal tilt, is investigated. 8 refs., 42 figs

  15. Atomic resolution of Lithium Ions in LiCoO

    Energy Technology Data Exchange (ETDEWEB)

    Shao-Horn, Yang; Croguennec, Laurence; Delmas, Claude; Nelson, Chris; O' Keefe, Michael A.

    2003-03-18

    LiCoO2 is the most common lithium storage material for lithium rechargeable batteries, used widely to power portable electronic devices such as laptop computers. Lithium arrangements in the CoO2 framework have a profound effect on the structural stability and electrochemical properties of LixCoO2 (0 < x < 1), however, probing lithium ions has been difficult using traditional X-ray and neutron diffraction techniques. Here we have succeeded in simultaneously resolving columns of cobalt, oxygen, and lithium atoms in layered LiCoO2 battery material using experimental focal series of LiCoO2 images obtained at sub-Angstrom resolution in a mid-voltage transmission electron microscope. Lithium atoms are the smallest and lightest metal atoms, and scatter electrons only very weakly. We believe our observations of lithium to be the first by electron microscopy, and that they show promise to direct visualization of the ordering of lithium and vacancy in LixCoO2.

  16. STM mapped real surface of W(112) with atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Losovyj, Ya.B. [National Univ. of Lviv (Ukraine). Faculty of Physics; Ciszewski, A.; Zuber, Z. [Wroclaw Univ. (Poland). Inst. of Experimental Physics

    2001-05-01

    The surfaces with high anisotropy of the unit cell such as (112) of W and Mo are excellent substrates for the investigation of the long-range lateral interaction between adsorbed atoms at low coverages. Such surfaces are often used for the induction of the anomalous strain of adsorbed films, for example Gd on Mo(112). It is interesting that the expansion of the Gd overlayers is extremely sensitive to the difference in the surface geometry of the furrowed and smooth substrates. But the information on the real atomic structure of such furrowed substrates coming generally from LEED investigations is rather poor. Only recently McAvoy et al. reached atomic resolution for Mo(112) and Madey and coworkers obtained STM data for W(112). McAvoy et al. have shown that already minimal coverage of carbon (or oxygen) completely reconstructs the clean Mo(112) surface to a (9 x 3) structure. Recently we used a special procedure to check the cleanness of W(112). In this note we report our first STM results for the real W(112) surface obtained after the same cleaning process. (orig.)

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

    CERN Document Server

    Hood, J D; Asenjo-Garcia, A; Lu, M; Yu, S -P; Chang, D E; Kimble, H J

    2016-01-01

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the crossover from propagating fields $E(x) \\propto e^{\\pm ik_x x}$ outside the bandgap to localized fields $E(x) \\propto e^{-\\kappa_x |x|}$ 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 for the first time by shifting the band edge frequency of the PCW relative to the $\\rm D_1$ line of atomic cesium for $\\bar{N}=3.0\\pm 0.5$ atoms trapped along the PCW. Our results are the initial demonstration of this new paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

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

    Science.gov (United States)

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

    2014-12-01

    High-speed atomic force microscopy has attracted much attention due to its unique capability of visualizing nanoscale dynamic processes at a solid/liquid interface. However, its usability and resolution have yet to be improved. As one of the solutions for this issue, here we present a design of a high-speed Z-tip scanner with screw holding mechanism. We perform detailed comparison between designs with different actuator size and screw arrangement by finite element analysis. Based on the design giving the best performance, we have developed a Z tip scanner and measured its performance. The measured frequency response of the scanner shows a flat response up to ˜10 kHz. This high frequency response allows us to achieve wideband tip-sample distance regulation. We demonstrate the applicability of the scanner to high-speed atomic-resolution imaging by visualizing atomic-scale calcite crystal dissolution process in water at 2 s/frame.

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

    Energy Technology Data Exchange (ETDEWEB)

    Reza Akrami, Seyed Mohammad; Miyata, Kazuki [Division of Electrical Engineering and Computer Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192 (Japan); Asakawa, Hitoshi [Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192 (Japan); Fukuma, Takeshi, E-mail: fukuma@staff.kanazawa-u.ac.jp [Division of Electrical Engineering and Computer Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192 (Japan); ACT-C, Japan Science and Technology Agency, Honcho 4-1-9, Kawaguchi 332-0012 (Japan)

    2014-12-15

    High-speed atomic force microscopy has attracted much attention due to its unique capability of visualizing nanoscale dynamic processes at a solid/liquid interface. However, its usability and resolution have yet to be improved. As one of the solutions for this issue, here we present a design of a high-speed Z-tip scanner with screw holding mechanism. We perform detailed comparison between designs with different actuator size and screw arrangement by finite element analysis. Based on the design giving the best performance, we have developed a Z tip scanner and measured its performance. The measured frequency response of the scanner shows a flat response up to ∼10 kHz. This high frequency response allows us to achieve wideband tip-sample distance regulation. We demonstrate the applicability of the scanner to high-speed atomic-resolution imaging by visualizing atomic-scale calcite crystal dissolution process in water at 2 s/frame.

  20. Polarizable atomic multipole X-ray refinement: application to peptide crystals.

    Science.gov (United States)

    Schnieders, Michael J; Fenn, Timothy D; Pande, Vijay S; Brunger, Axel T

    2009-09-01

    Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA-IAS model lowered R(free) by 20-40% relative to the original spherically symmetric scattering model. PMID:19690373

  1. Structure of Alzheimer’s disease amyloid precursor protein copper-binding domain at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Geoffrey Kwai-Wai; Adams, Julian J. [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Cappai, Roberto [Department of Pathology and Centre for Neuroscience, The University of Melbourne, Victoria 3010 (Australia); The Mental Health Research Institute of Victoria, Parkville, Victoria 3052 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia); Parker, Michael W., E-mail: mparker@svi.edu.au [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia)

    2007-10-01

    An atomic resolution structure of the copper-binding domain of the Alzheimer’s disease amyloid precursor protein is presented. Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer’s disease, as its cleavage generates the Aβ peptide that is toxic to cells. APP is able to bind Cu{sup 2+} and reduce it to Cu{sup +} through its copper-binding domain (CuBD). The interaction between Cu{sup 2+} and APP leads to a decrease in Aβ production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 Å) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu{sup 2+} reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Aβ production.

  2. Structure of Alzheimer’s disease amyloid precursor protein copper-binding domain at atomic resolution

    International Nuclear Information System (INIS)

    An atomic resolution structure of the copper-binding domain of the Alzheimer’s disease amyloid precursor protein is presented. Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer’s disease, as its cleavage generates the Aβ peptide that is toxic to cells. APP is able to bind Cu2+ and reduce it to Cu+ through its copper-binding domain (CuBD). The interaction between Cu2+ and APP leads to a decrease in Aβ production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 Å) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu2+ reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Aβ production

  3. 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.

  4. Fractal analysis of crystalline surfaces at atomic resolution

    International Nuclear Information System (INIS)

    High-resolution images of ceramic oxide surfaces (e.g. MgO, NiO and BaTiO3) have been obtained in digitized form. Analytical techniques were designed to search for self-similar scaling (fractal) geometries. Three measures of surface roughness were investigated; namely coastline analysis, height-difference correlation function and variance scaling analysis. In some cases changes in surface topology occur with time. In principle this should be analyzed using self-affine fractal geometry and scaling concepts. The scaling behaviour was in all cases complicated by atomic surface facetting. Analytical results are reported for all crystalline surfaces imaged. The results are interpreted in terms of Brownian motion or self-diffusion and Brownian motion with geometrical restriction (lattice string animal models). 13 refs., 4 tabs., 9 figs

  5. High-Resolution Atom Interferometers with Suppressed Diffraction Phases.

    Science.gov (United States)

    Estey, Brian; Yu, Chenghui; Müller, Holger; Kuan, Pei-Chen; Lan, Shau-Yu

    2015-08-21

    We experimentally and theoretically study the diffraction phase of large-momentum transfer beam splitters in atom interferometers based on Bragg diffraction. We null the diffraction phase and increase the sensitivity of the interferometer by combining Bragg diffraction with Bloch oscillations. We demonstrate agreement between experiment and theory, and a 1500-fold reduction of the diffraction phase, limited by measurement noise. In addition to reduced systematic effects, our interferometer has high contrast with up to 4.4×10(6) radians of phase difference, and a resolution in the fine structure constant of δα/α=0.25  ppb in 25 h of integration time. PMID:26340186

  6. 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...

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

    International Nuclear Information System (INIS)

    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.

  8. 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

  9. 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.

  10. Atomic, Crystal, Elastic, Thermal, Nuclear, and Other Properties of Beryllium

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, A

    2006-02-01

    This report is part of a series of documents that provide a background to those involved in the construction of beryllium components and their applications. This report is divided into five sub-sections: Atomic/Crystal Structure, Elastic Properties, Thermal Properties, Nuclear Properties, and Miscellaneous Properties. In searching through different sources for the various properties to be included in this report, inconsistencies were at times observed between these sources. In such cases, the values reported by the Handbook of Chemistry and Physics was usually used. In equations, except where indicated otherwise, temperature (T) is in degrees Kelvin.

  11. Fresnel coefficients of a two-dimensional atomic crystal

    Science.gov (United States)

    Merano, Michele

    2016-01-01

    In general the experiments on the linear optical properties of a single-layer two-dimensional atomic crystal are interpreted by modeling it as a homogeneous slab with an effective thickness. Here I fit the most remarkable experiments in graphene optics by using the Fresnel coefficients, fixing both the surface susceptibility and the surface conductivity of graphene. It is shown that the Fresnel coefficients and the slab model are not equivalent. Experiments indicate that the Fresnel coefficients are able to simulate the overall experiments here analyzed, while the slab model fails to predict absorption and the phase of the reflected light.

  12. 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)

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. High-resolution SANS experiments by double-crystal technique

    International Nuclear Information System (INIS)

    Though small-angle scattering is a method suitable for investigation of microstructure in a wide mesoscopic size range (about 1 nm to 1 μm), the dynamic Q-range in a single SANS spectrum - defined as the ratio of the maximum value of the scattering vector Q to the Q-resolution of the instrument - is rarely better than about 10. The combination of measurements performed at different Q regions is therefore necessary for better evaluation of SANS experiments, particularly in case of polydisperse systems. Variation of instrument length, slit sizes and neutron wavelength is the usual way how to extend the Q-range accessible at a conventional pinhole SANS instrument. Nevertheless, this possibility is limited on the side of small Q values because of restrictions imposed on the physical length and luminosity of SANS facilities even if they are equipped with an efficient cold neutron source. Alternative techniques for SANS investigation of large objects requiring ultra high resolution were developed, based on the nondispersive arrangement of two perfect crystals. This contribution is focused on the double bent crystal (DBC) diffractometers operating in the intermediate Q-range of 10-4 to 10-2 A-1, which is difficult to access by both the types of instruments mentioned above. (author)

  19. High-resolution core-level photoemission measurements on the pentacene single crystal surface assisted by photoconduction.

    Science.gov (United States)

    Nakayama, Yasuo; Uragami, Yuki; Yamamoto, Masayuki; Yonezawa, Keiichirou; Mase, Kazuhiko; Kera, Satoshi; Ishii, Hisao; Ueno, Nobuo

    2016-03-01

    Upon charge carrier transport behaviors of high-mobility organic field effect transistors of pentacene single crystal, effects of ambient gases and resultant probable 'impurities' at the crystal surface have been controversial. Definite knowledge on the surface stoichiometry and chemical composites is indispensable to solve this question. In the present study, high-resolution x-ray photoelectron spectroscopy (XPS) measurements on the pentacene single crystal samples successfully demonstrated a presence of a few atomic-percent of (photo-)oxidized species at the first molecular layer of the crystal surface through accurate analyses of the excitation energy (i.e. probing depth) dependence of the C1s peak profiles. Particular methodologies to conduct XPS on organic single crystal samples, without any charging nor damage of the sample in spite of its electric insulating character and fragility against x-ray irradiation, is also described in detail. PMID:26871646

  20. 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...

  1. Near-atomic resolution visualization of human transcription promoter opening.

    Science.gov (United States)

    He, Yuan; Yan, Chunli; Fang, Jie; Inouye, Carla; Tjian, Robert; Ivanov, Ivaylo; Nogales, Eva

    2016-05-19

    In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB. PMID:27193682

  2. Advanced double-biprism holography with atomic resolution

    International Nuclear Information System (INIS)

    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

  3. 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.

  4. 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.

  5. 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

  6. 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)...

  7. 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.

  8. Atomic-Resolution Observations of Semi-Crystalline Integranular Thin Films in Silicon Nitride

    OpenAIRE

    Ziegler, Alexander; Idrobo, Juan C.; Cinibulk, Michael K.; Kisielowski, Christian; Nigel D. Browning; Ritchie, Robert O.

    2005-01-01

    The thin intergranular phase in a silicon nitride (Si3N4) ceramic, which has been regarded for decades as having an entirely amorphous morphology, is shown to have a semi-crystalline structure. Using two different but complementary high-resolution electron microscopy methods, the intergranular atomic structure was directly imaged at the atomic level. These high-resolution images show that the atomic arrangement of the dopand element cerium takes very periodic positions not only along the...

  9. In-line three-dimensional holography of nanocrystalline objects at atomic resolution

    OpenAIRE

    Chen, F.-R.; Van Dyck, D.; Kisielowski, C.

    2016-01-01

    Resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we report a general tomographic method to rec...

  10. 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.

  11. 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

  12. A crystal of a typical EF-hand protein grown under microgravity diffracts X-rays beyond 0.9 Å resolution

    OpenAIRE

    Declercq, Jean-Paul; Evrard, Christine; Carter, Daniel; Wright, Brenda; Etienne, Gérard; Parello, Joseph

    1999-01-01

    We report on our recent observation that crystals of a typical EF-hand protein (parvalbumin or Pa; Ca-loaded component from pike muscle with isoelectric point 4.10) grown under microgravity conditions diffract X-rays to a resolution better than 0.9 Å. The crystals were grown in the US space shuttle and characterized at 100 K, using an X-ray synchrotron beam. An effective atomic resolution has been achieved and substates in the conformation of the protein are observed. Large crystals up to 3 m...

  13. 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 ...

  14. 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. PMID:18044992

  15. 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...

  16. 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.

  17. 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.

  18. 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

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

    International Nuclear Information System (INIS)

    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

  20. 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

  1. 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.

  2. Achieving atomic resolution magnetic dichroism by controlling the phase symmetry of an electron probe

    OpenAIRE

    Rusz, Jan; Idrobo, Juan-Carlos; Bhowmick, Somnath

    2014-01-01

    The calculations presented here reveal that an electron probe carrying orbital angular momentum is just a particular case of a wider class of electron beams that can be used to measure electron magnetic circular dichroism (EMCD) with atomic resolution. It is possible to obtain an EMCD signal with atomic resolution by simply breaking the symmetry of the electron probe phase distribution using the aberration-corrected optics of an scanning transmission electron microscope. The required phase di...

  3. 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...

  4. Simultaneous nc-AFM/STM measurements with atomic resolution

    Czech Academy of Sciences Publication Activity Database

    Hapala, Prokop; Ondráček, Martin; Stetsovych, Oleksandr; Švec, Martin; Jelínek, Pavel

    Cham: Springer International Publishing, 2015 - (Morita, S.; Giessibl, F.; Meyer, E.; Wiesendanger, R.), s. 29-49. (NanoScience and Technology. 3). ISBN 978-3-319-15587-6 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : AFM * STM * DFT simulations * electron transport * atomic contrast Subject RIV: BM - Solid Matter Physics ; Magnetism

  5. In-line three-dimensional holography of nanocrystalline objects at atomic resolution

    Science.gov (United States)

    Chen, F.-R.; van Dyck, D.; Kisielowski, C.

    2016-02-01

    Resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we report a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose rate electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. We apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1-2 Å, which is smaller than inter-atomic distances.

  6. High-resolution atom interferometers with suppressed diffraction phases

    OpenAIRE

    Estey, B; C. Yu; Müller, H; Kuan, PC; Lan, SY

    2015-01-01

    © 2015 American Physical Society. We experimentally and theoretically study the diffraction phase of large-momentum transfer beam splitters in atom interferometers based on Bragg diffraction. We null the diffraction phase and increase the sensitivity of the interferometer by combining Bragg diffraction with Bloch oscillations. We demonstrate agreement between experiment and theory, and a 1500-fold reduction of the diffraction phase, limited by measurement noise. In addition to reduced systema...

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

    Czech Academy of Sciences Publication Activity Database

    Moreno, C.; Stetsovych, Oleksandr; Shimizu, T.K.; Custance, O.

    2015-01-01

    Roč. 15, č. 4 (2015), s. 2257-2262. ISSN 1530-6984 Institutional support: RVO:68378271 Keywords : noncontact atomic force microscopy (NC-AFM) * submolecular resolution * three-dimensional dynamic force spectroscopy * high-resolution imaging Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 13.592, year: 2014

  8. The mechanisms underlying the enhanced resolution of atomic force microscopy with functionalized tips

    International Nuclear Information System (INIS)

    By functionalizing the tip of an atomic force microscope (AFM) with a molecule or an atom that significantly contributes to the tip-sample interaction, the resolution can be dramatically enhanced. The interaction and therefore the resolution crucially depend on the chemical nature of the tip termination. Employing a tip functionalized with a CO molecule, atomic resolution of a pentacene molecule was recently demonstrated. In this work, the interaction between the CO tip and the pentacene imaged are studied with first principles calculations. The calculated frequency shifts compare very well with the experiment. The different energy contributions are analyzed and the Pauli energy is computed. We demonstrate that the source of the high resolution is Pauli repulsion, whereas van der Waals and electrostatic interactions only add a diffuse attractive background.

  9. 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.

  10. Atomic Resolution Crystallography Reveals how Changes in pH Shape the Protein Microenvironment

    Energy Technology Data Exchange (ETDEWEB)

    Lyubimov,A.; Lario, P.; Moustafa, I.; Vrielink, A.

    2006-01-01

    Hydrogen atoms are a vital component of enzyme structure and function. In recent years, atomic resolution crystallography ({ge}1.2 Angstroms) has been successfully used to investigate the role of the hydrogen atom in enzymatic catalysis. Here, atomic resolution crystallography was used to study the effect of pH on cholesterol oxidase from Streptomyces sp., a flavoenzyme oxidoreductase. Crystallographic observations of the anionic oxidized flavin cofactor at basic pH are consistent with the UV-visible absorption profile of the enzyme and readily explain the reversible pH-dependent loss of oxidation activity. Furthermore, a hydrogen atom, positioned at an unusually short distance from the main chain carbonyl oxygen of Met122 at high pH, was observed, suggesting a previously unknown mechanism of cofactor stabilization. This study shows how a redox active site responds to changes in the enzyme's environment and how these changes are able to influence the mechanism of enzymatic catalysis.

  11. 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

  12. 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...

  13. 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

  14. 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.

  15. Atomic resolution probe for allostery in the regulatory thin filament.

    Science.gov (United States)

    Williams, Michael R; Lehman, Sarah J; Tardiff, Jil C; Schwartz, Steven D

    2016-03-22

    Calcium binding and dissociation within the cardiac thin filament (CTF) is a fundamental regulator of normal contraction and relaxation. Although the disruption of this complex, allosterically mediated process has long been implicated in human disease, the precise atomic-level mechanisms remain opaque, greatly hampering the development of novel targeted therapies. To address this question, we used a fully atomistic CTF model to test both Ca(2+)binding strength and the energy required to remove Ca(2+)from the N-lobe binding site in WT and mutant troponin complexes that have been linked to genetic cardiomyopathies. This computational approach is combined with measurements of in vitro Ca(2+)dissociation rates in fully reconstituted WT and cardiac troponin T R92L and R92W thin filaments. These human disease mutations represent known substitutions at the same residue, reside at a significant distance from the calcium binding site in cardiac troponin C, and do not affect either the binding pocket affinity or EF-hand structure of the binding domain. Both have been shown to have significantly different effects on cardiac function in vivo. We now show that these mutations independently alter the interaction between the Ca(2+)ion and cardiac troponin I subunit. This interaction is a previously unidentified mechanism, in which mutations in one protein of a complex indirectly affect a third via structural and dynamic changes in a second to yield a pathogenic change in thin filament function that results in mutation-specific disease states. We can now provide atom-level insight that is potentially highly actionable in drug design. PMID:26957598

  16. Dependence of the energy resolution of a scintillating crystal on the readout integration time

    OpenAIRE

    Bocci, V.; Chao, D; Chiodi, G.; Faccini, R; Ferroni, F.(INFN Sezione di Roma, I-00185, Roma, Italy); Lunadei, R.; Martellotti, G; Penso, G.; Pinci, D.; L. Recchia

    2012-01-01

    The possibilty of performing high-rate calorimetry with a slow scintillating crystal is studied. In this experimental situation, to avoid pulse pile-up, it can be necessary to base the energy measurement on only a fraction of the emitted light, thus spoiling the energy resolution. This effect was experimentally studied with a BGO crystal and a photomultiplier followed by an integrator, by measuring the maximum amplitude of the signals. The experimental data show that the energy resolution is ...

  17. 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.

  18. Elucidating Common Structural Features of Human Pathogenic Variations Using Large-Scale Atomic-Resolution Protein Networks

    Science.gov (United States)

    Das, Jishnu; Lee, Hao Ran; Sagar, Adithya; Fragoza, Robert; Liang, Jin; Wei, Xiaomu; Wang, Xiujuan; Mort, Matthew; Stenson, Peter D.; Cooper, David N.; Yu, Haiyuan

    2016-01-01

    With the rapid growth of structural genomics, numerous protein crystal structures have become available. However, the parallel increase in knowledge of the functional principles underlying biological processes, and more specifically the underlying molecular mechanisms of disease, has been less dramatic. This notwithstanding, the study of complex cellular networks has made possible the inference of protein functions on a large scale. Here, we combine the scale of network systems biology with the resolution of traditional structural biology to generate a large-scale atomic-resolution interactome-network comprising 3,398 interactions between 2,890 proteins with a well-defined interaction interface and interface residues for each interaction. Within the framework of this atomic-resolution network, we have explored the structural principles underlying variations causing human-inherited disease. We find that in-frame pathogenic variations are enriched at both the interface and in the interacting domain, suggesting that variations not only at interface “hot-spots,” but in the entire interacting domain can result in alterations of interactions. Further, the sites of pathogenic variations are closely related to the biophysical strength of the interactions they perturb. Finally, we show that biochemical alterations consequent to these variations are considerably more disruptive than evolutionary changes, with the most significant alterations at the protein interaction interface. PMID:24599843

  19. 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

  20. New area detector for atomic-resolution scanning transmission electron microscopy.

    Science.gov (United States)

    Shibata, Naoya; Kohno, Yuji; Findlay, Scott D; Sawada, Hidetaka; Kondo, Yukihito; Ikuhara, Yuichi

    2010-01-01

    A new area detector for atomic-resolution scanning transmission electron microscopy (STEM) is developed and tested. The circular detector is divided into 16 segments which are individually optically coupled with photomultiplier tubes. Thus, 16 atomic-resolution STEM images which are sensitive to the spatial distribution of scattered electrons on the detector plane can be simultaneously obtained. This new detector can be potentially used not only for the simultaneous formation of common bright-field, low-angle annular dark-field and high-angle annular dark-field images, but also for the quantification of images by detecting the full range of scattered electrons and even for exploring novel atomic-resolution imaging modes by post-processing combination of the individual images. PMID:20406732

  1. 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.

  2. 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.

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

    International Nuclear Information System (INIS)

    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

  4. Influence of the wavelength on the spatial resolution of pulsed-laser atom probe

    Energy Technology Data Exchange (ETDEWEB)

    Gault, B. [Australian Centre for Microscopy and Microanalysis, Madsen Building F09, University of Sydney, NSW 2006 (Australia); Institute of Materials and Engineering Science, Australian Nuclear Science and Technology Organisation, Private Mail Bag 1, Menai, NSW 2234 (Australia); Chen, Y. M.; Hono, K. [Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-0047 (Japan); National Institute for Materials Science, Tsukuba 305-0047 (Japan); Moody, M. P.; Ringer, S. P. [Australian Centre for Microscopy and Microanalysis, Madsen Building F09, University of Sydney, NSW 2006 (Australia); Ohkubo, T. [National Institute for Materials Science, Tsukuba 305-0047 (Japan)

    2011-11-01

    Modern atom probes typically incorporate an ultrafast pulsed-laser source with wavelength ranging from infrared (IR) to ultraviolet (UV) depending on the specific instrument. In order to estimate the influence of the wavelength on the accuracy of the technique, the achievable in-depth spatial resolution has been measured for atom probe analyses of the same pure W specimen using three different wavelengths and across a range of laser pulse energies. UV illumination is shown to yield superior spatial resolution to both IR and visible (green) wavelengths. We propose that this improvement relates to a faster decay of temperature enabled by light absorption confined to the near apex region.

  5. 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)

  6. 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.

  7. A high-intensity beam of metastable helium atoms with good velocity resolution

    International Nuclear Information System (INIS)

    The excitation of a low-energy ground state helium beam to its metastable states by electron impact is analysed. It is shown that the narrowest velocity distribution for the resulting metastable helium beam is obtained by directing the helium and electron beams parallel or antiparallel. A source of metastable helium atoms was constructed according to this analysis which produced a beam of 3 x 1014 metastable atoms/s sr with a velocity resolution of 3% FWHM for a room-temperature beam (E = 66 MeV). A possible source of errors in time-of-flight experiments with metastable atoms is pointed out. (author)

  8. 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.

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

    International Nuclear Information System (INIS)

    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

  10. 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.

  11. 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)

  12. 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.

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

    International Nuclear Information System (INIS)

    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: ► Impact of the brightness on the reconstructed signal in electron holography. ► Factor 2.8 gain in signal quality by setup with a high brightness electron gun. ► Investigation of a grain boundary in gold with a state-of-the-art holography setup. ► A-posteriori aberration fine-tuning for true one Angstrom resolution in the object wave. ► Mistilt analysis on the atomic scale by numerical wave optics.

  14. Opto-structural studies of well-dispersed silicon nano-crystals grown by atom beam sputtering.

    Science.gov (United States)

    Saxena, Nupur; Kumar, Pragati; Kabiraj, Debulal; Kanjilal, Dinakar

    2012-01-01

    Synthesis and characterization of nano-crystalline silicon grown by atom beam sputtering technique are reported. Rapid thermal annealing of the deposited films is carried out in Ar + 5% H2 atmosphere for 5 min at different temperatures for precipitation of silicon nano-crystals. The samples are characterized for their optical and structural properties using various techniques. Structural studies are carried out by micro-Raman spectroscopy, Fourier transform infrared spectroscopy, transmission electron microscopy (TEM), high resolution transmission electron microscopy, and selected area electron diffraction. The optical properties are studied by photoluminescence and UV-vis absorption spectroscopy, and bandgaps are evaluated. The bandgaps are found to decrease after rapid thermal treatment. The micro-Raman studies show the formation of nano-crystalline silicon in as-deposited as well as annealed films. The shifting and broadening in Raman peak suggest formation of nano-phase in the samples. Results of micro-Raman, photoluminescence, and TEM studies suggest the presence of a bimodal crystallite size distribution for the films annealed at higher temperatures. The results show that atom beam sputtering is a suitable technique to synthesize nearly mono-dispersed silicon nano-crystals. The size of the nano-crystals may be controlled by varying annealing parameters. PMID:23031449

  15. Fabrication of specimens of metamorphic magnetite crystals for field ion microscopy and atom probe microanalysis.

    Science.gov (United States)

    Kuhlman, K R; Martens, R L; Kelly, T F; Evans, N D; Miller, M K

    2001-10-01

    Field ion specimens have been successfully fabricated from samples of metamorphic magnetite crystals (Fe3O4) extracted from a polymetamorphosed, granulite-facies marble with the use of a focused ion beam. These magnetite crystals contain nanometer-scale, disk-shaped inclusions making this magnetite particularly attractive for investigating the capabilities of atom probe field ion microscopy (APFIM) for geological materials. Field ion microscope images of these magnetite crystals were obtained in which the observed size and morphology of the precipitates agree with previous results. Samples were analyzed in the energy compensated optical position-sensitive atom probe. Mass spectra were obtained in which peaks for singly ionized 16O, 56Fe and 56FeO and doubly ionized 54Fe, 56Fe and 57Fe peaks were fully resolved. Manganese and aluminum were observed in a limited analysis of a precipitate in an energy compensated position sensitive atom probe. PMID:11770743

  16. Resolution for Forward and Phase-Conjugate Degenerate Four-Wave Mixing in Hot Atomic Media

    International Nuclear Information System (INIS)

    Resolutions of degenerate four-wave mixing with forward and phase-conjugate configurations (FDFWM and PCDFWM) are investigated and compared theoretically and experimentally in hot rubidium (Rb) atomic vapor. The theoretical simulations indicate that PCDFWM is of much higher resolution than FDFWM. The resolution of PCDFWM is less dependent on Doppler broadening. The experimental results are in good agreement with the theoretical expectation. PCDFWM can resolve the hyperfine transitions and crossover resonances of 87Rb which cannot be achieved by FDFWM. Additionally, with sample temperature increasing, the linewidth of FDFWM spectrum obviously broadens. In comparison, no obvious broadening can be observed in the PCDFWM spectrum. (fundamental areas of phenomenology(including applications))

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

    OpenAIRE

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

    1992-01-01

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

  18. Atomic-resolution single-spin magnetic resonance detection concept based on tunneling force microscopy

    Science.gov (United States)

    Payne, A.; Ambal, K.; Boehme, C.; Williams, C. C.

    2015-05-01

    A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single-electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy system noise. The results show that the approach could provide single-spin measurement of electrically isolated qubit states with atomic spatial resolution at room temperature.

  19. Concept for room temperature single-spin tunneling force microscopy with atomic spatial resolution

    Science.gov (United States)

    Payne, Adam

    A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy (AFM) system noise. The results show that the approach could provide single-spin measurement of electrically isolated defect states with atomic spatial resolution at room temperature.

  20. 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)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-01

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

  2. Atomic density functional and diagram of structures in the phase field crystal model

    Science.gov (United States)

    Ankudinov, V. E.; Galenko, P. K.; Kropotin, N. V.; Krivilyov, M. D.

    2016-02-01

    The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindrical tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.

  3. 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.)

  4. Polarizable atomic multipole X-ray refinement: application to peptide crystals

    OpenAIRE

    Schnieders, Michael J.; Fenn, Timothy D.; Pande, Vijay S.; Brunger, Axel T.

    2009-01-01

    Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (F...

  5. 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

  6. Atomic force microscopy characterization of a YBaCuO crystal surface patterned by proton irradiation

    International Nuclear Information System (INIS)

    A YBaCuO single crystal and a c-axis grown epitaxial YBaCuO film were irradiated with 200 keV protons to study the changes of the transport and especially of the structural properties. The single crystal was covered with a special grid-mask with strips of 5 μm periodicity in the irradiation procedure. The changes of the structural properties of the film and of the single crystal were studied by X-ray diffraction and by interference contrast and atomic force microscopy, respectively. The main structural effect of irradiation with moderate fluences is a lattice expansion of 0.8% in the film. The expansion of the irradiated parts of the crystal was 15-20 nm which is a factor of about 2 higher than in the film. This discrepancy can be resolved by considering the different energy deposition processes in the crystal and in the film. (orig.)

  7. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  9. Crystals of DhaA mutants from Rhodococcus rhodochrous NCIMB 13064 diffracted to ultrahigh resolution: crystallization and preliminary diffraction analysis

    International Nuclear Information System (INIS)

    Three mutants of the haloalkane dehalogenase DhaA derived from R. rhodochrous NCIMB 13064 were crystallized and diffracted to ultrahigh resolution. The enzyme DhaA from Rhodococcus rhodochrous NCIMB 13064 belongs to the haloalkane dehalogenases, which catalyze the hydrolysis of haloalkanes to the corresponding alcohols. The haloalkane dehalogenase DhaA and its variants can be used to detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Three mutants named DhaA04, DhaA14 and DhaA15 were constructed in order to study the importance of tunnels connecting the buried active site with the surrounding solvent to the enzymatic activity. All protein mutants were crystallized using the sitting-drop vapour-diffusion method. The crystals of DhaA04 belonged to the orthorhombic space group P212121, while the crystals of the other two mutants DhaA14 and DhaA15 belonged to the triclinic space group P1. Native data sets were collected for the DhaA04, DhaA14 and DhaA15 mutants at beamline X11 of EMBL, DESY, Hamburg to the high resolutions of 1.30, 0.95 and 1.15 Å, respectively

  10. 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.

  11. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-08-21

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

  13. 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.)

  14. 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.

  15. X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3 Å resolution using a twinned crystal

    International Nuclear Information System (INIS)

    The crystal structure of bilirubin oxidase (BOD) from M. verrucaria has been determined at 2.3 Å resolution using a merohedrally twinned crystal. BOD has four copper-coordination sites that are almost identical to those of other multicopper oxidases and is also very similar to them in overall structure. Bilirubin oxidase (BOD), a multicopper oxidase found in Myrothecium verrucaria, catalyzes the oxidation of bilirubin to biliverdin. Oxygen is the electron acceptor and is reduced to water. BOD is used for diagnostic analysis of bilirubin in serum and has attracted considerable attention as an enzymatic catalyst for the cathode of biofuel cells that work under neutral conditions. Here, the crystal structure of BOD is reported for the first time. Blue bipyramid-shaped crystals of BOD obtained in 2-methyl-2,4-pentanediol (MPD) and ammonium sulfate solution were merohedrally twinned in space group P63. Structure determination was achieved by the single anomalous diffraction (SAD) method using the anomalous diffraction of Cu atoms and synchrotron radiation and twin refinement was performed in the resolution range 33–2.3 Å. The overall organization of BOD is almost the same as that of other multicopper oxidases: the protein is folded into three domains and a total of four copper-binding sites are found in domains 1 and 3. Although the four copper-binding sites were almost identical to those of other multicopper oxidases, the hydrophilic Asn residue (at the same position as a hydrophobic residue such as Leu in other multicopper oxidases) very close to the type I copper might contribute to the characteristically high redox potential of BOD

  16. High-resolution kaonic-atom x-ray spectroscopy with transition-edge-sensor microcalorimeters

    CERN Document Server

    Okada, S; Doriese, W B; Fowler, J W; Irwin, K D; Ishimoto, S; Sato, M; Schmidt, D R; Swetz, D S; Tatsuno, H; Ullom, J N; Yamada, S

    2014-01-01

    We are preparing for an ultra-high resolution x-ray spectroscopy of kaonic atoms using an x-ray spectrometer based on an array of superconducting transition-edge-sensor microcalorimeters developed by NIST. The instrument has excellent energy resolutions of 2 - 3 eV (FWHM) at 6 keV and a large collecting area of about 20 mm^2. This will open new door to investigate kaon-nucleus strong interaction and provide new accurate charged-kaon mass value.

  17. High-Resolution Kaonic-Atom X-ray Spectroscopy with Transition-Edge-Sensor Microcalorimeters

    Science.gov (United States)

    Okada, S.; Bennett, D. A.; Doriese, W. B.; Fowler, J. W.; Irwin, K. D.; Ishimoto, S.; Sato, M.; Schmidt, D. R.; Swetz, D. S.; Tatsuno, H.; Ullom, J. N.; Yamada, S.

    2014-09-01

    We are preparing for an ultra-high resolution X-ray spectroscopy of kaonic atoms using an X-ray spectrometer based on an array of superconducting transition-edge-sensor microcalorimeters developed by NIST. The instrument has excellent energy resolutions of 2-3 eV (FWHM) at 6 keV and a large collecting area of about 20 mm. This will open new door to investigate kaon-nucleus strong interaction and provide new accurate charged-kaon mass value.

  18. 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

  19. Resolution of the hydroxyapatite crystal lattice in bone and dental enamel by electron microscopy

    International Nuclear Information System (INIS)

    The molecular and atomic structure of hydroxyapatite was studied by transmission electron microscopy. The form, size and packing of hydroxyapatite crystals in sections of bone and dental hard tissues could be determined. Lattice fringe patterns with repeat distances in the range 2.7-8.2 A occurred in images of individual crystals. On the basis of these fringes the true orientation of the crystals relative to the plane of sectioning was calculated. The observed crystal lattice spacings and interplanar angles were in close agreement with data derived from X-ray diffraction analysis. This study shows that the possibility exists of relating crystallographic analysis to the morphology and fine structure of calcified tissue in health and disease

  20. 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...

  1. Understanding the Formation Mechanism of Two-Dimensional Atomic Islands on Crystal Surfaces by the Condensing Potential Model

    Science.gov (United States)

    Yin, Cong; Lin, Zheng-Zhe; Li, Min; Tang, Hao

    2016-04-01

    A condensing potential (CP) model was established for predicting the geometric structure of two-dimensional (2D) atomic islands on crystal surfaces. To further verify the CP model, statistical molecular dynamics simulations are performed to investigate the trapping adatom process of atomic island steps on Pt (111). According to the detailed analysis on the adatom trapping process, the CP model should be a universal theory to understand the shape of the 2D atomic islands on crystal surfaces.

  2. Atomic-Resolution Observations of Semi-Crystalline IntegranularThin Films in Silicon Nitride

    Energy Technology Data Exchange (ETDEWEB)

    Ziegler, Alexander; Idrobo, Juan C.; Cinibulk, Michael K.; Kisielowski, Christian; Browning, Nigel D.; Ritchie, Robert O.

    2005-08-01

    The thin intergranular phase in a silicon nitride (Si3N4)ceramic, which has been regarded for decades as having an entirely amorphous morphology, is shown to have a semi-crystalline structure. Using two different but complementary high-resolution electron microscopy methods, the intergranular atomic structure was directly imaged at the atomic level. These high-resolution images show that the atomic arrangement of the dopand element cerium takes very periodic positions not only along the interface between the intergranular phase and the Si3N4 matrix grains, but it arranges in a semi-crystalline structure that spans the entire width of the intergranular phase between two adjacent matrix grains, in principle connecting the two separate matrix grains. The result will have implications on the approach of understanding the materials properties of ceramics, most significantly on the mechanical properties and the associated computational modeling of the atomic structure of the thin intergranular phase in Si3N4 ceramics.

  3. Dependence of the energy resolution of a scintillating crystal on the readout integration time

    CERN Document Server

    Bocci, V; Chiodi, G; Faccini, R; Ferroni, F; Lunadei, R; Martellotti, G; Penso, G; Pinci, D; Recchia, L

    2012-01-01

    The possibilty of performing high-rate calorimetry with a slow scintillator crystal is studied. In this experimental situation, to avoid pulse pile-up, it can be necessary to base the energy measurement on only a fraction of the emitted light, thus spoiling the energy resolution. This effect was experimentally studied with a BGO crystal and a photomultiplier followed by an integrator, by measuring the peak amplitude of the signals. The experimental data show that the energy resolution is exclusively due to the statistical fluctuations of the number of photoelectrons contributing to the peak amplitude. When such number is small its fluctuations are even smaller than those predicted by Poisson statistics. These results were confirmed by a Monte Carlo simulation which allows to estimate, in a general case, the energy resolution, given the total number of photoelectrons, the scintillation time and the integration time.

  4. Super-resolution focal area induced by super-convergence in a photonic crystal immersion lens

    International Nuclear Information System (INIS)

    In this paper, we numerically demonstrate that the negative refraction of a photonic crystal immersion lens can bend a beam by unconventionally large convergence angles over π/2 in free space. This super-convergence feature leads to constructive interference of high-spatial-frequency waves in both lateral and axial directions and forms super-resolution focal areas beyond the evanescent fields. As such, a 57% reduction in the focal area compared with the diffraction-limited case of an objective with numerical aperture of 0.95 has been numerically achieved at a normalized frequency of 0.3 in a photonic crystal immersion lens, corresponding to a lateral resolution of 0.32λ as well as an axial resolution of 0.70λ. (paper)

  5. 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.

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

    International Nuclear Information System (INIS)

    The radiation damage, in terms of atom displacements, induced by gamma irradiation in LYSO and LuYAP crystals is presented. 44Sc, 22Na and 48V 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

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

    Science.gov (United States)

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

    2016-05-01

    As the resolutions of Three Dimensional Electron Microscopic reconstructions of biological macromolecules are being improved, there is a need for better fitting and refinement methods at high resolutions and robust approaches for model assessment. Flex-EM/MODELLER has been used for flexible fitting of atomic models in intermediate-to-low resolution density maps of different biological systems. Here, we demonstrate the suitability of the method to successfully refine structures at higher resolutions (2.5-4.5Å) using both simulated and experimental data, including a newly processed map of Apo-GroEL. A hierarchical refinement protocol was adopted where the rigid body definitions are relaxed and atom displacement steps are reduced progressively at successive stages of refinement. For the assessment of local fit, we used the SMOC (segment-based Manders' overlap coefficient) score, while the model quality was checked using the Qmean score. Comparison of SMOC profiles at different stages of refinement helped in detecting regions that are poorly fitted. We also show how initial model errors can have significant impact on the goodness-of-fit. Finally, we discuss the implementation of Flex-EM in the CCP-EM software suite. PMID:26988127

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

    Science.gov (United States)

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

    2016-01-01

    As the resolutions of Three Dimensional Electron Microscopic reconstructions of biological macromolecules are being improved, there is a need for better fitting and refinement methods at high resolutions and robust approaches for model assessment. Flex-EM/MODELLER has been used for flexible fitting of atomic models in intermediate-to-low resolution density maps of different biological systems. Here, we demonstrate the suitability of the method to successfully refine structures at higher resolutions (2.5–4.5 Å) using both simulated and experimental data, including a newly processed map of Apo-GroEL. A hierarchical refinement protocol was adopted where the rigid body definitions are relaxed and atom displacement steps are reduced progressively at successive stages of refinement. For the assessment of local fit, we used the SMOC (segment-based Manders’ overlap coefficient) score, while the model quality was checked using the Qmean score. Comparison of SMOC profiles at different stages of refinement helped in detecting regions that are poorly fitted. We also show how initial model errors can have significant impact on the goodness-of-fit. Finally, we discuss the implementation of Flex-EM in the CCP-EM software suite. PMID:26988127

  9. 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).

  10. 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).

  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

    Presents the solution of a special scattering problem which may be important in the theory of slowing-down of atomic particles in crystals. A projectile moves along the centre axis of a regular ring of n equal atoms which are free and do not interact with each other. The interaction between 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...... asymptotic velocities of the ring atoms as well as the energy loss of the projectile. Furthermore, it can be decided whether the projectile is reflected by the ring. Both the feasibility of assumptions specifying the problem and the validity of different approximations made in the transformation from the...

  12. Synthesis of Sm3+-doped strontium barium niobate crystals in glass by samarium atom heat processing

    International Nuclear Information System (INIS)

    New glasses giving the crystallization of Sm3+-doped Sr x Ba1-x Nb2O6 (SBN) ferroelectrics have been developed in the Sm2O3-SrO-BaO-Nb2O5-B2O3 system, and the formation of SBN crystal dots and lines by continuous wave Nd:YAG laser (wavelength:1064 nm, power: 1 W) irradiations, i.e., samarium atom heat processing, has been examined. The formation of Sm3+-doped SBN non-linear optical crystals is confirmed from X-ray diffraction analyses, micro-Raman scattering spectra, second harmonic generations, and photoluminescence spectra. Sm3+-doped SBN crystal dots with the diameters of 20-70 μm and lines with the widths of 20-40 μm are written at the surface of some glasses such as 10Sm2O3.10SrO.10BaO.20Nb2O5.50B2O3 (mol%) by Nd:YAG laser irradiations with the irradiation times of 20-70 s for the dots and with the scanning speeds of 1-5 μm/s for the lines. The present study suggests that the samarium atom heat processing has a potential for the patterning of optical waveguides consisting of ferroelectric SBN crystals in glass substrates

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

    International Nuclear Information System (INIS)

    A high-resolution X-ray crystallographic study of the effects of solvent deuteration on the crystallization of proteinase K shows negligibly small degradations of the crystals owing to solvent deuteration and small structural differences between nondeuterated and deuterated crystals of proteinase K. Deuteration of macromolecules is an important technique in neutron protein crystallography. Solvent deuteration of protein crystals is carried out by replacing water (H2O) with heavy water (D2O) 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 NO3− anions were included in the PK crystal unit cell grown in NaNO3 solution. In this study, however, the PK crystal structure did not contain NO3− anions; consequently, distortions of amino acids arising from the presence of NO3− 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. 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.

  15. 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

  16. Simple statistical model for predicting thermal atom diffusion on crystal surfaces

    International Nuclear Information System (INIS)

    A simple model based on the statistics of single atoms is developed to predict the diffusion rate of thermal atoms in (or on) bulk materials without empirical parameters. Compared with vast classical molecular-dynamics simulations for predicting the self-diffusion rate of Pt, Cu, and Ar adatoms on crystal surfaces, the model is proved to be much more accurate than the Arrhenius law and the transition state theory. Applying this model, the theoretical predictions agree well with the experimental values in the presented paper about the self-diffusion of Pt (Cu) adatoms on the surfaces

  17. Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Egli, Martin; Minasov, George; Su, Li; Rich, Alexander (MIT); (Vanderbilt); (NWU)

    2010-03-05

    Many pathogenic viruses use programmed -1 ribosomal frameshifting to regulate translation of their structural and enzymatic proteins from polycistronic mRNAs. Frameshifting is commonly stimulated by a pseudoknot located downstream from a slippery sequence, the latter positioned at the ribosomal A and P sites. We report here the structures of two crystal forms of the frameshifting RNA pseudoknot from beet western yellow virus at resolutions of 1.25 and 2.85 {angstrom}. Because of the very high resolution of 1.25 {angstrom}, ten mono- and divalent metal ions per asymmetric unit could be identified, giving insight into potential roles of metal ions in stabilizing the pseudoknot. A magnesium ion located at the junction of the two pseudoknot stems appears to play a crucial role in stabilizing the structure. Because the two crystal forms exhibit mostly unrelated packing interactions and local crystallographic disorder in the high-resolution form was resolvable, the two structures offer the most detailed view yet of the conformational preference and flexibility of an RNA pseudoknot.

  18. Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution

    International Nuclear Information System (INIS)

    Many pathogenic viruses use programmed -1 ribosomal frameshifting to regulate translation of their structural and enzymatic proteins from polycistronic mRNAs. Frameshifting is commonly stimulated by a pseudoknot located downstream from a slippery sequence, the latter positioned at the ribosomal A and P sites. We report here the structures of two crystal forms of the frameshifting RNA pseudoknot from beet western yellow virus at resolutions of 1.25 and 2.85 (angstrom). Because of the very high resolution of 1.25 (angstrom), ten mono- and divalent metal ions per asymmetric unit could be identified, giving insight into potential roles of metal ions in stabilizing the pseudoknot. A magnesium ion located at the junction of the two pseudoknot stems appears to play a crucial role in stabilizing the structure. Because the two crystal forms exhibit mostly unrelated packing interactions and local crystallographic disorder in the high-resolution form was resolvable, the two structures offer the most detailed view yet of the conformational preference and flexibility of an RNA pseudoknot.

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

    Science.gov (United States)

    Litinskaya, Marina; Tignone, Edoardo; Pupillo, Guido

    2016-01-01

    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. PMID:27170160

  20. 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.

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

    Science.gov (United States)

    Litinskaya, Marina; Tignone, Edoardo; Pupillo, Guido

    2016-01-01

    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. PMID:27170160

  2. Preparing arrays of large atomically flat regions on single crystal substrates

    International Nuclear Information System (INIS)

    We report a simple and general procedure to create arrays of atomically flat terraces on single crystal surfaces. Facets of three-dimensional (3D) metal islands formed after hetero-epitaxial growth are often flat and, through annealing or growth at elevated temperature, the formation of rather large (micron-scale) atomically flat-top facets can be promoted. We find that the step-free nature of top facets on such islands can be transferred to the substrate surface through room-temperature ion-sputter etching, followed by an annealing step. We use low-energy electron microscopy (LEEM) and Auger electron spectroscopy (AES) for in situ monitoring of the process steps while fabricating arrays of step-free surface regions on W(110), Ru(0001), Cu(100), and Fe(100) single crystals.

  3. 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.

  4. 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/

  5. 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.

  6. The structure determination of Al20Cu2Mn3 by near atomic resolution chemical mapping

    International Nuclear Information System (INIS)

    Highlights: • The structure of Al20Cu2Mn3 with a space group of Bbmm is completely determined. • The actual formula of Al20Cu2Mn3 is Al31Cu3Mn5. • Al20Cu2Mn3 is formed by a parallel tessellation of hexagon subunits. • Al20Cu2Mn3 is prone to twinning by an alternate tessellation of hexagon subunits. • The Al20Cu2Mn3 is coherent with α-Al along its longitudinal axis. - Abstract: Al20Cu2Mn3 phase is one kind of common dispersoids in aluminum alloys; however, the atomic arrangement of Al20Cu2Mn3 has not yet been clearly identified. Combining the atomic resolution high angle annular dark field and chemical composition quantitative results, three structure models of Al20Cu2Mn3 were derived basing on the isostructural Mn11Ni4Al60. The formation enthalpies and total energy were calculated using the first-principles approach. The structure of the Al20Cu2Mn3 phase with the minimal energy was identified, giving a fully relaxed structure with lattice parameters of a = 23.98 Å, b = 12.54 Å, c = 7.66 Å, which belongs to a space group of Bbmm. The determined structure is in excellent agreement with the near atomic resolution chemical mapping results

  7. Transition metal atom heat processing for writing of crystal lines in glass

    International Nuclear Information System (INIS)

    A technique for the writing of crystal line in glass has been developed, in which a continuous-wave Nd:YAG laser (wavelength: λ=1064 nm) is irradiated to the glasses containing transition metal (TM) ions such as Fe2+, Ni2+, and V4+. Laser energies are absorbed through d-d transitions of TM ions and dissipated to the lattice surrounding TM ions by nonradiative relaxation process, giving the increase in temperature in the laser irradiated region and inducing crystallization. This technique has been demonstrated for the writing of crystal lines consisting of nonlinear optical fresnoite-type Ba2TiGe2O8 and Ba2TiSi2O8 crystals in NiO-, Fe2O3-, and V2O5-doped (0.3-1 mol %) BaO-TiO2-GeO2 and BaO-TiO2-SiO2 glasses. It is confirmed that crystals in the crystal lines are highly oriented along the laser scanning direction. The technique developed in this study is proposed to be called ''transition metal atom heat processing.''

  8. On crystallization of polypropylene on atomically flat silicate substrate and relationship to mechanical properties

    International Nuclear Information System (INIS)

    Research highlights: → Phyllosilicate was used to probe the nucleation and chain organization in thin films. → Crystal morphology was altered from leaf-like structure to fully developed spherulites. → The lamellae structure changed from well-oriented to cross-hatched implying epitaxial growth. → The good interfacial bonding favored by epitaxial crystallization is beneficial for toughness. - Abstract: Phyllosilicates including mica offer one of the easiest methods to obtain atomically flat surface of macroscopic size by cleavage. Thus, thin films of polypropylene crystallized at different pressure and as a function of polypropylene concentration were investigated. The objective was to probe the nucleation and chain organization in thin films on basal plane surface from the view point of relating the nucleation and growth process to the intergallery space between the clay layers. The crystal morphology was altered from leaf-like structure at high undercooling to fully developed spherulites at low undercooling. Furthermore, the lamellae structure change from well-oriented to cross-hatched with increase in the crystallization pressure was indicative of epitaxial growth between polymer matrix and mica surface. The possible epitaxial mechanism is discussed here. The study provides a method to explore the macro- and microstructure of polymer and epitaxy between polymer matrix and inorganic particle surface. The good interfacial bonding favored by epitaxial crystallization is beneficial for toughness.

  9. 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.)

  10. Energetically favorable sites of iodine atoms in zirconium crystal: an ab-initio approach

    International Nuclear Information System (INIS)

    This paper is devoted to the determination of the energetically favorable sites of iodine atoms in zirconium crystal within the density functional framework and using norm-conserving pseudopotentials. We show that the substitutional sites are preferentially occupied compared to the interstitial ones. Our conclusion is that the diffusion process of iodine in site zirconium is of substitutional type in perfect agreement with an experimental study. (authors)

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. High resolution electron imaging system for sub-micron sized metastable atom beams produced by Stern Gerlach interferometry

    Science.gov (United States)

    Milosavljevic, A. R.; Bocvarski, V.; Jureta, J.; Marinkovic, B. P.; Karam, J.-C.; Grucker, J.; Perales, F.; Vassilev, G.; Reinhardt, J.; Robert, J.; Baudon, J.

    2005-10-01

    The method of modulating an atom beam profile by an immaterial magnetic mask generated in a Stern-Gerlach interferometer is recalled. A special magnetic configuration aimed at producing a single central bright interference fringe (atomic spot) was used. The effects of velocity spread, source coherence and source size on the limiting spot size at large values of the magnetic gradient are discussed. The observation of such small sizes requires a high spatial resolution of the position-sensitive detector. A new electron optical device is described, which images the secondary electron source generated by the impact of the atomic beam on a metallic electrode (detection in real time). Magnifications as high as 65 are accessible, leading to a better than 100 nm resolution of the atomic beam profile when a position-sensitive detector of a few µm resolution is used. Geometric and chromatic aberrations are discussed and, according to simulations, they do not significantly deteriorate the resolution.

  20. 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

  1. 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

  2. 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.

  3. 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. PMID:26751171

  4. 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.

  5. 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

  6. Atomic resolution scanning tunneling microscopy in a cryogen free dilution refrigerator at 15 mK

    Energy Technology Data Exchange (ETDEWEB)

    Haan, A. M. J. den, E-mail: arthur.denhaan@gmail.com; Wijts, G. H. C. J.; Galli, F.; Oosterkamp, T. H. [Department of Interface Physics, Leiden University, Niels Bohrweg 2, 2333CA Leiden (Netherlands); Usenko, O. [Leiden Cryogenics, Kenauweg 11, 2331BA Leiden (Netherlands); Baarle, G. J. C. van; Zalm, D. J. van der [Leiden Spin Imaging (LSI), J.H. Oortweg 21, 2333CH Leiden (Netherlands)

    2014-03-15

    Pulse tube refrigerators are becoming more common, because they are cost efficient and demand less handling than conventional (wet) refrigerators. However, a downside of a pulse tube system is the vibration level at the cold-head, which is in most designs several micrometers. We implemented vibration isolation techniques which significantly reduced vibration levels at the experiment. These optimizations were necessary for the vibration sensitive magnetic resonance force microscopy experiments at milli-kelvin temperatures for which the cryostat is intended. With these modifications we show atomic resolution scanning tunneling microscopy on graphite. This is promising for scanning probe microscopy applications at very low temperatures.

  7. Atomic resolution scanning tunneling microscopy in a cryogen free dilution refrigerator at 15 mK.

    Science.gov (United States)

    den Haan, A M J; Wijts, G H C J; Galli, F; Usenko, O; van Baarle, G J C; van der Zalm, D J; Oosterkamp, T H

    2014-03-01

    Pulse tube refrigerators are becoming more common, because they are cost efficient and demand less handling than conventional (wet) refrigerators. However, a downside of a pulse tube system is the vibration level at the cold-head, which is in most designs several micrometers. We implemented vibration isolation techniques which significantly reduced vibration levels at the experiment. These optimizations were necessary for the vibration sensitive magnetic resonance force microscopy experiments at milli-kelvin temperatures for which the cryostat is intended. With these modifications we show atomic resolution scanning tunneling microscopy on graphite. This is promising for scanning probe microscopy applications at very low temperatures. PMID:24689625

  8. Atomic resolution STM in a cryogen free dilution refrigerator at 15 mK

    CERN Document Server

    Haan, A M J den; Galli, F; Usenko, O; van Baarle, G J C; van der Zalm, D J; Oosterkamp, T H

    2013-01-01

    Pulse tube refrigerators are becoming more common, because they are cost efficient and demand less handling than conventional (wet) refrigerators. However, a downside of a pulse tube system is the vibration level at the cold-head, which is in most designs several micrometers. We implemented vibration isolation techniques which significantly reduced vibration levels at the experiment. These optimizations were necessary for the vibration sensitive Magnetic Resonance Force Microscopy experiments (MRFM) at milli-kelvin temperatures for which the cryostat is intended. With these modifications we show atomic resolution STM on graphite. This is promising for scanning probe microscopy applications at very low temperatures.

  9. Atomic resolution scanning tunneling microscopy in a cryogen free dilution refrigerator at 15 mK

    International Nuclear Information System (INIS)

    Pulse tube refrigerators are becoming more common, because they are cost efficient and demand less handling than conventional (wet) refrigerators. However, a downside of a pulse tube system is the vibration level at the cold-head, which is in most designs several micrometers. We implemented vibration isolation techniques which significantly reduced vibration levels at the experiment. These optimizations were necessary for the vibration sensitive magnetic resonance force microscopy experiments at milli-kelvin temperatures for which the cryostat is intended. With these modifications we show atomic resolution scanning tunneling microscopy on graphite. This is promising for scanning probe microscopy applications at very low temperatures

  10. Atomic resolution scanning tunneling microscopy in a cryogen free dilution refrigerator at 15 mK

    Science.gov (United States)

    den Haan, A. M. J.; Wijts, G. H. C. J.; Galli, F.; Usenko, O.; van Baarle, G. J. C.; van der Zalm, D. J.; Oosterkamp, T. H.

    2014-03-01

    Pulse tube refrigerators are becoming more common, because they are cost efficient and demand less handling than conventional (wet) refrigerators. However, a downside of a pulse tube system is the vibration level at the cold-head, which is in most designs several micrometers. We implemented vibration isolation techniques which significantly reduced vibration levels at the experiment. These optimizations were necessary for the vibration sensitive magnetic resonance force microscopy experiments at milli-kelvin temperatures for which the cryostat is intended. With these modifications we show atomic resolution scanning tunneling microscopy on graphite. This is promising for scanning probe microscopy applications at very low temperatures.

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

    DEFF Research Database (Denmark)

    Stern, Stephan; Holmegaard, Lotte; Filsinger, Frank;

    2014-01-01

    We give a detailed account of the theoretical analysis and the experimental results of an x-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac 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....

  12. 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.

  13. 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...

  14. 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.

  15. 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

  16. 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 ...

  17. 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

  18. 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

  19. 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.

  20. Nanoscale capacitance imaging with attofarad resolution using ac current sensing atomic force microscopy

    International Nuclear Information System (INIS)

    Nanoscale capacitance imaging with attofarad resolution (∼1 aF) of a nano-structured oxide thin film, using ac current sensing atomic force microscopy, is reported. Capacitance images are shown to follow the topographic profile of the oxide closely, with nanometre vertical resolution. A comparison between experimental data and theoretical models shows that the capacitance variations observed in the measurements can be mainly associated with the capacitance probed by the tip apex and not with positional changes of stray capacitance contributions. Capacitance versus distance measurements further support this conclusion. The application of this technique to the characterization of samples with non-voltage-dependent capacitance, such as very thin dielectric films, self-assembled monolayers and biological membranes, can provide new insight into the dielectric properties at the nanoscale

  1. 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.

  2. 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.

  3. 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...

  4. 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

  5. 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.

  6. 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.

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

    International Nuclear Information System (INIS)

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

  8. 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.

  9. 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.

  10. 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....

  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. 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

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

    International Nuclear Information System (INIS)

    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

  14. 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.)

  15. 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

  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. 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

  19. Single-crystal diamond pyramids: synthesis and application for atomic force microscopy

    Science.gov (United States)

    Tuyakova, Feruza T.; Obraztsova, Ekaterina A.; Ismagilov, Rinat R.

    2016-03-01

    Here we present the results of investigations aimed at the development and testing of robust, chemically inert single-crystal diamond probes for atomic force microscopy (AFM). The probes were prepared by assembling common silicon probes with micrometer-sized pyramid-shaped single-crystal diamonds (SCD). The SCD were obtained by the selective thermal oxidation of the polycrystalline films grown by chemical vapor deposition. Electrostatic spray of adhesive coating onto silicon probes was used to attach individual SCD. Geometrical parameters of produced AFM SCD probes were revealed with transmission electron microscopy: the apex angle of the pyramidal diamond crystallite was ˜10 deg, and the curvature radius at the apex was ˜2 to 10 nm. The diamond AFM probes were used for surface imaging of deoxyribonucleic acid deposited on graphite substrate. Obtained results demonstrate high efficiency of the diamond AFM probes, allowing improvement of the image quality compared to standard silicon probes.

  20. 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.

  1. 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

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

    Science.gov (United States)

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

    2016-01-01

    A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data. PMID:26697868

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-10-19

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

  4. Role of current profiles and atomic force microscope tips on local electric crystallization of amorphous silicon

    Czech Academy of Sciences Publication Activity Database

    Verveniotis, Elisseos; Rezek, Bohuslav; Šípek, Emil; Stuchlík, Jiří; Kočka, Jan

    2010-01-01

    Roč. 518, č. 21 (2010), s. 5965-5970. ISSN 0040-6090 R&D Projects: GA ČR GD202/09/H041; GA MŠk(CZ) LC06040; GA AV ČR KAN400100701; GA MŠk LC510 Institutional research plan: CEZ:AV0Z10100521 Keywords : amorphous materials * atomic force microscopy (AFM) * conductivity * crystallization * nanostructures * silicon * nickel Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.909, year: 2010

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

    Science.gov (United States)

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

    1986-01-01

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

  6. 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.

  7. 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)

  8. Characterization of the (0001) cleavage surface of antimony single crystals using scanning probe microscopy: Atomic structure, vacancies, cleavage steps, and twinned interlayers

    Science.gov (United States)

    Stegemann, Bert; Ritter, Claudia; Kaiser, Bernhard; Rademann, Klaus

    2004-04-01

    Atomically resolved scanning tunneling microscopy images of the unreconstructed hexagonal structure of surface atoms on Sb(0001) are presented. Lateral and vertical lattice parameters have been determined. The interatomic spacing of 4.31 Å (±0.05 Å) on the Sb(0001) surface corresponds to the known bulk data. Cleavage has been found to occur always between adjacent double layers, yielding at least diatomic cleavage steps of 3.75 Å (±0.10 Å) height. Different kinds of defect structures on the cleavage plane have been imaged with atomic resolution. Point defects, caused by a single or by three missing surface atoms, have been uncovered. Stable imaging of cleavage steps, which were found to be straight along the atomic rows, has been achieved. Twinned interlayers formed upon cleavage of Sb even at room temperature have been revealed by atomic force microscopy. The mean twinning angle of 2.42° (±0.20°) is quantitatively in accord with the value of 2.45° predicted by the model of twinning in Sb crystals. The observed features are discussed with respect to other layered materials and with regard to their relevance for the use of Sb(0001) as a support of nanostructures.

  9. 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.

  10. 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

  11. Subwavelength resolution in a two-dimensional photonic-crystal-based superlens.

    Science.gov (United States)

    Cubukcu, E; Aydin, K; Ozbay, E; Foteinopoulou, S; Foteinopolou, S; Soukoulis, C M

    2003-11-14

    We experimentally and theoretically demonstrate single-beam negative refraction and superlensing in the valence band of a two-dimensional photonic crystal operating in the microwave regime. By measuring the refracted electromagnetic waves from a slab shaped photonic crystal, we find a refractive index of -1.94 that is very close to the theoretical value of -2.06. A scanning transmission measurement technique is used to measure the spatial power distribution of the focused electromagnetic waves that radiate from a point source. The full width at half maximum of the focused beam is measured to be 0.21 lambda, which is in good agreement with the finite difference time domain method simulations. We also report a subwavelength resolution for the image of two incoherent point sources, which are separated by a distance of lambda/3. PMID:14683392

  12. Spectroscopic Properties of Neodymium-Doped Yttrium Orthovanadate Single Crystals with High-Resolution Measurement

    Science.gov (United States)

    Sato, Yoichi; Taira, Takunori

    2002-10-01

    The absorption and fluorescence spectra of the neodymium-doped yttrium orthovanadate (Nd:YVO4) single crystal were investigated carefully. For the 808.8-nm absorption cross section, the published values varied between 18.4 and 25.6 × 10-20 cm2 for π-polarization. The authors evaluated this spectroscopic parameter with high resolution at 0.5 nm, and discovered 48.4 cm-1 at 808.8 nm even for the absorption of 1 at.% Nd3+-ion-doped YVO4 single crystal. This value is 1.3 times larger than the well-known value, and confirms that Nd:YVO4 is very suitable for microchip lasers, and that certain laser characteristics of Nd:YVO4 of previous works should be re-evaluated.

  13. 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

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

    Science.gov (United States)

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

    2012-06-14

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

  15. 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.

  16. Effects of dislocations and crystal defects on the energy resolution and response uniformity of mercuric iodide detectors

    Energy Technology Data Exchange (ETDEWEB)

    Randtke, P.T.; Ortale, C.

    1977-02-01

    The energy resolution and response uniformity of HgI/sub 2/ detectors to nuclear radiation depends strongly on dislocation density and distribution in the HgI/sub 2/ crystal bulk. Several large planar detectors fabricated from the interiors of large single crystals verified this dependence. Scanning with collimated low-energy (6 keV) and medium-energy (60 keV) gamma-rays confirmed the association of poor resolution and counting efficiency with regions of high dislocation density and crystal imperfection.

  17. Effects of dislocations and crystal defects on the energy resolution and response uniformity of mercuric iodide detectors

    International Nuclear Information System (INIS)

    The energy resolution and response uniformity of HgI2 detectors to nuclear radiation depends strongly on dislocation density and distribution in the HgI2 crystal bulk. Several large planar detectors fabricated from the interiors of large single crystals verified this dependence. Scanning with collimated low-energy (6 keV) and medium-energy (60 keV) gamma-rays confirmed the association of poor resolution and counting efficiency with regions of high dislocation density and crystal imperfection

  18. Effects of dislocations and crystal defects on the energy resolution and response uniformity of mercuric iodide detectors

    Energy Technology Data Exchange (ETDEWEB)

    Randtke, P.T.; Ortale, C.

    1976-01-01

    The energy resolution and response uniformity of HgI/sub 2/ detectors to nuclear radiation depends strongly on dislocation density and distribution in the HgI/sub 2/ crystal bulk. Several large planar detectors fabricated from the interiors of large single crystals verified this dependence. Scanning with collimated low-energy (6 keV) and medium-energy (60 keV) gamma-rays confirmed the association of poor resolution and counting efficiency with regions of high dislocation density and crystal imperfection.

  19. 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.

  20. 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.

  1. High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method

    International Nuclear Information System (INIS)

    Using the high-pressure cryocooling method, the high-resolution X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. This is the first ultra-high-resolution structure obtained from a high-pressure cryocooled crystal. Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005 ▶) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method

  2. High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method

    Energy Technology Data Exchange (ETDEWEB)

    Higashiura, Akifumi, E-mail: hgsur-a@protein.osaka-u.ac.jp [Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Ohta, Kazunori; Masaki, Mika; Sato, Masaru [Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505 (Japan); Inaka, Koji [Maruwa Foods and Biosciences Inc., Nara 639-1123 (Japan); Tanaka, Hiroaki [Confocal Science Inc., Tokyo 101-0032 (Japan); Nakagawa, Atsushi [Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan)

    2013-11-01

    Using the high-pressure cryocooling method, the high-resolution X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. This is the first ultra-high-resolution structure obtained from a high-pressure cryocooled crystal. Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005 ▶) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

  3. Influence of the atomic structure of crystal surfaces on the surface diffusion in medium temperature range

    International Nuclear Information System (INIS)

    In this work, we have studied the influence of atomic structure of crystal surface on surface self-diffusion in the medium temperature range. Two ways are followed. First, we have measured, using a radiotracer method, the self-diffusion coefficient at 820 K (0.6 T melting) on copper surfaces both the structure and the cleanliness of which were stable during the experiment. We have shown that the interaction between mobile surface defects and steps can be studied through measurements of the anisotropy of surface self diffusion. Second, the behavior of an adatom and a surface vacancy is simulated via a molecular dynamics method, on several surfaces of a Lennard Jones crystal. An inventory of possible migration mechanisms of these surface defects has been drawn between 0.35 and 0.45 Tsub(m). The results obtained with both the methods point out the influence of the surface atomic structure in surface self-diffusion in the medium temperature range

  4. 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 ...

  5. Control of spontaneous emission from a microwave-field-driven four-level atom in an anisotropic photonic crystal

    International Nuclear Information System (INIS)

    The spontaneous emission properties of a microwave-field-driven four-level atom embedded in anisotropic double-band photonic crystals (PCs) are investigated. We discuss the influences of the band-edge positions, Rabi frequency and detuning of the microwave field on the emission spectrum. It is found that several interesting features such as spectral-line enhancement, spectral-line suppression, spectral-line overlap, and multi-peak structures can be observed in the spectra. The proposed scheme can be achieved by use of a microwave-coupled field into hyperfine levels in rubidium atom confined in a photonic crystal. These theoretical investigations may provide more degrees of freedom to manipulate the atomic spontaneous emission. -- Highlights: ► Spontaneous emission properties of an atom embedded in PCs are investigated. ► Spectral-line enhancement, suppression and overlapping are observed. ► The results provide more degrees of freedom to control atomic spontaneous emission.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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%.

  11. Lattice location and annealing behaviour of helium atoms implanted in uranium dioxide single crystals

    Science.gov (United States)

    Belhabib, T.; Desgardin, P.; Sauvage, T.; Erramli, H.; Barthe, M. F.; Garrido, F.; Carlot, G.; Nowicki, L.; Garcia, P.

    2015-12-01

    Helium behaviour in irradiated uranium dioxide may play an important role in the mechanical stability of nuclear fuels during and after its use in nuclear power plants. Helium migration mechanisms in bulk UO2 have already been the subject of theoretical studies but there is a lack of experimental data relating to the most stable location in the crystal. To this end, we have studied uranium dioxide samples implanted with helium ions at low fluence before and after thermal annealing in the range 600 and 800 °C. UO2 single crystals were implanted with 50 keV-3He ions at the fluence of 1 × 1015 at cm-2 and the location in the lattice of helium atoms was investigated using NRA (Nuclear Reaction Analysis) based on the reaction of 3He with deuterons (3He (d,p) 4He) in a channelling mode, recording angular scans across axes and planes. Furthermore, the uranium sub-lattice was analysed by the classical RBS method. After implantation, the experimental angular scans recorded across the main crystallographic axes and along major planes show that the helium atoms in their large majority occupy octahedral interstitial sites. No modification of the occupied crystallographic site was found after annealing at 600 °C. Conversely, no crystallographic relationship between matrix and helium signals was revealed following annealing at 800 °C. The latter feature is likely related to the clustering of implanted helium atoms into gas-filled bubbles. These experimental results have been quantified and interpreted using Monte Carlo simulations with the McChasy code.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. Atomic resolution imaging of oxygen atoms close to heavy atoms by HRTEM and ED, using the superconductor SmFeAsO0.85F0.15 as an example.

    Science.gov (United States)

    Wang, Yumei; Ge, Binghui; Che, Guangcan

    2015-04-01

    Imaging of light atoms has always been a challenge in high-resolution electron microscopy. Image resolution is mainly limited by lens aberrations, especially the spherical aberration of the objective lens. Image deconvolution could correct for the image distortion by lens aberrations and restore the structure projection, the resolution of which is limited by the information limit of the microscope. Electron diffraction unrestricted by lens aberrations could overcome this resolution limit. Here we show a combination of electron diffraction and image deconvolution to reveal simultaneously the atomic columns of O and considerably heavier Sm at a very close distance (1.17 Å) in iron-based superconductor SmFeAsO0.85F0.15 using a conventional 200 kV electron microscope. The approach used here, starting from an image and an electron diffraction pattern, has an advantage for those radiation-sensitive samples. Besides, it can be applied to simultaneously imaging light and heavy atoms, even though they have a big difference in atomic number and a much smaller atomic distance than the microscope resolution. PMID:25635603

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

    Czech Academy of Sciences Publication Activity Database

    Campbellová, A.; Ondráček, Martin; Pou, P.; Pérez, R.; Klapetek, P.; Jelínek, Pavel

    2011-01-01

    Roč. 22, č. 29 (2011), 295710/1-295710/7. ISSN 0957-4484 R&D Projects: GA AV ČR IAA100100905; GA ČR GAP204/10/0952; GA ČR(CZ) GPP204/11/P578 Grant ostatní: AVČR(CZ) M100100904 Institutional research plan: CEZ:AV0Z10100521 Keywords : density functional theory * atomic force microscope * semiconductor surface * sub- atomic resolution Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.979, year: 2011 http://iopscience.iop.org/0957-4484/22/29/295710

  18. New crystal structure of the proteasome-dedicated chaperone Rpn14 at 1.6 Å resolution

    International Nuclear Information System (INIS)

    A new crystal structure of yeast Rpn14 with an E384A mutation was determined at 1.6 Å resolution. The improved high-resolution structure provides a framework for understanding proteasome assembly. The 26S proteasome is an ATP-dependent protease responsible for selective degradation of polyubiquitylated proteins. Recent studies have suggested that proteasome assembly is a highly ordered multi-step process assisted by specific chaperones. Rpn14, an assembly chaperone for ATPase-ring formation, specifically recognizes the ATPase subunit Rpt6. The structure of Rpn14 at 2.0 Å resolution in space group P64 has previously been reported, but the detailed mechanism of Rpn14 function remains unclear. Here, a new crystal structure of Rpn14 with an E384A mutation is presented in space group P21 at 1.6 Å resolution. This high-resolution structure provides a framework for understanding proteasome assembly

  19. 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

  20. Thermodynamics and kinetic behaviors of thickness-dependent crystallization in high-k thin films deposited by atomic layer deposition

    International Nuclear Information System (INIS)

    Atomic layer deposition is adopted to prepare HfO2 and Al2O3 high-k thin films. The HfO2 thin films are amorphous at the initial growth stage, but become crystallized when the film thickness (h) exceeds a critical value (hcritical*). This phase transition from amorphous to crystalline is enhanced at higher temperatures and is discussed, taking into account the effect of kinetic energy. At lower temperatures, the amorphous state can be maintained even when h>hcritical* owing to the small number of activated atoms. However, the number of activated atoms increases with the temperature, allowing crystallization to occur even in films with smaller thickness. The Al2O3 thin films, on the other hand, maintain their amorphous state independent of the film thickness and temperature owing to the limited number of activated atoms. A thermodynamic model is proposed to describe the thickness-dependent phase transition

  1. 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.

  2. 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

  3. A Phenylnorstatine Inhibitor Binding to HIV-1 Protease: Geometry, Protonation, and Subsite-Pocket Interactions Analyzed at Atomic Resolution

    Czech Academy of Sciences Publication Activity Database

    Brynda, Jiří; Řezáčová, Pavlína; Fábry, Milan; Hořejší, Magdalena; Štouračová, Renata; Sedláček, Juraj; Souček, Milan; Hradilek, Martin; Lepšík, Martin; Konvalinka, Jan

    2004-01-01

    Roč. 47, č. 8 (2004), s. 2030-2036. ISSN 0022-2623 Grant ostatní: V.program EU(XE) QLRI-2000-02360 Institutional research plan: CEZ:AV0Z5052915 Keywords : inhibitor * HIV protease * atomic resolution Subject RIV: CE - Biochemistry Impact factor: 5.076, year: 2004

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

    DEFF Research Database (Denmark)

    Brodersen, Ditlev Egeskov; Etzerodt, Michael; Madsen, Peder Søndergaard; Thøgersen, Hans Christian; Celis, J. E.; Nyborg, Jens; Kjeldgaard, Morten

    1998-01-01

    holmium-substituted psoriasin has been determined by multiple anomalous wavelength dispersion (MAD) phasing and refined to atomic resolution (1.05 A). The structure represents the most accurately determined structure of a calcium-binding protein. Although the overall structure of psoriasin is similar to...

  5. 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

  6. 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.

  7. 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.

  8. High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence

    Science.gov (United States)

    Heggelund, Julie Elisabeth; Burschowsky, Daniel; Bjørnestad, Victoria Ariel; Hodnik, Vesna; Anderluh, Gregor; Krengel, Ute

    2016-01-01

    Cholera is the prime example of blood-group-dependent diseases, with individuals of blood group O experiencing the most severe symptoms. The cholera toxin is the main suspect to cause this relationship. We report the high-resolution crystal structures (1.1–1.6 Å) of the native cholera toxin B-pentamer for both classical and El Tor biotypes, in complexes with relevant blood group determinants and a fragment of its primary receptor, the GM1 ganglioside. The blood group A determinant binds in the opposite orientation compared to previously published structures of the cholera toxin, whereas the blood group H determinant, characteristic of blood group O, binds in both orientations. H-determinants bind with higher affinity than A-determinants, as shown by surface plasmon resonance. Together, these findings suggest why blood group O is a risk factor for severe cholera. PMID:27082955

  9. Enhanced Transmittance and Resolution of Photonic Crystal Flat Lens by Surface-Edge Engineering

    Science.gov (United States)

    Guo, Hao; Wang, Cancan; Zhang, Peiyuan; Chen, Hongjun; Li, Yun; Wu, Lishu; Zhang, Xiong; Cui, Yiping

    We proposed a novel two-dimensional (2D) photonic crystal (PC) flat lens based on the surface-edge engineering of a PC slab, operating as an n = -1 superlens at λ = 1.55 μm. The cross-section at the truncated edge of the flat lens is similar to an "anti-reflection grating", which is employed to reduce the reflectivity of propagative waves. The PC flat lens with a low reflectance of 1% was realized by the proposed truncated surface-edge for an InP/InGaAsP/InP 2D PC slab. The simulation results obtained with finite-difference time-domain (FDTD) method show that a PC flat super lens with a far-field resolution of 0.41 λ and a high transmittance of 81.9% can be achieved by the engineering of the truncated surface-edge at hetero-interface.

  10. Atoms

    International Nuclear Information System (INIS)

    Completed by recent contributions on various topics (atoms and the Brownian motion, the career of Jean Perrin, the evolution of atomic physics since Jean Perrin, relationship between scientific atomism and philosophical atomism), this book is a reprint of a book published at the beginning of the twentieth century in which the author addressed the relationship between atomic theory and chemistry (molecules, atoms, the Avogadro hypothesis, molecule structures, solutes, upper limits of molecular quantities), molecular agitation (molecule velocity, molecule rotation or vibration, molecular free range), the Brownian motion and emulsions (history and general features, statistical equilibrium of emulsions), the laws of the Brownian motion (Einstein's theory, experimental control), fluctuations (the theory of Smoluchowski), light and quanta (black body, extension of quantum theory), the electricity atom, the atom genesis and destruction (transmutations, atom counting)

  11. 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

  12. 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

  13. 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.

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

    International Nuclear Information System (INIS)

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

  15. About effect of the Ramsauer-Townsend type at scattering of relativistic electrons by crystal atomic string

    International Nuclear Information System (INIS)

    It is shown that a considerable decrease in a total cross-section of the elastic scattering of relativistic electrons by a crystal atomic string can take place at certain values of particle incidence angles. This effect is similar to the Ramsauer-Townsend effect of slow electrons scattering by an atom. It is shown that the decrease in the angle of particles incidence on the atomic string essentially changes the process of particles scattering. The phenomena of the particle rainbow scattering and orbiting may occur in this case. 14 refs., 5 figs

  16. 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

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

    Science.gov (United States)

    Fraile, L. M.; Mach, H.; Vedia, V.; Olaizola, B.; Paziy, V.; Picado, E.; Udías, J. M.

    2013-02-01

    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.

  18. 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.

  19. Switchable liquid-crystal phase-shift mask for super-resolution photolithography based on Pancharatnam-Berry phase

    Science.gov (United States)

    Glazar, Nikolaus; Culbreath, Christopher; Li, Yannian; Yokoyama, Hiroshi

    2015-11-01

    We present a novel liquid-crystal-based phase-shift mask that utilizes the Pancharatnam-Berry phase for super-resolution photolithography. Using an automated maskless photoalignment technique, we pattern an azobenzene alignment layer in a nematic liquid-crystal cell to fabricate the mask. Since the image is formed by phase cancellation, the minimum feature size is not restricted by the diffraction limit; here, we obtain submicron features. The liquid-crystal properties of the cell allow the mask to be switched on and off by applying a voltage. The cost effectiveness and flexibility of this technique make it a promising new technology for photolithography.

  20. A DOI Detector With Crystal Scatter Identification Capability for High Sensitivity and High Spatial Resolution PET Imaging

    OpenAIRE

    Gu, Z; Prout, D. L.; Silverman, R W; Herman, H; Dooraghi, A.; Chatziioannou, A F

    2015-01-01

    A new phoswich detector is being developed at the Crump Institute, aiming to provide improvements in sensitivity, and spatial resolution for PET. The detector configuration is comprised of two layers of pixelated scintillator crystal arrays, a glass light guide and a light detector. The annihilation photon entrance (top) layer is a 48 × 48 array of 1.01 × 1.01 × 7 mm3 LYSO crystals. The bottom layer is a 32 × 32 array of 1.55 × 1.55 × 9 mm3 BGO crystals. A tapered, multiple-element glass ligh...

  1. A new crystal form of human histidine triad nucleotide-binding protein 1 (hHINT1) in complex with adenosine 5′-monophosphate at 1.38 Å resolution

    International Nuclear Information System (INIS)

    The atomic structure of a new crystal form of the human histidine triad nucleotide-binding protein 1 (hHINT1)–AMP complex is reported at 1.38 Å resolution. Histidine triad nucleotide-binding protein 1 (HINT1) represents the most ancient and widespread branch of the histidine triad protein superfamily. HINT1 plays an important role in various biological processes and has been found in many species. Here, the structure of the human HINT1–adenosine 5′-monophosphate (AMP) complex at 1.38 Å resolution obtained from a new monoclinic crystal form is reported. The final structure has Rcryst = 0.1207 (Rfree = 0.1615) and the model exhibits good stereochemical quality. Detailed analysis of the high-resolution data allowed the details of the protein structure to be updated in comparison to the previously published data

  2. 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.)

  3. Calculating Hyperfine Couplings in Large Ionic Crystals Containing Hundreds of QM Atoms: Subsystem DFT is the Key

    CERN Document Server

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

    2013-01-01

    We present an application of the linear scaling Frozen Density Embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfccs) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems considered 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 neither 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 hfccs 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.

  4. 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.

  5. A prototype high-resolution animal positron tomograph with avalanche photodiode arrays and LSO crystals

    International Nuclear Information System (INIS)

    To fully utilize positron emission tomography (PET) as a non-invasive tool for tissue characterization, dedicated instrumentation is being developed which is specially suited for imaging mice and rats. Semiconductor detectors, such as avalanche photodiodes (APDs), may offer an alternative to photomultiplier tubes for the readout of scintillation crystals. Since the scintillation characteristics of lutetium oxyorthosilicate (LSO) are well matched to APDs, the combination of LSO and APDs seems favourable, and the goal of this study was to build a positron tomograph with LSO-APD modules to prove the feasibility of such an approach. A prototype PET scanner based on APD readout of small, individual LSO crystals was developed for tracer studies in mice and rats. The tomograph consists of two sectors (86 mm distance), each comprising three LSO-APD modules, which can be rotated for the acquisition of complete projections. In each module, small LSO crystals (3.7 x 3.7 x 12 mm3) are individually coupled to one channel within matrices containing 2 x 8 square APDs (2.6 x 2.6 mm2 sensitive area per channel). The list-mode data are reconstructed with a penalized weighted least squares algorithm which includes the spatially dependent line spread function of the tomograph. Basic performance parameters were measured with phantoms and first experiments with rats and mice were conducted to introduce this methodology for biomedical imaging. The reconstructed field of view covers 68 mm, which is 80% of the total detector diameter. Image resolution was shown to be 2.4 mm within the whole reconstructed field of view. Using a lower energy threshold of 450 keV, the system sensitivity was 350 Hz/MBq for a line source in air in the centre of the field of view. In a water-filled cylinder of 4.6 cm diameter, the scatter fraction at the centre of the field of view was 16% (450 keV threshold). The count rate was linear up to 700 coincidence counts per second. In vivo studies of anaesthetized

  6. 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))

  7. 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

  8. 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

  9. 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.

  10. 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 ...

  11. 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

  12. Crystallization, high-resolution data collection and preliminary crystallographic analysis of Aura virus capsid protease and its complex with dioxane

    International Nuclear Information System (INIS)

    A 17 kDa capsid protease domain from Aura virus was purified, crystallized together with its complex with dioxane and characterized by the X-ray diffraction method. The C-terminal protease domain of capsid protein from Aura virus expressed in a bacterial expression system has been purified to homogeneity and crystallized. Crystals suitable for X-ray diffraction analysis were obtained by the vapour-diffusion method using 0.1 M bis-tris and polyethylene glycol monomethyl ether 2000. Crystals of the C-terminal protease domain of capsid protein in complex with dioxane were also produced and crystal data were obtained. Both crystals belonged to space group C2, with unit-cell parameters a = 79.6, b = 35.2, c = 49.5 Å. High-resolution data sets were collected to a resolution of 1.81 Å for the native protein and 1.98 Å for the complex. Preliminary crystallographic studies suggested the presence of a single molecule in the crystallographic asymmetric unit, with a solvent content of 38.5%

  13. 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.

  14. 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.

  15. A High Resolution Monolithic Crystal, DOI, MR Compatible, PET Detector. Final-Report

    International Nuclear Information System (INIS)

    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 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.

  16. 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. PMID:27303797

  17. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

    OpenAIRE

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano; Lindorff-Larsen, Kresten; Cerminara, Michele; Santiveri, Clara M.; Shaw, David E.; de Alba, Eva; Muñoz, Victor

    2015-01-01

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex patter...

  18. Development of two-color laser system for high-resolution polarization spectroscopy measurements of atomic hydrogen.

    Science.gov (United States)

    Bhuiyan, A H; Satija, A; Naik, S V; Lucht, R P

    2012-09-01

    We have developed a high-spectral-resolution laser system for two-photon pump, polarization spectroscopy probe (TPP-PSP) measurements of atomic hydrogen in flames. In the TPP-PSP technique, a 243-nm laser beam excites the two-photon 1S-2S transition, and excited n=2 atoms are then detected by polarization spectroscopy of the n=2 to n=3 transition using 656-nm laser radiation. The single-frequency-mode 243 and 656-nm beams are produced using injection-seeded optical parametric generators coupled with pulsed dye amplifiers. The use of single-mode lasers allows accurate measurement of signal line shapes and intensities even with significant pulse-to-pulse fluctuations in pulse energies. Use of single-mode lasers and introduction of a scheme to select nearly constant laser energies enable repeatable extraction of important spectral features in atomic hydrogen transitions. PMID:22940950

  19. 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

  20. 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

  1. Change in the local atomic and crystal structures in a martensitic transformation in TiNiCu shape memory alloys

    International Nuclear Information System (INIS)

    Changes in the local and crystal structures of Ti, Ni, and Cu atoms in Ti50Ni25Cu25 shape memory alloys have been investigated using X-ray diffraction and extended X-ray absorption fine structure spectroscopy (EXAFS) in the temperature range of direct and inverse martensitic transformations. The analysis of the EXAFS spectra shows that the bonds involving Ni atoms have the highest degree of disorder and the change in the local environment of Ni atoms is significant for the occurrence of the shape memory effect, while Cu atoms occupy the normal positions in the crystallographic structure and have the lowest displacement amplitude leading to the stabilization of both phases

  2. 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

  3. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Alloyeau, D.; Nelayah, J.; Wang, G.; Ricolleau, C. [Laboratoire Materiaux et Phenomenes Quantiques, Universite Paris Diderot/CNRS, UMR 7162, Batiment Condorcet, 4 rue Elsa Morante, 75205 Paris Cedex 13 (France); Oikawa, T. [Laboratoire Materiaux et Phenomenes Quantiques, Universite Paris Diderot/CNRS, UMR 7162, Batiment Condorcet, 4 rue Elsa Morante, 75205 Paris Cedex 13 (France); JEOL Ltd, 1-2 Musashino 3-Chome, Akishima, Tokyo 196-8558 (Japan)

    2012-09-17

    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.

  5. 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...

  6. Surface atoms core-level shifts in single crystal GaAs surfaces: Interactions with trimethylaluminum and water prepared by atomic layer deposition

    International Nuclear Information System (INIS)

    The surface As/Ga atoms 3d core-level spectra of the atomically clean GaAs(1 1 1)A-2 × 2, GaAs(0 0 1)-2 × 4, and GaAs(0 0 1)-4 × 6 surfaces were firstly presented using high-resolution synchrotron radiation photoemission as a probe. The technique clearly explicates behaviors of the As atoms in different surface reconstruction. For GaAs(1 1 1)A-2 × 2, the surface As sits in the same plane as the Ga atoms. As to the GaAs(0 0 1)-2 × 4 surface, the As–As dimers dominate the surface layer, while for GaAs(001)-4 × 6, the As existed in two forms, the As in the As–Ga dimer and the 3-fold coordinated As. Next, we present a microscopic view of in situ atomic layer deposition (ALD) of Al2O3 on GaAs taking the two (0 0 1) surfaces as examples. The precursors were trimethylaluminum (TMA) and water. TMA could exist in either a chemisorbed or physisorbed form, depending on the charge environment of the associated surface atoms. The subsequent water purge resulted in both adsorbed forms being etched off or transformed the physisorbed TMA into the As-O-Al(CH3)2 configuration. We found that the ALD process rendered the precursors partially and selectively in forming bonds with the surface atoms without disturbing the atoms in the subsurface layer. Upon annealing, the interfacial bonding was dominated with the As-Al as well as Ga-O bonds.

  7. Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals.

    Science.gov (United States)

    Schnieders, Michael J; Fenn, Timothy D; Pande, Vijay S

    2011-04-12

    Refinement of macromolecular models from X-ray crystallography experiments benefits from prior chemical knowledge at all resolutions. As the quality of the prior chemical knowledge from quantum or classical molecular physics improves, in principle so will resulting structural models. Due to limitations in computer performance and electrostatic algorithms, commonly used macromolecules X-ray crystallography refinement protocols have had limited support for rigorous molecular physics in the past. For example, electrostatics is often neglected in favor of nonbonded interactions based on a purely repulsive van der Waals potential. In this work we present advanced algorithms for desktop workstations that open the door to X-ray refinement of even the most challenging macromolecular data sets using state-of-the-art classical molecular physics. First we describe theory for particle mesh Ewald (PME) summation that consistently handles the symmetry of all 230 space groups, replicates of the unit cell such that the minimum image convention can be used with a real space cutoff of any size and the combination of space group symmetry with replicates. An implementation of symmetry accelerated PME for the polarizable atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field is presented. Relative to a single CPU core performing calculations on a P1 unit cell, our AMOEBA engine called Force Field X (FFX) accelerates energy evaluations by more than a factor of 24 on an 8-core workstation with a Tesla GPU coprocessor for 30 structures that contain 240 000 atoms on average in the unit cell. The benefit of AMOEBA electrostatics evaluated with PME for macromolecular X-ray crystallography refinement is demonstrated via rerefinement of 10 crystallographic data sets that range in resolution from 1.7 to 4.5 Å. Beginning from structures obtained by local optimization without electrostatics, further optimization using AMOEBA with PME electrostatics improved

  8. 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.

  9. 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.

  10. Atomic relocation in ion-bombarded ultra-thin films analyzed with sub-nm spatial resolution

    International Nuclear Information System (INIS)

    The displacement of atoms in a magnetic trilayer Fe (10 nm)/Cr (0.7 nm)/Fe (10 nm) system by 30 keV Ga+ ion irradiation was studied by 3D Atom Probe Tomography (APT). From APT, the positions of individual Cr and Fe atoms could be located with sub-nm spatial resolution, both before and after ion bombardment. In the pristine specimen the presence of the 0.7-nm Cr layer was identified and individual lattice planes with a distance of ∼0.15 nm were observed which would correspond to the monolayer spacing of the Fe lattice, in agreement with the growth process. Upon irradiation, the Cr layer broadens to ∼1.2 nm at a fluence of 3 × 1014 Ga+/cm2 and to ∼3.4 nm at 3 × 1015 Ga+/cm2. From this broadening the mean squared relocation distance of (Cr) atoms was derived, 〈r2〉 ∼0.4 nm2. Computer simulations indicate that, at a fluence of 3 × 1014 Ga+/cm2, each Cr atom in the intermediate layer is displaced on average once in the collision processes. The distribution of implanted Ga ions appears to exhibit discontinuities at the Fe/Cr interfaces which might be caused by a demixing of Ga at the Cr layer

  11. 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.

  12. 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. PMID:26470814

  13. High resolution infrared absorption spectra, crystal field, and relaxation processes in CsCdBr_3:Pr^3+

    OpenAIRE

    Popova, M. N.; Chukalina, E. P.; Malkin, B. Z.; Iskhakova, A. I.; Antic-Fidancev, E.; P Porcher; Chaminade, J.P.

    2000-01-01

    High resolution low-temperature absorption spectra of 0.2% Pr^3+ doped CsCdBr_3 were measured in the spectral region 2000--7000 cm-1. Positions and widths of the crystal field levels within the 3H5, 3H4, 3F2, and 3F3 multiplets of the Pr^3+ main center have been determined. Hyperfine structure of several spectral lines has been found. Crystal field calculations were carried out in the framework of the semiphenomenological exchange charge model (ECM). Parameters of the ECM were determined by f...

  14. 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.

  15. Tapping-mode atomic force microscopy produces faithful high-resolution images of protein surfaces.

    OpenAIRE

    Möller, C; Allen, M.; Elings, V; Engel, A.; Müller, D J

    1999-01-01

    Compared to contact-mode atomic force microscopy (CMAFM), tapping-mode atomic force microscopy (TMAFM) has the advantage of allowing imaging surfaces of macromolecules, even when they are only weakly attached to the support. In this study, TMAFM is applied to two different regular protein layers whose structures are known to great detail, the purple membrane from Halobacterium salinarum and the hexagonally packed intermediate (HPI) layer from Deinococcus radiodurans, to assess the faithfulnes...

  16. 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.

  17. 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.

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

    International Nuclear Information System (INIS)

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

  19. 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

  20. 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

  1. 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. PMID:26491820

  2. 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.

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

    Science.gov (United States)

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

    2015-06-01

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

  4. 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.

  5. 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.

  6. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations.

    Science.gov (United States)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano; Lindorff-Larsen, Kresten; Cerminara, Michele; Santiveri, Clara M; Shaw, David E; de Alba, Eva; Muñoz, Victor

    2015-05-27

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue-residue couplings associated with cooperative folding emerges. Such thermodynamic residue-residue couplings appear to be linked to the order of mechanistically significant events that take place during the folding process. Our results on gpW indicate that the methods employed in this study are likely to prove broadly applicable to the fine analysis of folding mechanisms in fast folding proteins. PMID:25924808

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

    OpenAIRE

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

    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...

  8. 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.

  9. A Phenylnorstatine Inhibitor Binding to HIV-1 Protease: Geometry, Protonation and Subsite-Pocket Interactions Analyzed at Atomic Resolution

    Czech Academy of Sciences Publication Activity Database

    Brynda, Jiří; Řezáčová, Pavlína; Fábry, Milan; Hořejší, Magdalena; Štouračová, Renata; Sedláček, Juraj; Souček, Milan; Hradilek, Martin; Lepšík, Martin; Konvalinka, Jan

    Praha : Czech and Slovak Crystallographic Association, 2004 - (Kužel, R.; Hašek, J.; Fiala, J.; Weiss, Z.), s. 62 ISSN 1211-5894. - (Bulletin of the Czech and Slovak Crystallographic Association.. 11). [Meeting of the Czech and Slovak structural biologists /3./. Nové hrady (CZ), 11.03.2004-13.03.2004] R&D Projects: GA MŠk OE67/1 Institutional research plan: CEZ:AV0Z5052915 Keywords : inhibitor * HIV protease * atomic resolution Subject RIV: CE - Biochemistry

  10. Atomic-resolution STM study of a structural phase transition of steps on vicinal As/Ge(100)

    International Nuclear Information System (INIS)

    Scanning tunneling microscope images of arsenic-exposed vicinal Ge(100) surfaces show that most As/Ge steps are reconstructed and that a variety of different step structures exist. The entire family of reconstructed As/Ge steps can be divided into two types, which we have chosen to call ''single-row'' (SR) steps and ''double-row'' (DR) steps. By changing the sample preparation conditions, we are able to consistently change the ratio of SR/DR steps. In other words, we have observed a structural phase transition in the reconstruction of As/Ge steps at atomic resolution. (c) 1999 The American Physical Society

  11. A photonic crystal realization of a phase driven two-level atom

    CERN Document Server

    Rodríguez-Lara, B M; Soto-Eguibar, Francisco; Moya-Cessa, Héctor Manuel

    2012-01-01

    We propose a set of photonic crystals that realize a nonlinear quantum Rabi model equivalent to a two-level system driven by the phase of a quantized electromagnetic field. The crystals are exactly soluble in the weak-coupling regime and their dispersion relation is discrete. The system is diagonalized by normal modes equivalent to a dressed state basis. In the strong-coupling regime, we use perturbation theory and find that the dispersion relation is continuous and give the normal modes of the crystal in terms of continued fractions. We show that these photonic crystals allow state reconstruction in the form of coherent oscillations in the weak-coupling regime.

  12. Probing the antibody-catalyzed water-oxidation pathway at atomic resolution

    OpenAIRE

    Zhu, Xueyong; Wentworth, Paul; Wentworth, Anita D.; Eschenmoser, Albert; Lerner, Richard A.; Wilson, Ian A.

    2004-01-01

    Antibodies can catalyze the generation of hydrogen peroxide (H2O2) from singlet dioxygen (1O*2) and water via the postulated intermediacy of dihydrogen trioxide (H2O3) and other trioxygen species. Nine different crystal structures were determined to elucidate the chemical consequences to the antibody molecule itself of exposure to such reactive intermediates and to provide insights into the location on the antibody where these species could be generated. Herein, we report structural evidence ...

  13. 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\\.

  14. 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

  15. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Friedman, E., E-mail: elifried@cc.huji.ac.il [Racah Institute of Physics, The Hebrew University, 91904 Jerusalem (Israel); Okada, S. [RIKEN Nishina Center, RIKEN, Wako 351-0198 (Japan)

    2013-10-03

    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{sup −}–nucleon interaction in the nuclear medium.

  17. 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.

  18. 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

  19. 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.

  20. 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...

  1. 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

  2. Three-dimensional evaluation of gettering ability for oxygen atoms at small-angle tilt boundaries in Czochralski-grown silicon crystals

    International Nuclear Information System (INIS)

    Three-dimensional distribution of oxygen atoms at small-angle tilt boundaries (SATBs) in Czochralski-grown p-type silicon ingots was investigated by atom probe tomography combined with transmission electron microscopy. Oxygen gettering along edge dislocations composing SATBs, post crystal growth, was observed. The gettering ability of SATBs would depend both on the dislocation strain and on the dislocation density. Oxygen atoms would agglomerate in the atomic sites under the tensile hydrostatic stress larger than about 2.0 GPa induced by the dislocations. It was suggested that the density of the atomic sites, depending on the tilt angle of SATBs, determined the gettering ability of SATBs

  3. 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...

  4. [Determination of aluminum in wheat flour food by microwave digestion-high resolution continuum source graphite furnace atomic absorption spectrometry].

    Science.gov (United States)

    Ren, Ting; Zhao, Li-jiao; Zhong, Ru-gang

    2011-12-01

    The contents of aluminum (Al) in four kinds of wheat flour food (noodle, dumpling wrapper, twisted cruller and soda biscuit) were determined by high resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS GFAAS) combined with microwave digestion. The samples were completely digested by the mixture of HNO3 and H2O2 in closed polytetrafluoroethylene (PTFE) vessels. The conditions for microwave digestion, pyrolysis temperature and atomization temperature were optimized. The optimum experimental conditions were determined as follows. The microwave digestion was performed with HNO3/H2O2 7:1 (volume ratio), microwave power 1000 W and 190 degrees C for 40 minutes. The optimum pyrolysis temperature was 1350 degrees C and the optimum atomization temperature was 2400 degrees C. Magnesium nitrate solution with the concentration of 1 g x L(-1) was used as the matrix modifier. The correlation coefficient for the standard curve was 0.9999, the relative standard deviation (RSD) was from 1.7% to 2.4%, and the recovery for the samples was from 98.16% to 102.67%. The assay method for the determination of Al in wheat flour food established in this study has referential importance for the constituent of the correlated food standards. PMID:22295801

  5. Direct determination of P in biodiesel by high-resolution continuum source graphite furnace atomic absorption spectrometry

    International Nuclear Information System (INIS)

    The direct determination of P in biodiesel by high-resolution continuum source graphite furnace atomic absorption spectrometry has been investigated. A slow drying stage proved to be essential for good repeatability. Optimization was performed by a D optimal planning. The atomization temperature and modifier composition were the most relevant parameters. Thus, using a mixture of Pd (30 μg) and Mg(NO3)2 (20 μg) as the modifier, previously deposited onto the platform of the graphite tube and dried, a five step drying stage, and pyrolysis and atomization temperatures of 1000 and 2700 deg. C, respectively, a limit of detection of 0.5 μg g-1 was obtained. The analysis of biodiesel of different origins confirmed that external calibration with organic P standard solutions, diluted in P-free biodiesel, could be used. In this way, excellent agreement between the found and expected results was observed in the analysis of an ANP interlaboratorial exercise sample.

  6. 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...

  7. Acoustic Imaging of Ferroelectric Domains in BaTiO3 Single Crystals Using Atomic Force Microscope

    Science.gov (United States)

    Zeng, Huarong; Shimamura, Kiyoshi; Kannan, Chinna Venkadasamy; Villora, Encarnacion G.; Takekawa, Shunji; Kitamura, Kenji; Yin, Qingrui

    2007-01-01

    An “alternating-force-modulated” atomic force microscope (AFM) operating in the acoustic mode, generated by launching acoustic waves on the piezoelectric transducer that is attached to the cantilever, was used to visualize the ferroelectric domains in barium titanate (BaTiO3) single crystals by detecting acoustic vibrations generated by the tip and transmitted through the sample placed beneath it to the transducer. The acoustic signal was found to reflect locally elastic microstructures at low frequencies, while high-frequency acoustic images revealed strip like domain configurations of internal substructures in BaTiO3 single crystals. The underlying acoustic imaging mechanism using the AFM was discussed in terms of the interaction between the excited acoustic wave and ferroelectric domains.

  8. Thermal annealing and recoil reactions of 128I atoms in thermal neutron activated iodate-nitrate mixed crystals

    International Nuclear Information System (INIS)

    Recoil reaction of 128I atoms in neutron irradiated mixed crystals (iodate-nitrate) have been studied by thermal annealing methods. The retention of 128I (i.e. radioactivity of 128I retained in the parent chemi cal form) decreases sharply in the beginning and then attains saturation value with the increase in concentration of nitrate. The annealing followed the usual characteristic pattern, viz., a steep rise in retention within the first few minutes and then a saturation value thereafter but these saturation values in case of mixed crystals are lower in comparison to those of pure iodate targets. The process obeys simple first order kinetics and the activation energy obtained are of lower order than those obtained in case of pure targets. The results are discussed in the light of present ideas and the role of nitrate ion and its radiolytic products have also been invoked. (author)

  9. Integrated reflectivity measurements of hydrogen phthalate crystals for high-resolution soft x-ray spectroscopy

    International Nuclear Information System (INIS)

    The integrated x-ray reflectivity of Potassium Hydrogen Phthalate (KAP) and Rubidium Hydrogen Phthalate (RAP) crystals is studied at a photon energy of (1740±14) eV using a double-crystal setup. The absolute measured reflectivities are in < 5% agreement with the values predicted by the dynamic diffraction theory for perfect crystals when absorption is included. Within 4% experimental error margins, specimen that were exposed to ambient conditions over many years show identical reflectivity as specimen that were cleaved just before the measurement. No differences are observed between cleaving off a 10 μm surface layer and splitting the entire crystal bulk of 2 mm thickness. We conclude that at 1.7 keV photon energy the penetration depth of ∼ 1 μm is large compared to a potentially deteriorated surface layer of a few 10 nm

  10. 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.

  11. Probe integrated scattering cross sections in the analysis of atomic resolution HAADF STEM images

    International Nuclear Information System (INIS)

    The physical basis for using a probe-position integrated cross section (PICS) for a single column of atoms as an effective way to compare simulation and experiment in high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) is described, and the use of PICS in order to make quantitative use of image intensities is evaluated. It is based upon the calibration of the detector and the measurement of scattered intensities. Due to the predominantly incoherent nature of HAADF STEM, it is found to be robust to parameters that affect probe size and shape such as defocus and source coherence. The main imaging parameter dependencies are on detector angle and accelerating voltage, which are well known. The robustness to variation in other parameters allows for a quantitative comparison of experimental data and simulation without the need to fit parameters. By demonstrating the application of the PICS to the chemical identification of single atoms in a heterogeneous catalyst and in thin, layered-materials, we explore some of the experimental considerations when using this approach. - Highlights: • Probe-position integrated cross section (PICS) used to quantitatively compare experimental images of HAADF STEM to simulations. • Theoretical treatment based on the object function approximation is presented. • PICS shown to be robust to experimental parameters. • Considerations for accuracy of experimental analysis and simulations discussed. • Application of PICS analysis to low dimensional, beam sensitive samples show excellent agreement between experiment and simulations

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

    OpenAIRE

    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-centered-cubic (fcc) ordering of spherical voids in the inverse opal-like structure with unit cell dimension of 750±10nm. The diffuse scattering data were used to map defects in the fcc structure as a f...

  13. 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

  14. Confocal and Atomic Force Microscopies of Color Centers Produced by Ultrashort Laser Irradiation in LiF Crystals

    Science.gov (United States)

    Courrol, Lilia Coronato; Martinez, Oscar; Samad, Ricardo Elgul; Gomes, Laércio; Ranieri, Izilda Márcia; Baldochi, Sonia Licia; de Freitas, Anderson Zanardi; Junior, Nilson Dias Vieira

    2008-04-01

    We report properties of the spatial and spectral distribution of color centers produced in LiF single crystals by ultrashort high intensity laser pulses (60 fs, 10 GW) using confocal spectral microscopy and atomic force microscopy. We could identify a large amount of F centers that gave rise to aggregates such as F2, F4, F2+ and F3+ distributed in cracked shape brownish areas. We have taken a 3D image using confocal microscopy of the sample (luminescent image) and no difference is observed in the different planes. The atomic force microscopy image clearly shows the presence of defects on the modified surface. The formation of micrometer or sub-micrometer voids, filaments and void strings was observed and related to filamentation process.

  15. Comparison of Process of Diffusion of Interstitial Oxygen Atoms and Interstitial Hydrogen Molecules in Silicon and Germanium Crystals: Quantumchemical Simulation

    OpenAIRE

    Gusakov, Vasilii

    2006-01-01

    The theoretical analysis of the process of diffusion of interstitial oxygen atoms and hydrogen molecules in silicon and germanium crystals has been performed. The calculated values of the activation energy and pre-exponential factor for an interstitial oxygen atom Ea(Si) = 2.59 eV, Ea(Ge) = 2.05 eV, D(Si)= 0.28 cm2s-1, D(Ge)= 0.39 cm2s-1 and interstitial hydrogen molecule Ea(Si) = 0.79-0.83 eV, Ea(Ge) = 0.58-0.62 eV, D(Si)= 7.4 10(-4) cm2s-1, D(Ge)= 6.5 10(-4) cm2s-1 are in an excellent agree...

  16. 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).

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

    Science.gov (United States)

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

    2016-07-01

    The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped (3)He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambers are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001). PMID:27475560

  18. 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).

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  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. Application of atomic layer deposited microchannel plates to imaging photodetectors with high time resolution

    International Nuclear Information System (INIS)

    Novel microchannel plates have been constructed using borosilicate glass micro-capillary array substrates with 20 µm and 10 µm pores and coated with resistive, and secondary electron emissive, layers by atomic layer deposition. Microchannel plates in 33 mm, 50 mm and 20 cm square formats have been made and tested. Although their amplification, imaging, and timing properties are comparable to standard glass microchannel plates, the background rates and lifetime characteristics are considerably improved. Sealed tube detectors based on the Planacon tube, and a 25 mm cross delay line readout tube with a GaN(Mg) opaque photocathode deposited on borosilicate microchannel plates have been fabricated. Considerable progress has also been made with 20 cm microchannel plates for a 20 cm format sealed tube sensor with strip-line readout that is being developed for Cherenkov light detection

  3. Application of atomic layer deposited microchannel plates to imaging photodetectors with high time resolution

    Energy Technology Data Exchange (ETDEWEB)

    Siegmund, O.H.W., E-mail: ossy@ssl.berkeley.edu [Experimental Astrophysics Group, Space Sciences Laboratory, 7 Gauss Way, University of California, Berkeley, CA 94720 (United States); McPhate, J.B.; Tremsin, A.S.; Vallerga, J.V.; Ertley, C.D.; Richner, N.J.; Gerard, T.M. [Experimental Astrophysics Group, Space Sciences Laboratory, 7 Gauss Way, University of California, Berkeley, CA 94720 (United States); Frisch, H.J. [University of Chicago, 5640 S. Ellis Ave., Chicago, Il 60637 (United States); Elam, J.W.; Mane, A.U.; Wagner, R.G. [Argonne National Laboratory, 9700 S. Cass Ave. Lemont, Il 60439 (United States); Minot, M.J.; O' Mahony, A.; Craven, C.A. [Incom Inc., 294 Southbridge Road, Charlton, MA, 01507 (United States)

    2015-07-01

    Novel microchannel plates have been constructed using borosilicate glass micro-capillary array substrates with 20 µm and 10 µm pores and coated with resistive, and secondary electron emissive, layers by atomic layer deposition. Microchannel plates in 33 mm, 50 mm and 20 cm square formats have been made and tested. Although their amplification, imaging, and timing properties are comparable to standard glass microchannel plates, the background rates and lifetime characteristics are considerably improved. Sealed tube detectors based on the Planacon tube, and a 25 mm cross delay line readout tube with a GaN(Mg) opaque photocathode deposited on borosilicate microchannel plates have been fabricated. Considerable progress has also been made with 20 cm microchannel plates for a 20 cm format sealed tube sensor with strip-line readout that is being developed for Cherenkov light detection.

  4. 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.

  5. High-resolution transmission electron microscopy of crystal structures, defects, surface and interfaces in bismuth-based superconductors

    International Nuclear Information System (INIS)

    Since the discovery of high Tc superconductors many investigations have been performed to clarify the origin of the superconductivity. The High-Resolution Transmission Electron Microscopy is one of the most effective instruments to obtain more information and understanding of the superconducting mechanism of oxide superconductors. This paper reviews and discusses the result of studies on Bi-Sr-Ca-Cu-O superconductors which have been performed at the Japanese National Institute for Research in Inorganic Materials. Special attention has been paid to crystal structures, defects, surfaces and interfaces of examined samples. (author). 19 refs, 9 figs

  6. Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution.

    OpenAIRE

    Johnston, S. C.; Larsen, C N; Cook, W.J.; Wilkinson, K. D.; Hill, C. P.

    1997-01-01

    Ubiquitin C-terminal hydrolases catalyze the removal of adducts from the C-terminus of ubiquitin. We have determined the crystal structure of the recombinant human Ubiquitin C-terminal Hydrolase (UCH-L3) by X-ray crystallography at 1.8 A resolution. The structure is comprised of a central antiparallel beta-sheet flanked on both sides by alpha-helices. The beta-sheet and one of the helices resemble the well-known papain-like cysteine proteases, with the greatest similarity to cathepsin B. This...

  7. 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

  8. Enhance the resolution of photonic crystal negative refraction imaging by metal grating.

    Science.gov (United States)

    Shi, Peng; Huang, Kun; Li, Yong-ping

    2012-02-01

    The resolution of imaging is limited by the missing of high-frequencies information. The superlens employing negative refraction can compensate for these components. But for the directional coupling of Bloch waves and the low coupling efficiency of large-angle waves, the resolution of subwavelength imaging is not satisfactory. However, the subwavelength metallic grating can produce high-order diffracted waves carrying a lot of high-frequencies information. Therefore, this structure is used to inhibit the zero-order diffraction and enhance the high-order diffraction to achieve super-resolution. PMID:22297352

  9. 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...

  10. Relaxed atomic structure of the interphase boundary in a heterosystem of semi-spherical nanoparticles - crystal

    International Nuclear Information System (INIS)

    The structure of a fcc(001) interphase boundary in a nickel hemispherical crystal nanoparticle - palladium crystal substrate system is investigated as a function of the angle of rotation of the nanoparticle. Relaxation transformations are found to occur in a component of the system under investigation with a larger lattice parameter. It is demonstrated that the annealing leaves the location of large islands virtually unchanged but brings about a rotation of small nanoparticles into a parallel orientation or an orientation with a local energy minimum

  11. 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.

  12. High-resolution optical spectroscopy of Os-with a view to laser cooling of atomic anions

    Science.gov (United States)

    Kellerbauer, Alban; Fritzsche, Stephan

    2012-11-01

    Atomic anions are generally not amenable to optical spectroscopy because they are loosely bound systems and rarely have bound excited states. Until recently, there was only one known negative ion with a strong bound-bound electronic transition, the osmium anion Os-. The electric-dipole transition between the 4Fe9/2 ground and 6DoJ excited state of this ion provides unique insight into the structure of atomic anions. In addition, it may enable the preparation of ultracold ensembles of negative ions. Laser excitation of the electric-dipole transition in Os- ions could be used to laser-cool them to microkelvin temperatures. If demonstrated to be successful, the technique would allow the cooling of any species of negatively charged ions - from subatomic particles to molecular anions - to ultracold temperatures by sympathetic cooling. We have been investigating the bound-bound electric-dipole transition in Os- by high-resolution laser spectroscopy with a view to using it for the first laser cooling of negative ions. The principle of the method, its potential applications, as well as experimental results are presented.

  13. 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.

  14. 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

  15. 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...

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

    Science.gov (United States)

    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, A. V.; Grigoriev, S. V.

    2014-10-01

    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-centered-cubic (fcc) ordering of spherical voids in the inverse opal-like structure with unit cell dimension of 750±10nm. The diffuse scattering data were used to map defects in the fcc structure as a function of the number of layers in the Ni inverse opal-like structure. The average lateral size of mesoscopic domains is found to be independent of the number of layers. 3D reconstruction of the reciprocal space for the inverse opal crystals with different thickness provided an indirect study of original opal templates in a depth-resolved way. The microstructure and thermal response of the framework of the porous inverse opal crystal was examined using wide-angle powder x-ray diffraction. This artificial porous structure is built from nickel crystallites possessing stacking faults and dislocations peculiar for the nickel thin films.

  17. Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes.

    Science.gov (United States)

    Birmanns, Stefan; Rusu, Mirabela; Wriggers, Willy

    2011-03-01

    We describe an integrated software system called Sculptor that combines visualization capabilities with molecular modeling algorithms for the analysis of multi-scale data sets. Sculptor features extensive special purpose visualization techniques that are based on modern GPU programming and are capable of representing complex molecular assemblies in real-time. The integration of graphics and modeling offers several advantages. The user interface not only eases the usually steep learning curve of pure algorithmic techniques, but it also permits instant analysis and post-processing of results, as well as the integration of results from external software. Here, we implemented an interactive peak-selection strategy that enables the user to explore a preliminary score landscape generated by the colors tool of Situs. The interactive placement of components, one at a time, is advantageous for low-resolution or ambiguously shaped maps, which are sometimes difficult to interpret by the fully automatic peak selection of colors. For the subsequent refinement of the preliminary models resulting from both interactive and automatic peak selection, we have implemented a novel simultaneous multi-body docking in Sculptor and Situs that softly enforces shape complementarities between components using the normalization of the cross-correlation coefficient. The proposed techniques are freely available in Situs version 2.6 and Sculptor version 2.0. PMID:21078392

  18. 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

  19. 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.)

  20. Investigation of the crystallization features, atomic structure, and microstructure of chromium-doped monticellite

    International Nuclear Information System (INIS)

    A series of Cr4+:CaMgSiO4 single crystals is grown using floating zone melting, and their microstructure, composition, and crystal structure are investigated. It is shown that regions with inclusions of second phases, such as forsterite, akermanite, MgO, and Ca4Mg2Si3O12, can form over the length of the sample. The composition of the single-phase regions of the single crystals varies from the stoichiometric monticellite CaMgSiO4 to the solid solution Ca(1-x)Mg(1+x)SiO4(x = 0.22). The Cr:(Ca0.88Mg0.12)MgSiO4 crystal is studied using X-ray diffraction. It is revealed that, in this case, the olivine-like orthorhombic crystal lattice is distorted to the monoclinic lattice with the parameters a = 6.3574(5) A, b = 4.8164(4) A, c = 11.0387(8) A, β = 90.30(1)o, Z = 4, V = 337.98 A3, and space group P21/c. In the monoclinic lattice, the M(1) position of the initial olivine structure is split into two nonequivalent positions with the center of symmetry, which are occupied only by Mg2+ cations with the average length of the Mg-O bond Rav = 2.128 A. The overstoichiometric Mg2+ cations partially replace Ca2+ cations (in the M(2) position of the orthorhombic prastructure) with the average bond length of 2.347 A in the [(Ca,Mg)-O6] octahedron. The average distance in SiO4 distorted tetrahedra is 1.541 A.

  1. Impact on the Spatial Resolution Performance of a Monolithic Crystal PET Detector Due to Different Sensor Parameters.

    Science.gov (United States)

    Li, Xiaoli; Lockhart, Cate; Lewellen, Tom K; Miyaoka, Robert S

    2009-10-24

    The performance characteristics of a monolithic crystal PET detector utilizing a novel sensor on the entrance surface (SES) design is reported. To facilitate this design, we propose to utilize a 2D silicon photomultiplier (SiPM) array device. SiPMs are a form of Geiger-Muller mode avalanche photodiodes (GMAPD) that can provide signal gain similar to a photomultiplier tube (PMT). Since these devices are still under active development, their performance parameters are changing. Using a multi-step simulation process, we investigated how different SiPM parameters affect the performance of a monolithic crystal PET detector. These parameters include gain variability between different channels; gain instability; and dark count noise. The detector simulated was a 49.6 mm by 49.6 mm by 15 mm LYSO crystal detector readout by a 16 by 16 array of 2.8 mm by 2.8 mm SiPM elements. To reduce the number of signal channels that need to be collected, the detector utilizes row-column summing. A statistics based positioning method is used for event positioning and depth of interaction (DOI) decoding. Of the variables investigated, the dark count noise had the largest impact on the intrinsic spatial resolution. Gain differences of 5-10% between detector calibration and detector testing had a modest impact on the intrinsic spatial resolution performance and led to a slight bias in positioning. There was no measurable difference with a gain variability of up to 25% between the individual SiPM channels. Based upon these results we are planning to cool our detectors below room temperature to reduce dark count noise and to actively control the temperature of the SiPMs to reduce drifts in gain over time. PMID:20806058

  2. Time resolution study of staged photomultiplier with a plastic scintillation crystal

    International Nuclear Information System (INIS)

    The time resolution of a plastic scintillator mounted onto an Rca 8575 staged photomultiplier has been measured using a fast-fast coincidence technique. A new and accurate procedure for the walk adjustment is employed. The time calibration (≤ 2 psec/channel) has been performed using the two sources method. A best time resolution of 200 ± 0.329 psec(FWHM) at 1.3 MeV is also obtained. A detailed descriptions of the walk adjustment and the time calibration are give which ensure reproducibility of the time resolution within a few psec. Application of this technique in the measurement of short lifetime using a delayed coincidence system is illustrated in measuring the lifetime of the 570 keV level IR207 Pb. 6 fig

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. Laser crystallization of amorphous silicon films investigated by Raman spectroscopy and atomic force microscopy

    International Nuclear Information System (INIS)

    The intrinsic and phosphorous (P)-doped hydrogenated amorphous silicon thin films were crystallized by laser annealing. The structural properties during crystallization process can be investigated. Observed redshifts of the Si Raman transverse optical phonon peak indicate tensile stress present in the films and become intense with the effect of doping, which can be relieved in P-doped films by introducing buffer layer structures. Based on experimental results, the established correlation between the stress and crystalline fraction (XC) suggests that the relatively high stress can limit the increase in XC and the highest crystalline fraction is obtained by a considerable stress release. At high laser energy density of 1250 mJ/cm2, the poorer crystalline quality and disordered structure of the film originating from the irradiation damage and defects lead to the low electron mobility.

  8. A high resolution electromagnetic calorimeter based on lead-tungstate crystals

    Czech Academy of Sciences Publication Activity Database

    Aleksandrov, D. V.; Burachas, S.F.; Ippolitov, M.S.; Mareš, Jiří A.; Polák, Karel

    2005-01-01

    Roč. 550, - (2005), s. 169-184. ISSN 0168-9002 Institutional research plan: CEZ:AV0Z10100521 Keywords : PbWO 3 * high resolution electromagnetic calorimeter Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.224, year: 2005

  9. 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...

  10. 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.

  11. 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 ...

  12. Matter Waves in Reduced Dimensions: Dipolar-Induced Resonances and Atomic Artificial Crystals

    OpenAIRE

    Bartolo, Nicola

    2014-01-01

    The experimental achievement of Bose-Einstein condensation and Fermi degeneracy with ultracold gases boosted tremendous progresses both in theoretical methods and in the development of new experimental tools. Among them, intriguing possibilities have been opened by the implementation of optical lattices: periodic potentials for neutral atoms created by interfering laser beams. Degenerate gases in optical lattices can be forced in highly anisotropic traps, reducing the effective dimensionality...

  13. Damage creation in silicon single crystals irradiated with 200 keV/atom Aun+ clusters

    International Nuclear Information System (INIS)

    Silicon wafers of (1 0 0) orientation were irradiated with Aun cluster beams (1≤n≤7) produced by the 2.5 MV Van de Graaff accelerator of the Institut de Physique Nucleaire de Lyon equipped with a liquid metal source. The incident energy was of 200 keV per gold atom, which corresponds to a slowing-down mainly governed by elastic processes (nuclear energy loss of Au+ ions: 3 keV nm-1). All the irradiations were performed at room temperature with fluences up to 5x1014 Au (at. cm-2). The typical beam currents varied from 1.5 nA for Au+ down to 20 pA for Au7+. The radiation-induced disorder was measured by means of Rutherford backscattering spectrometry in channeling geometry (RBS-C), using a 4He+ beam accelerated at 2 MV. From the fluence evolution of the lattice disorder at the target surface, we evidence that polyatomic projectiles produce more defects per incident atom than single Au+ ions. As an example we measured damage cross-sections per incident Au atom of 12.5 and 2.7 nm2 for Au7+ and Au+ projectiles, respectively. This cluster effect was ascribed to the high density of nuclear energy deposited within the cascade. Transmission electron microscopy (TEM) was performed on samples irradiated at low fluences (109 at. cm-2) in order to visualize each projectile impact

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Concentration methods for high-resolution THz spectroscopy of nucleic-acid biomolecules and crystals

    Science.gov (United States)

    Brown, E. R.; Zhang, W.; Mendoza, E. A.; Kuznetsova, Y.; Brueck, S. R. J.; Rahman, M.; Norton, M. L.

    2012-03-01

    Biomolecules can exhibit low-lying vibrational modes in the THz region which are detectable in transmission given a strong molecular dipole moment and optical depth, and a spectrometer of adequate sensitivity. The nucleic acids are particularly interesting because of applications such as label-free gene assay, bio-agent detection, etc. However for nucleic acids, sample preparation and THz coupling are of paramount importance because of the strong absorption by liquid water and the small concentration of molecules present in physiological solutions. Concentration methods become necessary to make the THz vibrational modes detectable, either by concentrating the nucleic-acid sample itself in a small volume but large area, or by concentrating the THz radiation down to the volume of the sample. This paper summarizes one type of the first method: nanofluidic channel arrays for biological nucleic acids; and two types of the second method: (1) a circular-waveguide pinhole, and (2) a circular-waveguide, conical-horn coupling structure, both for DNA crystals. The first method has been demonstrated on a very short artificial nucleic acid [small-interfering (si) RNA (17-to-25 bp)] and a much longer, biological molecule [Lambda-phage DNA (48.5 kbp)]. The second method has been demonstrated on small (~100 micron) single crystals of DNA grown by the sitting-drop method.

  19. Crystal Dynamics of (delta) fcc Pu-Ga by High Resolution Inelastic X-Ray Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Wong, J; Krisch, M; Farber, D; Occelli, F; Xu, R; Chiang, T C; Clatterbuck, D; Schwartz, A J; Wall, M; Boro, C

    2004-09-28

    We have used a microbeam on large grain sample concept to carry out an inelastic x-ray scattering experiment to map the full phonon dispersion curves of an fcc {delta}-phase Pu-Ga alloy. This approach obviates experimental difficulties with conventional inelastic neutron scattering due to the high absorption cross section of the common {sup 239}Pu isotope and the non-availability of large (mm size) single crystal materials for Pu and its alloys. A classical Born von-Karman force constant model was used to model the experimental results, and no less than 4th nearest neighbor interactions had to be included to account for the observation. Several unusual features including, a large elastic anisotropy, a small shear elastic modulus, (C{sub 11}-C{sub 12})/2, a Kohn-like anomaly in the T{sub 1}[011] branch, and a pronounced softening of the T[111] branch towards the L point in the Brillouin are found. These features can be related to the phase transitions of plutonium and to strong coupling between the crystal structure and the 5f valence instabilities. Our results represent the first full phonon dispersions ever obtained for any Pu-bearing material, thus ending a 40-year quest for this fundamental data. The phonon data also provide a critical test for theoretical treatments of highly correlated 5f electron systems as exemplified by recent dynamical mean field theory (DMFT) calculations for {delta}-plutonium.

  20. Determination of cobalt in biological samples by line-source and high-resolution continuum source graphite furnace atomic absorption spectrometry using solid sampling or alkaline treatment

    International Nuclear Information System (INIS)

    Two procedures for the determination of Co in biological samples by graphite furnace atomic absorption spectrometry (GF AAS) were compared: solid sampling (SS) and alkaline treatment with tetramethylammonium hydroxide (TMAH) using two different instruments for the investigation: a conventional line-source (LS) atomic absorption spectrometer and a prototype high-resolution continuum source atomic absorption spectrometer. For the direct introduction of the solid samples, certified reference materials (CRM) were ground to a particle size ≤50 μm. Alkaline treatment was carried out by placing about 250 mg of the sample in polypropylene flasks, adding 2 mL of 25% m/v tetramethylammonium hydroxide and de-ionized water. Due to its unique capacity of providing a 3-D spectral plot, a high-resolution continuum source (HR-CS) graphite furnace atomic absorption spectrometry was used as a tool to evaluate potential spectral interferences, including background absorption for both sample introduction procedures, revealing that a continuous background preceded the atomic signal for pyrolysis temperatures lower than 700 deg. C. Molecular absorption bands with pronounced rotational fine structure appeared for atomization temperatures >1800 deg. C probably as a consequence of the formation of PO. After optimization had been carried out using high resolution continuum source atomic absorption spectrometry, the optimized conditions were adopted also for line-source atomic absorption spectrometry. Six biological certified reference materials were analyzed, with calibration against aqueous standards, resulting in agreement with the certified values (according to the t-test for a 95% confidence level) and in detection limits as low as 5 ng g-1

  1. High-Resolution Imaging of Plasmid DNA in Liquids in Dynamic Mode Atomic Force Microscopy Using a Carbon Nanofiber Tip

    Science.gov (United States)

    Kitazawa, Masashi; Ito, Shuichi; Yagi, Akira; Sakai, Nobuaki; Uekusa, Yoshitugu; Ohta, Ryo; Inaba, Kazuhisa; Hayashi, Akari; Hayashi, Yasuhiko; Tanemura, Masaki

    2011-08-01

    To understand the motion of DNA and DNA complexes, the real-time visualization of living DNA in liquids is quite important. Here, we report the high-resolution imaging of plasmid DNA in water using a rapid-scan atomic force microscopy (AFM) system equipped with a carbon nanofiber (CNF) probe. To achieve a rapid high-resolution scan, small SiN cantilevers with dimensions of 2 (width) × 0.1 (thickness) × 9 µm (length) and a bent end (tip view structure) were employed as base cantilevers onto which single CNFs were grown. The resonant frequencies of the cantilever were 1.5 MHz in air and 500 kHz in water, and the spring constant was calculated to be 0.1 N/m. Single CNFs, typically 88 nm in length, were formed on an array of the cantilevers in a batch process by the ion-irradiation method. An AFM image of a plasmid DNA taken in water at 0.2 fps (5 s/image) using a batch-fabricated CNF-tipped cantilever clearly showed the helix turns of the double strand DNA. The average helical pitch measured 3.4 nm (σ: 0.5 nm), which was in good agreement with that determined by the X-ray diffraction method, 3.4 nm. Thus, it is presumed that the combined use of the rapid-scan AFM system with the ion-induced CNF probe is promising for the dynamic analysis of biomolecules.

  2. 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.

  3. 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...

  4. Local atomic disordering by high-density electronic excitation in spinel crystal

    International Nuclear Information System (INIS)

    The atomic disordering in magnesium aluminate spinel irradiated with 200 MeV Xe14+ or 350 MeV Au28+ was examined quantitatively by electron channeling X-ray spectroscopy of analytical TEM. The structure of ion tracks keeps spinel structure, but it was indicated that cation were randomly disordered. The radius of the disordered region by the single swift heavy ion was estimated about 6.0 nm, which was larger than the radius of ion tracks estimated by TEM observation. (author)

  5. 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

  6. 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.

  7. Quartz crystal microbalance study of tungsten atomic layer deposition using WF6 and Si2H6

    International Nuclear Information System (INIS)

    The atomic layer deposition (ALD) of tungsten can be accomplished using sequential exposures of WF6 and Si2H6 (disilane). In this paper, W ALD is explored using in situ quartz crystal microbalance (QCM) measurements as a function of the reactant exposure and deposition temperature. The QCM measurements revealed that the WF6 reaction is self-limiting. In contrast, W ALD growth rates exhibited a slow and continual increase for disilane exposures > 4 x 104 L. The W ALD growth rate was also weakly temperature-dependent with an activation energy of 1.5 ± 0.1 kcal/mol at T 275 deg. C. The QCM results and previous Auger results for W ALD yield the relationship between the silicon coverage deposited during the Si2H6 exposure and the tungsten coverage deposited during the WF6 exposure. The W/Si atomic ratio of ∼ 1:1 is consistent with earlier Auger investigations of the surface chemistry during W ALD at 200 deg. C. The QCM measurements are also consistent with silicon coverages of 1.7-2.1 monolayers after the Si2H6 exposures. These high silicon coverages are believed to result by silylene insertion from Si2H6 into surface Si-H bonds

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

    International Nuclear Information System (INIS)

    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 ≤ 400 kcps per channel. We selected Ce-doped (Lu,Y)2(SiO4)O (Ce:LYSO) and a 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.

  9. 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.

  10. 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

  11. 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

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

    International Nuclear Information System (INIS)

    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 ΔλInstr and the absorption line width ΔλAbs, 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.

  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. PMID:26598693

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. Surface-aligned photochemistry: Aiming reactive oxygen atoms along a single crystal surface

    International Nuclear Information System (INIS)

    Surface-aligned photo-oxidation of CO with O2 was demonstrated on two stepped surfaces, Pt(335) and Pt(779). UV light photolysis of O2, localized exclusively on step sites, generates reactive oxygen atoms which oxidize preferentially the step-site CO. This effect was observed by monitoring labeled-CO consumption from step and terrace sites by reflection-absorption infrared spectroscopy, and also by monitoring labeled-CO2 desorbed in the gas phase from step and terrace sites by mass spectrometry. Photo-oxidation of step-CO was found to be about 2 times more efficient than photo-oxidation of terrace-CO, irrespective of the surface step density. This effect was attributed to the initial alignment of the O2 intramolecular axis on stepped Pt surfaces, parallel to the step edge. (c) 2000 American Institute of Physics

  2. 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.

  3. High-resolution electron microscope study of lamellar boundaries in Ti-rich TiAl polysynthetically twinned crystals

    International Nuclear Information System (INIS)

    The lamellar structure of Ti-rich TiAl has been investigated on an atomistic scale by high-resolution electron microscopy (HREM). The interfaces studied include those of TiAlsub([1anti 10])/ TiAlsub([0anti 10]), TiAlsub([1anti 1])/TiAlsub([01anti 1]), TiAlsub([1anti 10])/TiAlsub([01anti 1]), TiAlsub([1anti 10])/ Ti3Alsub([11anti 20]) and TiAlsub([01anti 1])/TiAlsub([11anti 20]). Interfaces between differently oriented TiAl variants are atomistically flat except for the presence of ledges two (111)TiAl planes high, and in most cases contain no Ti3Al phase. Interfaces between TiAl and Ti3Al are also atomistically flat and perfectly coherent but contain somewhat more ledges two (111)TiAl planes high. Close examination of HREM images taken at TiAlsub([1anti 10])/TiAlsub([11anti 20]) interfaces has revealed that the atomic rows composed of Ti atoms only are aligned across the interface between the two phases. The formation mechanism of the lamellar structure are the factors governing the ductility of TiAl are briefly discussed based on the results obtained. (orig.)

  4. Statistical distribution of single atoms and clusters of supported Au catalyst analyzed by global high-resolution HAADF-STEM observation with morphological image-processing operation.

    Science.gov (United States)

    Yamamoto, Yuta; Arai, Shigeo; Esaki, Akihiko; Ohyama, Junya; Satsuma, Atsushi; Tanaka, Nobuo

    2014-06-01

    We have developed a quantitative particle size analytical method at the single atomic level employing electron microscopy and image processing for the investigation of supported metal catalysts. In the present study, a supported gold (Au) catalyst containing sub-nano clusters and individual atoms was globally observed by high-resolution high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) using spherical aberration (Cs)-corrected TEM. To fully extract structural information of the Au clusters and individual atoms from the HAADF-STEM images, a morphological image-processing operation was applied. The resulting mean particle size was in good agreement with particle sizes estimated from average information provided by X-ray absorption fine structure analysis. It is demonstrated that the present HAADF-STEM image analysis gives a quantitative particle size distribution measurement of supported Au clusters and individual atoms. PMID:24489113

  5. 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.

    2016-01-01

    The norepinephrine pathway is believed to modulate behavioral and physiological processes, such as mood, overall arousal, and attention. Furthermore, abnormalities in the pathway have been linked to numerous diseases, for example hypertension, depression, anxiety, Parkinson’s disease, schizophrenia, Alzheimer’s disease, attention deficit hyperactivity disorder, and cocaine dependence. We report the crystal structure of human dopamine β-hydroxylase, which is the enzyme converting dopamine to norepinephrine. The structure of the DOMON (dopamine β-monooxygenase N-terminal) domain, also found in >1600 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.

  6. X-ray diffraction analysis of LiCu{sub 2}O{sub 2} crystals with additives of silver atoms

    Energy Technology Data Exchange (ETDEWEB)

    Sirotinkin, V. P., E-mail: irotinkin.vladimir@mail.ru; Bush, A. A.; Kamentsev, K. E. [Moscow State Technical University of Radio Engineering, Electronics, and Automation (Russian Federation); Dau, H. S. [People’s Friendship University of Russia (Russian Federation); Yakovlev, K. A. [Moscow State Technical University of Radio Engineering, Electronics, and Automation (Russian Federation); Tishchenko, E. A. [People’s Friendship University of Russia (Russian Federation)

    2015-09-15

    Silver-containing LiCu{sub 2}O{sub 2} crystals up to 4 × 8 × 8 mm in size were grown by the crystallization of 80(1-x)CuO · 20{sub x}AgNO{sub 3} · 20Li{sub 2}CO{sub 3} (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 LiCu{sub 2}O{sub 2} 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 LiCu{sub 2}O{sub 2} rhombic unit cell, a slight increase in parameter a, and a slight decrease in parameter b.

  7. 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.

  8. 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. PMID:27219352

  9. 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

  10. 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.

  11. A HIGH-RESOLUTION STUDY OF THE ATOMIC HYDROGEN IN CO-RICH EARLY-TYPE GALAXIES

    International Nuclear Information System (INIS)

    We present an analysis of new and archival Very Large Array H I observations of a sample of 11 early-type galaxies rich in CO, with detailed comparisons of CO and H I distributions and kinematics. The early-type sample consists of both lenticular and elliptical galaxies in a variety of environments. A range of morphologies and environments were selected in order to give a broader understanding of the origins, distribution, and fate of the cold gas in early-type galaxies. Six of the eleven galaxies in the sample are detected in both H I and CO. The H2 to H I mass ratios for this sample range from 0.2 to 120. The H I morphologies of the sample are consistent with that of recent H I surveys of early-type galaxies, which also find a mix of H I morphologies and masses, low H I peak surface densities, and a lack of H I in early-type galaxies that reside in high-density environments. The HI-detected galaxies have a wide range of H I masses (1.4 × 106 to 1.1 × 1010 M☉). There does not appear to be any correlation between the H I mass and morphology (E versus S0). When H I is detected, it is centrally peaked—there are no central kiloparsec-scale central H I depressions like those observed for early-type spiral galaxies at similar spatial resolutions and scales. A kinematic comparison between the H I and CO indicates that both cold gas components share the same origin. The primary goal of this and a series of future papers is to better understand the relationship between the atomic and molecular gas in early-type galaxies, and to compare the observed relationships with those of spiral galaxies where this relationship has been studied in depth.

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

    International Nuclear Information System (INIS)

    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. - Highlights: • Three-dimensional atomic structural reconstruction demonstrated using simulated diffraction data in a tilt series. • Using diffraction patterns allows alignment free tomography reconstruction. • This method can be applied to general image based tomography by using the power spectra of the images as input. • Reconstruction is based on an iterative transformation algorithm (ITA) using polar fast Fourier transform. • The ITA algorithm is accelerated using graphics processing unit (GPU) for competitive high performance

  13. 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...

  14. 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...

  15. 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 in the...

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. High-resolution absorption spectrum of atomic calcium in the vicinity of the 4p 2P1/2,3/2 thresholds

    International Nuclear Information System (INIS)

    The absorption spectrum of atomic Ca has been observed photographically in the wavelength region between 1410-1330 A with the high-resolution spectrograph at the Photon Factory. Complex structures of the observed spectrum just below the 4p 2P1/2 threshold are found to be well reproduced by the recent ab-initio calculation done by Kim and Greene. (orig.)

  1. Effect of the accumulation of excess Ni atoms in the crystal structure of the intermetallic semiconductor n-ZrNiSn

    International Nuclear Information System (INIS)

    The crystal structure, electron density distribution, and energy, kinetic, and magnetic properties of the n-ZrNiSn intermetallic semiconductor heavily doped with a Ni impurity are investigated. The effect of the accumulation of an excess number of Ni1+x atoms in tetrahedral interstices of the crystal structure of the semiconductor is found and the donor nature of such structural defects that change the properties of the semiconductor is established. The results obtained are discussed within the Shklovskii-Efros model of a heavily doped and strongly compensated semiconductor

  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. 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.

  6. Determination of total mercury for marine environmental monitoring studies by solid sampling continuum source high resolution atomic absorption spectrometry

    International Nuclear Information System (INIS)

    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

  7. 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.

  8. Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state

    International Nuclear Information System (INIS)

    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

  9. 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.

  10. The non-proportional response of NaI(Tl) to γ-rays and electrons and its effect upon the crystal resolution

    International Nuclear Information System (INIS)

    Measurements have been made of the scintillation efficiency (light output L, per unit energy input, E) for γ-rays absorbed in NaI(Tl) crystals. The results were sufficiently accurate to allow the evaluation of dL/dE for γ-rays and hence to demonstrate the variation of dL/dE with density of ionization along the path of the photo-electrons ejected by the primary γ-rays. The resolution of a crystal for the total absorption of γ-rays was shown to vary in a similar way to previously published results. Experiments indicated that variations throughout a crystal in the efficiency of light collection do not appreciably affect the resolution. Owing to the non-proportional response of NaI(Tl) to electrons, the light output resulting from the total absorption of a γ-ray varies according to the number and energy of electrons amongst which its energy is distributed. Approximate calculations show that this effect makes a considerable contribution to the anomalous crystal resolution. (author)

  11. 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

  12. 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.

  13. 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.

  14. 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.; Larsen, K.; Berthet-Colominas, C.; Leberman, R.; Beijer, B.; Sproat, B.; Als-Nielsen, J.; Grübel, G.; Legrand, J.-F.; Lehmann, M.; Cusack, S.

    1994-01-01

    crystal from adenosine triphosphate (ATP) and serine hydroxamate, and the second is with a synthetic analog of seryl adenylate (5'-O-[N-(L-seryl)-sulfamoyl]adenosine), which is a strong inhibitor of the enzyme. Both molecules are bound in a similar fashion by a network of hydrogen bond interactions in a......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 in the...

  15. The relationship between crystal growth and defect structure: a study of potassium hydrogen phthalate using x-ray topography and atomic force microscopy

    International Nuclear Information System (INIS)

    An investigation of the defect structure of crystals of potassium hydrogen phthalate (KAP) and its relationship to the crystallization behaviour has been carried out using x-ray diffraction topography and atomic force microscopy (AFM). Crystals of KAP grown from aqueous solution were found to exhibit very low defect densities in the range 5 to 15 cm-2 and remarkably low levels of strain. The character and distribution of the dominant growth dislocation types were determined using x-ray topography. The most significant features of the dislocation structure were a tendency for certain dislocation types to nucleate in pairs and at growth sector boundaries. X-ray topography revealed sectorial variations in solvent inclusions and the complementary use of AFM has shown the relationship of this to growth spiral anisotropy on the (010) face of KAP crystals. Changes in KAP crystal morphology have been observed which result from extreme variations in dislocation density, leading to either spiral growth or, in the case of dislocation-free growth sectors, a two-dimensional nucleation mechanism. The bending of dislocations from one growth sector to another and the tendency of dislocations in this material to nucleate in pairs are discussed in the context of size-dependent crystal growth rates. (author)

  16. 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.

  17. 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

  18. Enhancement of electrical characteristics and reliability in crystallized ZrO2 gate dielectrics treated with in-situ atomic layer doping of nitrogen

    International Nuclear Information System (INIS)

    The crystallized ZrO2 high-K gate dielectrics treated with in-situ atomic layer doping of nitrogen using remote N2 and NH3 plasma were investigated, to suppress the capacitance equivalent thickness (CET), leakage current density (Jg), and interfacial state density (Dit). The stress-induced leakage current (SILC) was reduced significantly as well. The tetragonal/cubic phase of ZrO2 was formed by post metallization annealing at a low temperature of 450 °C to offer a high dielectric constant of the gate oxide. The in-situ atomic layer doping of nitrogen using the remote NH3 plasma contributes to the deactivation of the oxygen vacancies and the well passivation of Dit. Accordingly, a suppressed Jg of 4.79 × 10−5 A cm−2 and Dit of 3.96 × 1011 cm−2 eV−1 were realized in the crystallized ZrO2 gate oxide with a low CET of 1.35 nm. The gate dielectrics were also optically examined by the photoluminescence from the high-K/Si interface, indicating that the Dit is highly correlated with the hydrogen passivation originating from the remote NH3 plasma. The results indicate that in-situ atomic layer doping of nitrogen is an applicable and effective technique to improve the electrical properties of crystallized gate dielectrics in the advanced metal-oxide-semiconductor devices.

  19. 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.)

  20. 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.