WorldWideScience

Sample records for atomic resolution crystal

  1. Protein crystal structure analysis using synchrotron radiation at atomic resolution

    International Nuclear Information System (INIS)

    Nonaka, Takamasa

    1999-01-01

    We can now obtain a detailed picture of protein, allowing the identification of individual atoms, by interpreting the diffraction of X-rays from a protein crystal at atomic resolution, 1.2 A or better. As of this writing, about 45 unique protein structures beyond 1.2 A resolution have been deposited in the Protein Data Bank. This review provides a simplified overview of how protein crystallographers use such diffraction data to solve, refine, and validate protein structures. (author)

  2. Deducing 2D Crystal Structure at the Solid/Liquid Interface with Atomic Resolution by Combined STM and SFG Study

    Science.gov (United States)

    McClelland, Arthur; Ahn, Seokhoon; Matzger, Adam J.; Chen, Zhan

    2009-03-01

    Supplemented by computed models, Scanning Tunneling Microscopy (STM) can provide detailed structure of 2D crystals formed at the liquid/solid interface with atomic resolution. However, some structural information such as functional group orientations in such 2D crystals needs to be tested experimentally to ensure the accuracy of the deduced structures. Due to the limited sensitivity, many other experimental techniques such as Raman and infrared spectroscopy have not been allowed to provide such structural information of 2D crystals. Here we showed that Sum Frequency Generation Vibrational Spectroscopy (SFG) can measure average orientation of functional groups in such 2D crystals, or physisorbed monolayers, providing key experimental data to aid in the modeling and interpretation of the STM images. The usefulness of combining these two techniques is demonstrated with a phthalate diesters monolayer formed at the 1-phenyloctane/ highly oriented pyrolytic graphite (HOPG) interface. The spatial orientation of the ester C=O of the monolayer was successfully determined using SFG.

  3. 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

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

    Directory of Open Access Journals (Sweden)

    Sam Horrell

    2016-07-01

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

  5. Electron microscopy at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Gronsky, R.

    1983-11-01

    The direct imaging of atomic structure in solids has become increasingly easier to accomplish with modern transmission electron microscopes, many of which have an information retrieval limit near 0.2 nm point resolution. Achieving better resolution, particularly with any useful range of specimen tilting, requires a major design effort. This presentation describes the new Atomic Resolution Microscope (ARM), recently put into operation at the Lawrence Berkeley Laboratory. Capable of 0.18 nm or better interpretable resolution over a voltage range of 400 kV to 1000 kV with +- 40/sup 0/ biaxial specimen tilting, the ARM features a number of new electron-optical and microprocessor-control designs. These are highlighted, and its atomic resolution performance demonstrated for a selection of inorganic crystals.

  6. Electron microscopy at atomic resolution

    International Nuclear Information System (INIS)

    Gronsky, R.

    1983-11-01

    The direct imaging of atomic structure in solids has become increasingly easier to accomplish with modern transmission electron microscopes, many of which have an information retrieval limit near 0.2 nm point resolution. Achieving better resolution, particularly with any useful range of specimen tilting, requires a major design effort. This presentation describes the new Atomic Resolution Microscope (ARM), recently put into operation at the Lawrence Berkeley Laboratory. Capable of 0.18 nm or better interpretable resolution over a voltage range of 400 kV to 1000 kV with +- 40 0 biaxial specimen tilting, the ARM features a number of new electron-optical and microprocessor-control designs. These are highlighted, and its atomic resolution performance demonstrated for a selection of inorganic crystals

  7. Atomic-resolution neutron holography

    International Nuclear Information System (INIS)

    Cser, L.; Toeroek, Gy.; Krexner, G.

    2001-01-01

    Atomic-resolution neutron holography can be realised by two different schemes. In the frame of the first approach a point-like source of slow neutrons is produced inside the investigated crystal. Due to the extremely large value of the incoherent-scattering cross-section of the proton, hydrogen atoms imbedded in a metal single-crystal lattice may serve as point-like sources when the sample is irradiated by a monochromatic beam of slow neutrons. The second approach utilizes the registration of the interference between the incident and scattered waves by means of a point-like detector inserted in the lattice of the crystal under investigation. In addition, neutron-induced electron holography is considered. The feasibility of these ideas is discussed. (orig.)

  8. Deducing 2D crystal structure at the liquid/solid interface with atomic resolution: a combined STM and SFG study.

    Science.gov (United States)

    McClelland, Arthur A; Ahn, Seokhoon; Matzger, Adam J; Chen, Zhan

    2009-11-17

    Sum frequency generation vibrational spectroscopy (SFG) has been applied to study two-dimensional (2D) crystals formed by an isophthalic acid diester on the surface of highly oriented pyrolytic graphite, providing complementary measurements to scanning tunneling microscopy (STM) and computational modeling. SFG results indicate that both aromatic and C=O groups in the 2D crystal tilt from the surface. This study demonstrates that a combination of SFG and STM techniques can be used to gain a more complete picture of 2D crystal structure, and it is necessary to consider solvent-2D crystal interactions and dynamics in the computer models to achieve an accurate representation of interfacial structure.

  9. Monolayer atomic crystal molecular superlattices

    Science.gov (United States)

    Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

    2018-03-01

    Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

  10. Crystallization Process of Protein Rv0731c from Mycobacterium Tuberculosis for a Successful Atomic Resolution Crystal Structure at 1.2 Angstrom

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Liang Cong

    2009-06-08

    Proteins are bio-macromolecules consisting of basic 20 amino acids and have distinct three-dimensional folds. They are essential parts of organisms and participate in every process within cells. Proteins are crucial for human life, and each protein within the body has a specific function, such as antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins and transport proteins. Determining three-dimensional structure of a protein can help researchers discover the remarkable protein folding, binding site, conformation and etc, in order to understand well of protein interaction and aid for possible drug design. The research on protein structure by X-ray protein crystallography carried by Li-Wei Hung's research group in the Physical Bioscience Division at Lawrence Berkeley National Laboratory (LBNL) is focusing on protein crystallography. The research in this lab is in the process of from crystallizing the proteins to determining the three dimensional crystal structures of proteins. Most protein targets are selected from Mycobacterium Tuberculosis. TB (Tuberculosis) is a possible fatal infectious disease. By studying TB target protein can help discover antituberculer drugs, and find treatment for TB. The high-throughput mode of crystallization, crystal harvesting, crystal screening and data collection are applied to the research pipeline (Figure 1). The X-ray diffraction data by protein crystals can be processed and analyzed to result in a three dimensional representation of electron density, producing a detailed model of protein structure. Rv0731c is a conserved hypothetical protein with unknown function from Mycobacterium Tuberculosis. This paper is going to report the crystallization process and brief structure information of Rv0731c.

  11. Atomic crystals resistive switching memory

    International Nuclear Information System (INIS)

    Liu Chunsen; Zhang David Wei; Zhou Peng

    2017-01-01

    Facing the growing data storage and computing demands, a high accessing speed memory with low power and non-volatile character is urgently needed. Resistive access random memory with 4F 2 cell size, switching in sub-nanosecond, cycling endurances of over 10 12 cycles, and information retention exceeding 10 years, is considered as promising next-generation non-volatile memory. However, the energy per bit is still too high to compete against static random access memory and dynamic random access memory. The sneak leakage path and metal film sheet resistance issues hinder the further scaling down. The variation of resistance between different devices and even various cycles in the same device, hold resistive access random memory back from commercialization. The emerging of atomic crystals, possessing fine interface without dangling bonds in low dimension, can provide atomic level solutions for the obsessional issues. Moreover, the unique properties of atomic crystals also enable new type resistive switching memories, which provide a brand-new direction for the resistive access random memory. (topical reviews)

  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)

    Burgess, Benjamin R.; Dobson, Renwick C. J.; Dogovski, Con; Jameson, Geoffrey B.; Parker, Michael W.; Perugini, Matthew A.

    2008-01-01

    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 (V M ) was 2.34 Å 3 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. Studying atomic-resolution by X-ray fluorescence holography

    International Nuclear Information System (INIS)

    Gao Hongyi; Chen Jianwen; Xie Honglan; Zhu Huafeng; Li Ruxin; Xu Zhizhan

    2005-01-01

    In this work, the results of numerical simulations of X-ray fluorescence holograms and the reconstructed atomic images for Fe single crystal are given. The influences of the recording angles ranges and the polarization effect on the reconstruction of the atomic images are discussed. The process for removing twin images by multiple energy fluorescence holography and expanding the energy range of the incident X-rays to improve the resolution of the reconstructed images is presented

  15. HRTEM imaging of atoms at sub-Angstroem resolution

    International Nuclear Information System (INIS)

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

    2005-01-01

    John Cowley and his group at Arizona State University pioneered the use of transmission electron microscopy for high-resolution imaging. Images were achieved three decades ago showing the crystal unit cell content at better than 4 A 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-Angstroem 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-Angstroem imaging, initially achieved by focal-series reconstruction of the specimen exit surface wave, will become commonplace for next-generation electron microscopes with C s -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 microscope 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. (author)

  16. 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.

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

    NARCIS (Netherlands)

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

    1994-01-01

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

  18. 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.

  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. Numerical simulation study for atomic-resolution x-ray fluorescence holography

    International Nuclear Information System (INIS)

    Xie Honglan; Gao Hongyi; Chen Jianwen; Xiong Shisheng; Xu Zhizhan; Wang Junyue; Zhu Peiping; Xian Dingchang

    2003-01-01

    Based on the principle of x-ray fluorescence holography, an iron single crystal model of a body-centred cubic lattice is numerically simulated. From the fluorescence hologram produced numerically, the Fe atomic images were reconstructed. The atomic images of the (001), (100), (010) crystallographic planes were consistent with the corresponding atomic positions of the model. The result indicates that one can obtain internal structure images of single crystals at atomic-resolution by using x-ray fluorescence holography

  1. Semiconductor crystal high resolution imager

    Science.gov (United States)

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

    2011-01-01

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

  2. 40 keV atomic resolution TEM

    International Nuclear Information System (INIS)

    Bell, David C.; Russo, Christopher J.; Kolmykov, Dmitry V.

    2012-01-01

    Here we present the first atomic resolution TEM imaging at 40 keV using an aberration-corrected, monochromated source TEM. Low-voltage High-Resolution Electron Microscopy (LVHREM) has several advantages, including increased cross-sections for inelastic and elastic scattering, increased contrast per electron and improved spectroscopy efficiency, decreased delocalization effects and reduced knock-on damage. Together, these often improve the contrast to damage ratio obtained on a large class of samples. Third-order aberration correction now allows us to operate the TEM at low energies while retaining atomic resolution, which was previously impossible. At low voltage the major limitation to resolution becomes the chromatic aberration limit. We show that using a source monochromator we are able to reduce the effect of chromatic aberration and achieve a usable high-resolution limit at 40 keV to less than 1 Å. We show various materials' examples of the application of the technique to image graphene and silicon, and compare atomic resolution images with electron multislice simulations. -- Highlights: ► We present the first atomic resolution images recorded at 40 keV using an aberration-corrected, monochromated TEM. ► We show information transfer measured to better than 1 Å. ► At 40 keV an aberration-corrected monochromated TEM is limited by fifth-order spherical aberration. ► We show that using a monochromator the effect of chromatic aberration is reduced to enable high resolution imaging. ► Low voltage high resolution electron microscopy will be beneficial for imaging the organic/inorganic materials interface.

  3. 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...

  4. Point defects and atomic transport in crystals

    International Nuclear Information System (INIS)

    Lidiard, A.B.

    1981-02-01

    There are two principle aspects to the theory of atomic transport in crystals as caused by the action of point defects, namely (1) the calculation of relevant properties of the point defects (energies and other thermodynamic characteristics of the different possible defects, activation energies and other mobility parameters) and (2) the statistical mechanics of assemblies of defects, both equilibrium and non-equilibrium assemblies. In the five lectures given here both these aspects are touched on. The first two lectures are concerned with the calculation of relevant point defect properties, particularly in ionic crystals. The first lecture is more general, the second is concerned particularly with some recent calculations of the free volumes of formation of defects in various ionic solids; these solve a rather long-standing problem in this area. The remaining three lectures are concerned with the kinetic theory of defects mainly in relaxation, drift and diffusion situations

  5. Atomic lattice excitons: from condensates to crystals

    International Nuclear Information System (INIS)

    Kantian, A; Daley, A J; Toermae, P; Zoller, P

    2007-01-01

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

  6. Atomic lattice excitons: from condensates to crystals

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-11-15

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

  7. High Resolution Displays Using NCAP Liquid Crystals

    Science.gov (United States)

    Macknick, A. Brian; Jones, Phil; White, Larry

    1989-07-01

    Nematic curvilinear aligned phase (NCAP) liquid crystals have been found useful for high information content video displays. NCAP materials are liquid crystals which have been encapsulated in a polymer matrix and which have a light transmission which is variable with applied electric fields. Because NCAP materials do not require polarizers, their on-state transmission is substantially better than twisted nematic cells. All dimensional tolerances are locked in during the encapsulation process and hence there are no critical sealing or spacing issues. By controlling the polymer/liquid crystal morphology, switching speeds of NCAP materials have been significantly improved over twisted nematic systems. Recent work has combined active matrix addressing with NCAP materials. Active matrices, such as thin film transistors, have given displays of high resolution. The paper will discuss the advantages of NCAP materials specifically designed for operation at video rates on transistor arrays; applications for both backlit and projection displays will be discussed.

  8. Streptavidin and its biotin complex at atomic resolution

    International Nuclear Information System (INIS)

    Le Trong, Isolde; Wang, Zhizhi; Hyre, David E.; Lybrand, Terry P.; Stayton, Patrick S.; Stenkamp, Ronald E.

    2011-01-01

    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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  10. Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures.

    Science.gov (United States)

    Silvaroli, Josie A; Arne, Jason M; Chelstowska, Sylwia; Kiser, Philip D; Banerjee, Surajit; Golczak, Marcin

    2016-04-15

    Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by CRBP1 remain unclear. Here we report the first structure of CRBP1 in a ligand-free form as well as ultra-high resolution structures of this protein bound to either all-trans-retinol or retinylamine, the latter a therapeutic retinoid that prevents light-induced retinal degeneration. Superpositioning of human apo- and holo-CRBP1 revealed major differences within segments surrounding the entrance to the retinoid-binding site. These included α-helix II and hairpin turns between β-strands βC-βD and βE-βF as well as several side chains, such as Phe-57, Tyr-60, and Ile-77, that change their orientations to accommodate the ligand. Additionally, we mapped hydrogen bond networks inside the retinoid-binding cavity and demonstrated their significance for the ligand affinity. Analyses of the crystallographic B-factors indicated several regions with higher backbone mobility in the apoprotein that became more rigid upon retinoid binding. This conformational flexibility of human apo-CRBP1 facilitates interaction with the ligands, whereas the more rigid holoprotein structure protects the labile retinoid moiety during vitamin A transport. These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular retinol-binding proteins. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Atomic resolution imaging of ferroelectric domains

    International Nuclear Information System (INIS)

    Bursill, L.A.

    1997-01-01

    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

  12. Laser guiding of cold atoms in photonic crystals

    International Nuclear Information System (INIS)

    Tarasishin, A V; Magnitskiy, Sergey A; Shuvaev, V A; Zheltikov, Aleksei M

    2000-01-01

    The possibility of using photonic crystals with a lattice defect for the laser guiding of cold atoms is analysed. We have found a configuration of a photonic-crystal lattice and a defect ensuring the distribution of a potential in the defect mode of the photonic crystal allowing the guiding of cold atoms along the defect due to the dipole force acting on atoms. Based on quantitative estimates, we have demonstrated that photonic crystals with a lattice defect permit the guiding of atoms with much higher transverse temperatures and a much higher transverse localisation degree than in the case of hollow-core fibres. (laser applications and other topics in quantum electronics)

  13. High resolution crystal calorimetry at LHC

    International Nuclear Information System (INIS)

    Schneegans, M.; Ferrere, D.; Lebeau, M.; Vivargent, M.

    1991-01-01

    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/c 2 , 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

  14. William Barlow and the Determination of Atomic Arrangement in Crystals.

    Science.gov (United States)

    Mauskopf, Seymour H

    2015-04-01

    William Barlow (1845-1934) was an important if unconventional scientist, known for having developed the 'closest-packing' atomic models of crystal structure. He resumed an early nineteenth-century tradition of utilizing crystallographical and chemical data to determine atomic arrangements in crystals. This essay recounts Barlow's career and scientific activity in three parts: (a) His place in the tradition of determining atomic arrangement in context of this earlier tradition and of contemporaneous developments of crystallography and chemistry, (b) his unconventional career, and (c) the 'success' of his program to determine atomic arrangements in crystals and its influence on the work of William Lawrence Bragg.

  15. Protein crystals as scanned probes for recognition atomic force microscopy.

    Science.gov (United States)

    Wickremasinghe, Nissanka S; Hafner, Jason H

    2005-12-01

    Lysozyme crystal growth has been localized at the tip of a conventional silicon nitride cantilever through seeded nucleation. After cross-linking with glutaraldehyde, lysozyme protein crystal tips image gold nanoparticles and grating standards with a resolution comparable to that of conventional tips. Force spectra between the lysozyme crystal tips and surfaces covered with antilysozyme reveal an adhesion force that drops significantly upon blocking with free lysozyme, thus confirming that lysozyme crystal tips can detect molecular recognition interactions.

  16. Direct detection of antihydrogen atoms using a BGO crystal

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-12-21

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

  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. Atomic scale resolution with correlation holography

    International Nuclear Information System (INIS)

    Csonka, P.L.

    1979-01-01

    For many atoms (including atoms of interest in biology) the elastic and inelastic photon scattering cross sections (denoted respectively by sigma/sub el/ and sigma/sub inel/) for photons in the wavelength region of interest, satisfy sigma/sub el/ << sigma/sub inel/. Therefore, the probability is high that when illuminated with photons, such an atom will decay before a holographic picture of it can be taken. On the other hand, if certain nonlinear phenomena: correlations between photons are taken into account, a hologram of such atoms can nevertheless be generated. Observation of small objects is compatible with the principles of quantum mechanics, even if the probability of disturbing the object as a result of observation is arbitrarily small

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

    International Nuclear Information System (INIS)

    Krehl, Jonas; Lubk, Axel

    2015-01-01

    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

  20. 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.

  1. Atomic-Resolution Spectrum Imaging of Semiconductor Nanowires.

    Science.gov (United States)

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

    2018-03-14

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

  2. Fast resolution change in neutral helium atom microscopy

    Science.gov (United States)

    Flatabø, R.; Eder, S. D.; Ravn, A. K.; Samelin, B.; Greve, M. M.; Reisinger, T.; Holst, B.

    2018-05-01

    In neutral helium atom microscopy, a beam of atoms is scanned across a surface. Though still in its infancy, neutral helium microscopy has seen a rapid development over the last few years. The inertness and low energy of the helium atoms (less than 0.1 eV) combined with a very large depth of field and the fact that the helium atoms do not penetrate any solid material at low energies open the possibility for a non-destructive instrument that can measure topology on the nanoscale even on fragile and insulating surfaces. The resolution is determined by the beam spot size on the sample. Fast resolution change is an attractive property of a microscope because it allows different aspects of a sample to be investigated and makes it easier to identify specific features. However up till now it has not been possible to change the resolution of a helium microscope without breaking the vacuum and changing parts of the atom source. Here we present a modified source design, which allows fast, step wise resolution change. The basic design idea is to insert a moveable holder with a series of collimating apertures in front of the source, thus changing the effective source size of the beam and thereby the spot size on the surface and thus the microscope resolution. We demonstrate a design with 3 resolution steps. The number of resolution steps can easily be extended.

  3. Principle and Reconstruction Algorithm for Atomic-Resolution Holography

    Science.gov (United States)

    Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

    2018-06-01

    Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

  4. Shallow surface depth profiling with atomic resolution

    International Nuclear Information System (INIS)

    Xi, J.; Dastoor, P.C.; King, B.V.; O'Connor, D.J.

    1999-01-01

    It is possible to derive atomic layer-by-layer composition depth profiles from popular electron spectroscopic techniques, such as X-ray photoelectron spectroscopy (XPS) or Auger electron spectroscopy (AES). When ion sputtering assisted AES or XPS is used, the changes that occur during the establishment of the steady state in the sputtering process make these techniques increasingly inaccurate for depths less than 3nm. Therefore non-destructive techniques of angle-resolved XPS (ARXPS) or AES (ARAES) have to be used in this case. In this paper several data processing algorithms have been used to extract the atomic resolved depth profiles of a shallow surface (down to 1nm) from ARXPS and ARAES data

  5. Protein nanocrystallography: growth mechanism and atomic structure of crystals induced by nanotemplates.

    Science.gov (United States)

    Pechkova, E; Vasile, F; Spera, R; Fiordoro, S; Nicolini, C

    2005-11-01

    Protein nanocrystallography, a new technology for crystal growth based on protein nanotemplates, has recently been shown to produce diffracting, stable and radiation-resistant lysozyme crystals. This article, by computing these lysozyme crystals' atomic structures, obtained by the diffraction patterns of microfocused synchrotron radiation, provides a possible mechanism for this increased stability, namely a significant decrease in water content accompanied by a minor but significant alpha-helix increase. These data are shown to be compatible with the circular dichroism and two-dimensional Fourier transform spectra of high-resolution H NMR of proteins dissolved from the same nanotemplate-based crystal versus those from a classical crystal. Finally, evidence for protein direct transfer from the nanotemplate to the drop and the participation of the template proteins in crystal nucleation and growth is provided by high-resolution NMR spectrometry and mass spectrometry. Furthermore, the lysozyme nanotemplate appears stable up to 523 K, as confirmed by a thermal denaturation study using spectropolarimetry. The overall data suggest that heat-proof lysozyme presence in the crystal provides a possible explanation of the crystal's resistance to synchrotron radiation.

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

    Science.gov (United States)

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

    2016-09-20

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

  7. Application of GRID to Foreign Atom Localization in Single Crystals.

    Science.gov (United States)

    Karmann, A; Wesch, W; Weber, B; Börner, H G; Jentschel, M

    2000-01-01

    The application of GRID (Gamma Ray Induced Doppler broadening) spectroscopy to the localization of foreign atoms in single crystals is demonstrated on erbium in YAP. By the investigation of the Doppler broadened secondary γ line for two crystalline directions, the Er was determined to be localized on the Y site. Conditions for the nuclear parameters of the impurity atoms used for the application of GRID spectroscopy are discussed.

  8. A high resolution ion microscope for cold atoms

    International Nuclear Information System (INIS)

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

    2017-01-01

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

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

    Science.gov (United States)

    Ho, Phuong T; Reddy, Vijay S

    2018-01-01

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

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

    Science.gov (United States)

    Zhang, Daliang; Zhu, Yihan; Liu, Lingmei; Ying, Xiangrong; Hsiung, Chia-En; Sougrat, Rachid; Li, Kun; Han, Yu

    2018-02-01

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

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

    KAUST Repository

    Zhang, Daliang

    2018-01-18

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

  12. 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.

  13. Atomic imaging of an InSe single-crystal surface with atomic force microscope

    OpenAIRE

    Uosaki, Kohei; Koinuma, Michio

    1993-01-01

    The atomic force microscope was employed to observed in air the surface atomic structure of InSe, one of III-VI compound semiconductors with layered structures. Atomic arrangements were observed in both n-type and p-type materials. The observed structures are in good agreement with those expected from bulk crystal structures. The atomic images became less clear by repeating the imaging process. Wide area imaging after the imaging of small area clearly showed that a mound was created at the sp...

  14. Waves in periodic medium. Atomic matter waves in light crystals

    International Nuclear Information System (INIS)

    Oberthaler, M. K.

    1997-07-01

    This work deals with the propagation of matter waves inside a periodic potential. In analogy to photon optics a potential can be described by a refractive index for matter waves. A real potential leads to a refractive spatial structure while an imaginary potential leads to an absorptive structure. A general theoretical description is given in the framework of Floquet theory. The equivalent approach of dynamical diffraction theory will be treated in detail. The analytic solution for weak potentials are given in a general form so that they are applicable for every kind of wave and medium. For our experiments an open two level atom (metastable Argon) propagating inside a standing light wave was used. Detuning the frequency of the light wave from the atomic resonance leads to a real (refractive) periodic potential. Tuning the laser exact on resonance gives rise to a pure imaginary (absorptive) periodic potential. In analogy to solid state crystals in X-ray and neutron optics we call a standing light wave a light crystal. Tuning the standing light field on resonance we demonstrated experimentally the Borrmann effect. This effect describes the increase of the total transmission through a crystal for Bragg incidence. Furthermore, we confirmed that this effect is coherent and that a sinusoidal wave field is formed inside the crystal. The nodes of the wave field were found to coincide with the maxima of absorption. For a detuned standing light field a refractive crystal was realized, for which the expected Pendelloesung effect was demonstrated. In this case the maximum of the wave field inside the crystal was found at the steepest gradient of the potential as predicted by dynamical diffraction theory. Superposing an absorptive and a refractive light crystal a complex light crystal was realized. With such a crystal the violation of Friedel's law was demonstrated in a very clear way. (author)

  15. Ultrafast terahertz scanning tunneling microscopy with atomic resolution

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  16. CO tip functionalization in subatomic resolution atomic force microscopy

    International Nuclear Information System (INIS)

    Kim, Minjung; Chelikowsky, James R.

    2015-01-01

    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

  17. Spectrum of a one-atom laser in photonic crystals

    International Nuclear Information System (INIS)

    Florescu, Lucia

    2006-01-01

    The emission spectrum of a single-emitter laser in a photonic crystal is presented. We consider a coherently pumped two-level emitter strongly coupled to a high-quality microcavity engineered within a photonic crystal. We show that the cavity spectrum consists of both elastic and inelastic components, for which we derive analytical expressions. Our study reveals enhanced, spectrally narrower emission resulting from the radiation reservoir of the photonic crystal. The cavity field spectral characteristics are fundamentally distinct from those of a corresponding microcavity in ordinary vacuum. At high pump intensities and for large discontinuities in the photon density of states between Mollow spectral components of atomic resonance fluorescence, the emitted intensity originating from the elastic spectral component increases with the intensity of the pump and the elastic component dominates the spectrum. In the case of a vanishing photon density of states in the spectral range surrounding the lower Mollow sideband and no dipolar dephasing, the cavity spectrum is elastic

  18. Clean Floquet Time Crystals: Models and Realizations in Cold Atoms

    Science.gov (United States)

    Huang, Biao; Wu, Ying-Hai; Liu, W. Vincent

    2018-03-01

    Time crystals, a phase showing spontaneous breaking of time-translation symmetry, has been an intriguing subject for systems far away from equilibrium. Recent experiments found such a phase in both the presence and the absence of localization, while in theories localization by disorder is usually assumed a priori. In this work, we point out that time crystals can generally exist in systems without disorder. A series of clean quasi-one-dimensional models under Floquet driving are proposed to demonstrate this unexpected result in principle. Robust time crystalline orders are found in the strongly interacting regime along with the emergent integrals of motion in the dynamical system, which can be characterized by level statistics and the out-of-time-ordered correlators. We propose two cold atom experimental schemes to realize the clean Floquet time crystals, one by making use of dipolar gases and another by synthetic dimensions.

  19. Investigation of phosphorus atomization using high-resolution continuum source electrothermal atomic absorption spectrometry

    International Nuclear Information System (INIS)

    Dessuy, Morgana B.; Vale, Maria Goreti R.; Lepri, Fabio G.; Welz, Bernhard; Heitmann, Uwe

    2007-01-01

    The atomization of phosphorus in electrothermal atomic absorption spectrometry has been investigated using a high-resolution continuum source atomic absorption spectrometer and atomization from a graphite platform as well as from a tantalum boat inserted in a graphite tube. A two-step atomization mechanism is proposed for phosphorus, where the first step is a thermal dissociation, resulting in a fast atomization signal early in the atomization stage, and the second step is a slow release of phosphorus atoms from the graphite tube surface following the adsorption of molecular phosphorus at active sites of the graphite surface. Depending on experimental conditions only one of the mechanisms or both might be active. In the absence of a modifier and with atomization from a graphite or tantalum platform the second mechanism appears to be dominant, whereas in the presence of sodium fluoride as a modifier both mechanisms are observed. Intercalation of phosphorus into the graphite platform in the condensed phase has also been observed; this phosphorus, however, appears to be permanently trapped in the structure of the graphite and does not contribute to the absorption signal

  20. High resolution atomic spectra of rare earths : progress report

    International Nuclear Information System (INIS)

    Saksena, G.D.; Ahmad, S.A.

    1976-01-01

    High resolution studies of atomic spectra of neodymium and gadolinium are being carried out on a recording Fabry-Perot spectrometer. The present progress report concerns work done on new assignments as well as confirmation of recently assigned electronic configurations and evaluation of isotope shifts of energy levels which have been possible from the isotope shift data obtained for several transitions of NdI, NdII and GdI, GdII respectively. (author)

  1. Modeling noncontact atomic force microscopy resolution on corrugated surfaces

    Directory of Open Access Journals (Sweden)

    Kristen M. Burson

    2012-03-01

    Full Text Available Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO2 as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid. The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-07-31

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

  3. Atomic-scale friction on stepped surfaces of ionic crystals.

    Science.gov (United States)

    Steiner, Pascal; Gnecco, Enrico; Krok, Franciszek; Budzioch, Janusz; Walczak, Lukasz; Konior, Jerzy; Szymonski, Marek; Meyer, Ernst

    2011-05-06

    We report on high-resolution friction force microscopy on a stepped NaCl(001) surface in ultrahigh vacuum. The measurements were performed on single cleavage step edges. When blunt tips are used, friction is found to increase while scanning both up and down a step edge. With atomically sharp tips, friction still increases upwards, but it decreases and even changes sign downwards. Our observations extend previous results obtained without resolving atomic features and are associated with the competition between the Schwöbel barrier and the asymmetric potential well accompanying the step edges.

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

    Science.gov (United States)

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

    2016-09-01

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields E(x)∝e±ikxxE(x)∝e±ikxx outside the bandgap to localized fields E(x)∝e-κx|x|E(x)∝e-κx|x| within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the D1D1 line of atomic cesium for N¯=3.0±0.5N¯=3.0±0.5 atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

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

    Directory of Open Access Journals (Sweden)

    Christian Jelsch

    2017-03-01

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

  6. Two-energy twin image removal in atomic-resolution x-ray holography

    International Nuclear Information System (INIS)

    Nishino, Y.; Ishikawa, T.; Hayashi, K.; Takahashi, Y.; Matsubara, E.

    2002-01-01

    We propose a two-energy twin image removal algorithm for atomic-resolution x-ray holography. The validity of the algorithm is shown in a theoretical simulation and in an experiment of internal detector x-ray holography using a ZnSe single crystal. The algorithm, compared to the widely used multiple-energy algorithm, allows efficient measurement of holograms, and is especially important when the available x-ray energies are fixed. It enables twin image free holography using characteristic x rays from laboratory generators and x-ray pulses of free-electron lasers

  7. Phase contrast scanning transmission electron microscopy imaging of light and heavy atoms at the limit of contrast and resolution.

    Science.gov (United States)

    Yücelen, Emrah; Lazić, Ivan; Bosch, Eric G T

    2018-02-08

    Using state of the art scanning transmission electron microscopy (STEM) it is nowadays possible to directly image single atomic columns at sub-Å resolution. In standard (high angle) annular dark field STEM ((HA)ADF-STEM), however, light elements are usually invisible when imaged together with heavier elements in one image. Here we demonstrate the capability of the recently introduced Integrated Differential Phase Contrast STEM (iDPC-STEM) technique to image both light and heavy atoms in a thin sample at sub-Å resolution. We use the technique to resolve both the Gallium and Nitrogen dumbbells in a GaN crystal in [[Formula: see text

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

    Science.gov (United States)

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

    2015-07-01

    The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron

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

    Directory of Open Access Journals (Sweden)

    Matthew P. Blakeley

    2015-07-01

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

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

    CERN Document Server

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

    2000-01-01

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

  11. Resolution of VISION, a crystal-analyzer spectrometer

    International Nuclear Information System (INIS)

    Seeger, Philip A.; Daemen, Luke L.; Larese, John Z.

    2009-01-01

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

  12. Effect of atomic initial phase difference on spontaneous emission of an atom embedded in photonic crystal

    International Nuclear Information System (INIS)

    Bing, Zhang; Xiu-Dong, Sun; Xiang-Qian, Jiang

    2010-01-01

    We investigate the effect of initial phase difference between the two excited states of a V-type three-level atom on its steady state behaviour of spontaneous emission. A modified density of modes is introduced to calculate the spontaneous emission spectra in photonic crystal. Spectra in free space are also shown to compare with that in photonic crystal with different relative positions of the excited levels from upper band-edge frequency. It is found that the initial phase difference plays an important role in the quantum interference property between the two decay channels. For a zero initial phase, destructive property is presented in the spectra. With the increase of initial phase difference, quantum interference between the two decay channels from upper levels to ground level turns to be constructive. Furthermore, we give an interpretation for the property of these spectra. (atomic and molecular physics)

  13. Simulation and understanding of atomic and molecular quantum crystals

    Science.gov (United States)

    Cazorla, Claudio; Boronat, Jordi

    2017-07-01

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

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

    International Nuclear Information System (INIS)

    Wood, G.J.; Beeching, M.J.

    1990-01-01

    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. Structural atlas of dynein motors at atomic resolution.

    Science.gov (United States)

    Toda, Akiyuki; Tanaka, Hideaki; Kurisu, Genji

    2018-04-01

    Dynein motors are biologically important bio-nanomachines, and many atomic resolution structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy. This review provides a historical perspective of structural studies of cytoplasmic and axonemal dynein including accessory proteins. We describe representative structural studies of every component of dynein and summarize them as a structural atlas that classifies the cytoplasmic and axonemal dyneins. Based on our review of all dynein structures in the Protein Data Bank, we raise two important points for understanding the two types of dynein motor and discuss the potential prospects of future structural studies.

  16. Describing intrinsically disordered proteins at atomic resolution by NMR

    International Nuclear Information System (INIS)

    Ringkjobing Jensen, Malene; Blackledge, Martin; Ruigrok, Rob WH

    2013-01-01

    There is growing interest in the development of physical methods to study the conformational behaviour and biological activity of intrinsically disordered proteins (IDPs). In this review recent advances in the elucidation of quantitative descriptions of disordered proteins from nuclear magnetic resonance spectroscopy are presented. Ensemble approaches are particularly well adapted to map the conformational energy landscape sampled by the protein at atomic resolution. Significant advances in development of calibrated approaches to the statistical representation of the conformational behaviour of IDPs are presented, as well as applications to some biologically important systems where disorder plays a crucial role. (authors)

  17. Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.

    Science.gov (United States)

    Gardberg, Anna S; Del Castillo, Alexis Rae; Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew P; Myles, Dean A A

    2010-05-01

    The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

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

    International Nuclear Information System (INIS)

    Mueller, H.

    1993-01-01

    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 K 2 O s Cl 6 -K 2 O s Br 6 (n,γ) 38 Cl. The reaction of the 38 Cl, the information about recoil atom reactions which increased with the complexity of target substances, and the resulted informations are reported. (K.I.)71 refs

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

    DEFF Research Database (Denmark)

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

    1965-01-01

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

  20. 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...

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  2. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-12-10

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

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

    International Nuclear Information System (INIS)

    Chen, Liqing; Wang, Yujun; Wells, David; Toh, Diana; Harold, Hunt; Zhou, Jing; DiGiammarino, Enrico; Meehan, Edward J.

    2006-01-01

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

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

    Science.gov (United States)

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

    2014-07-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

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

    2017-06-01

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

  9. Towards structural studies of the old yellow enzyme homologue SYE4 from Shewanella oneidensis and its complexes at atomic resolution

    International Nuclear Information System (INIS)

    Elegheert, Jonathan; Hemel, Debbie van den; Dix, Ina; Stout, Jan; Van Beeumen, Jozef; Brigé, Ann; Savvides, Savvas N.

    2009-01-01

    Of the four old yellow enzyme homologues found in S. oneidensis, SYE4 is the homologue most implicated in resistance to oxidative stress. SYE4 was recombinantly expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. Shewanella oneidensis is an environmentally versatile Gram-negative γ-proteobacterium that is endowed with an unusually large proteome of redox proteins. Of the four old yellow enzyme (OYE) homologues found in S. oneidensis, SYE4 is the homologue most implicated in resistance to oxidative stress. SYE4 was recombinantly expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the orthorhombic space group P2 1 2 1 2 1 and were moderately pseudo-merohedrally twinned, emulating a P422 metric symmetry. The native crystals of SYE4 were of exceptional diffraction quality and provided complete data to 1.10 Å resolution using synchrotron radiation, while crystals of the reduced enzyme and of the enzyme in complex with a wide range of ligands typically led to high-quality complete data sets to 1.30–1.60 Å resolution, thus providing a rare opportunity to dissect the structure–function relationships of a good-sized enzyme (40 kDa) at true atomic resolution. Here, the attainment of a number of experimental milestones in the crystallographic studies of SYE4 and its complexes are reported, including isolation of the elusive hydride–Meisenheimer complex

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

    Science.gov (United States)

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

    2013-02-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-11-22

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

  12. 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.

  13. An atomic-scale model of fcc crystal-growth

    Energy Technology Data Exchange (ETDEWEB)

    Waal, B.W. van de (Technische Hogeschool Twente, Enschede (Netherlands). Dept. of Physics)

    1991-01-01

    Nearly perfect fcc growth may be simulated by the application of a simple growth-algorithm - only sites that are at least 4-coordinated are occupied - to a selected seed. The seed is a 22-atom cluster, being the smallest close-packed structure with two crossing stacking-faults. The stacking-faults produce active surface-sites, that can not be exhausted by occupation; they are arranged in non-vanishing steps, similar to those produced by screw-dislocations. The algorithm prevents further stacking-faults, and ensures ABC-stacking of close-packed (111)-layers, characteristic of the fcc structure. The same algorithm would not produce further growth of perfect fcc clusters or of Mackay icosahedra. It is proposed that the ability to grow fast under near-equilibrium conditions is a better criterion to select clusters as precursors of the bulk-structure than their cohesive energy. The crystal structure problem of the rare gases - why fcc, not hcp - is discussed in connection with the apparent impossibility to simulate hcp growth by an analogous procedure. (orig.).

  14. Ex situ investigation of the step bunching on crystal surfaces by atomic force microscopy

    Science.gov (United States)

    Krasinski, Mariusz J.

    1997-07-01

    We are describing ex situ observation of step bunching on the surfaces of solution grown potassium dihydrogen phosphate (KDP) and sodium chlorate monocrystals. The measurements have been done with the use of atomic force microscope. The use of this equipment allowed us to see directly the structure of macrosteps. Observation confirmed the existence of step pinning which is one of the proposed mechanisms of step bunching. Despite the very high resolution of AFM it was not possible to determine the nature of pinning point. The monatomic steps on KDP and sodium chlorate crystal surfaces are mainly one unit cell high what seems to be the result of the steps pairing. The origin of observed step pattern is discussed in frames of existing theories.

  15. 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.

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

    International Nuclear Information System (INIS)

    Larese, J.Z.

    1998-01-01

    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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    is lightweight and is mounted directly on an ultra-high vacuum scanning tunneling microscope capable of atomic resolution. We report the simultaneous acquisition of an atomic resolution image, while the relative lateral displacement of the tip along the sample distance is measured with the new tunable diode...

  18. Dynamics of Transformation from Platinum Icosahedral Nanoparticles to Larger FCC Crystal at Millisecond Time Resolution

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Wenpei [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering and Fredrick Seitz Materials Research Lab.; Wu, Jianbo [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering, Fredrick Seitz Materials Research Lab. and Dept. of Chemical and Biomolecular Engineering; Shanghai Jiao Tong Univ. (China). School of Materials Science and Engineering; Yoon, Aram [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering and Fredrick Seitz Materials Research Lab.; Lu, Ping [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Qi, Liang [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Materials Science and Engineering; Wen, Jianguo [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials and Electron Microscopy Center; Miller, Dean J. [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials and Electron Microscopy Center; Mabon, James C. [Univ. of Illinois at Urbana-Champaign, IL (United States). Fredrick Seitz Materials Research Lab.; Wilson, William L. [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering and Fredrick Seitz Materials Research Lab.; Yang, Hong [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Chemical and Biomolecular Engineering; Zuo, Jian-Min [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering and Fredrick Seitz Materials Research Lab.

    2017-12-08

    Atomic motion at grain boundaries is essential to microstructure development, growth and stability of catalysts and other nanostructured materials. However, boundary atomic motion is often too fast to observe in a conventional transmission electron microscope (TEM) and too slow for ultrafast electron microscopy. We report on the entire transformation process of strained Pt icosahedral nanoparticles (ICNPs) into larger FCC crystals, captured at 2.5 ms time resolution using a fast electron camera. Results show slow diffusive dislocation motion at nm/s inside ICNPs and fast surface transformation at μm/s. By characterizing nanoparticle strain, we show that the fast transformation is driven by inhomogeneous surface stress. And interaction with pre-existing defects led to the slowdown of the transformation front inside the nanoparticles. Particle coalescence, assisted by oxygen-induced surface migration at T ≥ 300°C, also played a critical role. Thus by studying transformation in the Pt ICNPs at high time and spatial resolution, we obtain critical insights into the transformation mechanisms in strained Pt nanoparticles.

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

    International Nuclear Information System (INIS)

    Cabello, J.; Barrillon, P.; Barrio, J.; Bisogni, M.G.; Del Guerra, A.; Lacasta, C.; Rafecas, M.; Saikouk, H.; Solaz, C.; Solevi, P.; La Taille, C. de; Llosá, G.

    2013-01-01

    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

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

    International Nuclear Information System (INIS)

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

    1999-01-01

    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

  1. The digital structural analysis of cadmium selenide crystals by a method of ion beam thinning for high resolution electron microscopy

    International Nuclear Information System (INIS)

    Kanaya, Koichi; Baba, Norio; Naka, Michiaki; Kitagawa, Yukihisa; Suzuki, Kunio

    1986-01-01

    A digital processing method using a scanning densitometer system for structural analysis of electron micrographs was successfully applied to a study of cadmium selenide crystals, which were prepared by an argon-ion beam thinning method. Based on Fourier techniques for structural analysis from a computer-generated diffractogram, it was demonstrated that when cadmium selenide crystals were sufficiently thin to display the higher order diffraction spots at a high resolution approaching the atomic level, they constitute an alternative hexagonal lattice of imperfect wurtzite phase from a superposition of individual harmonic images by the enhanced scattering amplitude and corrected phase. From the structural analysis data, a Fourier synthetic lattice image was reconstructed, representing the precise location and three-dimensional arrangement of each of the atoms in the unit cell. Extensively enhanced lattice defect images of dislocations and stacking faults were also derived and shown graphically. (author)

  2. Application of two-dimensional crystallography and image processing to atomic resolution Z-contrast images.

    Science.gov (United States)

    Morgan, David G; Ramasse, Quentin M; Browning, Nigel D

    2009-06-01

    Zone axis images recorded using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM or Z-contrast imaging) reveal the atomic structure with a resolution that is defined by the probe size of the microscope. In most cases, the full images contain many sub-images of the crystal unit cell and/or interface structure. Thanks to the repetitive nature of these images, it is possible to apply standard image processing techniques that have been developed for the electron crystallography of biological macromolecules and have been used widely in other fields of electron microscopy for both organic and inorganic materials. These methods can be used to enhance the signal-to-noise present in the original images, to remove distortions in the images that arise from either the instrumentation or the specimen itself and to quantify properties of the material in ways that are difficult without such data processing. In this paper, we describe briefly the theory behind these image processing techniques and demonstrate them for aberration-corrected, high-resolution HAADF-STEM images of Si(46) clathrates developed for hydrogen storage.

  3. Water polygons in high-resolution protein crystal structures.

    Science.gov (United States)

    Lee, Jonas; Kim, Sung-Hou

    2009-07-01

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

  4. Modification of calcite crystal growth by abalone shell proteins: an atomic force microscope study.

    OpenAIRE

    Walters, D A; Smith, B L; Belcher, A M; Paloczi, G T; Stucky, G D; Morse, D E; Hansma, P K

    1997-01-01

    A family of soluble proteins from the shell of Haliotis rufescens was introduced over a growing calcite crystal being scanned in situ by an atomic force microscope (AFM). Atomic step edges on the crystal surface were altered in shape and speed of growth by the proteins. Proteins attached nonuniformly to the surface, indicating different interactions with crystallographically different step edges. The observed changes were consistent with the habit modification induced by this family of protei...

  5. Description of the atomic disorder (local order) in crystals by the mixed-symmetry method

    Science.gov (United States)

    Dudka, A. P.; Novikova, N. E.

    2017-11-01

    An approach to the description of local atomic disorder (short-range order) in single crystals by the mixed-symmetry method based on Bragg scattering data is proposed, and the corresponding software is developed. In defect-containing crystals, each atom in the unit cell can be described by its own symmetry space group. The expression for the calculated structural factor includes summation over different sets of symmetry operations for different atoms. To facilitate the search for new symmetry elements, an "atomic disorder expert" was developed, which estimates the significance of tested models. It is shown that the symmetry lowering for some atoms correlates with the existence of phase transitions (in langasite family crystals) and the anisotropy of physical properties (in rare-earth dodecaborides RB12).

  6. Atomic resolution three-dimensional electron diffraction microscopy

    International Nuclear Information System (INIS)

    Miao Jianwei; Ohsuna, Tetsu; Terasaki, Osamu; Hodgson, Keith O.; O'Keefe, Michael A.

    2002-01-01

    We report the development of a novel form of diffraction-based 3D microscopy to overcome resolution barriers inherent in high-resolution electron microscopy and tomography. By combining coherent electron diffraction with the oversampling phasing method, we show that the 3D structure of a nanocrystal can be determined ab initio at a resolution of 1 Angstrom from 29 simulated noisy diffraction patterns. This new form of microscopy can be used to image the 3D structures of nanocrystals and noncrystalline samples, with resolution limited only by the quality of sample diffraction

  7. Hydrothermal crystallization of amorphous titania films deposited using low temperature atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, D.R.G. [Institute of Materials Engineering, ANSTO, PMB 1, Menai, NSW 2234 (Australia)], E-mail: drm@ansto.gov.au; Triani, G.; Zhang, Z. [Institute of Materials Engineering, ANSTO, PMB 1, Menai, NSW 2234 (Australia)

    2008-10-01

    A two stage process (atomic layer deposition, followed by hydrothermal treatment) for producing crystalline titania thin films at temperatures compatible with polymeric substrates (< 130 deg. C) has been assessed. Titania thin films were deposited at 80 deg. C using atomic layer deposition. They were extremely flat, uniform and almost entirely amorphous. They also contained relatively high levels of residual Cl from the precursor. After hydrothermal treatment at 120 deg. C for 1 day, > 50% of the film had crystallized. Crystallization was complete after 10 days of hydrothermal treatment. Crystallization of the film resulted in the formation of coarse grained anatase. Residual Cl was completely expelled from the film upon crystallization. As a result of the amorphous to crystalline transformation voids formed at the crystallization front. Inward and lateral crystal growth resulted in voids being localized to the film/substrate interface and crystallite perimeters resulting in pinholing. Both these phenomena resulted in films with poor adhesion and film integrity was severely compromised.

  8. High-resolution X-ray spectroscopy of hollow atoms created in plasma heated by subpicosecond laser radiation

    International Nuclear Information System (INIS)

    Faenov, A.Ya.; Magunov, A.I.; Pikuz, T.A.

    1997-01-01

    The investigations of ultrashort (0.4-0.6 ps) laser pulse radiation interaction with solid targets have been carried out. The Trident subpicosecond laser system was used for plasma creation. The X-ray plasma emission was investigated with the help of high-resolution spectrographs with spherically bent mica crystals. It is shown that when high contrast ultrashort laser pulses were used for plasma heating its emission spectra could not be explained in terms of commonly used theoretical models, and transitions in so called hollow atoms must be taken into account for adequate description of plasma radiation

  9. From Atomic Resolution to Molecular Giants: an Overview of Crystallographic Studies of Biological Macromolecules with Synchrotron Radiation

    International Nuclear Information System (INIS)

    Jaskolski, M.

    2010-01-01

    Protein crystals have huge unit cells ( ≅100 A) filled not only with ordered protein molecules but also in about 50% with liquid water. The phase problem in protein crystallography can be solved by molecular replacement (using a suitable model molecule), by isomorphous replacement (using heavy atom derivatives), or by multiwavelength anomalous diffraction (using resonant scattering of synchrotron-generated X-rays by anomalous atoms, such as Se). X-ray diffraction by protein crystals produces thousands of reflections but since the models are very complex (many thousands of atoms), paucity of data is a serious problem and stereochemical restraints are necessary. In consequence, the highest possible resolution (minimum d-spacing in Bragg's Equation) should always be the experimental goal. Protein structures determined by crystallography are deposited in protein data bank, which currently holds more than 62000 entries. Recent methodological advancements, stimulated by a wide-spread use of powerful synchrotron sources and by structural genomics, have resulted in rapid acceleration of the structure elucidation process, and in addition help to obtain a better data. Protein crystallography has produced atomic models of gigantic macromolecular assemblies, including the ribosome. It is also providing accurate targets for structure-guided development of drugs. (author)

  10. From atomic resolution to molecular giants: an overview of crystallographic studies of biological macromolecules with synchrotron radiation

    International Nuclear Information System (INIS)

    Jaskolski, M.

    2010-01-01

    Protein crystals have huge unit cells (∼ 100 A) filled not only with ordered protein molecules but also in about 50% with liquid water. The phase problem in protein crystallography can be solved by molecular replacement (using a suitable model molecule), by isomorphous replacement (using heavy atom derivatives), or by multiwavelength anomalous diffraction (using resonant scattering of synchrotron-generated X-rays by anomalous atoms, such as Se). X-ray diffraction by protein crystals produces thousands of reflections but since the models are very complex (many thousands of atoms), paucity of data is a serious problem and stereochemical restraints are necessary. In consequence, the highest possible resolution (minimum d-spacing in Bragg's Equation) should always be the experimental goal. Protein structures determined by crystallography are deposited in Protein Data Bank, which currently holds more than 65 000 entries. Recent methodological advancements, stimulated by a wide-spread use of powerful synchrotron sources and by structural genomics, have resulted in rapid acceleration of the structure elucidation process, and in addition help to obtain better data. Protein crystallography has produced atomic models of gigantic macromolecular assemblies, including the ribosome. It is also providing accurate targets for structure-guided development of drugs. (author)

  11. 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...

  12. 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

  13. A model for the interaction between F centers and H atoms in ionic crystals

    International Nuclear Information System (INIS)

    Dumke, V.R.; Souza, M. de

    1975-01-01

    The interaction between an F center and neutral hydrogen atoms, the most simple paramagnetic defects in ionic crystals, is described in terms of a perturbation theory of two square potential wells. The good agreement with experimental data indicates that lattice distortion due to the presence of the hydrogen atoms is negligible [pt

  14. The method of intersecting spheres for determination of coordination numbers of atoms in crystal structures

    International Nuclear Information System (INIS)

    Serezhkin, V.N.; Buslaev, Yu.A.; Mikhajlov, Yu.N.

    1997-01-01

    New method for determination of coordination numbers (CN) of atoms in crystal structures, based on the model of interatomic interaction, within the frames whereof each atom is approximated by two spheres with the common center in the atom nuclei, is proposed. One of the spheres specifies conditionally isolated (chemically unbound) atom and its radius is a constant, which for atoms of the given chemical sort in the structure of any compound is equal to quasi-orbital Sleiter radius. The sphere of the other radius specifies chemically bound atom and coincides with the sphere, the volume whereof is equal to the volume of the Voronoj-Dirichlet polyhedron of the corresponding atom in the structure of the concrete crystal. Using a series of examples, workability of the given method for CN determination of atoms in structures of both simple substances and chemical compounds (alkali, transition metals, U, Th). Good agreement of the obtained results with the generally accepted CN s of atoms for the considered crystals is noted and a number of principal advantages of the new method, as compared to classical one of the CNs evaluation, is demonstrated

  15. Atomic structures and mechanical properties of single-crystal GaN nanotubes

    International Nuclear Information System (INIS)

    Xu, B.; Lu, A.J.; Pan, B.C.; Yu, Q.X.

    2005-01-01

    An approach is proposed to theoretically construct a realistic single-crystal GaN nanotube at atomic scale. The generated atomic structures of the single-crystal GaN nanotubes match the structural aspects from experiment very well. Our energetic calculations show that a single-crystal GaN nanotube with [100]-oriented lateral facets is more stable than that with [110]-oriented lateral facets, when they have around the same wall thickness. For a specified orientation of the lateral facets on the single-crystal GaN nanotubes, the energetic stabilities of the tubes obey a P rule, in which P is the ratio of the number of four-coordinated atoms to the number of three-coordinated atoms. Furthermore, the Young's modulus of the considered GaN nanotubes decrease with increasing the ratio of the number of bulk atoms to the number of surface atoms in each type of tube. Our calculations and analysis demonstrate that the surface effect of a single-crystal nanotube enhances its Young's modulus significantly

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

    Science.gov (United States)

    Teschke, Omar; Soares, David Mendez

    2016-03-29

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

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

    NARCIS (Netherlands)

    van der Heijden, N.J.

    2017-01-01

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

  18. muSR-Investigation of a Liquid Crystal Containing Iron Atoms

    CERN Document Server

    Mamedov, T N; Galyametdinov, Yu G; Gritsaj, K I; Herlach, D; Kormann, O; Major, J V; Rochev, V Ya; Stoikov, A V; Zimmermann, U

    2000-01-01

    The work is devoted to the investigation of properties of a liquid crystal whose molecule contains iron atom. The compounds of this type are of interest from the point of view of obtaining liquid crystals with magnetic properties. The temperature dependence of the polarization and relaxation rate of positive muon spin in the liquid crystal was measured in the temperature range 4-300 K. The results obtained do not contradict the suggestion that the iron ions from an antiferromagnetically-ordered structure in this liquid crystal at the temperatures below 80 K.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-04-12

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    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

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

    Science.gov (United States)

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

    2016-02-01

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

  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. 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: 13.779, year: 2015

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  5. Study on light output and energy resolution of PbWO4 crystal

    International Nuclear Information System (INIS)

    Su Guanghui; Yue Ke; Sun Zhiyu

    2010-01-01

    The light output and energy resolution of PbWO 4 crystal are studied with different wrapping materials and methods. The Wrapping condition was optimized by analyzing the experimental data to gain higher light output and better energy resolution. A GEANT4-based package has been developed to simulate the corresponding features of PbWO 4 crystal, and the simulation results are consistent with the experimental data. (authors)

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

    Science.gov (United States)

    Niermann, T; Lehmann, M

    2014-08-01

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

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

    International Nuclear Information System (INIS)

    Moll, Nikolaj; Gross, Leo; Mohn, Fabian; Curioni, Alessandro; Meyer, Gerhard

    2010-01-01

    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.

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

    Science.gov (United States)

    Neumann, Piotr; Tittmann, Kai

    2014-12-01

    Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Enhanced Resolution Maps of Energetic Neutral Atoms from IBEX

    Science.gov (United States)

    Teodoro, L. A.; Elphic, R. C.; Janzen, P.; Reisenfeld, D.; Wilson, J. T.

    2017-12-01

    The discovery by the Interstellar Boundary Explorer (IBEX) of a "Ribbon" in the measurements of Energetic Neutral Particles (ENA) was a major surprise that lead to the re-thinking of the Physics underpinning the heliosphere-intergalactic medium boundary dynamics. Several physical models have been proposed and tested in their ability to mimic the IBEX observations. Some of the ENA IBEX's include the following features: 1) The presence of fine structure within the ribbon suggests that the physical properties of it exhibit small-scale spacial structure and possibly rapid small-scale variations. 2) The ribbon is a fairly narrow feature at low energies and broadens with increasing energy;The IBEX detectors were designed to maximize count rate by incorporating wide angular and broad energy acceptance. Thus far, the existing mapping software used by the IBEX Science Operation Center has not been design with the "Ribbon" ( 20o wide) in mind: the current generation of maps are binned in 6o longitude pixels by 6o latitude pixels (so the pixels are all of the same size in angle and are quite "blocky"). Furthermore, the instrumental point spread function has not been deconvolved, making any potential narrow features broader than they are. An improvement in the spatial resolution of the IBEX maps would foster a better understanding of the Ribbon and its substructure, and thus reply to some of the basic and profound questions related to its origin, the nature of the outer boundaries of the our solar system and the surrounding interstellar Galactic medium.Here we report on the application of the Bayesian image reconstruction algorithm "Speedy Pixons" to the ENA data with the aim to sharpen the ENA IBEX maps. A preliminary application allow us to conclude that: The peaks in the count rate do appear to be more enhanced in the reconstruction; The reconstruction is clearly denoised; The "Ribbon" is better defined in the reconstruction. We are currently studying the implications of

  10. 1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Reddy, Bharat G.; Moates, Derek B.; Kim, Heung-Bok; Green, Todd J.; Kim, Chang-Yub; Terwilliger, Thomas C.; DeLucas, Lawrence J.

    2014-01-01

    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

  11. 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.

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

    Science.gov (United States)

    2016-08-26

    OPEN ORIGINAL ARTICLE Atomically phase-matched second-harmonic generation in a 2D crystal Mervin Zhao1,2,*, Ziliang Ye1,2,*, Ryuji Suzuki3,4,*, Yu...photoluminescence mapping, Raman spectroscopy and atomic -force microscopy. (b) Image produced via scanning and gathering the SH light produced by the 3R-MoS2...arising from a single atomic layer, where the SH light elucidated important information such as the grain boundaries and electronic structure in these ultra

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-09-25

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

  14. Toward electron exit wave tomography of amorphous materials at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Borisenko, Konstantin B., E-mail: konstantin.borisenko@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Moldovan, Grigore [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Kirkland, Angus I., E-mail: angus.kirkland@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Van Dyck, Dirk [Department of Physics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Tang, Hsin-Yu; Chen, Fu-Rong [Department of Engineering and System Science, National Tsing Hua University, Kuang-Fu Road, 300 Hsinchu, Taiwan (China)

    2012-09-25

    Highlights: Black-Right-Pointing-Pointer We suggest a novel electron exit wave tomography approach to obtain three dimensional atomic structures of amorphous materials. Black-Right-Pointing-Pointer Theoretical tests using a model of amorphous Si doped with Au show that it is feasible to reconstruct both Si and Au atoms positions. Black-Right-Pointing-Pointer Reconstructions of the strongly scattering Au atoms positions appear to be insensitive to typical experimental errors. - Abstract: We suggest to use electron exit wave phase for tomographic reconstruction of structure of Au-doped amorphous Si with atomic resolution. In the present theoretical investigation into the approach it is found that the number of projections and the accuracy of defocus in the focal series restoration are the main factors that contribute to the final resolution. Although resolution is ultimately limited by these factors, phase shifts in the exit wave are sufficient to identify the position of Au atoms in an amorphous Si needle model, even when only 19 projections with defocus error of 4 nm are used. Electron beam damage will probably further limit the resolution of such tomographic reconstructions, however beam damage can be mitigated using lower accelerating voltages.

  15. 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.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. 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%

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-15

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    Zoest, J.M. van.

    1986-01-01

    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 H 2 + 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.)

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

    Science.gov (United States)

    2013-01-01

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

  1. Visualising reacting single atoms under controlled conditions: Advances in atomic resolution in situ Environmental (Scanning) Transmission Electron Microscopy (E(S)TEM)

    Science.gov (United States)

    Boyes, Edward D.; Gai, Pratibha L.

    2014-02-01

    Advances in atomic resolution Environmental (Scanning) Transmission Electron Microscopy (E(S)TEM) for probing gas-solid catalyst reactions in situ at the atomic level under controlled reaction conditions of gas environment and temperature are described. The recent development of the ESTEM extends the capability of the ETEM by providing the direct visualisation of single atoms and the atomic structure of selected solid state heterogeneous catalysts in their working states in real-time. Atomic resolution E(S)TEM provides a deeper understanding of the dynamic atomic processes at the surface of solids and their mechanisms of operation. The benefits of atomic resolution-E(S)TEM to science and technology include new knowledge leading to improved technological processes with substantial economic benefits, improved healthcare, reductions in energy needs and the management of environmental waste generation. xml:lang="fr"

  2. Controllable optical bistability in photonic-crystal one-atom laser

    International Nuclear Information System (INIS)

    Guo Xiaoyong; Lue Shuchen

    2009-01-01

    We investigate the property of optical bistability in a photonic-crystal one-atom laser when nonlinear microcavity is present. The physical system consists of a coherently driven two-level light emitter strongly coupled to a high-quality microcavity which is embedded within a photonic crystal and another coherent probing field which has incident into the microcavity. In our case, the microcavity is fabricated by nonlinear material and placed as an impurity in photonic crystal. This study reveals that such a system can exhibit optical bistability. The dependence of threshold value and hysteresis loop on the photonic band gap of the photonic crystal, driving field Rabi frequency and dephasing processes, are studied. Our results clearly illustrate the ability to control optical bistability through suitable photonic-crystal architectures and external coherent driving field, and this study suggests that in a photonic-crystal nonlinear microcavity, the one-atom laser acts as an effective controllable bistable device in the design of all-light digital computing systems in the near future.

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

    OpenAIRE

    Lazzerini, GM; Paterno, GM; Tregnago, G; Treat, N; Stingelin, N; Yacoot, A; Cacialli, F

    2016-01-01

    We report high-resolution, traceable atomic force microscopymeasurements 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 cr...

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

    OpenAIRE

    Lazzerini, G. M.; Paterno, G. M.; Tregnago, G.; Treat, N.; Stingelin, N.; Yacoot, A.; Cacialli, F.

    2016-01-01

    We report high-resolution, traceable atomic force microscopymeasurements 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 crys...

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

    International Nuclear Information System (INIS)

    Linck, Martin; Freitag, Bert; Kujawa, Stephan; Lehmann, Michael; Niermann, Tore

    2012-01-01

    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.

  6. The Use of Atomic-Force Microscopy for Studying the Crystallization Process of Amorphous Alloys

    Science.gov (United States)

    Elmanov, G. N.; Ivanitskaya, E. A.; Dzhumaev, P. S.; Skrytniy, V. I.

    The crystallization process of amorphous alloys is accompanied by the volume changes as a result of structural phase transitions. This leads to changes in the surface topography, which was studied by atomic force microscopy (AFM). The changes of the surface topography, structure and phase composition during multistage crystallization process of the metallic glasses with composition Ni71,5Cr6,8Fe2,7B11,9Si7,1 and Ni63,4Cr7,4Fe4,3Mn0,8B15,6Si8,5 (AWS BNi2) has been investigated. The obtained results on changing of the surface topography in crystallization process are in good agreement with the data of X-ray diffraction analysis (XRD). The nature of redistribution of some alloy components in the crystallization process has been suggested.

  7. 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.

  8. 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.

  9. Optimal thickness of a monocrystal line object in atomic plane visualization on its image in a high-resolution electron microscope

    International Nuclear Information System (INIS)

    Grishina, T.A.; Sviridova, V.Yu.

    1983-01-01

    Theoretical and experimental investigation of the influence of the FCC-lattice crystal (gold, nickel) thickness on conditions of visulization of atomic plane projections (APP) on the crystal image in a transmission high-resolution electron microscope (THREM) is reported. Results of electron diffraction theory are used for theoretical investigation. Calculation analysis of the influence of the monocrystal thickness and orientation on conitions of visualization of APP and atomic columns in monocrystal images formed in THREM in multibeam regimes with inclined and axial illumination is conducted. It is shown that, to visualize the atomic column projections in a crystal image formed in the multibeam regime with axial illumination, optimal are the thicknesses from 0.1 xisub(min) to 0.25 xisub(min) and at some object orientations also the thicknesses from 0.8 xisub(min) to 0.9 xisub(min), where xisub(min) is the extinction length minimum for the given orientation. It is shown that, to realize the ultimate resolutions in multibeam regimes both with inclined and axial illumination the optimal thickness of the object is 0.63 xisub(min). Satisfactory coincidence of theoretical and experimental data is obtained

  10. 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.

  11. Mechanisms of heterogeneous crystal growth in atomic systems: insights from computer simulations.

    Science.gov (United States)

    Gulam Razul, M S; Hendry, J G; Kusalik, P G

    2005-11-22

    In this paper we analyze the atomic-level structure of solid/liquid interfaces of Lennard-Jones fcc systems. The 001, 011, and 111 faces are examined during steady-state growth and melting of these crystals. The mechanisms of crystallization and melting are explored using averaged configurations generated during these steady-state runs, where subsequent tagging and labeling of particles at the interface provide many insights into the detailed atomic behavior at the freezing and melting interfaces. The interfaces are generally found to be rough and we observe the structure of freezing and melting interfaces to be very similar. Large structural fluctuations with solidlike and liquidlike characteristics are apparent in both the freezing and melting interfaces. The behavior at the interface observed under either growth or melting conditions reflects a competition between ordering and disordering processes. In addition, we observe atom hopping that imparts liquidlike characteristics to the solid side of the interfaces for all three crystal faces. Solid order is observed to extend as rough, three-dimensional protuberances through the interface, particularly for the 001 and 011 faces. We are also able to reconcile our different measures for the interfacial width and address the onset of asymmetry in the growth rates at high rates of crystal growth/melting.

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

    International Nuclear Information System (INIS)

    Poulsen, O.

    1984-01-01

    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 51 V I, and in 235 U 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.)

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

    International Nuclear Information System (INIS)

    Stsiapanava, Alena; Koudelakova, Tana; Lapkouski, Mikalai; Pavlova, Martina; Damborsky, Jiri; Kuta Smatanova, Ivana

    2008-01-01

    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 P2 1 2 1 2 1 , 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

  14. 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

  15. Properties of the localized field emitted from degenerate Λ-type atoms in photonic crystals

    International Nuclear Information System (INIS)

    Foroozani, N.; Golshan, M. M.; Mahjoei, M.

    2007-01-01

    The spontaneous emission from a degenerate Λ-type three-level atom, embedded in a photonic crystal, is studied. The emitted field, as a function of time and position, is calculated by solving the three coupled differential equations governing the amplitudes. We show that the spontaneously emitted field is characterized by three components (as in the case of two-level and V-type atoms): a localized part, a traveling part, and a t -3/2 decaying part. Our calculations indicate that under specific conditions the atoms do not emit propagating fields, while the localized field, having shorter localization length and time, is intensified. As a consequence, the population of the upper level, after a short period of oscillations, approaches a constant value. It is also shown that this steady value, under the same conditions, is much larger than its counterpart in V-type atoms

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

    International Nuclear Information System (INIS)

    Mizutani, Kimihiko; Toyoda, Mayuko; Sagara, Kenta; Takahashi, Nobuyuki; Sato, Atsuko; Kamitaka, Yuji; Tsujimura, Seiya; Nakanishi, Yuji; Sugiura, Toshiyuki; Yamaguchi, Shotaro; Kano, Kenji; Mikami, Bunzo

    2010-01-01

    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 P6 3 . 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

  17. Effect of Ge atoms on crystal structure and optoelectronic properties of hydrogenated Si-Ge films

    Science.gov (United States)

    Li, Tianwei; Zhang, Jianjun; Ma, Ying; Yu, Yunwu; Zhao, Ying

    2017-07-01

    Optoelectronic and structural properties of hydrogenated microcrystalline silicon-germanium (μc-Si1-xGex:H) alloys prepared by radio-frequency plasma-enhanced chemical vapor deposition (RF-PECVD) were investigated. When the Ge atoms were predominantly incorporated in amorphous matrix, the dark and photo-conductivity decreased due to the reduced crystalline volume fraction of the Si atoms (XSi-Si) and the increased Ge dangling bond density. The photosensitivity decreased monotonously with Ge incorporation under higher hydrogen dilution condition, which was attributed to the increase in both crystallization of Ge and the defect density.

  18. Zigzag phosphorene nanoribbons: one-dimensional resonant channels in two-dimensional atomic crystals

    Science.gov (United States)

    Páez, Carlos J; Pereira, Ana L C; Schulz, Peter A

    2016-01-01

    We theoretically investigate phosphorene zigzag nanoribbons as a platform for constriction engineering. In the presence of a constriction at one of the edges, quantum confinement of edge-protected states reveals conductance peaks, if the edge is uncoupled from the other edge. If the constriction is narrow enough to promote coupling between edges, it gives rise to Fano-like resonances as well as antiresonances in the transmission spectrum. These effects are shown to mimic an atomic chain like behavior in a two dimensional atomic crystal. PMID:28144546

  19. Zigzag phosphorene nanoribbons: one-dimensional resonant channels in two-dimensional atomic crystals

    Directory of Open Access Journals (Sweden)

    Carlos. J. Páez

    2016-12-01

    Full Text Available We theoretically investigate phosphorene zigzag nanoribbons as a platform for constriction engineering. In the presence of a constriction at one of the edges, quantum confinement of edge-protected states reveals conductance peaks, if the edge is uncoupled from the other edge. If the constriction is narrow enough to promote coupling between edges, it gives rise to Fano-like resonances as well as antiresonances in the transmission spectrum. These effects are shown to mimic an atomic chain like behavior in a two dimensional atomic crystal.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    International Nuclear Information System (INIS)

    Selvig, K.A.

    1975-01-01

    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

  2. Design and development of high-resolution atomic beam fluorescence spectroscopy facility for isotope shift and hyperfine structure measurements

    International Nuclear Information System (INIS)

    Acharyulu, G.V.S.G.; Sankari, M.; Kiran Kumar, P.V.; Suryanarayana, M.V.

    2012-01-01

    A high-resolution atomic beam fluorescence spectroscopy facility for the determination of isotope shifts and hyperfine structure in atomic species has been designed and developed. A resistively heated graphite tube atomic beam source was designed, tested and integrated into a compact interaction chamber for atomic beam fluorescence experiments. The design of the laser-atom interaction chamber and the source has been modified in a phased manner so as to achieve sub-Doppler resolution. The system has been used to record the hyperfine spectrum of the D2 transitions of Rb and K isotopes. The spectral resolution achieved is ∼ 26 MHz and is adequate to carry out high resolution measurement of isotope shifts and hyperfine structure of various atomic species. The other major advantage of the source is that it requires very small amounts of sample for achieving very good signal to noise ratio. (author)

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

    NARCIS (Netherlands)

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

    2016-01-01

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

  4. Complete Chiral Resolution Using Additive-Induced Crystal Size Bifurcation During Grinding

    NARCIS (Netherlands)

    Noorduin, Wim L.; Asdonk, Pim van der; Meekes, Hugo; Enckevort, Willem J.P. van; Kaptein, Bernard; Leeman, Michel; Kellogg, Richard M.; Vlieg, Elias

    2009-01-01

    Grinding them down: By using a tailor-made additive, even in the absence of racemization in solution, abrasive grinding can yield an enantiopure solid state. This novel chiral resolution technique is based on an asymmetric bifurcation in the crystal size distribution as a result of stereoselective

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

    International Nuclear Information System (INIS)

    Huang, H.Z.; Yuan, Q.; Misra, R.D.K.

    2011-01-01

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-06-21

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

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

    Science.gov (United States)

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

    2009-06-22

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

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

    International Nuclear Information System (INIS)

    Cooper, David; Pan, Cheng-Ta; Haigh, Sarah

    2014-01-01

    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.

  9. Crystal structure of the alkaline proteinase Savinase from Bacillus lentus at 1.4 A resolution.

    Science.gov (United States)

    Betzel, C; Klupsch, S; Papendorf, G; Hastrup, S; Branner, S; Wilson, K S

    1992-01-20

    Savinase (EC3.4.21.14) is secreted by the alkalophilic bacterium Bacillus lentus and is a representative of that subgroup of subtilisin enzymes with maximum stability in the pH range 7 to 10 and high activity in the range 8 to 12. It is therefore of major industrial importance for use in detergents. The crystal structure of the native form of Savinase has been refined using X-ray diffraction data to 1.4 A resolution. The starting model was that of subtilisin Carlsberg. A comparison to the structures of the closely related subtilisins Carlsberg and BPN' and to the more distant thermitase and proteinase K is presented. The structure of Savinase is very similar to those of homologous Bacillus subtilisins. There are two calcium ions in the structure, equivalent to the strong and the weak calcium-binding sites in subtilisin Carlsberg and subtilisin BPN', well known for their stabilizing effect on the subtilisins. The structure of Savinase shows novel features that can be related to its stability and activity. The relatively high number of salt bridges in Savinase is likely to contribute to its high thermal stability. The non-conservative substitutions and deletions in the hydrophobic binding pocket S1 result in the most significant structural differences from the other subtilisins. The different composition of the S1 binding loop as well as the more hydrophobic character of the substrate-binding region probably contribute to the alkaline activity profile of the enzyme. The model of Savinase contains 1880 protein atoms, 159 water molecules and two calcium ions. The crystallographic R-factor [formula; see text].

  10. Experimental evaluation of interfaces using atomic-resolution high angle annular dark field (HAADF) imaging

    International Nuclear Information System (INIS)

    Robb, Paul D.; Finnie, Michael; Longo, Paolo; Craven, Alan J.

    2012-01-01

    Aberration-corrected high angle annular dark field (HAADF) imaging in scanning transmission electron microscopy (STEM) can now be performed at atomic-resolution. This is an important tool for the characterisation of the latest semiconductor devices that require individual layers to be grown to an accuracy of a few atomic layers. However, the actual quantification of interfacial sharpness at the atomic-scale can be a complicated matter. For instance, it is not clear how the use of the total, atomic column or background HAADF signals can affect the measured sharpness or individual layer widths. Moreover, a reliable and consistent method of measurement is necessary. To highlight these issues, two types of AlAs/GaAs interfaces were studied in-depth by atomic-resolution HAADF imaging. A method of analysis was developed in order to map the various HAADF signals across an image and to reliably determine interfacial sharpness. The results demonstrated that the level of perceived interfacial sharpness can vary significantly with specimen thickness and the choice of HAADF signal. Individual layer widths were also shown to have some dependence on the choice of HAADF signal. Hence, it is crucial to have an awareness of which part of the HAADF signal is chosen for analysis along with possible specimen thickness effects for future HAADF studies performed at the scale of a few atomic layers. -- Highlights: ► Quantification of interfaces using atomic-scale HAADF imaging is considered. ► The sharpness of AlAs/GaAs interfaces is investigated. ► A method of analysis was developed to map the various HAADF signals in an image. ► Measured sharpness varies with specimen thickness and HAADF signal type.

  11. Inhomogenous Dislocation Nucleation Based on Atom Potential in Hexagonal Noncentrosymmetric Crystal Sheet

    International Nuclear Information System (INIS)

    Xue-Chuan, Zhao; Xiao-Ming, Liu; Zhuo, Zhuang; Zhan-Li, Liu; Yuan, Gao

    2010-01-01

    By introducing internal degree, the deformation of hexagonal noncentrosymmetric crystal sheet can be described by the revised Cauchy–Born rule based on atomic potential. The instability criterion is deduced to investigate the inhomogeneous dislocation nucleation behavior of the crystal sheet under simple loading. The anisotropic characters of dislocation nucleation under uniaxial tension are studied by using the continuum method associated with the instability criterion. The results show a strong relationship between yield stress and crystal sheet chirality. The results also indicate that the instability criterion has sufficient ability to capture the dislocation nucleation site and expansion. To observe the internal dislocation phenomenon, the prediction of the dislocation nucleation site and expansion domain is illustrated by MD simulations. The developed method is another way to explain the dislocation nucleation phenomenon. (condensed matter: structure, mechanical and thermal properties)

  12. High-resolution compact Johann crystal spectrometer with the Livermore electron beam ion trap

    International Nuclear Information System (INIS)

    Robbins, D.L.; Chen, H.; Beiersdorfer, P.; Faenov, A.Ya.; Pikuz, T.A.; May, M.J.; Dunn, J.; Smith, A.J.

    2004-01-01

    A compact high-resolution (λ/Δλ≅10 000) spherically bent crystal spectrometer in the Johann geometry was recently installed and tested on the Lawrence Livermore National Laboratory SuperEBIT electron beam ion trap. The curvature of the mica (002) crystal grating allows for higher collection efficiency compared to the flat and cylindrically bent crystal spectrometers commonly used on the Livermore electron beam ion traps. The spectrometer's Johann configuration enables orientation of its dispersion plane to be parallel to the electron beam propagation. Used in concert with a crystal spectrometer, whose dispersion plane is perpendicular to the electron beam propagation, the polarization of x-ray emission lines can be measured

  13. Multiband super-resolution imaging of graded-index photonic crystal flat lens

    Science.gov (United States)

    Xie, Jianlan; Wang, Junzhong; Ge, Rui; Yan, Bei; Liu, Exian; Tan, Wei; Liu, Jianjun

    2018-05-01

    Multiband super-resolution imaging of point source is achieved by a graded-index photonic crystal flat lens. With the calculations of six bands in common photonic crystal (CPC) constructed with scatterers of different refractive indices, it can be found that the super-resolution imaging of point source can be realized by different physical mechanisms in three different bands. In the first band, the imaging of point source is based on far-field condition of spherical wave while in the second band, it is based on the negative effective refractive index and exhibiting higher imaging quality than that of the CPC. However, in the fifth band, the imaging of point source is mainly based on negative refraction of anisotropic equi-frequency surfaces. The novel method of employing different physical mechanisms to achieve multiband super-resolution imaging of point source is highly meaningful for the field of imaging.

  14. Partially slotted crystals for a high-resolution γ-camera based on a position sensitive photomultiplier

    International Nuclear Information System (INIS)

    Giokaris, N.; Loudos, G.; Maintas, D.; Karabarbounis, A.; Lembesi, M.; Spanoudaki, V.; Stiliaris, E.; Boukis, S.; Gektin, A.; Pedash, V.; Gayshan, V.

    2005-01-01

    Partially slotted crystals have been designed and constructed and have been used to evaluate the performance with respect to the spatial resolution of a γ-camera based on a position-sensitive photomultiplier. It is shown that the resolution obtained with such a crystal is only slightly worse than the one obtained with a fully pixelized one whose cost, however, is much higher

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

    Science.gov (United States)

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

    2017-08-01

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

  16. Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS.

    Science.gov (United States)

    Neelon, Kelly; Roberts, Mary F; Stec, Boguslaw

    2011-12-07

    1-L-myo-inositol-phosphate synthase (mIPS) catalyzes the first step of the unique, de novo pathway of inositol biosynthesis. However, details about the complex mIPS catalytic mechanism, which requires oxidation, enolization, intramolecular aldol cyclization, and reduction, are not fully known. To gain further insight into this mechanism, we determined the crystal structure of the wild-type mIPS from Archaeoglobus fulgidus at 1.7 Å, as well as the crystal structures of three active-site mutants. Additionally, we obtained the structure of mIPS with a trapped 5-keto-glucose-6-phosphate intermediate at 2 Å resolution by a novel (to our knowledge) process of activating the crystal at high temperature. A comparison of all of the crystal structures of mIPS described in this work suggests a novel type of catalytic mechanism that relies on the forced atomic proximity of functional groups. The lysine cluster is contained in a small volume in the active site, where random motions of these side chains are responsible for the progress of the complex multistep reaction as well as for the low rate of catalysis. The mechanism requires that functional groups of Lys-274, Lys-278, Lys-306, and Lys-367 assume differential roles in the protonation/deprotonation steps that must occur during the mIPS reaction. This mechanism is supported by the complete loss of activity of the enzyme caused by the Leu-257 mutation to Ala that releases the lysine containment. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Signal Tracking Beyond the Time Resolution of an Atomic Sensor by Kalman Filtering

    Science.gov (United States)

    Jiménez-Martínez, Ricardo; Kołodyński, Jan; Troullinou, Charikleia; Lucivero, Vito Giovanni; Kong, Jia; Mitchell, Morgan W.

    2018-01-01

    We study causal waveform estimation (tracking) of time-varying signals in a paradigmatic atomic sensor, an alkali vapor monitored by Faraday rotation probing. We use Kalman filtering, which optimally tracks known linear Gaussian stochastic processes, to estimate stochastic input signals that we generate by optical pumping. Comparing the known input to the estimates, we confirm the accuracy of the atomic statistical model and the reliability of the Kalman filter, allowing recovery of waveform details far briefer than the sensor's intrinsic time resolution. With proper filter choice, we obtain similar benefits when tracking partially known and non-Gaussian signal processes, as are found in most practical sensing applications. The method evades the trade-off between sensitivity and time resolution in coherent sensing.

  18. High-resolution measurements of x rays from ion-atom collisions

    International Nuclear Information System (INIS)

    Knudson, A.R.

    1974-01-01

    High resolution measurements of K x-ray spectra produced by ion-atom collisions at MeV energies are presented. These measurements indicate that a distribution of L-shell vacancies accompanies K-shell excitation. The variation of these spectra as a function of incident ion energy and atomic number is discussed. Difficulties in the analysis of these spectra due to rearrangement of vacancies between the time of the collision and the time of x-ray emission are considered. The use of high resolution x-ray measurements to obtain information on projectile ion vacancy configurations is demonstrated by data for Ar ions in KCl. X-ray spectra from Al projectiles in a variety of targets were measured and the effect of target composition on these spectra is discussed

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

    International Nuclear Information System (INIS)

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

    2009-01-01

    We describe a type of scanning electron microscope that works by directly imaging the electron field-emission sites on a nanotip. Electrons are extracted from the nanotip through a nanoscale aperture, accelerated in a high electric field, and focused to a spot using a microscale Einzel lens. If the whole microscope (accelerating section and lens) and the focal length are both restricted in size to below 10 μm, then computer simulations show that the effects of aberration are extremely small and it is possible to have a system with approximately unit magnification at electron energies as low as 300 eV. Thus a typical emission site of 1 nm diameter will produce an image of the same size, and an atomic emission site will give a resolution of 0.1-0.2 nm (1-2 A). Also, because the beam is not allowed to expand beyond 100 nm in diameter, the depth of field is large and the contribution to the beam spot size from chromatic aberrations is less than 0.02 nm (0.2 A) for 500 eV electrons. Since it is now entirely possible to make stable atomic sized emitters (nanopyramids), it is expected that this instrument will have atomic resolution. Furthermore the brightness of the beam is determined only by the field emission and can be up to 1x10 6 times larger than in a typical (high energy) electron microscope. The advantages of this low energy, bright-beam electron microscope with atomic resolution are described and include the possibility of it being used to rapidly sequence the human genome from a single strand of DNA as well as being able to identify atomic species directly from the elastic scattering of electrons

  20. Instrumentation at the National Center for Electron Microscopy: the Atomic Resolution Microscope

    International Nuclear Information System (INIS)

    Gronsky, R.; Thomas, G.

    1983-01-01

    The Atomic Resolution Microscope (ARM) is one of two unique high voltage electron microscopes at the Lawrence Berkeley Laboratory's National Center for Electron Microscopy (NCEM). The latest results from this new instrument which was manufactured by JEOL, Ltd. to the performance specifications of the NCEM, delivered in January of 1983, and soon to be open to access by the entire microscopy community are given. Details of its history and development are given and its performance specifications are reviewed

  1. High Resolution Numerical Simulations of Primary Atomization in Diesel Sprays with Single Component Reference Fuels

    Science.gov (United States)

    2015-09-01

    NC. 14. ABSTRACT A high-resolution numerical simulation of jet breakup and spray formation from a complex diesel fuel injector at diesel engine... diesel fuel injector at diesel engine type conditions has been performed. A full understanding of the primary atomization process in diesel fuel... diesel liquid sprays the complexity is further compounded by the physical attributes present including nozzle turbulence, large density ratios

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

    CSIR Research Space (South Africa)

    Malwela, T

    2014-01-01

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

  3. Chromatic Aberration Correction for Atomic Resolution TEM Imaging from 20 to 80 kV.

    Science.gov (United States)

    Linck, Martin; Hartel, Peter; Uhlemann, Stephan; Kahl, Frank; Müller, Heiko; Zach, Joachim; Haider, Max; Niestadt, Marcel; Bischoff, Maarten; Biskupek, Johannes; Lee, Zhongbo; Lehnert, Tibor; Börrnert, Felix; Rose, Harald; Kaiser, Ute

    2016-08-12

    Atomic resolution in transmission electron microscopy of thin and light-atom materials requires a rigorous reduction of the beam energy to reduce knockon damage. However, at the same time, the chromatic aberration deteriorates the resolution of the TEM image dramatically. Within the framework of the SALVE project, we introduce a newly developed C_{c}/C_{s} corrector that is capable of correcting both the chromatic and the spherical aberration in the range of accelerating voltages from 20 to 80 kV. The corrector allows correcting axial aberrations up to fifth order as well as the dominating off-axial aberrations. Over the entire voltage range, optimum phase-contrast imaging conditions for weak signals from light atoms can be adjusted for an optical aperture of at least 55 mrad. The information transfer within this aperture is no longer limited by chromatic aberrations. We demonstrate the performance of the microscope using the examples of 30 kV phase-contrast TEM images of graphene and molybdenum disulfide, showing unprecedented contrast and resolution that matches image calculations.

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

    International Nuclear Information System (INIS)

    Van Aert, S.; Verbeeck, J.; Erni, R.; Bals, S.; Luysberg, M.; Dyck, D. Van; Tendeloo, G. Van

    2009-01-01

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

  5. Positron states and nanoobjects in proton-irradiated quartz single crystals: Positronium atom in quartz

    International Nuclear Information System (INIS)

    Grafutin, V. I.; Zaluzhnyi, A. G.; Timoshenkov, S. P.; Britkov, O. M.; Ilyukhina, O. V.; Myasishcheva, G. G.; Prokop'ev, E. P.; Funtikov, Yu. V.

    2008-01-01

    The influence of proton bombardment and metal atom impurities on the structure of quartz single crystals has been studied. The related defects have been studied using positron annihilation spectroscopy (angular correlation of positron-annihilation photons), acoustic absorption, and optical absorption measurements. It is shown that the presence of a narrow component f in the angular distribution of annihilation photons (ADAP), which is related to the formation of parapositronium, determines a high sensitivity of this method with respect to features of the crystal structure of quartz. It is established that the defectness of the structure of irradiated quartz crystals can be characterized by the ratio f/f 0 of the relative intensities of narrow components in the ADAP curves measured before (f 0 ) and after (f) irradiation. Any process leading to a decrease in the probability of positronium formation (e.g., positron loss as a result of the trapping on defects and the interaction with impurity atoms and lattice distortions) decreases the intensity of the narrow component. Based on the ADAP data, estimates of the radii and concentrations of nanodefects in quartz have been obtained and their variation upon annealing at temperatures up to T = 873 K has been studied

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

    Science.gov (United States)

    Ren, He

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

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

    Science.gov (United States)

    Stsiapanava, Alena; Koudelakova, Tana; Lapkouski, Mikalai; Pavlova, Martina; Damborsky, Jiri; Smatanova, Ivana Kuta

    2008-02-01

    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 P2(1)2(1)2(1), 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 A, respectively.

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

    International Nuclear Information System (INIS)

    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 (λ/Δλ ∼ 3000) with fast time resolution (4 msec per spectrum) and good spatial resolution (3 cm). The spectral bandwidth is Δλ/λ 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. 43 refs., 23 figs

  9. High spatial resolution measurement of depth-of-interaction of a PET LSO crystal

    International Nuclear Information System (INIS)

    Simon, A.; Kalinka, G.; Novak, D.; Sipos, A.; Vegh, J.; Molnar, J.

    2004-01-01

    Complete text of publication follows. A new type of experimental technique to investigate the depth-of-interaction (DOI) dependence in small scintillator elements designed for high-resolution animal PET [1] has been introduced at our institute, recently. A lutetium oxyorthosilicate (LSO) crystal (2x2x10 mm 3 ) was irradiated with a highly focused 2 MeV He + beam at the ATOMKI nuclear microprobe laboratory. Pulse height spectra from a photomultiplier (PMT) attached to one end of the LSO crystal were collected in list mode. Sequential scans of 1000x1000 μm 2 areas along the 10 mm long crystal were made to get high lateral resolution images of pulse height spectra at different distances from the window of the PMT. A mean pulse height algorithm was applied to each pixel to generate two dimensional intensity images and the corresponding spectra of 100 μmx1 mm areas. Representative pulse height spectra are shown in Fig. 1 for different distances between the position of irradiation and the PMT. The mean value of the pulse height spectrum describing the position of the full energy peak is a way to measure DOI effects. It is seen that the closer the DOI to the PMT-end of the crystal the higher the energy of the peak. The centre of the detected peak varies about 30 % along the lateral side of the crystal. This effect is due to the increasing number of reflections with associated loss of light when the distance between the DOI position and the light collecting PMT grows. Further these results, no difference in the light intensity was found depending on which position across (perpendicular to the length of) the crystal was irradiated with the microbeam. The obtained results of the overall DOI dependence confirm previous measurements on LSO crystals with similar geometry and wrapping but based on collimated gamma-ray irradiation. Since the present experimental setup allows obtaining data with several orders of magnitude better spatial resolution (from μm up to mm) than with

  10. High resolution monochromatic X-ray imaging system based on spherically bent crystals

    International Nuclear Information System (INIS)

    Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C.M.; Seely, J.; Feldman, U.; Holland, G.

    1997-01-01

    We have developed a new X-ray imaging system based on spherically curved crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser [1,2]. The imaging system is used for plasma diagnostics of the main target and for characterization of potential backlighters. A spherically curved quartz crystal (2d=6.687 Angstrom, R=200mm) is used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the X-ray optical system is 3 endash 4 μm. Time resolved backlit monochromatic images of CH planar targets driven by the Nike facility have been obtained with 6 endash 7 μm spatial resolution. copyright 1997 American Institute of Physics

  11. High resolution monochromatic X-ray imaging system based on spherically bent crystals

    International Nuclear Information System (INIS)

    Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C. M.; Seely, J.; Feldman, U.; Holland, G.

    1997-01-01

    We have developed a new X-ray imaging system based on spherically curved crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser. The imaging system is used for plasma diagnostics of the main target and for characterization of potential backlighters. A spherically curved quartz crystal (2d=6.687 A, R=200 mm) is used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the X-ray optical system is 3-4 μm. Time resolved backlit monochromatic images of CH planar targets driven by the Nike facility have been obtained with 6-7 μm spatial resolution

  12. High-resolution monochromatic x-ray imaging system based on spherically bent crystals

    International Nuclear Information System (INIS)

    Aglitskiy, Y.; Lehecka, T.; Obenschain, S.; Bodner, S.; Pawley, C.; Gerber, K.; Sethian, J.; Brown, C.M.; Seely, J.; Feldman, U.; Holland, G.

    1998-01-01

    We have developed an improved x-ray imaging system based on spherically curve crystals. It is designed and used for diagnostics of targets ablatively accelerated by the Nike KrF laser. A spherically curved quartz crystal (2d=6.687 Angstrom, R=200 mm) has been used to produce monochromatic backlit images with the He-like Si resonance line (1865 eV) as the source of radiation. The spatial resolution of the x-ray optical system is 1.7 μm in selected places and 2 - 3 μm over a larger area. Time-resolved backlit monochromatic images of polystyrene planar targets driven by the Nike facility have been obtained with a spatial resolution of 2.5 μm in selected places and 5 μm over the focal spot of the Nike laser. copyright 1998 Optical Society of America

  13. Atomic resolution chemical bond analysis of oxygen in La2CuO4

    Science.gov (United States)

    Haruta, M.; Nagai, T.; Lugg, N. R.; Neish, M. J.; Nagao, M.; Kurashima, K.; Allen, L. J.; Mizoguchi, T.; Kimoto, K.

    2013-08-01

    The distorted CuO6 octahedron in La2CuO4 was studied using aberration-corrected scanning transmission electron microscopy at atomic resolution. The near-edge structure in the oxygen K-edge electron energy-loss spectrum was recorded as a function of the position of the electron probe. After background subtraction, the measured spectrum image was processed using a recently developed inversion process to remove the mixing of signals on the atomic columns due to elastic and thermal scattering. The spectra were then compared with first-principles band structure calculations based on the local-density approximation plus on-site Coulomb repulsion (LDA + U) approach. In this article, we describe in detail not only anisotropic chemical bonding of the oxygen 2p state with the Cu 3d state but also with the Cu 4p and La 5d/4f states. Furthermore, it was found that buckling of the CuO2 plane was also detectable at the atomic resolution oxygen K-edge. Lastly, it was found that the effects of core-hole in the O K-edge were strongly dependent on the nature of the local chemical bonding, in particular, whether it is ionic or covalent.

  14. Influence of spatial and temporal coherences on atomic resolution high angle annular dark field imaging

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Andreas, E-mail: andreas.beyer@physik.uni-marburg.de; Belz, Jürgen; Knaub, Nikolai; Jandieri, Kakhaber; Volz, Kerstin

    2016-10-15

    Aberration-corrected (scanning) transmission electron microscopy ((S)TEM) has become a widely used technique when information on the chemical composition is sought on an atomic scale. To extract the desired information, complementary simulations of the scattering process are inevitable. Often the partial spatial and temporal coherences are neglected in the simulations, although they can have a huge influence on the high resolution images. With the example of binary gallium phosphide (GaP) we elucidate the influence of the source size and shape as well as the chromatic aberration on the high angle annular dark field (HAADF) intensity. We achieve a very good quantitative agreement between the frozen phonon simulation and experiment for different sample thicknesses when a Lorentzian source distribution is assumed and the effect of the chromatic aberration is considered. Additionally the influence of amorphous layers introduced by the preparation of the TEM samples is discussed. Taking into account these parameters, the intensity in the whole unit cell of GaP, i.e. at the positions of the different atomic columns and in the region between them, is described correctly. With the knowledge of the decisive parameters, the determination of the chemical composition of more complex, multinary materials becomes feasible. - Highlights: • Atomic resolution high angle annular dark field images of gallium phosphide are compared quantitatively with simulated ones. • The influence of partial spatial and temporal coherence on the HAADF-intensity is investigated. • The influence of amorphous layers introduced by the sample preparation is simulated.

  15. High-efficiency transmision neutron polarizer for high-resolution double crystal diffractometer

    International Nuclear Information System (INIS)

    Ioffe, A.; Krist, T.; Mezei, F.; Gordeev, G.; Ibrayev, B.

    1997-01-01

    An efficient transmission geometry neutron polarizer for the high-resolution double crystal diffractometer at HMI (λ=4.8 A) is described. A polarization of about 94% was achieved and the polarized neutron beam intensity amounts to 40% of the nonpolarized beam intensity. This opens up wide possibilities for the study of magnetic small-angle scattering for extremely small momentum transfer (Q∝10 -5 A -1 ). (orig.)

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

    International Nuclear Information System (INIS)

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

    1988-01-01

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

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

    International Nuclear Information System (INIS)

    Millo, O.; Katz, D.

    1999-01-01

    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

  18. Quartz-crystal microbalance study for characterizing atomic oxygen in plasma ash tools

    International Nuclear Information System (INIS)

    Srivastava, A.K.; Sakthivel, P.

    2001-01-01

    This article discusses the measurement of atomic oxygen (AO) concentrations in an oxygen discharge using a quartz-crystal microbalance (QCM). This is a device that has been previously used for monitoring thin-film deposition, among several other applications. The sensor consists of a silver-coated quartz crystal that oscillates at its specific resonant frequency (typically, at about 6 MHz), which is dependent on the mass of the crystal. When exposed to AO, the silver oxidizes rapidly, resulting in a change in its mass, and a consequent change in this frequency. The frequency change is measured with a counter, and when plotted versus time, it may be fit to a standard diffusion-limited oxide-growth model. This model is then used to determine the specific AO flux to the crystal, and by inference, to the wafer. Initial results of QCM measurements in the FusionGemini Plasma Asher (GPL TM -standard downstream microwave asher) and FusionGemini Enhanced Strip (GES TM -fluorine compatible enhanced strip asher) are presented in this article. The results indicate AO densities of the order of 10 12 cm -3 on the wafer. There is a marked increase in AO concentration with addition of nitrogen into the plasma, and a decrease in AO concentration with increasing pressure at constant flow. Effects of increasing the total plasma volume in the enhanced strip tool on AO production are discussed

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

    International Nuclear Information System (INIS)

    Tronrud, Dale E.; Karplus, P. Andrew

    2011-01-01

    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/

  20. 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...

  1. Translational-rotational interaction in dynamics and thermodynamics of 2D atomic crystal with molecular impurity

    International Nuclear Information System (INIS)

    Antsygina, T.N.; Poltavskaya, M.I.; Chishko, K.A.

    2003-01-01

    The interaction between the rotational degrees of freedom of a diatomic molecular impurity and the phonon excitations of a two-dimensional atomic matrix commensurate with a substrate is investigated theoretically. It is shown, that the translational-rotational interaction changes the form of the rotational kinetic energy operator as compared to the corresponding expression for a free rotator, and also renormalized the parameters of the crystal field without change in its initial form. The contribution of the impurity rotational degrees of freedom to the low-temperature heat capacity for a dilute solution of diatomic molecules in an atomic two-dimensional matrix is calculated. The possibility of experimental observation of the effects obtained is discussed

  2. Optical coupling between atomically thin black phosphorus and a two dimensional photonic crystal nanocavity

    Science.gov (United States)

    Ota, Yasutomo; Moriya, Rai; Yabuki, Naoto; Arai, Miho; Kakuda, Masahiro; Iwamoto, Satoshi; Machida, Tomoki; Arakawa, Yasuhiko

    2017-05-01

    Atomically thin black phosphorus (BP) is an emerging two dimensional (2D) material exhibiting bright photoluminescence in the near infrared region. Coupling its radiation to photonic nanostructures will be an important step toward the realization of 2D material based nanophotonic devices that operate efficiently in the near infrared region, which includes the technologically important optical telecommunication wavelength bands. In this letter, we demonstrate the optical coupling between atomically thin BP and a 2D photonic crystal nanocavity. We employed a home-build dry transfer apparatus for placing a thin BP flake on the surface of the nanocavity. Their optical coupling was analyzed through measuring cavity mode emission under optical carrier injection at room temperature.

  3. Ion beam focusing by the atomic chains of a crystal lattice

    International Nuclear Information System (INIS)

    Shulga, V.I.

    1975-01-01

    A study is made of the focusing of a parallel ion beam by a pair of close packed atomic chains of a crystal. The focal length of this system has been calculated to the approximation of continuous potential of chain in the general form and also for a number of specific potentials of ion-atom interactions. Ar ion beam focusing by a Cu chain pair is discusssed in detail. For this case, the focal length has been calculated as a function of ion energy using the method of computer simulation of ion trajectories in the chain field. The calculations were made on the basis of the Born-Mayer potential with various constants. A pronounced dependence of focal length on the constant in this potential has been found. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-28

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

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

    Science.gov (United States)

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

    2012-10-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

    International Nuclear Information System (INIS)

    Fumagalli, L; Ferrari, G; Sampietro, M; Casuso, I; MartInez, E; Samitier, J; Gomila, G

    2006-01-01

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Fumagalli, L [Dipartimento di Elettronica e Informazione, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 (Italy); Ferrari, G [Dipartimento di Elettronica e Informazione, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 (Italy); Sampietro, M [Dipartimento di Elettronica e Informazione, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 (Italy); Casuso, I [Departament d' Electronica, Universitat de Barcelona, C/MartIi Franques 1, 08028 Barcelona (Spain); MartInez, E [Plataforma de Nanotecnologia, Parc Cientific de Barcelona, C/ Josep Samitier 1-5, 08028-Barcelona (Spain); Samitier, J [Departament d' Electronica, Universitat de Barcelona, C/MartIi Franques 1, 08028 Barcelona (Spain); Gomila, G [Departament d' Electronica, Universitat de Barcelona, C/MartIi Franques 1, 08028 Barcelona (Spain)

    2006-09-28

    Nanoscale capacitance imaging with attofarad resolution ({approx}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.

  9. 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.

  10. Improvement of optical imaging resolution by a negative refraction photonic crystal with a solid immersion lens

    International Nuclear Information System (INIS)

    Tseng, M.-C.; Chen, L.-W.; Liu, C.-Y.

    2008-01-01

    Photonic crystals (PCs) have many potential applications because of their ability to control light-wave propagation. We have investigated the solid immersion lens (SIL) technology in imaging system based on negative refraction PCs and analyzed the influence of refractive index and geometric parameters of SIL on imaging resolution. In the finite element method calculation, the resolution of our optical system has improved greatly. The high performance of imaging resolution was achieved with shorter radius and larger refractive index of SIL. Furthermore, the effects of the three kinds of SILs at the same radius were analyzed. Such a mechanism of negative refraction PCs and SILs should open up a new application for designing components in optical imaging systems

  11. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Duo, E-mail: zhangduo10@gmail.com [Wuhan National Laboratory for Optoelectronics and School of Physics, Huazhong University of Science and Technology, Wuhan 430074 (China); School of Electrical and Electronic Engineering, Wuhan Polytechnic University, Wuhan 430023 (China); Li, Jiahua, E-mail: huajia_li@163.com [Wuhan National Laboratory for Optoelectronics and School of Physics, Huazhong University of Science and Technology, Wuhan 430074 (China); Ding, Chunling; Yang, Xiaoxue [Wuhan National Laboratory for Optoelectronics and School of Physics, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2012-05-21

    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.

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

    International Nuclear Information System (INIS)

    Zhang, Duo; Li, Jiahua; Ding, Chunling; Yang, Xiaoxue

    2012-01-01

    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.

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

    Science.gov (United States)

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

    2017-11-01

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

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

    International Nuclear Information System (INIS)

    Cousty, J.P.

    1981-12-01

    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 [fr

  16. Irradiation induced defects containing oxygen atoms in germanium crystal as studied by deep level transient spectroscopy

    International Nuclear Information System (INIS)

    Fukuoka, Noboru; Kambe, Yoshiyuki; Saito, Haruo; Matsuda, Koji.

    1984-05-01

    Deep level transient spectroscopy was applied to the electron trapping levels which are associated with the irradiation induced lattice defects in germanium crystals. The germanium crystals used in the study were doped with oxygen, antimony or arsenic and the defects were formed by electron irradiation of 1.5MeV or 10MeV. The nature of so called ''thermal defect'' formed by heat treatment at about 670K was also studied. The trapping levels at Esub(c)-0.13eV, Esub(c)-0.25eV and Esub(c)-0.29eV were found to be associated with defects containing oxygen atoms. From the experimental results the Esub(c)-0.25eV level was attributed to the germanium A-center (interstitial oxygen atom-vacancy pair). Another defect associated with the 715cm -1 infrared absorption band was found to have a trapping level at the same position at Esub(c)-0.25eV. The Esub(c)-0.23eV and Esub(c)-0.1eV levels were revealed to be associated with thermal donors formed by heat treatment at about 670K. Additional two peaks (levels) were observed in the DLTS spectrum. The annealing behavior of the levels suggests that the thermal donors originate from not a single type but several types of defects. (author)

  17. Lattice location of diffused Zn atoms in GaAs and InP single crystals

    International Nuclear Information System (INIS)

    Chan, L.Y.; Yu, K.M.; Ben-Tzur, M.; Haller, E.E.; Jaklevic, J.M.; Walukiewicz, W.; Hanson, C.M.

    1991-01-01

    We have investigated the saturation phenomenon of the free carrier concentration in p-type GaAs and InP single crystals doped by zinc diffusion. The free hole saturation occurs at 10 20 cm -3 for GaAs, but the maximum concentration for InP appears at mid 10 18 cm -3 . The difference in the saturation hole concentrations for these materials is investigated by studying the incorporation and the lattice location of the impurity zinc, an acceptor when located on a group III atom site. Zinc is diffused into the III-V wafers in a sealed quartz ampoule. Particle-induced x-ray emission with ion-channeling techniques are employed to determine the exact lattice location of the zinc atoms. We have found that over 90% of all zinc atoms occupy Ga sites in the diffused GaAs samples, while for the InP case, the zinc substitutionality is dependent on the cooling rate of the sample after high-temperature diffusion. For the slowly cooled sample, a large fraction (∼90%) of the zinc atoms form random precipitates of Zn 3 P 2 and elemental Zn. However, when rapidly cooled only 60% of the zinc forms such precipitates while the rest occupies specific sites in the InP. We analyze our results in terms of the amphoteric native defect model. We show that the difference in the electrical activity of the Zn atoms in GaAs and InP is a consequence of the different location of the Fermi level stabilization energy in these two materials

  18. Precision controlled atomic resolution scanning transmission electron microscopy using spiral scan pathways

    Science.gov (United States)

    Sang, Xiahan; Lupini, Andrew R.; Ding, Jilai; Kalinin, Sergei V.; Jesse, Stephen; Unocic, Raymond R.

    2017-03-01

    Atomic-resolution imaging in an aberration-corrected scanning transmission electron microscope (STEM) can enable direct correlation between atomic structure and materials functionality. The fast and precise control of the STEM probe is, however, challenging because the true beam location deviates from the assigned location depending on the properties of the deflectors. To reduce these deviations, i.e. image distortions, we use spiral scanning paths, allowing precise control of a sub-Å sized electron probe within an aberration-corrected STEM. Although spiral scanning avoids the sudden changes in the beam location (fly-back distortion) present in conventional raster scans, it is not distortion-free. “Archimedean” spirals, with a constant angular frequency within each scan, are used to determine the characteristic response at different frequencies. We then show that such characteristic functions can be used to correct image distortions present in more complicated constant linear velocity spirals, where the frequency varies within each scan. Through the combined application of constant linear velocity scanning and beam path corrections, spiral scan images are shown to exhibit less scan distortion than conventional raster scan images. The methodology presented here will be useful for in situ STEM imaging at higher temporal resolution and for imaging beam sensitive materials.

  19. Quantitative atomic resolution elemental mapping via absolute-scale energy dispersive X-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Z. [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia); Weyland, M. [Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800 (Australia); Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800 (Australia); Sang, X.; Xu, W.; Dycus, J.H.; LeBeau, J.M. [Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695 (United States); D' Alfonso, A.J.; Allen, L.J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Findlay, S.D., E-mail: scott.findlay@monash.edu [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia)

    2016-09-15

    Quantitative agreement on an absolute scale is demonstrated between experiment and simulation for two-dimensional, atomic-resolution elemental mapping via energy dispersive X-ray spectroscopy. This requires all experimental parameters to be carefully characterized. The agreement is good, but some discrepancies remain. The most likely contributing factors are identified and discussed. Previous predictions that increasing the probe forming aperture helps to suppress the channelling enhancement in the average signal are confirmed experimentally. It is emphasized that simple column-by-column analysis requires a choice of sample thickness that compromises between being thick enough to yield a good signal-to-noise ratio while being thin enough that the overwhelming majority of the EDX signal derives from the column on which the probe is placed, despite strong electron scattering effects. - Highlights: • Absolute scale quantification of 2D atomic-resolution EDX maps is demonstrated. • Factors contributing to remaining small quantitative discrepancies are identified. • Experiment confirms large probe-forming apertures suppress channelling enhancement. • The thickness range suitable for reliable column-by-column analysis is discussed.

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

    Science.gov (United States)

    Lu, Shih-I.

    2018-01-01

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

  1. Improved self-control system for the DR1 high resolution focusing neutron crystal diffractometer operation

    International Nuclear Information System (INIS)

    Ionita, I; Florescu, V.

    2010-01-01

    During the last decade new principles for the design of high-resolution configurations for crystal neutron diffractometry have been developed leading to the concept of Q-space high-resolution configuration which proved to be an alternative to the existing conventional configuration. The characteristics of such a focusing configuration are the use of open beam geometry (absence of the Soller collimators), use of the bent crystals in asymmetric reflection as monochromators and the rotation of the sample during the diffraction pattern raise, to fulfill the focusing conditions. High-resolution is obtained with no collimators by controlling the curvature and reflectivity of bent monochromators. At the sample position the beam width is rather wide offering the possibility to use wide plate-like samples with a significant raise of intensity; still high-resolution can be obtained by rotating the sample to get the focusing condition (to compensate the sample width contribution to the line-width) for each value of the scattering angle. This paper aims to clarify in which conditions such a Q-space focusing configuration, particularly that existing at INR Pitesti, can be used for stress determinations. Taking account of the characteristics of such measurements, it is quite obvious that the sample cannot be placed in focusing position appearing a limitation of the dimension of the sample region for which stress determinations are made, if we want still to have a reasonable good resolution. This can be done by using corresponding diaphragms in front of the sample holder but, if an optimal use of the available neutron beam is desired, a real-space focusing at sample position is required. For a two crystals monochromators unit the conditions to get real-space focusing were extensively analyzed by M. Popovici and W.B.Yelon. For the case of a single crystal monochromator, though such instruments are used at HMI Berlin or NRI Rez, a real space focusing is not possible to be achieved

  2. A high resolution reflecting crystal spectrometer to measure 3 keV pionic hydrogen and deuterium X-rays

    International Nuclear Information System (INIS)

    Badertscher, A.; Bogdan, M.; Goudsmit, P.F.A.; Knecht, L.; Leisi, H.J.; Schroeder, H.C.; Sigg, D.; Zhao, Z.G.; Chatellard, D.; Egger, J.P.; Jeannet, E.; Aschenauer, E.C.; Gabathuler, K.; Simons, L.M.; Rusi El Hassani, A.J.

    1993-01-01

    A reflecting crystal spectrometer consisting of three cylindrically bent quartz (110) crystals is described. It was designed to measure the 3 keV K β X-rays from pionic hydrogen and deuterium. Charge coupled devices (CCDs) were used as X-ray detectors. Projecting the reflexes of all three crystals on one common focus, an instrumental energy resolution below 1 eV was obtained at an energy of 2.9 keV. (orig.)

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

    Science.gov (United States)

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

    2014-01-01

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

  4. Torsional tapping atomic force microscopy for molecular resolution imaging of soft matter

    Science.gov (United States)

    Hobbs, Jamie; Mullin, Nic

    2012-02-01

    Despite considerable advances in image resolution on challenging, soft systems, a method for obtaining molecular resolution on `real' samples with significant surface roughness has remained elusive. Here we will show that a relatively new technique, torsional tapping AFM (TTAFM), is capable of imaging with resolution down to 3.7 Angrstrom on the surface of `bulk' polymer films [1]. In TTAFM T-shaped cantilevers are driven into torsional oscillation. As the tip is offset from the rotation axis this provides a tapping motion. Due to the high frequency and Q of the oscillation and relatively small increase in spring constant, improved cantilever dynamics and force sensitivity are obtained. As the tip offset from the torsional axis is relatively small (typically 25 microns), the optical lever sensitivity is considerably improved compared to flexural oscillation. Combined these give a reduction in noise floor by a factor of 12 just by changing the cantilever geometry. The ensuing low noise allows the use of ultra-sharp `whisker' tips with minimal blunting. As the cantilevers remain soft in the flexural axis, the force when imaging with error is also reduced, further protecting the tip. We will show that this combination allows routine imaging of the molecular structure of semicrystalline polymer films, including chain folds, loose loops and tie-chains in polyethylene, and the helical conformation of polypropylene within the crystal, using a standard, commercial AFM. [4pt] [1] N Mullin, JK Hobbs, PRL 107, 197801 (2011)

  5. Length-extension resonator as a force sensor for high-resolution frequency-modulation atomic force microscopy in air.

    Science.gov (United States)

    Beyer, Hannes; Wagner, Tino; Stemmer, Andreas

    2016-01-01

    Frequency-modulation atomic force microscopy has turned into a well-established method to obtain atomic resolution on flat surfaces, but is often limited to ultra-high vacuum conditions and cryogenic temperatures. Measurements under ambient conditions are influenced by variations of the dew point and thin water layers present on practically every surface, complicating stable imaging with high resolution. We demonstrate high-resolution imaging in air using a length-extension resonator operating at small amplitudes. An additional slow feedback compensates for changes in the free resonance frequency, allowing stable imaging over a long period of time with changing environmental conditions.

  6. High-resolution studies of momentum distributions using perfect crystal gamma diffractometry

    International Nuclear Information System (INIS)

    Krexner, G.; Bischof, G.; Jentschel, M.; Boerner, H.

    2006-01-01

    Full text: Positron annihilation spectroscopy has turned out to be highly successful in the investigation of Fermi surfaces, electronic structures and various kinds of defects. On the other hand, algorithms based on density functional theory have made enormous progress in recent years and calculations for the contributions of both delocalized and core electrons in a rapidly increasing number of systems is either already feasible today or to be expected in the near future. By comparison, over the last decades there has been little improvement in the experimental limitations which are still set by the energy resolution of germanium detectors (slightly above 1 keV for annihilation photons close to 500 keV) and the angular resolution in ACAR studies (superior by about one order of magnitude). In addition, coincidence techniques are hampered by low count rates. An alternative is suggested by the fact that, in principle, Bragg diffraction techniques using perfect single crystals provide a way for the precise determination of wavelengths corresponding to energies in the MeV range. The single crystal analyzer instrument PN3 at the Institute Laue-Langevin (Grenoble, France) offers the unique possibility to determine the energy of annihilation photons with an accuracy close to about 1 eV, i.e. an improvement of up to three orders of magnitude in comparison to conventional semiconductor detectors. We discuss possible applications of this spectrometer in high-resolution studies of momentum distributions for both delocalized and core electrons. (author)

  7. Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.

    Science.gov (United States)

    Organtini, Lindsey J; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E; Makhov, Alexander M; Conway, James F; Parrish, Colin R; Hafenstein, Susan

    2016-11-01

    Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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

    International Nuclear Information System (INIS)

    Lee, Z.; Rose, H.; Lehtinen, O.; Biskupek, J.; Kaiser, U.

    2014-01-01

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

  9. Sub-nanometer-resolution imaging of peptide nanotubes in water using frequency modulation atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Sugihara, Tomoki; Hayashi, Itsuho; Onishi, Hiroshi [Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Kimura, Kenjiro, E-mail: kimura@gold.kobe-u.ac.jp [Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Tamura, Atsuo [Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan)

    2013-06-20

    Highlights: ► Peptide nanotubes were aligned on highly oriented pyrolytic graphite surface. ► We visualized sub-nanometer-scale structure on peptide nanotube surface in water. ► We observed hydration structure at a peptide nanotube/water interface. - Abstract: Peptide nanotubes are self-assembled fibrous materials composed of cyclic polypeptides. Recently, various aspects of peptide nanotubes have been studied, in particular the utility of different methods for making peptide nanotubes with diverse designed functions. In order to investigate the relationship between formation, function and stability, it is essential to analyze the precise structure of peptide nanotubes. Atomic-scale surface imaging in liquids was recently achieved using frequency modulation atomic force microscopy with improved force sensing. Here we provide a precise surface structural analysis of peptide nanotubes in water without crystallizing them obtained by imaging the nanotubes at the sub-nanometer scale in water. In addition, the local hydration structure around the peptide nanotubes was observed at the nanotube/water interface.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-01

    The theory and practical problems of continuum source simultaneous multi-element electrothermal atomic absorption spectrometry (SMET AAS) are discussed by the example of direct analysis of underground water. The experimental methodology is based on pulse vaporization of the sample in a fast heated graphite tube and measurement of transient absorption of continuum spectrum radiation from D{sub 2} and Xe lamps within 200–400 nm wavelengths range with a low resolution spectral instrument and linear charge-coupled device. The setup permits the acquisition of 200 spectra during 1 s atomization pulse. Respective data matrix absorbance vs wavelength/time is employed for the quantification of elements in the sample. The calculation algorithm developed includes broad band and continuum background correction, linearization of function absorbance vs. concentration of atomic vapor and integration of thus modified absorbance at the resonance lines of the elements to be determined. Practical application shows that the method can be employed for the direct simultaneous determination of about 20 elements above microgram per liter level within 3–5 orders of the magnitude concentration range. The investigated sources of measurement errors are mainly associated with the atomization and vapor transportation problems, which are aggravated for the simultaneous release of major and minor sample constituents. Respective corrections concerning the selection of analytical lines, optimal sampling volume, matrix modification and cleaning of the atomizer have been introduced in the SMET AAS analytical technology. Under the optimized experimental conditions the calibration curves in Log-Log coordinates for all the investigated analytes in the single or multi-element reference solutions are approximated by the first order equations. The use of these equations as permanent characteristics of the setup enables instant quantification of Al, Ca, Co, Cr, Cu, Fe, Mg, Mn and Ni in the underground

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

    International Nuclear Information System (INIS)

    Katskov, Dmitri

    2015-01-01

    The theory and practical problems of continuum source simultaneous multi-element electrothermal atomic absorption spectrometry (SMET AAS) are discussed by the example of direct analysis of underground water. The experimental methodology is based on pulse vaporization of the sample in a fast heated graphite tube and measurement of transient absorption of continuum spectrum radiation from D 2 and Xe lamps within 200–400 nm wavelengths range with a low resolution spectral instrument and linear charge-coupled device. The setup permits the acquisition of 200 spectra during 1 s atomization pulse. Respective data matrix absorbance vs wavelength/time is employed for the quantification of elements in the sample. The calculation algorithm developed includes broad band and continuum background correction, linearization of function absorbance vs. concentration of atomic vapor and integration of thus modified absorbance at the resonance lines of the elements to be determined. Practical application shows that the method can be employed for the direct simultaneous determination of about 20 elements above microgram per liter level within 3–5 orders of the magnitude concentration range. The investigated sources of measurement errors are mainly associated with the atomization and vapor transportation problems, which are aggravated for the simultaneous release of major and minor sample constituents. Respective corrections concerning the selection of analytical lines, optimal sampling volume, matrix modification and cleaning of the atomizer have been introduced in the SMET AAS analytical technology. Under the optimized experimental conditions the calibration curves in Log-Log coordinates for all the investigated analytes in the single or multi-element reference solutions are approximated by the first order equations. The use of these equations as permanent characteristics of the setup enables instant quantification of Al, Ca, Co, Cr, Cu, Fe, Mg, Mn and Ni in the underground water

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-03-15

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

  13. Local atomic and crystal structure rearrangement during the martensitic transformation in Ti50Ni25Cu25 shape memory alloy

    International Nuclear Information System (INIS)

    Menushenkov, Alexey; Grishina, Olga; Shelyakov, Alexander; Yaroslavtsev, Alexander; Zubavichus, Yan; Veligzhanin, Alexey; Bednarcik, Jozef; Chernikov, Roman; Sitnikov, Nikolay

    2014-01-01

    Highlights: • Local crystalline structure of TiNiCu SMA is investigated using EXAFS. • Peculiarities of Ni and Cu local environment are found. • Ti atoms show greater mobility relative to Ni atoms. • Ni local environment change is significant for shape memory effect. -- Abstract: The changes of crystal structure and local crystalline environment of Ti, Ni and Cu atoms in Ti 50 Ni 25 Cu 25 shape memory alloy are investigated using X-ray diffraction and extended X-ray absorption fine structure spectroscopy (EXAFS) in temperature range of martensite transformation. 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 around 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

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

    KAUST Repository

    Roldan, Manuel

    2016-12-21

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

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

    International Nuclear Information System (INIS)

    Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

    2013-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    H Ichinose

    2000-01-01

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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Suharso Suharso

    2010-06-01

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

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

    Science.gov (United States)

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

    2012-06-13

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

  20. 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.

  1. Super-resolution with an optically-addressable liquid crystal spatial light modulator

    International Nuclear Information System (INIS)

    McOrist, J.; Sharma, M.D.; Sheppard, C.J.R.

    2002-01-01

    Full text: An optically-addressable liquid crystal spatial light modulator has been used to generate super-resolving masks. This approach avoids problems of low efficiency and coupling between amplitude and phase modulation, that occur when using conventional liquid crystal modulators. When addressed by a programmed light intensity distribution, it allows filters to be changed rapidly to modify the response of a system or permit the investigation of different filter designs. The device used is not pixellated, with a spatial resolution of 30 line pairs/mm over an area 18mm X 18mm, and can achieve continuously-variable phase modulation up to 1.5 wavelengths. The system consists of a write-beam that is collimated from a white-light source. An input mask was used in our experiments determines the modulation pattern of the read-beam. The read-beam from a HeNe laser reflects from the modulator and is focused by a microscope objective. The value of the phase change induced by the transparent regions of the mask can be altered continuously by adjusting the brightness of the write-beam. We have used this system to attain super-resolution by simple Toraldo filters, consisting of arrays of rings. Copyright (2002) Australian Society for Electron Microscopy Inc

  2. Investigation of chemical modifiers for phosphorus in a graphite furnace using high-resolution continuum source atomic absorption spectrometry

    International Nuclear Information System (INIS)

    Lepri, Fabio G.; Dessuy, Morgana B.; Vale, Maria Goreti R.; Borges, Daniel L.G.; Welz, Bernhard; Heitmann, Uwe

    2006-01-01

    Phosphorus is not one of the elements that are typically determined by atomic absorption spectrometry, but this technique nevertheless offers several advantages that make it attractive, such as the relatively great freedom from interferences. As the main resonance lines for phosphorus are in the vacuum-ultraviolet, inaccessible by conventional atomic absorption spectrometry equipment, L'vov and Khartsyzov proposed to use the non-resonance doublet at 213.5 / 213.6 nm. Later it turned out that with conventional equipment it is necessary to use a chemical modifier in order to get reasonable sensitivity, and lanthanum was the first one suggested for that purpose. In the following years more than 30 modifiers have been proposed for the determination of this element, and there is no consensus about the best one. In this work high-resolution continuum source atomic absorption spectrometry has been used to investigate the determination of phosphorus without a modifier and with the addition of selected modifiers of very different nature, including the originally recommended lanthanum modifier, several palladium-based modifiers and sodium fluoride. As high-resolution continuum source atomic absorption spectrometry is revealing the spectral environment of the analytical line at high resolution, it became obvious that without the addition of a modifier essentially no atomic phosphorus is formed, even at 2700 deg. C . The absorption measured with line source atomic absorption spectrometry in this case is due to the PO molecule, the spectrum of which is overlapping with the atomic line. Palladium, with or without the addition of calcium or ascorbic acid, was found to be the only modifier to produce almost exclusively atomic phosphorus. Lanthanum and particularly sodium fluoride produced a mixture of P and PO, depending on the atomization temperature. This fact can explain at least some of the discrepancies found in the literature and some of the phenomena observed in the

  3. 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.

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

    Science.gov (United States)

    Wang, Yu; Li, Jia-xi

    2009-05-01

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

  5. Clustered atom-replaced structure in single-crystal-like metal oxide

    Science.gov (United States)

    Araki, Takeshi; Hayashi, Mariko; Ishii, Hirotaka; Yokoe, Daisaku; Yoshida, Ryuji; Kato, Takeharu; Nishijima, Gen; Matsumoto, Akiyoshi

    2018-06-01

    By means of metal organic deposition using trifluoroacetates (TFA-MOD), we replaced and localized two or more atoms in a single-crystalline structure having almost perfect orientation. Thus, we created a new functional structure, namely, clustered atom-replaced structure (CARS), having single-crystal-like metal oxide. We replaced metals in the oxide with Sm and Lu and localized them. Energy dispersive x-ray spectroscopy results, where the Sm signal increases with the Lu signal in the single-crystalline structure, confirm evidence of CARS. We also form other CARS with three additional metals, including Pr. The valence number of Pr might change from 3+ to approximately 4+, thereby reducing the Pr–Ba distance. We directly observed the structure by a high-angle annular dark-field image, which provided further evidence of CARS. The key to establishing CARS is an equilibrium chemical reaction and a combination of additional larger and smaller unit cells to matrix cells. We made a new functional metal oxide with CARS and expect to realize CARS in other metal oxide structures in the future by using the above-mentioned process.

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

    International Nuclear Information System (INIS)

    Shul'ga, N.F.; Truten', V.I.

    1999-01-01

    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

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

    International Nuclear Information System (INIS)

    1992-01-01

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

  8. High-resolution and large dynamic range nanomechanical mapping in tapping-mode atomic force microscopy

    International Nuclear Information System (INIS)

    Sahin, Ozgur; Erina, Natalia

    2008-01-01

    High spatial resolution imaging of material properties is an important task for the continued development of nanomaterials and studies of biological systems. Time-varying interaction forces between the vibrating tip and the sample in a tapping-mode atomic force microscope contain detailed information about the elastic, adhesive, and dissipative response of the sample. We report real-time measurement and analysis of the time-varying tip-sample interaction forces with recently introduced torsional harmonic cantilevers. With these measurements, high-resolution maps of elastic modulus, adhesion force, energy dissipation, and topography are generated simultaneously in a single scan. With peak tapping forces as low as 0.6 nN, we demonstrate measurements on blended polymers and self-assembled molecular architectures with feature sizes at 1, 10, and 500 nm. We also observed an elastic modulus measurement range of four orders of magnitude (1 MPa to 10 GPa) for a single cantilever under identical feedback conditions, which can be particularly useful for analyzing heterogeneous samples with largely different material components.

  9. High-resolution continuum-source atomic absorption spectrometry: what can we expect?

    Directory of Open Access Journals (Sweden)

    Welz Bernhard

    2003-01-01

    Full Text Available A new instrumental concept has been developed for atomic absorption spectrometry (AAS, using a high-intensity xenon short-arc lamp as continuum radiation source, a high-resolution double-echelle monochromator and a CCD array detector, providing a resolution of ~2 pm per pixel. Among the major advantages of the system are: i an improved signal-to-noise ratio because of the high intensity of the radiation source, resulting in improved photometric precision and detection limits; ii for the same reason, there are no more 'weak' lines, i.e. secondary lines can be used without compromises; iii new elements might be determined, for which no radiation source has been available; iv the entire spectral environment around the analytical line becomes 'visible', giving a lot more information than current AAS instruments; v the CCD array detector allows a truly simultaneous background correction close to the analytical line; vi the software is capable of storing reference spectra, e.g. of a molecular absorption with rotational fine structure, and of subtracting such spectra from the spectra recorded for a sample, using a least squares algorithm; vii although not yet realized, the system makes possible a truly simultaneous multi-element AAS measurement when an appropriate two-dimensional detector is used, as is already common practice in optical emission spectrometry; vii preliminary experiments have indicated that the instrumental concept could result in a more rugged analytical performance in the determination of trace elements in complex matrices.

  10. High mobility In2O3:H transparent conductive oxides prepared by atomic layer deposition and solid phase crystallization

    NARCIS (Netherlands)

    Macco, B.; Wu, Y.; Vanhemel, D.; Kessels, W.M.M.

    2014-01-01

    The preparation of high-quality In2O3:H, as transparent conductive oxide (TCO), is demonstrated at low temperatures. Amorphous In2O3:H films were deposited by atomic layer deposition at 100 °C, after which they underwent solid phase crystallization by a short anneal at 200 °C. TEM analysis has shown

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

    NARCIS (Netherlands)

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-06-15

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

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

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov; Møller, Per

    1994-01-01

    The influence of surface drift velocities on in situ scanning tunnelling microscopy (STM) experiments with atomic resolution is analysed experimentally and mathematically. Constant drift velocities much smaller than the speed of scanning can in many in situ STM experiments with atomic resolution ...... as well as the vectors of the non-distorted surface lattice can be determined. The calibration of distances can thus be carried out also when the image is influenced by drift. Results with gold surfaces and graphite surfaces are analysed and discussed....

  14. High resolution electron microscopy. Visualization of crystal lattices and of their defects

    International Nuclear Information System (INIS)

    Desseaux, J.

    1981-10-01

    A great number of fault characterization results may be obtained without calculations simply by observing the pictures: determination of Burgers' vector of dislocations, dissociation of the dislocations, presence of precipitates in the heart of the dislocations, presence of micro-twin-crystals, phase boundaries, etc. Determining the position of the atoms will be facilitated if the phase system approximation can be applied. In those cases where it is necessary to use the calculated image-experimental image comparison, it is fundamental to check the parameters on which the image depends. For the simplicity of the interpretation it is always necessary to obtain images taken in conditions where the structure is the most directly projected and where the image contrast is as stable as possible for a small variation in the parameters: thickness, focusing and crystalline parameters. A few examples are given on silicon [fr

  15. 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.

  16. Scanning tunneling microscopy of the atomically smooth (001) surface of vanadium pentoxide V_2O_5 crystals

    International Nuclear Information System (INIS)

    Muslimov, A. E.; Butashin, A. V.; Kanevsky, V. M.

    2017-01-01

    The (001) cleavage surface of vanadium pentoxide (V_2O_5) crystal has been studied by scanning tunneling spectroscopy (STM). It is shown that the surface is not reconstructed; the STM image allows geometric lattice parameters to be determined with high accuracy. The nanostructure formed on the (001) cleavage surface of crystal consists of atomically smooth steps with a height multiple of unit-cell parameter c = 4.37 Å. The V_2O_5 crystal cleavages can be used as references in calibration of a scanning tunneling microscope under atmospheric conditions both along the (Ñ…, y) surface and normally to the sample surface (along the z axis). It is found that the terrace surface is not perfectly atomically smooth; its roughness is estimated to be ~0.5 Å. This circumstance may introduce an additional error into the microscope calibration along the z coordinate.

  17. Defect formation and desorption of metal atoms from alkali halide crystals under low energy electron bombardment studied by optical absorption and mass spectroscopy

    International Nuclear Information System (INIS)

    Seifert, N.R.

    1993-04-01

    This work presents an extensive investigation of electronically induced desorption of ground-state alkali atoms from alkali halides and for the first time correlates directly the desorption with the stability and spatial distribution of the defects formed during bombardment. The electron impact results in the formation of stable F-centers and F-center clusters in the bulk of the crystals. In striking contrast a significant metallization of the surface is observed. Even at temperatures as low as 90 deg C the metallization is achieved within the time resolution of our detection system, which can only be explained by the rapid diffusion of hot holes. Superimposed to the fast and short diffusion of hot holes is the slow F-center diffusion. Measuring the distribution of defects with low energy ion sputtering techniques indicates that at least in the case of LiF the observed diffusion constant of F-centers agrees with values derived by using methods different from that applied here. At low temperatures the formation of F-center clusters and metal on the surface dominates. Colloid formation clearly requires higher temperatures (typically around 200 deg C). This is a strong evidence that efficient F-center diffusion is necessary for the formation of metallic particles (colloids) in the bulk of the crystals. Desorption of alkali atoms from alkali halides at temperatures around room temperature is due to weakly bound alkali atoms. For elevated temperatures the stability of the metallic clusters in the bulk of the crystals (i.e. colloids) are the rate limiting process. (author)

  18. Atoms

    International Nuclear Information System (INIS)

    Fuchs, Alain; Villani, Cedric; Guthleben, Denis; Leduc, Michele; Brenner, Anastasios; Pouthas, Joel; Perrin, Jean

    2014-01-01

    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)

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

    Science.gov (United States)

    Zhang, Duo; Li, Jiahua; Ding, Chunling; Yang, Xiaoxue

    2012-05-01

    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.

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

    International Nuclear Information System (INIS)

    Sirotinkin, V. P.; Bush, A. A.; Kamentsev, K. E.; Dau, H. S.; Yakovlev, K. A.; Tishchenko, E. A.

    2015-01-01

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

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

    KAUST Repository

    Cong, Chunxiao; Li, Kun; Zhang, Xixiang; Yu, Ting

    2013-01-01

    In-plane and out-of-plane arrangements of carbon atoms in graphene layers play critical roles in the fundamental physics and practical applications of these novel two-dimensional materials. Here, we report initial results on the edge

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

    International Nuclear Information System (INIS)

    Morita, Mizuki; Katta, AVSK Mohan; Ahmad, Shandar; Mori, Takaharu; Sugita, Yuji; Mizuguchi, Kenji

    2011-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    Morita Mizuki

    2011-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Gonnissen, J.; De Backer, A. [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Dekker, A.J. den [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Delft Center for Systems and Control (DCSC), Delft University of Technology, Mekelweg 2, 2628 CD Delft (Netherlands); Sijbers, J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)

    2016-11-15

    In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramér–Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms. - Highlights: • The optimal detector design to detect and locate light atoms in HR STEM is derived. • The probability of error is quantified and used to detect light atoms. • The Cramér–Rao lower bound is calculated to determine the atomic column precision. • Both measures are evaluated and result in the single optimal LAADF detector regime. • The incoming electron dose is optimised for both research goals.

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

    Science.gov (United States)

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

    2015-02-02

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

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

    International Nuclear Information System (INIS)

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

    1994-01-01

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

    Science.gov (United States)

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

    2017-08-01

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

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

    International Nuclear Information System (INIS)

    1992-01-01

    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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2015-10-01

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

  11. Investigation of the martensitic phase transformations in CoFe single crystals using high-resolution transmission electron microscopy

    International Nuclear Information System (INIS)

    Waitz, T.

    1999-06-01

    In CoFe crystals containing 0.85, 1.5, 5.75 and 6.0at.% Fe the thermally induced martensitic phase transformations between the close packed lattices face centered cubic (fcc), double hexagonal close packed (dhcp) and hexagonal close packed (hcp) were studied. Transmission electron microscopy methods were applied including in-situ experiments; both high-resolution transmission electron microscopy (HRTEM) images and lattice fringe images were used to analyze the transformations at an atomic scale. Based on the results of both the transformations in the bulk and the in-situ transformations it is concluded that the phase transitions occur by the formation of lamellae on the close packed habit planes. The lamellae have a minimum thickness of 10 to 15 close packed planes; therefore transformation models that are based on random overlap of stacking faults can be excluded. The glissile transformation fronts of the lamellae contain transformation dislocations (partials) that are correlated on an atomic scale. In the HRTEM images partials that are only about 0.2 nm apart were resolved and analyzed in detail by circuits that are similar to Burgers circuits. Two attracting partials on adjacent close packed planes are the structural units of the transformation fronts; they are dipoles and paired partials (with a total Burgers vector of a single partial) in the case of the transformations hcp dhcp and fcc dhcp, respectively. Different arrangements of the partials at the transformation fronts lead to two different modes A and B of the phase transition. These two modes seem to be competitive processes that can be favored by different parameters of the material (as chemical composition and microstructure). Partials of mode A transformations have the same Burgers vectors; therefore the partials repel each other causing long range internal stresses and large transformation shear strains that can lead to a surface relief. Whereas, partials of mode B transformations have different

  12. Atomic-resolution environmental TEM for quantitative in-situ microscopy in materials science.

    Science.gov (United States)

    Takeda, Seiji; Yoshida, Hideto

    2013-02-01

    We have compiled our recent in-situ quantitative environmental transmission electron microscopy (ETEM) studies on typical gold nanoparticulate catalysts for the low-temperature oxidation of CO to describe the issues surrounding the application of ETEM, with a special regard to catalyst chemistry. Thanks to the recent development of high-resolution environmental transmission electron microscopes that can work robustly to accumulate observation data in controlled environments, we can deal with the electron irradiation effects and heterogeneity of real catalysts. We established a structural evolution diagram that summarizes the structure of catalysts under electron irradiation as a function of the electron current density ϕ and the electron dose, D. By extrapolating to ϕ = 0, D = 0, we could deduce the intrinsic catalysis structure (without electron irradiation) in various environments, including reaction environments. By numerically and statistically analyzing a substantial number of ETEM images of gold nanoparticles, we established a morphology phase diagram that summarizes how the majority of gold nanoparticles change their morphology systematically as a function of the partial pressures of CO and O(2). Similar diagrams will be helpful in elucidating the phenomena that directly correlate with the catalytic activity determined from ETEM observations. Using these quantitative analyses, we could analyze Cs-corrected ETEM images of the catalysts. The surfaces of gold nanoparticles were structurally reconstructed under reaction conditions, via interactions with CO molecules. CO molecules were observed on the surfaces of catalysts under reaction conditions using high-resolution ETEM. Finally, we discuss the potential of environmental transmission electron microscopy for quantitative in-situ microscopy at the atomic scale.

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

    NARCIS (Netherlands)

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

    2016-01-01

    In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of

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

    KAUST Repository

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

    2015-01-01

    . 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

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

    Science.gov (United States)

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

    2017-10-01

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

  16. Band structure of one-dimensional doped photonic crystal with three level atoms using the Fresnel coefficients method

    Science.gov (United States)

    Jafari, A.; Rahmat, A.; Bakkeshizadeh, S.

    2018-01-01

    We consider a one-dimensional photonic crystal (1DPC) composed of double-layered dielectrics. Electric permittivity and magnetic permeability of this crystal depends on the incident electromagnetic wave frequency. We suppose that three level atoms have been added to the second layer of each dielectric and this photonic crystal (PC) has been doped. These atoms can be added to the layer with different rates. In this paper, we have calculated and compared the band structure of the mentioned PC considering the effect of added atoms to the second layer with different rates through the Fresnel coefficients method. We find out that according to the effective medium theory, the electric permittivity of the second layer changes. Also the band structure of PC for both TE and TM polarizations changes, too. The width of bandgaps related to “zero averaged refractive index” and “Bragg” increases. Moreover, new gap branches appear in new frequencies at both TE and TM polarizations. In specific state, two branches of “zero permittivity” gap appear in the PC band structure related to TM polarization. With increasing the amount of the filling rate of total volume with three level atoms, we observe a lot of changes in the PC band structure.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-05-15

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Shane D. Trask

    2010-06-01

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

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

    Science.gov (United States)

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

    2017-08-01

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

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

    Science.gov (United States)

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

    2016-12-01

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

  2. Galvanomagnetic properties of atomic-disordered Sr2RuO4 single crystals

    International Nuclear Information System (INIS)

    Kar'kin, A.E.; Naumov, S.V.; Goshchitskij, V.N.; Balbashov, A.M.

    2005-01-01

    The effect of neutron-bombardment-induced atomic disorder on the galvanomagnetic properties of Sr 2 RuO 4 single crystals has been experimentally studied in a broad range of temperatures (1.7-380 K) and magnetic fields (up to 13.6 T). The disorder leads to the appearance of negative temperature coefficients for both the in-plane electric resistivity (ρ a ) and that along the c axis (ρ c ), as well as the negative magnetoresistance Δρ, which is strongly anisotropic to the magnetic field orientation (H || a and H || c), with the easy magnetization direction along the c axis and a weak dependence on the probing current direction in the low-temperature region. The experimental ρ a (T) and ρ c (T) curves obtained for the initial and radiation-disordered samples can be described in the framework of a theoretical model with two conductivity channels. The first channel corresponds to the charge carriers with increased effective masses and predominantly electron-electron scattering, the second channel corresponds to the charge carriers with lower effective masses exhibiting magnetic scattering at low temperatures [ru

  3. Mechanisms for the reflection of light atoms from crystal surfaces at kilovolt energies

    International Nuclear Information System (INIS)

    Hou, M.; Robinson, M.T.

    1978-01-01

    The computer program MARLOWE was used to investigate the backscattering of protons from the (110) surface of a nickel crystal. Grazing incidence was considered so that anisotropic effects originated mainly from the surface region. The contribution of aligned scattering was studied by comparing the results with similar calculations for an amorphous target. Energy distributions of backscattered particles were investigated for incident energies ranging from 0.1 to 5 keV. The structure of these distributions was explained by making calculations for several target thickness. Specular reflection was found to depend on the structure of the first few atomic planes only. The (110) rows in the surface plane were responsible for focusing into surface semichannels. Focusing in these semichannels was found to be the strongest under total reflection conditions (below about 1.3 keV) while the scattering intensity from surface rows increased with increasing incident energy. The orientation of the plane of incidence was found to have large influence on the relative contributions of the reflection mechanisms involved. (orig.) [de

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

    International Nuclear Information System (INIS)

    Pal, M.; Erskine, P. T.; Gill, R. S.; Wood, S. P.; Cooper, J. B.

    2010-01-01

    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 R free 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 R free 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

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

    International Nuclear Information System (INIS)

    Ziegler, S.I.; Pichler, B.J.; Rafecas, M.; Schwaiger, M.

    2001-01-01

    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 mm 3 ) are individually coupled to one channel within matrices containing 2 x 8 square APDs (2.6 x 2.6 mm 2 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. Investigations of the dynamics and growth of insulator films by high resolution helium atom scattering. Final report, May 1, 1985--April 30, 1997

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-07-01

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

  7. High-resolution 3D imaging of polymerized photonic crystals by lab-based x-ray nanotomography with 50-nm resolution

    Science.gov (United States)

    Yin, Leilei; Chen, Ying-Chieh; Gelb, Jeff; Stevenson, Darren M.; Braun, Paul A.

    2010-09-01

    High resolution x-ray computed tomography is a powerful non-destructive 3-D imaging method. It can offer superior resolution on objects that are opaque or low contrast for optical microscopy. Synchrotron based x-ray computed tomography systems have been available for scientific research, but remain difficult to access for broader users. This work introduces a lab-based high-resolution x-ray nanotomography system with 50nm resolution in absorption and Zernike phase contrast modes. Using this system, we have demonstrated high quality 3-D images of polymerized photonic crystals which have been analyzed for band gap structures. The isotropic volumetric data shows excellent consistency with other characterization results.

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

    International Nuclear Information System (INIS)

    Yu, Wentao

    2009-01-01

    In this work, the characteristic inversion domain microstructures of In 2 O 3 (ZnO) m (m=30) compounds were investigated by TEM methods. At bright-atom contrast condition, atomically resolved HR-TEM images of In 2 O 3 (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 In 2 O 3 (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 In 2 O 3 (ZnO) m compounds by using phase-contrast and Z-contrast imaging at atomic resolution, In 3+ atoms are determined with trigonal bi-pyramidal co-ordination and are distributed at the pyramidal IDBs. (orig.)

  9. 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 ...

  10. Phonon interference control of atomic-scale metamirrors, meta-absorbers, and heat transfer through crystal interfaces

    Science.gov (United States)

    Kosevich, Yu. A.; Potyomina, L. G.; Darinskii, A. N.; Strelnikov, I. A.

    2018-03-01

    The paper theoretically studies the possibility of using the effects of phonon interference between paths through different interatomic bonds for the control of phonon heat transfer through internal crystal interfaces and for the design of phonon metamirrors and meta-absorbers. These metamirrors and meta-absorbers are considered to be defect nanolayers of atomic-scale thicknesses embedded in a crystal. Several analytically solvable three-dimensional lattice-dynamics models of the phonon metamirrors and meta-absorbers at the internal crystal planes are described. It is shown that due to destructive interference in the two or more phonon paths, the internal crystal planes, fully or partially filled with weakly bound or heavy-isotope defect atoms, can completely reflect or completely absorb phonons at the transmission antiresonances, whose wavelengths are larger than the effective thickness of the metamirror or meta-absorber. Due to cooperative superradiant effect, the spectral widths of the two-path interference antiresonances for the plane waves are given by the square of partial filling fraction in the defect crystal plane. Our analysis reveals that the presence of two or more phonon paths plays the dominant role in the emergence of the transmission antiresonances in phonon scattering at the defect crystal planes and in reduction of the thermal interface conductance in comparison with the Fano-resonance concept. We study analytically phonon transmission through internal crystal plane in a model cubic lattice of Si-like atoms, partially filled with Ge-like defect atoms. Such a plane can serve as interference phonon metamirror with the transmission antiresonances in the vicinities of eigenmode frequencies of Ge-like defect atoms in the terahertz frequency range. We predict the extraordinary phonon transmission induced by the two-path constructive interference of the lattice waves in resonance with the vibrations of rare host atoms, periodically distributed in the

  11. Atom

    International Nuclear Information System (INIS)

    Auffray, J.P.

    1997-01-01

    The atom through centuries, has been imagined, described, explored, then accelerated, combined...But what happens truly inside the atom? And what are mechanisms who allow its stability? Physicist and historian of sciences, Jean-Paul Auffray explains that these questions are to the heart of the modern physics and it brings them a new lighting. (N.C.)

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

    International Nuclear Information System (INIS)

    Miyaoka, Robert S.

    2012-01-01

    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.

  13. The 1.1 Å resolution structure of a periplasmic phosphate-binding protein from Stenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank.

    Science.gov (United States)

    Keegan, Ronan; Waterman, David G; Hopper, David J; Coates, Leighton; Taylor, Graham; Guo, Jingxu; Coker, Alun R; Erskine, Peter T; Wood, Steve P; Cooper, Jonathan B

    2016-08-01

    During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from Alcaligenes sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this new structure as the search model did not give a convincing solution with the original atomic resolution data set. Hence, it was considered that these crystals might have arisen from a protein impurity, although molecular replacement using the structures of common crystallization contaminants as search models again failed. A script to perform molecular replacement using MOLREP in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate-binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron-density map at 1.1 Å resolution based on the solution obtained with PDB entry 2q9t allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate-binding protein from Stenotrophomonas maltophilia (UniProt ID B4SL31; gene ID Smal_2208), and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked to the virulence of antibiotic-resistant strains of pathogenic bacteria and with biofilm formation. The structure of the S. maltophilia protein has been refined to an R factor of 10.15% and an Rfree of 12.46% at 1.1 Å resolution. The molecule adopts the type II periplasmic binding protein (PBP) fold with a number of extensively elaborated loop regions. A fully dehydrated phosphate

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

    Science.gov (United States)

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

    2017-05-01

    The increasing use of energy dispersive X-ray spectroscopy in atomic resolution scanning transmission electron microscopy invites the question of whether its success in precision composition determination at lower magnifications can be replicated in the atomic resolution regime. In this paper, we explore, through simulation, the prospects for composition measurement via the model system of Al x Ga 1-x As, discussing the approximations used in the modelling, the variability in the signal due to changes in configuration at constant composition, and the ability to distinguish between different compositions. Results are presented in such a way that the number of X-ray counts, and thus the expected variation due to counting statistics, can be gauged for a range of operating conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Sites of Au atoms in Sn crystals as determined by channeling

    International Nuclear Information System (INIS)

    Miller, J.W.; Gemmell, D.S.; Holland, R.E.; Poizat, J.C.; Worthington, J.N.; Loess, R.E.

    1974-01-01

    The position of Au atoms diffused into Sn monocrystals has been studied by channeling and backscattering of 2.5-MeV Ne ions. For equilibrium conditions at 217 0 C, Au atoms are found almost entirely in substitutional positions, so that the unusually fast diffusion of Au in Sn most likely arises from a small fraction of Au atoms migrating interstitially

  16. High-resolution photoluminescence spectroscopy of Sn-doped ZnO single crystals

    International Nuclear Information System (INIS)

    Kumar, E. Senthil; Mohammadbeigi, F.; Boatner, L.A.; Watkins, S.P.

    2016-01-01

    Group IV donors in ZnO are poorly understood, despite evidence that they are effective n-type dopants. Here we present high-resolution photoluminescence (PL) spectroscopy studies of unintentionally doped and Sn-doped ZnO single crystals grown by the chemical vapor transport method. Doped samples showed greatly increased emission from the I 10 bound exciton transition that was recently proven to be related to the incorporation of Sn impurities based on radio-isotope studies. The PL linewidths are exceptionally sharp for these samples, enabling a clear identification of several donor species. Temperature-dependent PL measurements of the I 10 line emission energy and intensity dependence reveal a behavior that is similar to other shallow donors in ZnO. Ionized donor bound-exciton and two-electron satellite transitions of the I 10 transition are unambiguously identified and yield a donor binding energy of 71 meV. In contrast to recent reports of Ge-related donors in ZnO, the spectroscopic binding energy for the Sn-related donor bound exciton follows a linear relationship with donor binding energy (Haynes rule) similar to recently observed carbon related donors, and confirming the shallow nature of this defect center, which was recently attributed to a Sn Zn double donor compensated by an unknown single acceptor.

  17. In situ study of the growth and degradation processes in tetragonal lysozyme crystals on a silicon substrate by high-resolution X-ray diffractometry

    Science.gov (United States)

    Kovalchuk, M. V.; Prosekov, P. A.; Marchenkova, M. A.; Blagov, A. E.; D'yakova, Yu. A.; Tereshchenko, E. Yu.; Pisarevskii, Yu. V.; Kondratev, O. A.

    2014-09-01

    The results of an in situ study of the growth of tetragonal lysozyme crystals by high-resolution X-ray diffractometry are considered. The crystals are grown by the sitting-drop method on crystalline silicon substrates of different types: both on smooth substrates and substrates with artificial surface-relief structures using graphoepitaxy. The crystals are grown in a special hermetically closed crystallization cell, which enables one to obtain images with an optical microscope and perform in situ X-ray diffraction studies in the course of crystal growth. Measurements for lysozyme crystals were carried out in different stages of the crystallization process, including crystal nucleation and growth, developed crystals, the degradation of the crystal structure, and complete destruction.

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

    International Nuclear Information System (INIS)

    Hazemann, I.; Dauvergne, M.T.; Blakeley, M.P.; Meilleur, Flora; Haertlein, M.; Van Dorsselaer, A.; Mitschler, A.; Myles, Dean A.A.; Podjarny, A.

    2005-01-01

    Neutron diffraction data have been collected to 2.2 (angstrom) resolution from a small (0.15 mm 3 ) 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 mm 3 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.

  19. On the possibilities of high-resolution continuum source graphite furnace atomic absorption spectrometry for the simultaneous or sequential monitoring of multiple atomic lines

    International Nuclear Information System (INIS)

    Resano, M.; Rello, L.; Florez, M.; Belarra, M.A.

    2011-01-01

    This paper explores the potential of commercially available high-resolution continuum source graphite furnace atomic absorption spectrometry instrumentation for the simultaneous or sequential monitoring of various atomic lines, in an attempt to highlight the analytical advantages that can be derived from this strategy. In particular, it is demonstrated how i) the monitoring of multiplets may allow for the simple expansion of the linear range, as shown for the measurement of Ni using the triplet located in the vicinity of 234.6 nm; ii) the use of a suitable internal standard may permit improving the precision and help in correcting for matrix-effects, as proved for the monitoring of Ni in different biological samples; iii) direct and multi-element analysis of solid samples may be feasible on some occasions, either by monitoring various atomic lines that are sufficiently close (truly simultaneous monitoring, as demonstrated in the determination of Co, Fe and Ni in NIST 1566a Oyster tissue) or, alternatively, by opting for a selective and sequential atomization of the elements of interest during every single replicate. Determination of Cd and Ni in BCR 679 White cabbage is attempted using both approaches, which permits confirming that both methods can offer very similar and satisfactory results. However, it is important to stress that the second approach provides more flexibility, since analysis is no longer limited to those elements that show very close atomic lines (closer than 0.3 nm in the ultraviolet region) with a sensitivity ratio similar to the concentration ratio of the analytes in the samples investigated.

  20. High resolution diffraction imaging of mercuric iodide: Demonstration of the necessity for alternate crystal processing techniques for highly purified material

    International Nuclear Information System (INIS)

    Steiner, B.; Berg, L. van den; Laor, U.

    1995-01-01

    The overall crystalline lattice uniformity in recently available, highly purified mercuric iodide single crystals has been shown to be impacted by crystal handling techniques that were previously satisfactory. High resolution diffraction imaging of the surface regularity of crystals of various levels of purity and growth orientation shows: (1) that the newer materials have a generally lower level of precipitates, (2) that the incidence of these precipitates is now closely correlated with growth direction, and (3) that the deformation resistance and resulting sensitivity to crystal handling procedures are also closely correlated with these factors in this soft material. As a result, gentler cutting and polishing procedures have been developed and are shown to be effective in preserving overall lattice regularity in the new material. The polishing required to remove residual surface scratches affect the lattice orientation of the softer, precipitate-free regions, while not affecting those regions with detectable levels of precipitates. These results correlate closely with the electrical properties of devices made from these crystals. Mercuric iodide single crystals have proved to be particularly useful for x and γ ray detectors because their room temperature operation allow for simple, efficient, and compact instrumentation

  1. 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\\.

  2. Annealing as grown large volume CZT single crystals for increased spectral resolution

    International Nuclear Information System (INIS)

    Li, Longxia

    2008-01-01

    The spectroscopic performance of current large-volume Cadmium 10% Zinc Telluride, Cd 0.9 Zn 0.1 Te, (CZT) detectors is impaired by cumulative effect of tellurium precipitates (secondary phases) presented in CZT single-crystal grown by low-pressure Bridgman techniques(1). This statistical effect may limit the energy resolution of large-volume CZT detectors (typically 2-5% at 662 keV for 12-mm thick devices). The stochastic nature of the interaction prevents the use of any electronic or digital charge correction techniques without a significant reduction in the detector efficiency. This volume constraint hampers the utility of CZT since the detectors are inefficient at detecting photons >1MeV and/or in low fluency situations. During the project, seven runs CZT ingots have been grown, in these ingots the indium dopant concentrations have been changed in the range between 0.5ppm to 6ppm. The I-R mapping imaging method has been employed to study the Te-precipitates. The Teprecipitates in as-grown CZT wafers, and after annealing wafers have been systematically studied by using I-R mapping system (home installed, resolution of 1.5 (micro)m). We employed our I-R standard annealing CZT (Zn=4%) procedure or two-steps annealing into radiation CZT (Zn=10%), we achieved the 'non'-Te precipitates (size 10 9-10 (Omega)-cm. We believe that the Te-precipitates are the p-type defects, its reducing number causes the CZT became n+-type, therefore we varied or reduced the indium dapant concentration during the growth and changed the Te-precipitates size and density by using different Cd-temperature and different annealing procedures. We have made the comparisons among Te-precipitates size, density and Indium dopant concentrations, and we found that the CZT with smaller size of Te-precipitates is suitable for radiation uses but non-Te precipitates is impossible to be used in the radiation detectors, because the CZT would became un-dopant or 'intrinsic' with non radiation affection (we

  3. Neutral-helium-atom diffraction from a micron-scale periodic structure: Photonic-crystal-membrane characterization

    Science.gov (United States)

    Nesse, Torstein; Eder, Sabrina D.; Kaltenbacher, Thomas; Grepstad, Jon Olav; Simonsen, Ingve; Holst, Bodil

    2017-06-01

    Surface scattering of neutral helium beams created by supersonic expansion is an established technique for measuring structural and dynamical properties of surfaces on the atomic scale. Helium beams have also been used in Fraunhofer and Fresnel diffraction experiments. Due to the short wavelength of the atom beams of typically 0.1 nm or less, Fraunhofer diffraction experiments in transmission have so far been limited to grating structures with a period (pitch) of up to 200 nm. However, larger periods are of interest for several applications, for example, for the characterization of photonic-crystal-membrane structures, where the period is typically in the micron to high submicron range. Here we present helium atom diffraction measurements of a photonic-crystal-membrane structure with a two-dimensional square lattice of 100 ×100 circular holes. The nominal period and the hole radius were 490 and 100 nm, respectively. To our knowledge this is the largest period that has been measured with helium diffraction. The helium diffraction measurements are interpreted using a model based on the helium beam characteristics. It is demonstrated how to successfully extract values from the experimental data for the average period of the grating, the hole diameter, and the width of the virtual source used to model the helium beam.

  4. Investigation of artifacts caused by deuterium background correction in the determination of phosphorus by electrothermal atomization using high-resolution continuum source atomic absorption spectrometry

    International Nuclear Information System (INIS)

    Dessuy, Morgana B.; Vale, Maria Goreti R.; Lepri, Fabio G.; Borges, Daniel L.G.; Welz, Bernhard; Silva, Marcia M.; Heitmann, Uwe

    2008-01-01

    The artifacts created in the measurement of phosphorus at the 213.6-nm non-resonance line by electrothermal atomic absorption spectrometry using line source atomic absorption spectrometry (LS AAS) and deuterium lamp background correction (D 2 BC) have been investigated using high-resolution continuum source atomic absorption spectrometry (HR-CS AAS). The absorbance signals and the analytical curves obtained by LS AAS without and with D 2 BC, and with HR-CS AAS without and with automatic correction for continuous background absorption, and also with least-squares background correction for molecular absorption with rotational fine structure were compared. The molecular absorption due to the suboxide PO that exhibits pronounced fine structure could not be corrected by the D 2 BC system, causing significant overcorrection. Among the investigated chemical modifiers, NaF, La, Pd and Pd + Ca, the Pd modifier resulted in the best agreement of the results obtained with LS AAS and HR-CS AAS. However, a 15% to 100% higher sensitivity, expressed as slope of the analytical curve, was obtained for LS AAS compared to HR-CS AAS, depending on the modifier. Although no final proof could be found, the most likely explanation is that this artifact is caused by a yet unidentified phosphorus species that causes a spectrally continuous absorption, which is corrected without problems by HR-CS AAS, but which is not recognized and corrected by the D 2 BC system of LS AAS

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

    Science.gov (United States)

    Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

    2013-11-01

    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.

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

    International Nuclear Information System (INIS)

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

    1984-01-01

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

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

    KAUST Repository

    Zhu, Yihan; Wang, Qingxiao; Zhao, Lan; Teng, Baiyang; Lu, Weimin; Han, Yu

    2012-01-01

    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

  8. Hard x-ray monochromator with milli-electron volt bandwidth for high-resolution diffraction studies of diamond crystals

    Energy Technology Data Exchange (ETDEWEB)

    Stoupin, Stanislav; Shvyd' ko, Yuri; Shu Deming; Khachatryan, Ruben; Xiao, Xianghui; DeCarlo, Francesco; Goetze, Kurt; Roberts, Timothy; Roehrig, Christian; Deriy, Alexey [Advanced Photon Source, Argonne National Laboratory, Illinois 60439 (United States)

    2012-02-15

    We report on design and performance of a high-resolution x-ray monochromator with a spectral bandwidth of {Delta}E{sub X}{approx_equal} 1.5 meV, which operates at x-ray energies in the vicinity of the backscattering (Bragg) energy E{sub H} = 13.903 keV of the (008) reflection in diamond. The monochromator is utilized for high-energy-resolution diffraction characterization of diamond crystals as elements of advanced x-ray crystal optics for synchrotrons and x-ray free-electron lasers. The monochromator and the related controls are made portable such that they can be installed and operated at any appropriate synchrotron beamline equipped with a pre-monochromator.

  9. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. 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.

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Loisel, G. P., E-mail: gploise@sandia.gov; Wu, M.; Lake, P.; Dunham, G. S.; Bailey, J. E.; Rochau, G. A. [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States); Stolte, W. [National Security Technologies, LLC, Livermore, California 94551 (United States); Kruschwitz, C. [National Security Technologies, LLC, Los Alamos, New Mexico 87544 (United States)

    2016-11-15

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

  13. X-ray diffraction from ideal mosaic crystals in external fields of certain types. I. Atomic displacements and the corresponding diffraction patterns

    International Nuclear Information System (INIS)

    Treushnikov, E.N.

    2000-01-01

    The problem of the theoretical description of X-ray diffraction from ideal mosaic crystals under the effect of various external fields has been formulated. Electric, magnetic, electromagnetic, and acoustic perturbations are considered. The atomic displacements in crystals under the effect of external fields and the types of the corresponding diffraction patterns are analyzed for various types of perturbations. The crystal classes are determined in which atomic displacements can be recorded experimentally. Diffraction patterns formed under the effect of various external factors are considered on the basis of the derived dependence of the structure factor on the characteristics of an applied force field

  14. Growth of potassium sulfate crystals in the presence of organic dyes: in situ characterization by atomic force microscopy

    Science.gov (United States)

    Mauri, Andrea; Moret, Massimo

    2000-01-01

    In situ atomic force microscopy (AFM) has been used to observe potassium sulfate crystals growing in the presence of acid fuchsin and pyranine. These polysulfonated dyes are well known for their ability to adsorb onto the {1 1 0} and {0 1 0} (pyranine only) crystal faces. Using AFM, we analyzed the changes in surface micromorphology induced by the additives on advancing steps for the {1 1 0} and {0 1 0} surfaces. In situ AFM showed that layers grow by step flow at pre-existing steps by the addition of growth units at the step edges. It has been found that dye concentrations as low as ˜2×10 -6 M for pyranine and ˜4×10 -4 M for acid fuchsin produce significant changes in the step morphology and growth rates. The additive molecules attach to the terraces and pin the growing front. As a consequence, the edges of the growing steps become jagged as the dye molecules are adsorbed onto the crystal surface. At critical dye concentrations crystal growth is heavily hampered or even stopped along certain crystallographic directions producing, on a macroscopic scale, strong habit modifications. The formation of dye inclusions by means of macrosteps overgrowing the poisoned surface was also imaged. Interestingly, comparison of the in situ AFM experiments with previous habit modification studies showed acid fuchsin is also able to enter the {0 1 0} surfaces, a previously unnoticed phenomenon.

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

    International Nuclear Information System (INIS)

    Mishra, S.P.; Sharma, R.B.

    1983-01-01

    Recoil reaction of 128 I atoms in neutron irradiated mixed crystals (iodate-nitrate) have been studied by thermal annealing methods. The retention of 128 I (i.e. radioactivity of 128 I 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)

  16. Magnetic dichroism in photoemission: a new element-specific magnetometer with atomic-layer resolution

    International Nuclear Information System (INIS)

    Starke, K.; Arenholz, E.; Kaindl, G.

    1998-01-01

    Full text: Magnetic coupling in layered metallic structures has become a key issue in thin-film magnetism since the observation of oscillatory exchange coupling across non-ferromagnetic spacer layers. Although this phenomenon was discovered in rare earths (RE) superlattices, mostly transition-metal systems have been studied and are now applied in data-storage industry. An understanding of the coupling mechanisms has been reached after a fabrication of high-quality interfaces became possible. It allowed, in particular, the experimental finding of induced ferromagnetic order in 'nonmagnetic' atomic layers near an interface, using element-specific probes such as magnetic circular dichroism in x-ray absorption. - In layered RE systems, by contrast, the well known intermiscibility has prevented a preparation of atomically sharp interfaces, and all RE superlattices studied so far showed interdiffusion zones of several atomic layers. In the present overview, we report the first fabrication of atomically flat heteromagnetic RE interfaces, their structural characterization and their magnetic analysis using magnetic dichroism in photoemission (MDPE). This new tool gives access to the magnetization of individual atomic layers near interfaces in favourite cases. Merits of MDPE as a magnetometer are demonstrated at the example of Eu/Gd(0001), where chemical shifts of core-level photoemission lines allow to spectroscopically separate up to four different atomic layers. The high surface sensitivity of MDPE, together with the well known dependence of the core-level binding energies on the coordination number of the photo emitting atom, opens the door to future site-specific studies of magnetism in sub-monolayer systems such as 'nanowires'

  17. 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...

  18. Modification and control of the spontaneous emission from an M-type atom embedded in an anisotropic photonic crystal

    International Nuclear Information System (INIS)

    Ding Chunling; Li Jiahua; Yang Xiaoxue; Lue Xinyou

    2011-01-01

    We describe the spontaneous emission properties of an M-type five-level atom embedded in a photonic crystal (PC), which is coherently driven by two external laser fields. It leads to two types of quantum interference: reservoir-induced interference and laser-induced interference. Considering different detunings of atomic transition frequencies from band edges, we reveal some interesting phenomena such as spectral-line enhancement, spectral-line suppression, spectral-line narrowing, reservoir-induced cancellation of spontaneous emission and the appearance of dark lines, which originate from the quantum interference effects and the control of external laser fields. These investigations suggest possible applications in quantum optics, optical communications and in the fabrication of novel optoelectronic devices.

  19. Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

    Science.gov (United States)

    Robb, Paul D; Craven, Alan J

    2008-12-01

    An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

  20. Column ratio mapping: A processing technique for atomic resolution high-angle annular dark-field (HAADF) images

    International Nuclear Information System (INIS)

    Robb, Paul D.; Craven, Alan J.

    2008-01-01

    An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [1 1 0]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 A-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

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

    International Nuclear Information System (INIS)

    Quin, Maureen; Newman, Joseph; Firbank, Susan; Lewis, Richard J.; Marles-Wright, Jon

    2008-01-01

    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 σ B . One of the gene products of this operon is RsbS, a single STAS-domain protein that is a component of higher order assemblies in Bacillus subtilis known as ‘stressosomes’. It is expected that similar complexes are found in M. thermoacetica, but in this instance regulating the biosynthesis of cyclic di-GMP, a ubiquitous secondary messenger. Selenomethionine-labelled MtRsbS protein was crystallized at room temperature using the hanging-drop vapour-diffusion method. Crystals belonging to space group P2 1 2 1 2 1 , with unit-cell parameters a = 51.07, b = 60.52, c = 89.28 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

  2. 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

    strength of the steel. The Cr content promotes Z-phase precipitation, making MN strengthening of these materials unfeasible, since 12%Cr is necessary for oxidation resistance. The authors have suggested an acceleration of Z-phase precipitation to obtain a fine and stable distribution of CrMN instead of MN...... 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......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...

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

    KAUST Repository

    Zhu, Yihan

    2012-08-28

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

  4. Comparison of CsI(Tl) and CsI(Na) partially slotted crystals for high-resolution SPECT imaging

    International Nuclear Information System (INIS)

    Giokaris, N.; Loudos, G.; Maintas, D.; Karabarbounis, A.; Lembesi, M.; Spanoudaki, V.; Stiliaris, E.; Boukis, S.; Sakellios, N.; Karakatsanis, N.; Gektin, A.; Boyarintsev, A.; Pedash, V.; Gayshan, V.

    2006-01-01

    Dedicated systems based on Position Sensitive Photomultiplier Tubes (PSPMTs) coupled to scintillators, have been used over the past years for the construction of compact systems, suitable for applications such as small animal imaging and small organs imaging. Most of the proposed systems are based on fully pixelized scintillators. Previous studies have shown that partially slotted scintillators offer a good compromise between cost, energy resolution and spatial resolution. In this work, the performance of two sets of CsI(Tl) and CsI(Na) partially slotted crystals is compared. Initial results show that CsI(Tl) scintillators are more suitable for gamma-ray detection, since their performance in terms of sensitivity, spatial and energy resolution is superior than that of CsI(Na)

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

    Science.gov (United States)

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

    2017-12-01

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

  6. Atomic resolution ultrafast scanning tunneling microscope with scan rate breaking the resonant frequency of a quartz tuning fork resonator.

    Science.gov (United States)

    Li, Quanfeng; Lu, Qingyou

    2011-05-01

    We present an ultra-fast scanning tunneling microscope with atomic resolution at 26 kHz scan rate which surpasses the resonant frequency of the quartz tuning fork resonator used as the fast scan actuator. The main improvements employed in achieving this new record are (1) fully low voltage design (2) independent scan control and data acquisition, where the tuning fork (carrying a tip) is blindly driven to scan by a function generator with the scan voltage and tunneling current (I(T)) being measured as image data (this is unlike the traditional point-by-point move and measure method where data acquisition and scan control are switched many times).

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

    Science.gov (United States)

    Nakamura, Eiichi

    2017-06-20

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

  8. Dynamical theoretical model of the high-resolution double-crystal x-ray diffractometry of imperfect single crystals with microdefects

    International Nuclear Information System (INIS)

    Molodkin, V. B.; Olikhovskii, S. I.; Kislovskii, E. N.; Vladimirova, T. P.; Skakunova, E. S.; Seredenko, R. F.; Sheludchenko, B. V.

    2008-01-01

    The dynamical diffraction model has been developed for the quantitative description of rocking curves (RCs) measured in the Bragg diffraction geometry from single crystals containing homogeneously distributed microdefects of several types and with arbitrary sizes. The analytical expressions for coherent and diffuse RC components, which take self-consistently multiple-scattering effects into account and depend explicitly on microdefect characteristics (radius, concentration, strength, etc.), have been derived with taking into account the instrumental factors. The developed model has been applied to determine the characteristics of oxygen precipitates and dislocation loops in silicon crystals grown by Czochralsky and float-zone methods using RCs measured by the high-resolution double-crystal x-ray diffractometer. It has been shown, particularly, that completely dynamical consideration of Huang as well as Stockes-Wilson diffuse scattering (DS) in both diffuse RC component and coefficient of extinction of coherent RC component due to DS, together with taking asymmetry and thermal DS effects into account, provides the possibility to distinguish contributions into RC from defects of different types, which have equal or commensurable effective radii

  9. Resonant Coulomb excitation of atomic nuclei propagating through a crystal in the channeling mode

    International Nuclear Information System (INIS)

    Stepanov, A.V.

    1996-01-01

    The Coulomb-excitation total cross section and the distribution of decay products originating from a resonant state of a nucleus interacting with a crystal lattice has been calculated for the case of a single inelastic collision (with respect to internal degrees of freedom in a nucleus). These observables have been expressed in terms of time-dependent correlators which describe thermal oscillations of lattice nuclei and the motion of the center of mass of a nucleus propagating across a crystal target in the channelling mode. An expression generalizing the spectrum of equivalent photons calculated by the Weizsaecker-Williams method is given

  10. Influence of gamma radiation and impurity atoms on the photoconductivity of GeS single crystals

    International Nuclear Information System (INIS)

    Madatov, R.S.; Alekperov, A.S.

    2013-01-01

    Wide opportunities for using of layered semiconductors, particularly in optoelectronics have generated considerable interest to them. Recently it was created the unique device from GeS for the storage of solar energy. The investigated GeS 1 -xNd x S single crystals were grown by the Bridgman method. The samples were irradiated by gamma-quanta and was conducted to install 60Co at room temperature. Irradiation of p-GeS 1 -xNd x S single crystals by small doses of gamma rays increases the photoconductivity on 40%

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

    Science.gov (United States)

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

    2013-08-01

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

  12. 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.

  13. Submolecular resolution imaging of molecules by atomic force microscopy: the influence of the electrostatic force

    Czech Academy of Sciences Publication Activity Database

    van der Lit, J.; Di Cicco, F.; Hapala, Prokop; Jelínek, Pavel; Swart, I.

    2016-01-01

    Roč. 116, č. 9 (2016), 1-5, č. článku 096102. ISSN 0031-9007 R&D Projects: GA ČR(CZ) GC14-16963J Institutional support: RVO:68378271 Keywords : AFM * submolecular resolution * molecules * surface Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 8.462, year: 2016

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

    International Nuclear Information System (INIS)

    Blauth, David

    2010-01-01

    In the framework of the present dissertation the interactions of fast atoms with surfaces of bulk oxides, metals and thin films on metals were studied. The experiments were performed in the regime of grazing incidence of atoms with energies of some keV. The advantage of this scattering geometry is the high surface sensibility and thus the possibility to determine the crystallographic and electronic characteristics of the topmost surface layer. In addition to these experiments, the energy loss and the electron emission induced by scattered projectiles was investigated. The energy for electron emission and exciton excitation on Alumina/NiAl(110) and SiO 2 /Mo(112) are determined. By detection of the number of projectile induced emitted electrons as function of azimuthal angle for the rotation of the target surface, the geometrical structure of atoms forming the topmost layer of different adsorbate films on metal surfaces where determined via ion beam triangulation. (orig.)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-05-15

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

  16. 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.

  17. Visualization of drug-nucleic acid interactions at atomic resolution. II. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodocytidylyl(3'5')guanosine

    Energy Technology Data Exchange (ETDEWEB)

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

    1977-01-01

    Ethidium forms a second crystalline complex with the dinucleoside monophosphate 5-iodocytidyl(3'-5')guanosine (iodoCpG). These crystals are monoclinic, P2/sub 1/, with a = 14.06 A, b = 32.34 A, c = 16.53 A, ..beta.. = 117.8/sup 0/. The structure has been solved to atomic resolution using rigid-body Patterson vector search and Fourier methods, and refined by full matrix least-squares to a residual of 0.16 on 3180 observed reflections. Both iodoCpG molecules are hydrogen-bonded together by guanine.cytosine Watson--Crick base-pairing. Adjacent base-pairs within this paired iodoCpG structure and between neighboring iodoCpG molecules in adjoining unit cells are separated by 6.7 A. Approximate 2-fold symmetry is used in the interaction; this reflects the pseudo-2-fold symmetry axis of the phenanthridinium ring system in ethidium coinciding with the approximate 2-fold axis relating base-paired iodoCpG molecules. The phenyl and ethyl groups of the intercalated ethidium molecule lie in the narrow groove of the miniature iodoCpG double-helix. The stacked ethidium, however, lies in the opposite direction, its phenyl and ethyl groups neighboring iodine atoms on cytosine residues. Base-pairs within the paired nucleotide units are related by a twist of about 8/sup 0/. The magnitude of this angular twist reflects conformational changes in the sugar--phosphate chains accompanying intercalation. These primarily reflect the differences in ribose sugar ring puckering that are observed (i.e., both iodocytidine residues have C3' endo sugar conformations, while both guanosine residues have C2' endo sugar conformations), and alterations in the glycosidic torsional angles that describe the base-sugar orientation.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1977-01-01

    Ethidium forms a crystalline complex with the dinucleoside monophosphate 5-iodouridyly(3'-5')adenosine (iodoUpA). These crystals are monoclinic, space group C2, with unit cell dimensions, a = 28.45 A, b = 13.54 A, c = 34.13 A, ..beta.. = 98.6/sup 0/. The structure has been solved to atomic resolution by Patterson and Fourier methods, and refined by full matrix least-squares to a residual of 0.20 on 2017 observed reflections. The asymmetric unit contains two ethidium molecules, two iodoUpA molecules and 27 water molecules, a total of 155 atoms excluding hydrogens. The two iodoUpA molecules are held together by adenine.uracil Watson--Crick-type base-pairing. Adjacent base-pairs within this paired iodoUpA structure and between neighboring iodoUpA molecules in adjoining unit cells are separated by about 6.7 A; this separation results from intercalative binding by one ethidium molecule and stacking by the other ethidium molecule above and below the base-pairs. Non-crystallographic 2-fold symmetry is utilized in this model drug--nucleic acid interaction, the intercalated ethidium molecule being oriented such that its phenyl and ethyl groups lie in the narrow groove of the miniature nucleic acid double-helix. Base-pairs within the paired nucleotide units are related by a twist of 8/sup 0/. The magnitude of this angular twist is related to conformational changes in the sugar--phosphate chains that accompany drug intercalation. These changes partly reflect the differences in ribose sugar ring puckering that are observed. Additional small but systematic changes occur in torsional angles that involve the phosphodiester linkages and the C4'--C5' bond. Solution studies have indicated a marked sequence-specific binding preference in ethidium--dinucleotide interactions, and a probable structural explanation for this is provided by this study.

  19. Phase time delay and Hartman effect in a one-dimensional photonic crystal with four-level atomic defect layer

    Science.gov (United States)

    Jamil, Rabia; Ali, Abu Bakar; Abbas, Muqaddar; Badshah, Fazal; Qamar, Sajid

    2017-08-01

    The Hartman effect is revisited using a Gaussian beam incident on a one-dimensional photonic crystal (1DPC) having a defect layer doped with four-level atoms. It is considered that each atom of the defect layer interacts with three driving fields, whereas a Gaussian beam of width w is used as a probe light to study Hartman effect. The atom-field interaction inside the defect layer exhibits electromagnetically induced transparency (EIT). The 1DPC acts as positive index material (PIM) and negative index material (NIM) corresponding to the normal and anomalous dispersion of the defect layer, respectively, via control of the phase associated with the driving fields and probe detuning. The positive and negative Hartman effects are noticed for PIM and NIM, respectively, via control of the relative phase corresponding to the driving fields and probe detuning. The advantage of using four-level EIT system is that a much smaller absorption of the transmitted beam occurs as compared to three-level EIT system corresponding to the anomalous dispersion, leading to negative Hartman effect.

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

    DEFF Research Database (Denmark)

    Andersen, Hans Henrik; Sigmund, Peter

    1966-01-01

    the 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...... previously. Inelastic contributions to the energy loss can easily be included. The oscillator forces binding lattice atoms turn out to influence the scattering process only at very small energies. The validity of the so-called momentum approximation and a related perturbation method are also investigated....

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-12-15

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

  2. Transfer behavior of quantum states between atoms in photonic crystal coupled cavities

    International Nuclear Information System (INIS)

    Zhang Ke; Li Zhiyuan

    2010-01-01

    In this article, we discuss the one-excitation dynamics of a quantum system consisting of two two-level atoms each interacting with one of two coupled single-mode cavities via spontaneous emission. When the atoms and cavities are tuned into resonance, a wide variety of time-evolution behaviors can be realized by modulating the atom-cavity coupling strength g and the cavity-cavity hopping strength λ. The dynamics is solved rigorously via the eigenproblem of an ordinary coupled linear system and simple analytical solutions are derived at several extreme situations of g and λ. In the large hopping limit where g >λ, the time-evolution behavior of the system is characterized by the usual slowly varying carrier envelope superimposed upon a fast and violent oscillation. At a certain instant, the energy is fully transferred from the one quantum subsystem to the other. When the two interaction strengths are comparable in magnitude, the dynamics acts as a continuous pulse having irregular frequency and line shape of peaks and valleys, and the complicated time-evolution behaviors are ascribed to the violent competition between all the one-excitation quantum states. The coupled quantum system of atoms and cavities makes a good model to study cavity quantum electrodynamics with great freedoms of many-body interaction.

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

    International Nuclear Information System (INIS)

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

    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 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).

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

    Energy Technology Data Exchange (ETDEWEB)

    Allwörden, H. von; Ruschmeier, K.; Köhler, A.; Eelbo, T.; Schwarz, A., E-mail: aschwarz@physnet.uni-hamburg.de; Wiesendanger, R. [Department of Physics, University of Hamburg, Jungiusstrasse 11, 20355 Hamburg (Germany)

    2016-07-15

    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 {sup 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).

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

    Science.gov (United States)

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

    2016-01-15

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

  6. Irradiation of tungsten with metallic diatomic molecular ions: atomic-resolution observations of depleted zones

    International Nuclear Information System (INIS)

    Pramanik, D.; Seidman, D.N.

    1982-08-01

    Direct evidence, on an atomic scale, is presented for the enhancement of damage production per projectile ion in diatomic metallic molecular ion (dimer) irradiations of tungsten as compared to monatomic metallic ion (monomer) irradiations. Irradiations were performed in situ at less than or equal to 10 K, in a field-ion microscope, employing 20 keV Ag + or W + monomer ions and the results are compared with 40 keV W 2 + or Ag 2 + dimer ion bombardments; the average energy per ion was 20 keV. First, in the near-surface region the depleted zones produced by the W 2 + dimer ions give rise to void-like contrast effects. The W + monomer ions do not produce this void-like damage. The existence of voids was explained employing a nucleation and diffusion-limited growth model which suggests that the growth can occur on a time scale -9 s, if the effective diffusivity of an atom in the fully-developed collision cascade is > 3 x 10 -4 cm 2 s -1 . Second, by counting the number of vacancies in individual depleted zones, produced by the different ions, it was demonstrated that the number of vacancies produced per incoming ion of the dimer is 1.55 times greater than the number of vacancies produced per monomer ion

  7. Ion-atom collisions with laser-prepared target: High resolution study of single charge exchange process

    International Nuclear Information System (INIS)

    Leredde, Arnaud

    2012-01-01

    Single charge transfer in low-energy Na"++"8"7Rb(5s,5p) collisions is investigated using magneto-optically trapped Rb atoms and high-resolution recoil-ion momentum spectroscopy. The three-dimensional reconstruction of the recoil-ion momentum provides accurate relative cross-sections for the active channels and the projectile scattering angle distributions. Thanks to the high experimental resolution, scattering structures such as diffraction-like oscillations in angular distributions are clearly observed. The measurements are compared with molecular close-coupling calculations and an excellent agreement is found. To go further in the test of the theory, the target is prepared in an oriented state. It is the first time that such collision experiments with oriented target is performed with such a high resolution. The right-left asymmetry expected for the scattering angle distribution is evidenced. The agreement between MOCC calculations and experiments is very good. Simple models developed for collisions with oriented target are also discussed. (author) [fr

  8. Energy resolution measurements of LaBr3:Ce scintillating crystals with an ultra-high quantum efficiency photomultiplier tube

    International Nuclear Information System (INIS)

    Pani, R.; Cinti, M.N.; Scafe, R.; Pellegrini, R.; Vittorini, F.; Bennati, P.; Ridolfi, S.; Lo Meo, S.; Mattioli, M.; Baldazzi, G.; Pisacane, F.; Navarria, F.; Moschini, G.; Boccaccio, P.; Orsolini Cencelli, V.; Sacco, D.

    2009-01-01

    The performance of the new prototype of high quantum efficiency PMT (43% at 380 nm), Hamamatsu R7600U-200, was studied coupled to a LaBr 3 :Ce crystal with the size of o12.5 mmx12.5 mm. The energy resolution results were compared with ones from two PMTs, Hamamatsu R7600U and R6231MOD, with 22% and 30% quantum efficiency (QE), respectively. Moreover, the photodetectors were equipped with tapered and un-tapered voltage dividers to study the non-linearity effects on pulse height distribution, due to very high peak currents induced in the PMT by the fast and intense light pulse of LaBr 3 :Ce. The results show an energy resolution improvement with UBA PMT of about 20%, in the energy range of 80-662 keV, with respect to the BA one.

  9. Isomorphic Properties of Atoms, Molecules, Water, DNA, Crystals, Earth, SolarSystem and Galaxies

    Science.gov (United States)

    Gareev, F. A.; Gareeva, G. F.; Zhidkova, I. E.

    2009-03-01

    We discuss the cooperative resonance synchronization enhancement mechanisms of Low Energy Nuclear Reactions (LENR). Some of the low energy external fields can be used as triggers for starting and enhancing exothermic LENR. Any external field shortening distances between protons in nuclei and electrons in atoms should enhance beta-decay (capture) or double-beta decay (capture). We have proposed a new mechanism of LENR: cooperative resonance synchronization processes in the whole system nuclei+atoms+condensed matter+gaseuos+plasma medium, which we suggest can occur at a smaller threshold than the corresponding ones on free constituents. The cooperative processes can be induced and enhanced by low energy external fields. The excess heat is the emission of internal energy, and transmutations at LENR are the result of redistribution inner energy of the whole system.

  10. The scattering of low energy helium ions and atoms from a copper single crystal, ch. 2

    International Nuclear Information System (INIS)

    Verheij, L.K.; Poelsema, B.; Boers, A.L.

    1976-01-01

    The scattering of 4-10 keV helium ions from a copper surface cannot be completely described with elastic, single collisions. The general behaviour of the measured energy and width of the surface peak can be explained by differences in inelastic energy losses for scattering from an ideal surface and from surface structures (damage). Multiple scattering effects have a minor influence. Additional information about the inelastic processes is obtained from scattering experiments with a primary atom beam. For large angles of incidence, the energy of the reflected ions is reduced about 20 eV if the primary beam consists of atoms instead of ions. An explanation of this effect and an explanation of the different behaviour of small angles is given. In the investigated energy range, the electronic stopping power might depend on the charge state of the primary particles. The experimental results are rather well explained by the Lindhard, Scharff, Schioett theory

  11. Structures of adsorbed CO on atomically smooth and on stepped sngle crystal surfaces

    International Nuclear Information System (INIS)

    Madey, T.E.; Houston, J.E.

    1980-01-01

    The structures of molecular CO adsorbed on atomically smooth surfaces and on surfaces containing monatomic steps have been studied using the electron stimulated desorption ion angular distribution (ESDIAD) method. For CO adsorbed on the close packed Ru(001) and W(110) surfaces, the dominant bonding mode is via the carbon atom, with the CO molecular axis perpendicular to the plane of the surface. For CO on atomicaly rough Pd(210), and for CO adsorbed at step sites on four different surfaces vicinal to W(110), the axis of the molecule is tilted or inclined away from the normal to the surface. The ESDIAD method, in which ion desorption angles are related to surface bond angles, provides a direct determination of the structures of adsorbed molecules and molecular complexes on surfaces

  12. 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.

  13. Direct Atomic Force Microscopy Observation of DNA Tile Crystal Growth at the Single-Molecule Level

    OpenAIRE

    Evans, Constantine G.; Hariadi, Rizal F.; Winfree, Erik

    2012-01-01

    While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detach...

  14. crystal

    Science.gov (United States)

    Yu, Yi; Huang, Yisheng; Zhang, Lizhen; Lin, Zhoubin; Sun, Shijia; Wang, Guofu

    2014-07-01

    A Nd3+:Na2La4(WO4)7 crystal with dimensions of ϕ 17 × 30 mm3 was grown by the Czochralski method. The thermal expansion coefficients of Nd3+:Na2La4(WO4)7 crystal are 1.32 × 10-5 K-1 along c-axis and 1.23 × 10-5 K-1 along a-axis, respectively. The spectroscopic characteristics of Nd3+:Na2La4(WO4)7 crystal were investigated. The Judd-Ofelt theory was applied to calculate the spectral parameters. The absorption cross sections at 805 nm are 2.17 × 10-20 cm2 with a full width at half maximum (FWHM) of 15 nm for π-polarization, and 2.29 × 10-20 cm2 with a FWHM of 14 nm for σ-polarization. The emission cross sections are 3.19 × 10-20 cm2 for σ-polarization and 2.67 × 10-20 cm2 for π-polarization at 1,064 nm. The fluorescence quantum efficiency is 67 %. The quasi-cw laser of Nd3+:Na2La4(WO4)7 crystal was performed. The maximum output power is 80 mW. The slope efficiency is 7.12 %. The results suggest Nd3+:Na2La4(WO4)7 crystal as a promising laser crystal fit for laser diode pumping.

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

    International Nuclear Information System (INIS)

    Huang, Chih-Hsien; Hsieh, Wen-Feng; Wu, Jing-Nuo; Cheng, Szu-Cheng; Li, Yen-Yin

    2011-01-01

    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.

  17. From Modeling of Plasticity in Single-Crystal Superalloys to High-Resolution X-rays Three-Crystal Diffractometer Peaks Simulation

    Science.gov (United States)

    Jacques, Alain

    2016-12-01

    The dislocation-based modeling of the high-temperature creep of two-phased single-crystal superalloys requires input data beyond strain vs time curves. This may be obtained by use of in situ experiments combining high-temperature creep tests with high-resolution synchrotron three-crystal diffractometry. Such tests give access to changes in phase volume fractions and to the average components of the stress tensor in each phase as well as the plastic strain of each phase. Further progress may be obtained by a new method making intensive use of the Fast Fourier Transform, and first modeling the behavior of a representative volume of material (stress fields, plastic strain, dislocation densities…), then simulating directly the corresponding diffraction peaks, taking into account the displacement field within the material, chemical variations, and beam coherence. Initial tests indicate that the simulated peak shapes are close to the experimental ones and are quite sensitive to the details of the microstructure and to dislocation densities at interfaces and within the soft γ phase.

  18. Low-frequency-field-induced spontaneous-emission interference in a two-level atom placed in an anisotropic photonic crystal

    International Nuclear Information System (INIS)

    Li Gaoxiang; Evers, Joerg; Keitel, Christoph H

    2005-01-01

    We investigate the spontaneous-emission properties of a two-level atom embedded in a three-dimensional anisotropic photonic crystal. In addition to the modified density of states, the atom is driven by a coherent intense low-frequency field (LFF), which creates additional multiphoton decay channels with the exchange of two low-frequency photons and one spontaneous photon during an atomic transition. Due to the low frequency of the applied field, the various transition pathways may interfere with each other and thus give rise to a modified system dynamics. We find that even if all the atomic (bare and induced) transition frequencies are in the conducting band of the photonic crystal, there still may exist a photon-atom bound state in coexistence with propagating modes. The system also allows us to generate narrow lines in the spontaneous-emission spectrum. This spectrum is a function of the distance of the observer from the atom due to the band gap in the photonic crystal. The system properties depend on three characteristic frequencies, which are influenced by quantum interference effects. Thus these results can be attributed to a combination of interference and band-gap effects

  19. 3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution.

    Science.gov (United States)

    Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F

    2016-02-01

    The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution. Graphical Abstract ᅟ.

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

    Science.gov (United States)

    Ombaba, Jackson M.

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

  1. Interaction of Pd single atoms with different CeO2 crystal planes: A first-principles study

    Science.gov (United States)

    He, Bingling; Wang, Jinlong; Ma, Dongwei; Tian, Zhixue; Jiang, Lijuan; Xu, Yan; Cheng, Sujun

    2018-03-01

    The adsorption of single Pd atoms on the various CeO2 surfaces, including (111), (110), and (100), has been studied based on the first-principles calculations. It is found that, according to the calculated adsorption energy, interaction strength between Pd and the three CeO2 surfaces follows the order of (100) > (110) > (111). Interestingly, the effect of the electron localization on the surface Ce ions due to the Pd adsorption on its adsorption stability is more significant for the (110) surface than that for the (111) and (100) surfaces. We also find that the formal oxidation states of Pd0, Pdδ+ (δ < 1) and Pd1+ may appear on the CeO2 (111) surface, and Pdδ+ (δ < 1) and Pd1+ could coexist on the CeO2 (100) surfaces. However, under suitable conditions the CeO2 (110) surface may be covered with Pd2+ ions. Present theoretical results clearly suggest that the interaction between Pd and CeO2 nanocrystals significantly depends on the crystal planes of CeO2. It is expected that our study will give useful insights into the effect of CeO2 crystal plane on the physicochemical and catalytic properties of CeO2 supported Pd catalyst.

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

    Science.gov (United States)

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

    2014-04-17

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

  3. An atomic resolution scanning tunneling microscope that applies external tensile stress and strain in an ultrahigh vacuum

    International Nuclear Information System (INIS)

    Fujita, D; Kitahara, M; Onishi, K; Sagisaka, K

    2008-01-01

    We have developed an ultrahigh vacuum scanning tunneling microscope with an in situ external stress application capability in order to determine the effects of stress and strain on surface atomistic structures. It is necessary to understand these effects because controlling them will be a key technology that will very likely be used in future nanometer-scale fabrication processes. We used our microscope to demonstrate atomic resolution imaging under external tensile stress and strain on the surfaces of wafers of Si(111) and Si(001). We also successfully observed domain redistribution induced by applying uniaxial stress at an elevated temperature on the surface of a wafer of vicinal Si(100). We confirmed that domains for which an applied tensile stress is directed along the dimer bond become less stable and shrink. This suggests that it may be feasible to fabricate single domain surfaces in a process that controls surface stress and strain

  4. Direct determination of a radiation-damage profile with atomic resolution in ion-irradiated platinum. MSC report No. 5030

    International Nuclear Information System (INIS)

    Pramanik, D.; Seidman, D.N.

    1983-05-01

    The field-ion microscope (FIM) technique has been employed to determine directly a radiation damage profile, with atomic resolution, in a platinum specimen which had been irradiated at 80 0 K with 20-keV Kr + ions to a fluence of 5 x 10 12 cm - 2 . It is shown that the microscopic spatial-vacancy distribution (radiation-damage profile) is directly related to the elastically-deposited-energy profile. The experimentally constructed radiation-damage profile is compared with a theoretical damage profile - calculated employing the TRIM Monte Carlo code - and excellent agreement is obtained between the two, thus demonstrating that it is possible to go directly from a microscopic spatial distribution of vacancies to a continuous radiation-damage profile

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-03-15

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

  6. High-resolution inelastic X-ray scattering to study the high-frequency atomic dynamics of disordered systems

    International Nuclear Information System (INIS)

    Monaco, G.

    2008-01-01

    The use of momentum-resolved inelastic X-ray scattering with meV energy resolution to study the high-frequency atomic dynamics in disordered systems is here reviewed. The typical realization of this experiment is described together with some common models used to interpret the measured spectra and to extract parameters of interest for the investigation of disordered systems. With the help of some selected examples, the present status of the field is discussed. Particular attention is given to those results which are still open for discussion or controversial, and which will require further development of the technique to be fully solved. Such an instrumental development seems nowadays possible at the light of recently proposed schemes for advanced inelastic X-ray scattering spectrometers. (author)

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

    International Nuclear Information System (INIS)

    Kosmata, Marcel

    2011-01-01

    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. Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution.

    Science.gov (United States)

    Shen, Huaizong; Zhou, Qiang; Pan, Xiaojing; Li, Zhangqiang; Wu, Jianping; Yan, Nieng

    2017-03-03

    Voltage-gated sodium (Na v ) channels are responsible for the initiation and propagation of action potentials. They are associated with a variety of channelopathies and are targeted by multiple pharmaceutical drugs and natural toxins. Here, we report the cryogenic electron microscopy structure of a putative Na v channel from American cockroach (designated Na v PaS) at 3.8 angstrom resolution. The voltage-sensing domains (VSDs) of the four repeats exhibit distinct conformations. The entrance to the asymmetric selectivity filter vestibule is guarded by heavily glycosylated and disulfide bond-stabilized extracellular loops. On the cytoplasmic side, a conserved amino-terminal domain is placed below VSD I , and a carboxy-terminal domain binds to the III-IV linker. The structure of Na v PaS establishes an important foundation for understanding function and disease mechanism of Na v and related voltage-gated calcium channels. Copyright © 2017, American Association for the Advancement of Science.

  9. Leakage current analysis for dislocations in Na-flux GaN bulk single crystals by conductive atomic force microscopy

    Science.gov (United States)

    Hamachi, T.; Takeuchi, S.; Tohei, T.; Imanishi, M.; Imade, M.; Mori, Y.; Sakai, A.

    2018-04-01

    The mechanisms associated with electrical conduction through individual threading dislocations (TDs) in a Na-flux GaN crystal grown with a multipoint-seed-GaN technique were investigated by conductive atomic force microscopy (C-AFM). To focus on individual TDs, dislocation-related etch pits (DREPs) were formed on the Na-flux GaN surface by wet chemical etching, after which microscopic Pt electrodes were locally fabricated on the DREPs to form conformal contacts to the Na-flux GaN crystal, using electron beam assisted deposition. The C-AFM data clearly demonstrate that the leakage current flows through the individual TD sites. It is also evident that the leakage current and the electrical conduction mechanism vary significantly based on the area within the Na-flux GaN crystal where the TDs are formed. These regions include the c-growth sector (cGS) in which the GaN grows in the [0001 ] direction on top of the point-seed with a c-plane growth front, the facet-growth sector (FGS) in which the GaN grows with {10 1 ¯ 1 } facets on the side of the cGS, the boundary region between the cGS and FGS (BR), and the coalescence boundary region between FGSs (CBR). The local current-voltage (I-V) characteristics of the specimen demonstrate space charge limited current conduction and conduction related to band-like trap states associated with TDs in the FGS, BR, and CBR. A detailed analysis of the I-V data indicates that the electrical conduction through TDs in the cGS may proceed via the Poole-Frenkel emission mechanism.

  10. Real-Time Very High-Resolution Regional 4D Assimilation in Supporting CRYSTAL-FACE Experiment

    Science.gov (United States)

    Wang, Donghai; Minnis, Patrick

    2004-01-01

    To better understand tropical cirrus cloud physical properties and formation processes with a view toward the successful modeling of the Earth's climate, the CRYSTAL-FACE (Cirrus Regional Study of Tropical Anvils and Cirrus Layers - Florida Area Cirrus Experiment) field experiment took place over southern Florida from 1 July to 29 July 2002. During the entire field campaign, a very high-resolution numerical weather prediction (NWP) and assimilation system was performed in support of the mission with supercomputing resources provided by NASA Center for Computational Sciences (NCCS). By using NOAA NCEP Eta forecast for boundary conditions and as a first guess for initial conditions assimilated with all available observations, two nested 15/3 km grids are employed over the CRYSTAL-FACE experiment area. The 15-km grid covers the southeast US domain, and is run two times daily for a 36-hour forecast starting at 0000 UTC and 1200 UTC. The nested 3-km grid covering only southern Florida is used for 9-hour and 18-hour forecasts starting at 1500 and 0600 UTC, respectively. The forecasting system provided more accurate and higher spatial and temporal resolution forecasts of 4-D atmospheric fields over the experiment area than available from standard weather forecast models. These forecasts were essential for flight planning during both the afternoon prior to a flight day and the morning of a flight day. The forecasts were used to help decide takeoff times and the most optimal flight areas for accomplishing the mission objectives. See more detailed products on the web site http://asd-www.larc.nasa.gov/mode/crystal. The model/assimilation output gridded data are archived on the NASA Center for Computational Sciences (NCCS) UniTree system in the HDF format at 30-min intervals for real-time forecasts or 5-min intervals for the post-mission case studies. Particularly, the data set includes the 3-D cloud fields (cloud liquid water, rain water, cloud ice, snow and graupe/hail).

  11. The conditions for total reflection of low-energy atoms from crystal surfaces

    International Nuclear Information System (INIS)

    Hou, M.; Robinson, M.T.

    1978-01-01

    The critical angles for the total reflection of low-energy particles from Cu rows and (001) planes have been investigated, using the binary collision approximation computer simulation code MARLOWE Breakthrough angles were evaluated for H, N, Ne, Ar, Cu, Xe, and Au in the energy range from 0.1 to 7.5 keV. In both the axial and the planar cases, recoiling of the target atoms lowers the energy barrier which the target surface presents to the heavy projectiles. Consequently, the breakthrough angles are reduced for heavy projectiles below the values expected either from observations on light projectiles or from analytical channeling theory. (orig.) [de

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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 ∼10 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 4 tetrahedra, which efficiently transduce electric energy into elastic energy

  13. Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level.

    Science.gov (United States)

    Evans, Constantine G; Hariadi, Rizal F; Winfree, Erik

    2012-06-27

    While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly.

  14. Nanoprecipitates in single-crystal molybdenum-alloy nanopillars detected by TEM and atom probe tomography

    International Nuclear Information System (INIS)

    Oveisi, Emad; Bártová, Barbora; Gerstl, Stephan; Zimmermann, Julien; Marichal, Cécile; Van Swygenhoven, Helena; Hébert, Cécile

    2013-01-01

    Transmission electron microscopy (TEM) supported by various chemical analyses techniques as well as atom probe tomography is applied to characterize newly identified nanosized precipitates in Mo-alloy nanopillars that were prepared by directional solidification. It is shown that the α-Mo matrix contains Al-enriched face-centred cubic precipitates which have a 4.12 Å lattice parameter, and exhibit a Kurdjumov–Sachs crystallographic orientation relationship with the matrix. Such precipitates could be responsible for the unusual behaviour of the pillars during compression tests

  15. Probing the Surface Charge on the Basal Planes of Kaolinite Particles with High-Resolution Atomic Force Microscopy.

    Science.gov (United States)

    Kumar, N; Andersson, M P; van den Ende, D; Mugele, F; Siretanu, I

    2017-12-19

    High-resolution atomic force microscopy is used to map the surface charge on the basal planes of kaolinite nanoparticles in an ambient solution of variable pH and NaCl or CaCl 2 concentration. Using DLVO theory with charge regulation, we determine from the measured force-distance curves the surface charge distribution on both the silica-like and the gibbsite-like basal plane of the kaolinite particles. We observe that both basal planes do carry charge that varies with pH and salt concentration. The silica facet was found to be negatively charged at pH 4 and above, whereas the gibbsite facet is positively charged at pH below 7 and negatively charged at pH above 7. Investigations in CaCl 2 at pH 6 show that the surface charge on the gibbsite facet increases for concentration up to 10 mM CaCl 2 and starts to decrease upon further increasing the salt concentration to 50 mM. The increase of surface charge at low concentration is explained by Ca 2+ ion adsorption, while Cl - adsorption at higher CaCl 2 concentrations partially neutralizes the surface charge. Atomic resolution imaging and density functional theory calculations corroborate these observations. They show that hydrated Ca 2+ ions can spontaneously adsorb on the gibbsite facet of the kaolinite particle and form ordered surface structures, while at higher concentrations Cl - ions will co-adsorb, thereby changing the observed ordered surface structure.

  16. Polarization switching detection method using a ferroelectric liquid crystal for dichroic atomic vapor laser lock frequency stabilization techniques.

    Science.gov (United States)

    Dudzik, Grzegorz; Rzepka, Janusz; Abramski, Krzysztof M

    2015-04-01

    We present a concept of the polarization switching detection method implemented for frequency-stabilized lasers, called the polarization switching dichroic atomic vapor laser lock (PSDAVLL) technique. It is a combination of the well-known dichroic atomic vapor laser lock method for laser frequency stabilization with a synchronous detection system based on the surface-stabilized ferroelectric liquid crystal (SSFLC).The SSFLC is a polarization switch and quarter wave-plate component. This technique provides a 9.6 dB better dynamic range ratio (DNR) than the well-known two-photodiode detection configuration known as the balanced polarimeter. This paper describes the proposed method used practically in the VCSEL laser frequency stabilization system. The applied PSDAVLL method has allowed us to obtain a frequency stability of 2.7×10⁻⁹ and a reproducibility of 1.2×10⁻⁸, with a DNR of detected signals of around 81 dB. It has been shown that PSDAVLL might be successfully used as a method for spectra-stable laser sources.

  17. Contribution of a solute atoms in the relaxation phenomenon at high temperature in Cu-Al single crystal alloys

    Science.gov (United States)

    Belamri, C.; Belhas, S.; Rivière, A.

    2009-11-01

    Two Cu-Al single crystals with 7 and 14 at. % Al respectively have been studied using isothermal mechanical spectroscopy (IMS) technique. After a 1% cold work by torsion, the samples have been progressively heated to 1140 K and then cooled until room temperature. IMS experiments allow to compare the isothermal internal friction spectra obtained during the heating (in this case, the annealing temperature is equal to the temperature of measurement) with the measurements performed at various temperature during the cooling after the annealing at 1140 K. Three relaxation peaks were observed. The first one at about 0.4 TM (TM: melting point) is a Zener relaxation peak (PZ) due to the reorientation under constraint of pairs of aluminium atoms. The high temperature annealing does not influence PZ. At about 0.6TM, a peak (P1) related to a dislocation mechanism is evidenced. The relaxation strength of P1 peak decreases with the temperature and a new relaxation peak (P2) is progressively developed. The IMS spectra obtained during the cooling evidenced only P2. The relaxation parameters obtained by the Arrhenius plots and the evolution with the annealing temperature allow to assign P1 and P2 to an interaction between the dislocations and the solute atoms according to the Darinskiy model.

  18. Ultrahigh stability of atomically thin metallic glasses

    Energy Technology Data Exchange (ETDEWEB)

    Cao, C. R.; Huang, K. Q.; Zhao, N. J.; Sun, Y. T.; Bai, H. Y.; Gu, L., E-mail: l.gu@iphy.ac.cn, E-mail: dzheng@iphy.ac.cn, E-mail: whw@iphy.ac.cn; Zheng, D. N., E-mail: l.gu@iphy.ac.cn, E-mail: dzheng@iphy.ac.cn, E-mail: whw@iphy.ac.cn; Wang, W. H., E-mail: l.gu@iphy.ac.cn, E-mail: dzheng@iphy.ac.cn, E-mail: whw@iphy.ac.cn [Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

    2014-07-07

    We report the fabrication and study of thermal stability of atomically thin ZrCu-based metallic glass films. The ultrathin films exhibit striking dynamic properties, ultrahigh thermal stability, and unique crystallization behavior with discrete crystalline nanoparticles sizes. The mechanisms for the remarkable high stability and crystallization behaviors are attributed to the dewetting process of the ultrathin film. We demonstrated a promising avenue for understanding some fundamental issues such as glassy structure, crystallization, deformation, and glass formation through atomic resolution imaging of the two dimensional like metallic glasses.

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

    Science.gov (United States)

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

    2011-01-01

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

  20. High-resolution bistable nematic liquid crystal device realized on orientational surface patterns

    International Nuclear Information System (INIS)

    Kim, Jong-Hyun; Yoneya, Makoto; Yokoyama, Hiroshi

    2003-01-01

    The four-fold symmetry of a checkerboard-like surface alignment consisted of square domains arrived at the macroscopic orientational bistability of nematic liquid crystals. Switching between the two orientations took place with an appropriate electric field. Here the threshold field of bistable switching decreased as temperature increased, and the light could heat only the selected region in the cell including a light-absorbing medium. Irradiating the laser concurrently with an electric field, we addressed a selected region in the alignment pattern without the disturbance of neighboring regions. Extending this process, we realized an extremely fine bistable device of nematic liquid crystal with a pixel size down to about 2 μm

  1. Intrinsic spatial resolution evaluation of the X'tal cube PET detector based on a 3D crystal block segmented by laser processing.

    Science.gov (United States)

    Yoshida, Eiji; Tashima, Hideaki; Inadama, Naoko; Nishikido, Fumihiko; Moriya, Takahiro; Omura, Tomohide; Watanabe, Mitsuo; Murayama, Hideo; Yamaya, Taiga

    2013-01-01

    The X'tal cube is a depth-of-interaction (DOI)-PET detector which is aimed at obtaining isotropic resolution by effective readout of scintillation photons from the six sides of a crystal block. The X'tal cube is composed of the 3D crystal block with isotropic resolution and arrays of multi-pixel photon counters (MPPCs). In this study, to fabricate the 3D crystal block efficiently and precisely, we applied a sub-surface laser engraving (SSLE) technique to a monolithic crystal block instead of gluing segmented small crystals. The SSLE technique provided micro-crack walls which carve a groove into a monolithic scintillator block. Using the fabricated X'tal cube, we evaluated its intrinsic spatial resolution to show a proof of concept of isotropic resolution. The 3D grids of 2 mm pitch were fabricated into an 18 × 18 × 18 mm(3) monolithic lutetium yttrium orthosilicate (LYSO) crystal by the SSLE technique. 4 × 4 MPPCs were optically coupled to each surface of the crystal block. The X'tal cube was uniformly irradiated by (22)Na gamma rays, and all of the 3D grids on the 3D position histogram were separated clearly by an Anger-type calculation from the 96-channel MPPC signals. Response functions of the X'tal cube were measured by scanning with a (22)Na point source. The gamma-ray beam with a 1.0 mm slit was scanned in 0.25 mm steps by positioning of the X'tal cube at vertical and 45° incident angles. The average FWHM resolution at both incident angles was 2.1 mm. Therefore, we confirmed the isotropic spatial resolution performance of the X'tal cube.

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

    Science.gov (United States)

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

    2015-10-14

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

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

    CSIR Research Space (South Africa)

    Malwela, T

    2014-09-01

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

  4. Crystallization of isoelectrically homogeneous cholera toxin

    International Nuclear Information System (INIS)

    Spangler, B.D.; Westbrook, E.M.

    1989-01-01

    Past difficulty in growing good crystals of cholera toxin has prevented the study of the crystal structure of this important protein. The authors have determined that failure of cholera toxin to crystallize well has been due to its heterogeneity. They have now succeeded in overcoming the problem by isolating a single isoelectric variant of this oligomeric protein (one A subunit and five B subunits). Cholera toxin purified by their procedure readily forms large single crystals. The crystal form has been described previously. They have recorded data from native crystals of cholera toxin to 3.0-angstrom resolution with our electronic area detectors. With these data, they have found the orientation of a 5-fold symmetry axis within these crystals, perpendicular to the screw dyad of the crystal. They are now determining the crystal structure of cholera toxin by a combination of multiple heavy-atom isomorphous replacement and density modification techniques, making use of rotational 5-fold averaging of the B subunits

  5. 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

  6. Vacancies and atomic processes in intermetallics - From crystals to quasicrystals and bulk metallic glasses

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, Hans-Eckhardt [Institute of Theoretical and Applied Physics, Stuttgart University, Pfaffenwaldring 57, 70569 Stuttgart (Germany); Baier, Falko [Voith Turbo Comp., Alexanderstr. 2, 89552 Heidenheim (Germany); Mueller, Markus A. [GFT Technologies A. G., Filderhauptstr. 142, 70599 Stuttgart (Germany); Reichle, Klaus J. [Philipp-Matthaeus-Hahn School, Jakob-Beutter-Str. 15, 72336 Balingen (Germany); Reimann, Klaus [NXP Semiconductors, Central Research and Development, High Tech Campus 4, 5656 AE Eindhoven (Netherlands); Rempel, Andrey A. [Institute of Solid State Chemistry, Russian Academy of Sciences, Ul. Pervomaiskaya 91, 620041 Ekaterinburg (Russian Federation); Sato, Kiminori [Tokyo Gakugei University, Nukuikita 4-1-1, Koganei, Tokyo 184-8501 (Japan); Ye, Feng [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, 30 Xue Yuan Road, Beijing 100083 (China); Zhang, Xiangyi [Yanshan University, Qinhuangdao 066004 (China); Sprengel, Wolfgang [Institute of Materials Physics, Graz University of Technology, Petersgasse 16, 8010 Graz (Austria)

    2011-10-15

    A review is given on atomic vacancies in intermetallic compounds. The intermetallic compounds cover crystalline, quasicrystalline, and bulk metallic glass (BMG) structures. Vacancies can be specifically characterized by their positron lifetimes, by the coincident measurement of the Doppler broadening of the two quanta emitted by positron-electron annihilation, or by time-differential dilatometry. By these techniques, high concentrations and low mobilities of thermal vacancies were found in open-structured B2 intermetallics such as FeAl or NiAl, whereas the concentrations of vacancies are low and their mobilities high in close-packed structure as, e.g., L1{sub 2}-Ni{sub 3}Al. The activation volumes of vacancy formation and migration are determined by high-pressure experiments. The favorable sublattice for vacancy formation is found to be the majority sublattice in Fe{sub 61}Al{sub 39} and in MoSi{sub 2}. In the icosahedral quasicrystal Al{sub 70}Pd{sub 21}Mn{sub 9} the thermal vacancy concentration is low, whereas in the BMG Zr{sub 57}Cu{sub 15.4}Ni{sub 12.6}Nb{sub 3}Al{sub 10} thermal vacancies are found in high concentrations with low mobilities. This may determine the basic mechanisms of the glass transition. Making use of the experimentally determined vacancy data, the main features of atomic diffusion studies in crystalline intermetallics, in quasicrystals, and in BMGs can be understood. Manfred Faehnle and his group have substantially contributed to the theoretical understanding of vacancies and diffusion mechanisms in intermetallics. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Determination of silicon in biomass and products of pyrolysis process via high-resolution continuum source atomic absorption spectrometry.

    Science.gov (United States)

    Nakadi, Flávio V; Prodanov, Caroline; Boschetti, Wiliam; Vale, Maria Goreti R; Welz, Bernhard; de Andrade, Jailson B

    2018-03-01

    Thermochemical processes can convert the biomass into fuels, such as bio-oil. The biomass submitted to pyrolysis process, such as fibers, are generally rich in silicon, an element that can lead to damages in an engine when there is high concentration in a fuel. High-resolution continuum source atomic absorption spectrometry (HR-CS AAS) is an interesting alternative for Si determination in the products and byproducts of the pyrolysis process because, besides the flame (F) and graphite furnace (GF) atomizers, it has enhanced the application of direct analysis of solid samples (SS) within GF. This study aimed the development of methods to determine Si in biomass samples, their products and byproducts using HR-CS AAS. A high-resolution continuum source atomic absorption spectrometer contrAA 700 equipped with F and GF atomizers was used throughout the study. HR-CS F AAS (λ = 251.611nm, 1 detection pixel, N 2 O/C 2 H 2 flame) was used to evaluate Si content in biomass and ash, after a microwave-assisted acid digestion with HNO 3 and HF. HR-CS GF AAS (T pyr = 1400°C, T atom = 2650°C) has evaluated Si in pyrolysis water and bio-oil at 251.611nm, and in peach pit biomass and ash at 221.174nm using SS, both wavelengths with 1 detection pixel. Rhodium (300μg) was applied as permanent modifier and 10μgPd + 6μg Mg were pipetted onto the standards/samples at each analysis. Three different biomass samples were studied: palm tree fiber, coconut fiber and peach pit, and three certified reference materials (CRM) were used to verify the accuracy of the methods. The figures of merit were LOD 0.09-20mgkg -1 , and LOQ 0.3-20mgkg -1 , considering all the methods. There were no significant differences between the CRM certified values and the determined ones, using a Student t-test with a confidence interval of 95% (n = 5). Si concentration ranged from 0.11-0.92% mm -1 , 1.1-1.7mgkg -1 , 3.3-13mgkg -1 , and 0.41-1.4%mm -1 , in biomass, bio-oil, pyrolysis water and ash, respectively

  8. Algorithms for solving atomic structures of nanodimensional clusters in single crystals based on X-ray and neutron diffuse scattering data

    International Nuclear Information System (INIS)

    Andrushevskii, N.M.; Shchedrin, B.M.; Simonov, V.I.

    2004-01-01

    New algorithms for solving the atomic structure of equivalent nanodimensional clusters of the same orientations randomly distributed over the initial single crystal (crystal matrix) have been suggested. A cluster is a compact group of substitutional, interstitial or other atoms displaced from their positions in the crystal matrix. The structure is solved based on X-ray or neutron diffuse scattering data obtained from such objects. The use of the mathematical apparatus of Fourier transformations of finite functions showed that the appropriate sampling of the intensities of continuous diffuse scattering allows one to synthesize multiperiodic difference Patterson functions that reveal the systems of the interatomic vectors of an individual cluster. The suggested algorithms are tested on a model one-dimensional structure

  9. Scanning tunneling microscopy of the atomically smooth (001) surface of vanadium pentoxide V{sub 2}O{sub 5} crystals

    Energy Technology Data Exchange (ETDEWEB)

    Muslimov, A. E., E-mail: amuslimov@mail.ru; Butashin, A. V.; Kanevsky, V. M. [Russian Academy of Sciences, Shubnikov Institute of Crystallography, Federal Research Centre “Crystallography and Photonics” (Russian Federation)

    2017-01-15

    The (001) cleavage surface of vanadium pentoxide (V{sub 2}O{sub 5}) crystal has been studied by scanning tunneling spectroscopy (STM). It is shown that the surface is not reconstructed; the STM image allows geometric lattice parameters to be determined with high accuracy. The nanostructure formed on the (001) cleavage surface of crystal consists of atomically smooth steps with a height multiple of unit-cell parameter c = 4.37 Å. The V{sub 2}O{sub 5} crystal cleavages can be used as references in calibration of a scanning tunneling microscope under atmospheric conditions both along the (Ñ…, y) surface and normally to the sample surface (along the z axis). It is found that the terrace surface is not perfectly atomically smooth; its roughness is estimated to be ~0.5 Å. This circumstance may introduce an additional error into the microscope calibration along the z coordinate.

  10. The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution.

    OpenAIRE

    Czworkowski, J; Wang, J; Steitz, T A; Moore, P B

    1994-01-01

    Elongation factor G (EF-G) catalyzes the translocation step of protein synthesis in bacteria, and like the other bacterial elongation factor, EF-Tu--whose structure is already known--it is a member of the GTPase superfamily. We have determined the crystal structure of EF-G--GDP from Thermus thermophilus. It is an elongated molecule whose large, N-terminal domain resembles the G domain of EF-Tu, except for a 90 residue insert, which covers a surface that is involved in nucleotide exchange in E...

  11. Development of high-resolution gamma detector using sub-mm GAGG crystals coupled to TSV-MPPC array

    International Nuclear Information System (INIS)

    Lipovec, A.; Shimazoe, K.; Takahashi, H.

    2016-01-01

    In this study a high-resolution gamma detector based on an array of sub-millimeter Ce:GAGG (Cerium doped Gd 3 Al 2 Ga 3 O 12 ) crystals read out by an array of surface-mount type of TSV-MPPC was developed. MPPC sensor from Hamamatsu which has a 26 by 26 mm 2 detector area with 64 channels was used. One channel has a 3 by 3 mm 2 photosensitive area with 50 μ m pitch micro cells. MPPC sensor provides 576 mm 2 sensing area and was used to decode 48 by 48 array with 0.4 by 0.4 by 20 mm 3 Ce:GAGG crystals of 500 μ m pitch. The base of the detector with the crystal module was mounted to a read out board which consists of charge division circuit, thus allowing for a read out of four channels to identify the position of the incident event on the board. The read out signals were amplified using charge sensitive amplifiers. The four amplified signals were digitized and analyzed to produce a position sensitive event. For the performance analysis a 137 Cs source was used. The produced events were used for flood histogram and energy analysis. The effects of the glass thickness between the Ce:GAGG and MPPC were analyzed using the experimental flood diagrams and Geant4 simulations. The glass between the scintillator and the detector allows the spread of the light over different channels and is necessary if the channel's sensitive area is bigger than the scintillator's area. The initial results demonstrate that this detector module is promising and could be used for applications requiring compact and high-resolution detectors. Experimental results show that the detectors precision increases using glass guide thickness of 1.35 mm and 1.85 mm; however the precision using 2.5 mm are practically the same as if using 0.8 mm or 1.0 mm glass guide thicknesses. In addition, simulations using Geant4 indicate that the light becomes scarcer if thicker glass is used, thus reducing the ability to indicate which crystal was targeted. When 2.5 mm glass thickness is used, the scarce

  12. 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.

  13. A positron tomograph with 600 BGO [bismuth germanate] crystals and 2.6 mm resolution

    International Nuclear Information System (INIS)

    Derenzo, S.E.; Huesman, R.H.; Cahoon, J.L.; Geyer, A.B.; Moses, W.W.; Uber, D.C.; Vuletich, T.; Budinger, T.F.

    1987-10-01

    We describe the imaging performance of the Donner 600-Crystal Positron Tomograph, a single 600 cm diam ring of 3 mm wide bismuth germanate (BGO) crystals coupled individually to 14 mm phototubes. With a pulse height threshold of 200 keV and a slice thickness of 5 mm, the sensitivity is 7024 eventssec per μCiml in a 20 cm cyliner of water. The measured rates for 18 μCiml are 95,000 truessec plus 20,000 randomsec. A 0.3 mm diam 22 Na line source near the center of the tomograph has a circular point spread function (PSF) with a full-width at half-maximum (fwhm) of 2.6 mm. At 5 cm from the center the PSF is elliptical with a fwhm of 2.7 mm tangential /times/ 3.2 mm radial. At 10 cm the PSF has a fwhm of 2.8 mm tangential /times/ 4.8 mm radial. Attenuation data are accumulated with a 20 mCi 68 Ge orbiting transmission source and 100 million coincident events are collected in 200 sec. 20 refs., 9 figs., 5 tabs

  14. A positron tomograph with 600 BGO crystals and 2.6 mm resolution

    International Nuclear Information System (INIS)

    Derenzo, S.E.; Huesman, R.H.; Cahoon, J.L.; Geyer, A.B.; Moses, W.W.; Uber, D.C.; Vuletich, T.; Budinger, T.F.

    1988-01-01

    The authors describe the imaging performance of the Donner 600-Crystal Positron Tomograph, a single 60 cm diam ring of 3 mm wide bismuth germanate (BGO) crystals coupled individually to 14 mm phototubes. With a pulse height threshold of 200 keV and a slice thickness of 5 mm, the sensitivity is 7024 events/sec per μCi/ml in a 20 cm cylinder of water. The measured rates for 18 μCi/ml are 95,000 trues/sec plus 20,000 random/sec. A 0.3 mm diam /sup 22/Na line source near the center of the tomograph has a circular point spread function (PSF) with a full-width at half-maximum (fwhm) of 2.6 mm. At 5 cm from the center the PSF is elliptical with a fwhm of 2.7 mm tangential x 3.2 mm radial. At 10 cm the PSF has a fwhm of 2.8 mm tangential x 4.8 mm radial. Attenuation data are accumulated with a 20 mCi /sup 68/Ge orbiting transmission source and 100 million coincident events are collected in 200 sec

  15. 1.45 A resolution crystal structure of recombinant PNP in complex with a pM multisubstrate analogue inhibitor bearing one feature of the postulated transition state

    International Nuclear Information System (INIS)

    Chojnowski, Grzegorz; Breer, Katarzyna; Narczyk, Marta; Wielgus-Kutrowska, Beata; Czapinska, Honorata; Hashimoto, Mariko; Hikishima, Sadao; Yokomatsu, Tsutomu; Bochtler, Matthias; Girstun, Agnieszka; Staron, Krzysztof; Bzowska, Agnieszka

    2010-01-01

    Low molecular mass purine nucleoside phosphorylases (PNPs, E.C. 2.4.2.1) are homotrimeric enzymes that are tightly inhibited by immucillins. Due to the positive charge on the ribose like part (iminoribitol moiety) and protonation of the N7 atom of the purine ring, immucillins are believed to act as transition state analogues. Over a wide range of concentrations, immucillins bind with strong negative cooperativity to PNPs, so that only every third binding site of the enzyme is occupied (third-of-the-sites binding). 9-(5',5'-difluoro-5'-phosphonopentyl)-9-deazaguanine (DFPP-DG) shares with immucillins the protonation of the N7, but not the positive charge on the ribose like part of the molecule. We have previously shown that DFPP-DG interacts with PNPs with subnanomolar inhibition constant. Here, we report additional biochemical experiments to demonstrate that the inhibitor can be bound with the same K d (∼190 pM) to all three substrate binding sites of the trimeric PNP, and a crystal structure of PNP in complex with DFPP-DG at 1.45 A resolution, the highest resolution published for PNPs so far. The crystals contain the full PNP homotrimer in the asymmetric unit. DFPP-DG molecules are bound in superimposable manner and with full occupancies to all three PNP subunits. Thus the postulated third-of-the-sites binding of immucillins should be rather attribute to the second feature of the transition state, ribooxocarbenium ion character of the ligand or to the coexistence of both features characteristic for the transition state. The DFPP-DG/PNP complex structure confirms the earlier observations, that the loop from Pro57 to Gly66 covering the phosphate-binding site cannot be stabilized by phosphonate analogues. The loop from Glu250 to Gln266 covering the base-binding site is organized by the interactions of Asn243 with the Hoogsteen edge of the purine base of analogues bearing one feature of the postulated transition state (protonated N7 position).

  16. Surface phonon modes of the NaI(001) crystal surface by inelastic He atom scattering

    International Nuclear Information System (INIS)

    Brug, W.P.; Chern, G.; Duan, J.; Safron, S.A.; Skofronick, J.G.; Benedek, G.

    1990-01-01

    The present theoretical treatment of the surface dynamics of ionic insulators employs the shell model with parameters obtained from bulk materials. The approach has been generally very successful in comparisons with experiment. However, most of the experimental surface dynamics work has been on the low-mass alkali halides with very little effort on higher energy modes or on the heavier alkali halides, where effects from relaxation might be important. The work of this paper explores these latter two conditions. Inelastic scattering of He atoms from the left-angle 110 right-angle NaI(001) surface has been used to obtain the acoustic S 1 Rayleigh mode, the S 6 longitudinal mode, and the S 8 crossing mode, however, no gap S 4 optical mode was seen. The results compare favorably with reported theoretical models employing both slab calculations and the Green's function method thus indicating that bulk parameters and the shell model go a long way in explaining most of the observations

  17. Chemical state analysis of oxide thin films using a high resolution double crystal X-ray fluorescence spectrometer

    International Nuclear Information System (INIS)

    Masuda, Hirohisa; Morinaga, Kenji; Ohta, Yoshio.

    1995-01-01

    The chemical state analysis of r.f.-sputtered amorphous oxide thin films was determined by a high resolution X-ray fluorescence spectrometer with double crystals. The polymerization degree of silicate anions in the silicate film was as same as a target (α-Quartz). The oxygen coordination number of Al 3+ ions in the aluminate film was different from a target (α-Al 2 O 3 ), and it was a mixture of 4 and 6 in a spinel-like structure. In CaO-SiO 2 and CaO-Al 2 O 3 films, when the film thickness is thin at the beginning of sputtering, the composition of films are in the shortage of CaO. But when the film thickness become thicker, the composition of films become as same as the target. From the results above, the chemical state of films and their variations with film thickness can be clarified by using the apparatus. (author)

  18. Broadband high-resolution multi-species CARS in gas-filled hollow-core photonic crystal fiber.

    Science.gov (United States)

    Trabold, Barbara M; Hupfer, Robert J R; Abdolvand, Amir; St J Russell, Philip

    2017-09-01

    We report the use of coherent anti-Stokes Raman spectroscopy (CARS) in gas-filled hollow-core photonic crystal fiber (HC-PCF) for trace gas detection. The long optical path-lengths yield a 60 dB increase in the signal level compared with free-space arrangements. This enables a relatively weak supercontinuum (SC) to be used as Stokes seed, along with a ns pump pulse, paving the way for broadband (>4000  cm -1 ) single-shot CARS with an unprecedented resolution of ∼100  MHz. A kagomé-style HC-PCF provides broadband guidance, and, by operating close to the pressure-tunable zero dispersion wavelength, we can ensure simultaneous phase-matching of all gas species. We demonstrate simultaneous measurement of the concentrations of multiple trace gases in a gas sample introduced into the core of the HC-PCF.

  19. Overview of Three-Dimensional Atomic-Resolution Holography and Imaging Techniques: Recent Advances in Local-Structure Science

    Science.gov (United States)

    Daimon, Hiroshi

    2018-06-01

    Local three-dimensional (3D) atomic arrangements without periodicity have not been able to be studied until recently. Recently, several holographies and related techniques have been developed to reveal the 3D atomic arrangement around specific atoms with no translational symmetry. This review gives an overview of these new local 3D atomic imaging techniques.

  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)

    Ribeiro, Anderson Schwingel; Vieira, Mariana Antunes; Furtado da Silva, Alessandra; Borges, Daniel L. Gallindo; Welz, Bernhard; Heitmann, Uwe; Curtius, Adilson Jose

    2005-01-01

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

    Energy Technology Data Exchange (ETDEWEB)

    Hell, N. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Dr. Remeis-Sternwarte and ECAP, Universität Erlangen-Nürnberg, Bamberg 96049 (Germany); Beiersdorfer, P.; Magee, E. W.; Brown, G. V. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)

    2016-11-15

    We report the calibration of the Orion High-Resolution X-ray (OHREX) imaging crystal spectrometer at the EBIT-I electron beam ion trap at Livermore. Two such instruments, dubbed OHREX-1 and OHREX-2, are fielded for plasma diagnostics at the Orion laser facility in the United Kingdom. The OHREX spectrometer can simultaneously house two spherically bent crystals with a radius of curvature of r = 67.2 cm. The focusing properties of the spectrometer allow both for larger distance to the source due to the increase in collected light and for observation of extended sources. OHREX is designed to cover a 2.5°–3° spectral range at Bragg angles around 51.3°. The typically high resolving powers at these large Bragg angles are ideally suited for line shape diagnostics. For instance, the nominal resolving power of the instrument (>10 000) is much higher than the effective resolving power associated with the Doppler broadening due to the temperature of the trapped ions in EBIT-I. The effective resolving power is only around 3000 at typical EBIT-I conditions, which nevertheless is sufficient to set up and test the instrument’s spectral characteristics. We have calibrated the spectral range for a number of crystals using well known reference lines in the first and second order and derived the ion temperatures from these lines. We have also made use of the 50 μm size of the EBIT-I source width to characterize the spatial focusing of the spectrometer.

  2. High resolution crystal structure of the Grb2 SH2 domain with a phosphopeptide derived from CD28.

    Directory of Open Access Journals (Sweden)

    Kunitake Higo

    Full Text Available Src homology 2 (SH2 domains play a critical role in cellular signal transduction. They bind to peptides containing phosphotyrosine (pY with various specificities that depend on the flanking amino-acid residues. The SH2 domain of growth-factor receptor-bound protein 2 (Grb2 specifically recognizes pY-X-N-X, whereas the SH2 domains in phosphatidylinositol 3-kinase (PI3K recognize pY-X-X-M. Binding of the pY site in CD28 (pY-M-N-M by PI3K and Grb2 through their SH2 domains is a key step that triggers the CD28 signal transduction for T cell activation and differentiation. In this study, we determined the crystal structure of the Grb2 SH2 domain in complex with a pY-containing peptide derived from CD28 at 1.35 Å resolution. The peptide was found to adopt a twisted U-type conformation, similar to, but distinct from type-I β-turn. In all previously reported crystal structures, the peptide bound to the Grb2 SH2 domains adopts a type-I β-turn conformation, except those with a proline residue at the pY+3 position. Molecular modeling also suggests that the same peptide bound to PI3K might adopt a very different conformation.

  3. High resolution crystal structure of the Grb2 SH2 domain with a phosphopeptide derived from CD28.

    Science.gov (United States)

    Higo, Kunitake; Ikura, Teikichi; Oda, Masayuki; Morii, Hisayuki; Takahashi, Jun; Abe, Ryo; Ito, Nobutoshi

    2013-01-01

    Src homology 2 (SH2) domains play a critical role in cellular signal transduction. They bind to peptides containing phosphotyrosine (pY) with various specificities that depend on the flanking amino-acid residues. The SH2 domain of growth-factor receptor-bound protein 2 (Grb2) specifically recognizes pY-X-N-X, whereas the SH2 domains in phosphatidylinositol 3-kinase (PI3K) recognize pY-X-X-M. Binding of the pY site in CD28 (pY-M-N-M) by PI3K and Grb2 through their SH2 domains is a key step that triggers the CD28 signal transduction for T cell activation and differentiation. In this study, we determined the crystal structure of the Grb2 SH2 domain in complex with a pY-containing peptide derived from CD28 at 1.35 Å resolution. The peptide was found to adopt a twisted U-type conformation, similar to, but distinct from type-I β-turn. In all previously reported crystal structures, the peptide bound to the Grb2 SH2 domains adopts a type-I β-turn conformation, except those with a proline residue at the pY+3 position. Molecular modeling also suggests that the same peptide bound to PI3K might adopt a very different conformation.

  4. Thermal equilibrium concentration of intrinsic point defects in heavily doped silicon crystals - Theoretical study of formation energy and formation entropy in area of influence of dopant atoms-

    Science.gov (United States)

    Kobayashi, K.; Yamaoka, S.; Sueoka, K.; Vanhellemont, J.

    2017-09-01

    It is well known that p-type, neutral and n-type dopants affect the intrinsic point defect (vacancy V and self-interstitial I) behavior in single crystal Si. By the interaction with V and/or I, (1) growing Si crystals become more V- or I-rich, (2) oxygen precipitation is enhanced or retarded, and (3) dopant diffusion is enhanced or retarded, depending on the type and concentration of dopant atoms. Since these interactions affect a wide range of Si properties ranging from as-grown crystal quality to LSI performance, numerical simulations are used to predict and to control the behavior of both dopant atoms and intrinsic point defects. In most cases, the thermal equilibrium concentrations of dopant-point defect pairs are evaluated using the mass action law by taking only the binding energy of closest pair to each other into account. The impacts of dopant atoms on the formation of V and I more distant than 1st neighbor and on the change of formation entropy are usually neglected. In this study, we have evaluated the thermal equilibrium concentrations of intrinsic point defects in heavily doped Si crystals. Density functional theory (DFT) calculations were performed to obtain the formation energy (Ef) of the uncharged V and I at all sites in a 64-atom supercell around a substitutional p-type (B, Ga, In, and Tl), neutral (C, Ge, and Sn) and n-type (P, As, and Sb) dopant atom. The formation (vibration) entropies (Sf) of free I, V and I, V at 1st neighboring site from B, C, Sn, P and As atoms were also calculated with the linear response method. The dependences of the thermal equilibrium concentrations of trapped and total intrinsic point defects (sum of free I or V and I or V trapped with dopant atoms) on the concentrations of B, C, Sn, P and As in Si were obtained. Furthermore, the present evaluations well explain the experimental results of the so-called ;Voronkov criterion; in B and C doped Si, and also the observed dopant dependent void sizes in P and As doped Si

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

    International Nuclear Information System (INIS)

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

    2013-01-01

    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 × 10 5 at + 20 °C, gain fluctuation over the entire MPPC device is only ± 5.6%, and dark count rates (as measured at the 1 p.e. level) amount to ≤ 400 kcps per channel. We selected Ce-doped (Lu,Y) 2 (SiO 4 )O (Ce:LYSO) and a brand-new scintillator, Ce-doped Gd 3 Al 2 Ga 3 O 12 (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 mm 2 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 22 Na point source. These results suggest that the gamma-ray imagers offer excellent potential for applications in high spatial medical imaging.

  6. Design of a self-aligned, wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with 10 nm magnetic force microscope resolution

    Energy Technology Data Exchange (ETDEWEB)

    Karcı, Özgür [NanoMagnetics Instruments Ltd., Hacettepe - İvedik OSB Teknokent, 1368. Cad., No: 61/33, 06370, Yenimahalle, Ankara (Turkey); Department of Nanotechnology and Nanomedicine, Hacettepe University, Beytepe, 06800 Ankara (Turkey); Dede, Münir [NanoMagnetics Instruments Ltd., Hacettepe - İvedik OSB Teknokent, 1368. Cad., No: 61/33, 06370, Yenimahalle, Ankara (Turkey); Oral, Ahmet, E-mail: orahmet@metu.edu.tr [Department of Physics, Middle East Technical University, 06800 Ankara (Turkey)

    2014-10-01

    We describe the design of a wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with a self-aligned fibre-cantilever mechanism. An alignment chip with alignment groves and a special mechanical design are used to eliminate tedious and time consuming fibre-cantilever alignment procedure for the entire temperature range. A low noise, Michelson fibre interferometer was integrated into the system for measuring deflection of the cantilever. The spectral noise density of the system was measured to be ~12 fm/√Hz at 4.2 K at 3 mW incident optical power. Abrikosov vortices in BSCCO(2212) single crystal sample and a high density hard disk sample were imaged at 10 nm resolution to demonstrate the performance of the system.

  7. Design of a self-aligned, wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with 10 nm magnetic force microscope resolution

    International Nuclear Information System (INIS)

    Karcı, Özgür; Dede, Münir; Oral, Ahmet

    2014-01-01

    We describe the design of a wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with a self-aligned fibre-cantilever mechanism. An alignment chip with alignment groves and a special mechanical design are used to eliminate tedious and time consuming fibre-cantilever alignment procedure for the entire temperature range. A low noise, Michelson fibre interferometer was integrated into the system for measuring deflection of the cantilever. The spectral noise density of the system was measured to be ∼12 fm/√Hz at 4.2 K at 3 mW incident optical power. Abrikosov vortices in BSCCO(2212) single crystal sample and a high density hard disk sample were imaged at 10 nm resolution to demonstrate the performance of the system

  8. 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 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. Energy resolution of the CdTe-XPAD detector:calibration and potential for Laue diffractionmeasurements on protein crystals

    Energy Technology Data Exchange (ETDEWEB)

    Medjoubi K.; Idir M.; Thompson, A.; Berar, J-F.; Clemens, J-C.; Delpierre, P.; Da Silva, P.; Dinkespiler, B.; Itie, J-P.; Legrand, P.; Menneglier, C.; Mercere, P.; Picca, F.; Samama J-P.

    2012-02-02

    The XPAD3S-CdTe, a CdTe photon-counting pixel array detector, has been used to measure the energy and the intensity of the white-beam diffraction from a lysozyme crystal. A method was developed to calibrate the detector in terms of energy, allowing incident photon energy measurement to high resolution (approximately 140 eV), opening up new possibilities in energy-resolved X-ray diffraction. In order to demonstrate this, Laue diffraction experiments were performed on the bending-magnet beamline METROLOGIE at Synchrotron SOLEIL. The X-ray energy spectra of diffracted spots were deduced from the indexed Laue patterns collected with an imaging-plate detector and then measured with both the XPAD3S-CdTe and the XPAD3S-Si, a silicon photon-counting pixel array detector. The predicted and measured energy of selected diffraction spots are in good agreement, demonstrating the reliability of the calibration method. These results open up the way to direct unit-cell parameter determination and the measurement of high-quality Laue data even at low resolution. Based on the success of these measurements, potential applications in X-ray diffraction opened up by this type of technology are discussed.

  10. A novel stibacarbaborane cluster with adjacent antimony atoms exhibiting unique pnictogen bond formation that dominates its crystal packing.

    Science.gov (United States)

    Holub, Josef; Melichar, Petr; Růžičková, Zdeňka; Vrána, Jan; Wann, Derek A; Fanfrlík, Jindřich; Hnyk, Drahomír; Růžička, Aleš

    2017-10-17

    We have prepared nido-7,8,9,11-Sb 2 C 2 B 7 H 9 , the first cluster with simultaneous Sb-B, Sb-C and Sb-Sb atom pairs with interatomic separations with magnitudes that approach the respective sums of covalent radii. However, the length of the Sb-Sb separation in this cluster is slightly less than the sum of the covalent radii. Quantum chemical analysis has revealed that the crystal packing of nido-7,8,9,11-Sb 2 C 2 B 7 H 9 is predominantly dictated by pnictogen (Pn) bonding, an unconventional σ-hole interaction. Indeed, the interaction energy of a very strong Sb 2 H-B Pn-bond in the nido-7,8,9,11-Sb 2 C 2 B 7 H 9 dimer exceeds -6.0 kcal mol -1 . This is a very large value and is comparable to the strengths of known Pn-bonds in Cl 3 Pnπ complexes (Pn = As, Sb).

  11. Influence of crystal defects on the chemical reactivity of recoil atoms in oxygen-containing chromium compounds

    International Nuclear Information System (INIS)

    Costea, T.

    1969-01-01

    The influence of crystal defects on the chemical reactivity of recoil atoms produced by the reaction 50 Cr (n,γ) 51 Cr in oxygen-containing chromium compounds has been studied. Three methods have been used to introduce the defects: doping (K 2 CrO 4 doped with BaCrO 4 ), irradiation by ionizing radiation (K 2 CrO 4 irradiated in the presence of Li 2 CO 3 ) and non-stoichiometry (the semi-conducting oxides of the CrO 3 -Cr 2 O 3 series). The thermal annealing kinetics of the irradiated samples have been determined, and the activation energy has been calculated. In all cases it has been observed that there is a decrease in the activation energy for thermal annealing in the presence of the defects. In order to explain the annealing process, an electronic mechanism has been proposed based on the interaction between the recoil species and the charge-carriers (holes or electrons). (author) [fr

  12. A grid-enabled web service for low-resolution crystal structure refinement.

    Science.gov (United States)

    O'Donovan, Daniel J; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C; Schröder, Gunnar F; Brunger, Axel T; Sliz, Piotr

    2012-03-01

    Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.

  13. Detection of silver nanoparticles in parsley by solid sampling high-resolution-continuum source atomic absorption spectrometry.

    Science.gov (United States)

    Feichtmeier, Nadine S; Leopold, Kerstin

    2014-06-01

    In this work, we present a fast and simple approach for detection of silver nanoparticles (AgNPs) in biological material (parsley) by solid sampling high-resolution-continuum source atomic absorption spectrometry (HR-CS AAS). A novel evaluation strategy was developed in order to distinguish AgNPs from ionic silver and for sizing of AgNPs. For this purpose, atomisation delay was introduced as significant indication of AgNPs, whereas atomisation rates allow distinction of 20-, 60-, and 80-nm AgNPs. Atomisation delays were found to be higher for samples containing silver ions than for samples containing silver nanoparticles. A maximum difference in atomisation delay normalised by the sample weight of 6.27 ± 0.96 s mg(-1) was obtained after optimisation of the furnace program of the AAS. For this purpose, a multivariate experimental design was used varying atomisation temperature, atomisation heating rate and pyrolysis temperature. Atomisation rates were calculated as the slope of the first inflection point of the absorbance signals and correlated with the size of the AgNPs in the biological sample. Hence, solid sampling HR-CS AAS was proved to be a promising tool for identifying and distinguishing silver nanoparticles from ionic silver directly in solid biological samples.

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

    International Nuclear Information System (INIS)

    Bulanov, Alexey V.; Nagorny, Ivan G.

    2015-01-01

    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

  15. Atom optics

    International Nuclear Information System (INIS)

    Balykin, V. I.; Jhe, W.

    1999-01-01

    Atom optics, in analogy to neutron and electron optics, deals with the realization of as a traditional elements, such as lenes, mirrors, beam splitters and atom interferometers, as well as a new 'dissipative' elements such as a slower and a cooler, which have no analogy in an another types of optics. Atom optics made the development of atom interferometer with high sensitivity for measurement of acceleration and rotational possible. The practical interest in atom optics lies in the opportunities to create atom microprobe with atom-size resolution and minimum damage of investigated objects. (Cho, G. S.)

  16. Crystal structure of spinach major light-harvesting complex at 2.72Å resolution

    Science.gov (United States)

    Liu, Zhenfeng; Yan, Hanchi; Wang, Kebin; Kuang, Tingyun; Zhang, Jiping; Gui, Lulu; An, Xiaomin; Chang, Wenrui

    2004-03-01

    The major light-harvesting complex of photosystem II (LHC-II) serves as the principal solar energy collector in the photosynthesis of green plants and presumably also functions in photoprotection under high-light conditions. Here we report the first X-ray structure of LHC-II in icosahedral proteoliposome assembly at atomic detail. One asymmetric unit of a large R32 unit cell contains ten LHC-II monomers. The 14 chlorophylls (Chl) in each monomer can be unambiguously distinguished as eight Chla and six Chlb molecules. Assignment of the orientation of the transition dipole moment of each chlorophyll has been achieved. All Chlb are located around the interface between adjacent monomers, and together with Chla they are the basis for efficient light harvesting. Four carotenoid-binding sites per monomer have been observed. The xanthophyll-cycle carotenoid at the monomer-monomer interface may be involved in the non-radiative dissipation of excessive energy, one of the photoprotective strategies that have evolved in plants.

  17. 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...

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

    KAUST Repository

    Roldan, Manuel; Oxley, Mark; Li, Qiang; Gray, Kenneth; Mitchell, John; Pennycook, Stephen; Varela, Maria

    2016-01-01

    quality. No secondary phases or defects are observed. Figure 1 displays an atomic resolution image obtained with the c-axis perpendicular to the electron beam of a x=0.50 sample. The perovskite (P)-like planes and the rock salt (R)-like planes are clearly

  19. CRYSTAL-STRUCTURE OF DEOXYGENATED LIMULUS-POLYPHEMUS SUBUNIT-II HEMOCYANIN AT 2.18-ANGSTROM RESOLUTION - CLUES FOR A MECHANISM FOR ALLOSTERIC REGULATION

    NARCIS (Netherlands)

    HAZES, B; MAGNUS, KA; BONAVENTURA, C; BONAVENTURA, J; DAUTER, Z; KALK, KH; HOL, WGJ

    The crystal structure of Limulus polyphemus subunit type II hemocyanin in the deoxygenated state has been determined to a resolution of 2.18 angstrom. Phase information for this first structure of a cheliceratan hemocyanin was obtained by molecular replacement using the crustacean hemocyanin

  20. Modulation of Calcium Oxalate Crystallization by Proteins and Small Molecules Investigated by In Situ Atomic Force Microscopy

    Science.gov (United States)

    Qiu, R.; Orme, C.; Cody, A. M.; Wierzbicki, A.; Hoyer, J.; Nancollas, G.; de Yoreo, J.

    2002-12-01

    Understanding the physical mechanisms by which biological inhibitors control nucleation and growth of inorganic crystals is a major focus of biomineral research. Calcium oxalate monohydrate (COM), which plays a functional role in plant physiology, is also a source of pathogenesis in humans where it causes kidney stone disease. Although a great deal of research has been carried out on the modulation COM by proteins and small molecules, the basic mechanism has not yet been understood. However, because the proteins that play a role in COM growth have been identified and sequenced, COM provides an excellent model system for research into biomineral growth. In this study, in situ atomic force microscopy (AFM) was used to monitor the COM surface under controlled growth conditions both from pure solutions and those doped with citrate and osteopontin (OPN) in order to determine their effects on surface morphology and growth dynamics at the molecular level. As with other solution-grown crystals such as calcite, COM grows on complex dislocation hillocks. In pure solution, while growth on the (010) face is isotropic, hillocks on the (-101) face exhibit anisotropic step kinetics. Steps of [-10-1] and orientation are clearly delineated with the [-10-1] being the fast growing direction. When citrate is added to the solution, both growth rate and morphology are drastically changed on (-101) face, especially along the [-10-1] direction. This results in isotropic disc-shaped hillocks a shape that is then reflected in the macroscopic growth habit. In contrast, no large growth changes were observed on the (010) facet. At the same time, molecular modeling predicts an excellent fit of the citrate ion into the (-101) plane and a poor fit to the (010) face. Here we propose a model that reconciles the step-specific interactions implied by the AFM results with the face-specific predictions of the calculations. Finally, we present the results of doping with aspartic acid as well as OPN, an

  1. 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.

  2. Anelasticity of olivine single crystals investigated by stress-reduction tests and high-angular resolution electron backscatter diffraction

    Science.gov (United States)

    Wallis, D.; Hansen, L. N.; Kempton, I.; Wilkinson, A. J.

    2017-12-01

    Geodynamic phenomena, including glacial isostatic adjustment and postseismic deformation, can involve transient deformation in response to changes in differential stress acting on mantle rocks. As such, rheological models of transient deformation are incorporated in predictions of associated processes, including sea-level rise and stress redistribution after earthquakes. However, experimental constraints on rheological models for transient deformation of mantle materials are sparse. In particular, experiments involving stress reductions have been lacking. Moreover, a material's response to a reduction in stress can provide clues to the microphysical processes controlling deformation. To constrain models of transient deformation of mantle rocks we performed stress-reduction tests on single crystals of olivine at 1250-1300°C. Mechanical and piezoelectric actuators controlled constant initial stress during creep. At various strain intervals stress was reduced near-instantaneously using the piezoelectric actuator, inducing both elastic and anelastic (time-dependent) lengthening of the samples. A range of magnitudes of stress reduction were applied, typically unloading 10-90% of the initial stress. High-angular resolution electron backscatter diffraction (HR-EBSD), based on cross-correlation of diffraction patterns, was used to map dislocation density and elastic strain distributions in the recovered samples. Magnitudes of anelastic back-strain increase with increasing magnitudes of stress reduction and show a marked increase when stress reductions exceed 50% of the initial stress, consistent with previous observations in metals and alloys. This observation is inconsistent with the Burgers rheological model commonly used to describe transient behaviour and suggests that the style of rheological behaviour depends on the magnitude of stress change. HR-EBSD maps reveal that the crystal lattices are smoothly curved and generally lack subgrain boundaries and elastic strain

  3. Studying the InAs quantum points on the vicinal surface of a GaAs crystal by the atomic force microscopy

    CERN Document Server

    Evtikhiev, V P; Kotelnikov, E Y; Matveentsev, A V; Titkov, A N; Shkolnik, A S

    2002-01-01

    The methodology for processing the images, obtained through the atomic force microscopy, is proposed. It is shown by the concrete example, how the parameters of the InAs clusters on the vicinal surface of the GaAs crystal are determined. This makes it possible to calculate the energy levels of the electrons and holes in the quantum point with application of the previously developed cluster spherical model

  4. Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy.

    Science.gov (United States)

    Yan, Si; Guo, Changmiao; Hou, Guangjin; Zhang, Huilan; Lu, Xingyu; Williams, John Charles; Polenova, Tatyana

    2015-11-24

    Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

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

    International Nuclear Information System (INIS)

    Hassan, Noor; Kori, Lokesh D.; Gandini, Rosaria; Patel, Bharat K. C.; Divne, Christina; Tan, Tien Chye

    2015-01-01

    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 2+ at pH 6.5. The gene encoding the H. orenii GH43 enzyme has previously been annotated as a putative α-l-arabinofuranosidase. Activity was detected with p-nitrophenyl-α-l-arabinofuranoside as a substrate, and therefore the name HoAraf43 was suggested for the enzyme. In agreement with the conditions for optimal thermal stability against unfolding, the highest arabinofuranosidase activity was obtained in the presence of 4 M NaCl and Mn 2+ at pH 6.5, giving a specific activity of 20–36 µmol min −1 mg −1 . The active site is structurally distinct from those of other GH43 members, including arabinanases, arabinofuranosidases and xylanases. This probably reflects the special requirements for degrading the unique biomass available in highly saline aqueous ecosystems, such as halophilic algae and halophytes. The amino-acid distribution of HoAraf43 has similarities to those of mesophiles, thermophiles and halophiles, but also has unique features, for example more hydrophobic amino acids on the surface and fewer buried charged residues

  6. 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.

  7. Electron diffraction and high-resolution transmission electron microscopy of the high temperature crystal structures of GexSb2Te3+x (x=1,2,3) phase change material

    NARCIS (Netherlands)

    Kooi, B.J.; de Hosson, J.T.M.

    2002-01-01

    The crystal structures of GeSb2Te4, Ge2Sb2Te5, and Ge3Sb2Te6 were determined using electron diffraction and high-resolution transmission electron microscopy. The structure determined for the former two crystals deviates from the ones proposed in the literature. These crystal structures were

  8. Combined High Spectral Resolution Lidar and Millimeter Wavelength Radar Measurement of Ice Crystal Precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Eloranta, Edwin [Univ. of Wisconsin, Madison, WI (United States)

    2016-10-28

    The goal of this research has been to improve measurements of snowfall using a combination of millimeter-wavelength radar and High Spectral Resolution Lidar (HSRL) Observations. Snowflakes are large compared to the 532nm HSRL wavelength and small compared to the 3.2 and 8.6 mm wavelength radars used in this study. This places the particles in the optical scattering regime of the HSRL, where extinction cross-section is proportional to the projected area of the particles, and in the Rayleigh regime for the radar, where the backscatter cross-section is proportional to the mass-squared of the particles. Forming a ratio of the radar measured cross-section to the HSRL measured cross section eliminates any dependence on the number of scattering particles, yielding a quantity proportional to the average mass-squared of the snowflakes over the average area of the flakes. Using simultaneous radar measurements of particle fall velocities, which are dependent particle mass and cross-sectional area it is possible to derive the average mass of the snow flakes, and with the radar measured fall velocities compute the snowfall rate. Since this retrieval requires the optical extinction cross-section we began by considering errors this quantity. The HSRL is particularly good at measuring the backscatter cross-section. In previous studies of snowfall in the high Arctic were able to estimate the extinction cross-section directly as a fixed ratio to the backscatter cross-section. Measurements acquired in the STORMVEX experiment in Colorado showed that this approach was not valid in mid-latitude snowfalls and that direct measurement of the extinction cross-section is required. Attempts to measure the extinction directly uncovered shortcomings in thermal regulation and mechanical stability of the newly deployed DOE HSRL systems. These problems were largely mitigated by modifications installed in both of the DOE systems. We also investigated other sources of error in the HSRL direct

  9. Low resolution crystal structure of Arenicola erythrocruorin: influence of coiled coils on the architecture of a megadalton respiratory protein.

    Science.gov (United States)

    Royer, William E; Omartian, Michael N; Knapp, James E

    2007-01-05

    Annelid erythrocruorins are extracellular respiratory complexes assembled from 180 subunits into hexagonal bilayers. Cryo-electron microscopic experiments have identified two different architectural classes. In one, designated type I, the vertices of the two hexagonal layers are partially staggered, with one hexagonal layer rotated by about 16 degrees relative to the other layer, whereas in the other class, termed type II, the vertices are essentially eclipsed. We report here the first crystal structure of a type II erythrocruorin, that from Arenicola marina, at 6.2 A resolution. The structure reveals the presence of long continuous triple-stranded coiled-coil "spokes" projecting towards the molecular center from each one-twelfth unit; interdigitation of these spokes provides the only contacts between the two hexagonal layers of the complex. This arrangement contrasts with that of a type I erythrocruorin from Lumbricus terrestris in which the spokes are broken into two triple-stranded coiled coils with a disjointed connection. The disjointed connection allows formation of a more compact structure in the type I architecture, with the two hexagonal layers closer together and additional extensive contacts between the layers. Comparison of sequences of the coiled-coil regions of various linker subunits shows that the linker subunits from type II erythrocruorins possess continuous heptad repeats, whereas a sequence gap places these repeats out of register in the type I linker subunits, consistent with a disjointed coiled-coil arrangement.

  10. 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.

  11. 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)

    Blankenship, Elise; Vukoti, Krishna; Miyagi, Masaru; Lodowski, David T.

    2014-01-01

    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

  12. 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)

    Yap, Thai Leong; Chen, Yen Liang; Xu, Ting; Wen, Daying; Vasudevan, Subhash G.; Lescar, Julien

    2007-01-01

    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. 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.

  14. Mechanisms and energetics of surface atomic processes

    International Nuclear Information System (INIS)

    Tsong, T.T.

    1991-01-01

    The energies involved in various surface atomic processes such as surface diffusion, the binding of small atomic clusters on the surface, the interaction between two adsorbed atoms, the dissociation of an atom from a small cluster or from a surface layer, the binding of kink size atoms or atoms at different adsorption sites to the surface etc., can be derived from an analysis of atomically resolved field ion microscope images and a kinetic energy measurement of low temperature field desorbed ions using the time-of-flight atom-probe field ion microscope. These energies can be used to compare with theories and to understand the transport of atoms on the surface in atomic reconstructions, epitaxial growth of surface layers and crystal growth, adsorption layer superstructure formation, and also why an atomic ordering or atomic reconstruction at the surface is energetically favored. Mechanisms of some of the surface atomic processes are also clarified from these quantitative, atomic resolution studies. In this paper work in this area is bris briefly reviewed

  15. High-resolution inner-shell spectroscopies of free atoms and molecules using soft-x-ray beamlines at the third-generation synchrotron radiation sources

    International Nuclear Information System (INIS)

    Ueda, Kiyoshi

    2003-01-01

    This article reviews the current status of inner-shell spectroscopies of free atoms and molecules using high-resolution soft-x-ray monochromators installed in the soft-x-ray beamlines at the third-generation synchrotron radiation facilities. Beamlines and endstations devoted to atomic and molecular inner-shell spectroscopies and various types of experimental techniques, such as ion yield spectroscopy, resonant photoemission spectroscopy and multiple-coincidence momentum imaging, are described. Experimental results for K-shell excitation of Ne, O K-shell excitation of H 2 O and CO 2 , C K-shell excitation and ionization of CO 2 and B K-shell excitation of BF 3 , obtained at beamline 27SU of SPring-8 in Japan, are discussed as examples of atomic and molecular inner-shell spectroscopies using the third-generation synchrotron radiation sources. (topical review)

  16. On the solid phase crystallization of In{sub 2}O{sub 3}:H transparent conductive oxide films prepared by atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Macco, Bart; Verheijen, Marcel A.; Black, Lachlan E.; Melskens, J. [Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Barcones, Beatriz [NanoLab@TU/e, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Kessels, Wilhelmus M. M., E-mail: w.m.m.kessels@tue.nl [Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Solliance Solar Research, High Tech Campus 5, 5656 AE Eindhoven (Netherlands)

    2016-08-28

    Hydrogen-doped indium oxide (In{sub 2}O{sub 3}:H) has emerged as a highly transparent and conductive oxide, finding its application in a multitude of optoelectronic devices. Recently, we have reported on an atomic layer deposition (ALD) process to prepare high quality In{sub 2}O{sub 3}:H. This process consists of ALD of In{sub 2}O{sub 3}:H films at 100 °C, followed by a solid phase crystallization step at 150–200 °C. In this work, we report on a detailed electron microscopy study of this crystallization process which reveals new insights into the crucial aspects for achieving the large grain size and associated excellent properties of the material. The key finding is that the best optoelectronic properties are obtained by preparing the films at the lowest possible temperature prior to post-deposition annealing. Electron microscopy imaging shows that such films are mostly amorphous, but feature a very low density of embedded crystallites. Upon post-deposition annealing, crystallization proceeds merely from isotropic crystal grain growth of these embedded crystallites rather than by the formation of additional crystallites. The relatively high hydrogen content of 4.2 at. % in these films is thought to cause the absence of additional nucleation, thereby rendering the final grain size and optoelectronic properties solely dependent on the density of embedded crystallites. The temperature-dependent grain growth rate has been determined, from which an activation energy of (1.39 ± 0.04) eV has been extracted. Finally, on the basis of the observed crystallization mechanism, a simple model to fully describe the crystallization process has been developed. This model has been validated with a numerical implementation thereof, which accurately predicts the observed temperature-dependent crystallization behaviour.

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

    Science.gov (United States)

    Mandjukov, Petko; Orani, Anna Maria; Han, Eunmi; Vassileva, Emilia

    2015-01-01

    The most critical step in almost all commonly used analytical procedures for Hg determination is the sample preparation due to its extreme volatility. One of the possible solutions of this problem is the application of methods for direct analysis of solid samples. The possibilities for solid sampling high resolution continuum source atomic absorption spectrometry (HR CS AAS) determination of total mercury in various marine environmental samples e.g. sediments and biota are object of the present study. The instrumental parameters were optimized in order to obtain reproducible and interference free analytical signal. A calibration technique based on the use of solid standard certified reference materials similar to the nature of the analyzed sample was developed and applied to various CRMs and real samples. This technique allows simple and reliable evaluation of the uncertainty of the result and the metrological characteristics of the method. A validation approach in line with the requirements of ISO 17025 standard and Eurachem guidelines was followed. With this in mind, selectivity, working range (0.06 to 25 ng for biota and 0.025 to 4 ng for sediment samples, expressed as total Hg) linearity (confirmed by Student's t-test), bias (1.6-4.3%), repeatability (4-9%), reproducibility (9-11%), and absolute limit of detection (0.025 ng for sediment, 0.096 ng for marine biota) were systematically assessed using solid CRMs. The relative expanded uncertainty was estimated at 15% for sediment sample and 8.5% for marine biota sample (k = 2). Demonstration of traceability of measurement results is also presented. The potential of the proposed analytical procedure, based on solid sampling HR CS AAS technique was demonstrated by direct analysis of sea sediments form the Caribbean region and various CRMs. Overall, the use of solid sampling HR CS AAS permits obtaining significant advantages for the determination of this complex analyte in marine samples, such as straightforward

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

    Energy Technology Data Exchange (ETDEWEB)

    Mandjukov, Petko; Orani, Anna Maria; Han, Eunmi; Vassileva, Emilia, E-mail: e.vasileva-veleva@iaea.org

    2015-01-01

    The most critical step in almost all commonly used analytical procedures for Hg determination is the sample preparation due to its extreme volatility. One of the possible solutions of this problem is the application of methods for direct analysis of solid samples. The possibilities for solid sampling high resolution continuum source atomic absorption spectrometry (HR CS AAS) determination of total mercury in various marine environmental samples e.g. sediments and biota are object of the present study. The instrumental parameters were optimized in order to obtain reproducible and interference free analytical signal. A calibration technique based on the use of solid standard certified reference materials similar to the nature of the analyzed sample was developed and applied to various CRMs and real samples. This technique allows simple and reliable evaluation of the uncertainty of the result and the metrological characteristics of the method. A validation approach in line with the requirements of ISO 17025 standard and Eurachem guidelines was followed. With this in mind, selectivity, working range (0.06 to 25 ng for biota and 0.025 to 4 ng for sediment samples, expressed as total Hg) linearity (confirmed by Student's t-test), bias (1.6–4.3%), repeatability (4–9%), reproducibility (9–11%), and absolute limit of detection (0.025 ng for sediment, 0.096 ng for marine biota) were systematically assessed using solid CRMs. The relative expanded uncertainty was estimated at 15% for sediment sample and 8.5% for marine biota sample (k = 2). Demonstration of traceability of measurement results is also presented. The potential of the proposed analytical procedure, based on solid sampling HR CS AAS technique was demonstrated by direct analysis of sea sediments form the Caribbean region and various CRMs. Overall, the use of solid sampling HR CS AAS permits obtaining significant advantages for the determination of this complex analyte in marine samples, such as

  19. Stripping scattering of fast atoms on surfaces of metal-oxide crystals and ultrathin films; Streifende Streuung schneller Atome an Oberflaechen von Metalloxid-Kristallen und ultraduennen Filmen

    Energy Technology Data Exchange (ETDEWEB)

    Blauth, David

    2010-03-11

    In the framework of the present dissertation the interactions of fast atoms with surfaces of bulk oxides, metals and thin films on metals were studied. The experiments were performed in the regime of grazing incidence of atoms with energies of some keV. The advantage of this scattering geometry is the high surface sensibility and thus the possibility to determine the crystallographic and electronic characteristics of the topmost surface layer. In addition to these experiments, the energy loss and the electron emission induced by scattered projectiles was investigated. The energy for electron emission and exciton excitation on Alumina/NiAl(110) and SiO{sub 2}/Mo(112) are determined. By detection of the number of projectile induced emitted electrons as function of azimuthal angle for the rotation of the target surface, the geometrical structure of atoms forming the topmost layer of different adsorbate films on metal surfaces where determined via ion beam triangulation. (orig.)

  20. Quantum incommensurate skyrmion crystals and commensurate to in-commensurate transitions in cold atoms and materials with spin-orbit couplings in a Zeeman field

    Science.gov (United States)

    Sun, Fadi; Ye, Jinwu; Liu, Wu-Ming

    2017-08-01

    In this work, we study strongly interacting spinor atoms in a lattice subject to a two dimensional (2d) anisotropic Rashba type of spin orbital coupling (SOC) and an Zeeman field. We find the interplay between the Zeeman field and the SOC provides a new platform to host rich and novel classes of quantum commensurate and in-commensurate phases, excitations and phase transitions. These commensurate phases include two collinear states at low and high Zeeman field, two co-planar canted states at mirror reflected SOC parameters respectively. Most importantly, there are non-coplanar incommensurate Skyrmion (IC-SkX) crystal phases surrounded by the four commensurate phases. New excitation spectra above all the five phases, especially on the IC-SKX phase are computed. Three different classes of quantum commensurate to in-commensurate transitions from the IC-SKX to its four neighboring commensurate phases are identified. Finite temperature behaviors and transitions are discussed. The critical temperatures of all the phases can be raised above that reachable by current cold atom cooling techniques simply by tuning the number of atoms N per site. In view of recent impressive experimental advances in generating 2d SOC for cold atoms in optical lattices, these new many-body phenomena can be explored in the current and near future cold atom experiments. Applications to various materials such as MnSi, {Fe}}0.5 {Co}}0.5Si, especially the complex incommensurate magnetic ordering in Li2IrO3 are given.

  1. Investigations of the stability of the neutral silver atom in Nasub(x)Agsub(1-x)Cl-mixed crystals by EPR-spectroscopy

    International Nuclear Information System (INIS)

    Muessig, T.; Granzer, F.

    1983-01-01

    In most of the theories of the photographic process in the classical silver halide systems, the neutral silver atom, Ag 0 , still plays an important role. Up till now, however, all attempts failed to detect the Ag 0 in pure AgCl and AgBr, while its detection in NaCl, weakly doped with Ag does not impose any problems applying EPR-spectroscopy. Benefiting from some peculiarities of the NaCl-AgCl-phase diagram, Nasub(x)Agsub(1-x)Cl-mixed crystals were grown and the stability of the Ag 0 -centre was followed by EPR-measurements. From the results obtained by gradually augmenting the Ag-content up to 30 mol.% and cooling down the crystals to 20 K, there seems to be only little chance, to detect the neutral silver atom in pure AgCl, even at very low temperatures by EPR-spectroscopy. Simultaneously the-EPR signal of the Ag 2 + -centre was studied and the occurrence of a very strong EPR-line at g = 1.88 in decomposed mixed crystals was interpreted. (author)

  2. Effects of spin orbital coupling on atomic and electronic structures in Al2Cu and Al2Au crystal and liquid phases via ab initio molecular dynamics simulations

    International Nuclear Information System (INIS)

    Wang, Y.; Lu, Y.H.; Wang, X.D.; Cao, Q.P.; Zhang, D.X.; Jiang, J.Z.

    2014-01-01

    Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al 2 Cu and Al 2 Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al 2 Cu and Al 2 Au

  3. 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.)

  4. High-resolution diffraction from crystals of a membrane-protein complex: bacterial outer membrane protein OmpC complexed with the antibacterial eukaryotic protein lactoferrin

    International Nuclear Information System (INIS)

    Sundara Baalaji, N.; Acharya, K. Ravi; Singh, T. P.; Krishnaswamy, S.

    2005-01-01

    Crystals of the complex formed between the bacterial membrane protein OmpC and the antibacterial protein lactoferrin suitable for high-resolution structure determination have been obtained. The crystals belong to the hexagonal space group P6, with unit-cell parameters a = b = 116.3, c = 152.4 Å. Crystals of the complex formed between the outer membrane protein OmpC from Escherichia coli and the eukaryotic antibacterial protein lactoferrin from Camelus dromedarius (camel) have been obtained using a detergent environment. Initial data processing suggests that the crystals belong to the hexagonal space group P6, with unit-cell parameters a = b = 116.3, c = 152.4 Å, α = β = 90, γ = 120°. This indicated a Matthews coefficient (V M ) of 3.3 Å 3 Da −1 , corresponding to a possible molecular complex involving four molecules of lactoferrin and two porin trimers in the unit cell (4832 amino acids; 533.8 kDa) with 63% solvent content. A complete set of diffraction data was collected to 3 Å resolution at 100 K. Structure determination by molecular replacement is in progress. Structural study of this first surface-exposed membrane-protein complex with an antibacterial protein will provide insights into the mechanism of action of OmpC as well as lactoferrin

  5. Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels.

    Science.gov (United States)

    Stsiapanava, A; Dohnalek, J; Gavira, J A; Kuty, M; Koudelakova, T; Damborsky, J; Kuta Smatanova, I

    2010-09-01

    The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 is a bacterial enzyme that shows catalytic activity for the hydrolytic degradation of the highly toxic industrial pollutant 1,2,3-trichloropropane (TCP). Mutagenesis focused on the access tunnels of DhaA produced protein variants with significantly improved activity towards TCP. Three mutants of DhaA named DhaA04 (C176Y), DhaA14 (I135F) and DhaA15 (C176Y + I135F) were constructed in order to study the functional relevance of the tunnels connecting the buried active site of the protein with the surrounding solvent. All three protein variants were crystallized using the sitting-drop vapour-diffusion technique. The crystals of DhaA04 belonged to the orthorhombic space group P2(1)2(1)2(1), while the crystals of DhaA14 and DhaA15 had triclinic symmetry in space group P1. The crystal structures of DhaA04, DhaA14 and DhaA15 with ligands present in the active site were solved and refined using diffraction data to 1.23, 0.95 and 1.22 A, resolution, respectively. Structural comparisons of the wild type and the three mutants suggest that the tunnels play a key role in the processes of ligand exchange between the buried active site and the surrounding solvent.

  6. Human tRNAGly acceptor-stem microhelix: crystallization and preliminary X-ray diffraction analysis at 1.2 Å resolution

    International Nuclear Information System (INIS)

    Förster, Charlotte; Szkaradkiewicz, Karol; Perbandt, Markus; Brauer, Arnd B. E.; Borowski, Tordis; Fürste, Jens P.; Betzel, Christian; Erdmann, Volker A.

    2007-01-01

    The human tRNA Gly acceptor-stem microhelix was crystallized and preliminary X-ray diffraction analysis revealed diffraction to a resolution of up to 1.2 Å. The major dissimilarities between the eukaryotic/archaebacterial-type and eubacterial-type glycyl-tRNA synthetase systems (GlyRS; class II aminoacyl-tRNA synthetases) represent an intriguing example of evolutionarily divergent solutions to similar biological functions. The differences in the identity elements of the respective tRNA Gly systems are located within the acceptor stem and include the discriminator base U73. In the present work, the human tRNA Gly acceptor-stem microhelix was crystallized in an attempt to analyze the structural features that govern the correct recognition of tRNA Gly by the eukaryotic/archaebacterial-type glycyl-tRNA synthetase. The crystals of the human tRNA Gly acceptor-stem helix belong to the monoclinic space group C2, with unit-cell parameters a = 37.12, b = 37.49, c = 30.38 Å, α = γ = 90, β = 113.02°, and contain one molecule per asymmetric unit. A high-resolution data set was acquired using synchrotron radiation and the data were processed to 1.2 Å resolution

  7. Position Dependent Spontaneous Emission Spectra of a Λ-Type Atomic System Embedded in a Defective Photonic Crystal

    International Nuclear Information System (INIS)

    Entezar, S. Roshan

    2012-01-01

    We investigate the position dependent spontaneous emission spectra of a Λ-type three-level atom with one transition coupled to the free vacuum reservoir and the other one coupled to a double-band photonic band gap reservoir with a defect mode in the band gap. It is shown that, for the atom at the defect location, we have a two-peak spectrum with a wide dark line due to the strong coupling between the atom and the defect mode. While, when the atom is far from the defect location (or in the absence of the defect mode), the spectrum has three peaks with two dark lines due to the coupling between the atom and the photonic band gap reservoir with the largest density of states near the band edges. On the other hand, we have a four-peak spectrum for the atom at the space in between. Moreover, the average spontaneous emission spectra of the atoms uniformly embedded in high dielectric or low dielectric regions are described. It is shown that the atoms embedded in high (low) dielectric regions far from the defect location, effectively couple to the modes of the lower (upper) photonic band. However, the atoms embedded in high dielectric or low dielectric regions at the defect location, are coupled mainly to the defect modes. While, the atoms uniformly embedded in high (low) dielectric regions with a normal distance from the defect location, are coupled to both of defect and lower (upper) photonic band modes. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  8. DFT study of the effect of fluorine atoms on the crystal structure and semiconducting properties of poly(arylene-ethynylene) derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Moral, Mónica, E-mail: monica.moral@uclm.es [Renewable Energy Research Institute, University of Castilla-La Mancha, Paseo de la Investigación 1, 02071 Albacete (Spain); García, Gregorio [Department of Chemistry, University of Burgos, Plaza Misael Bañuelos, s/n, 09001 Burgos (Spain); Garzón, Andrés [Department of Physical Chemistry, Faculty of Pharmacy, University of Castilla-La Mancha, Paseo de los Estudiantes, 02071 Albacete (Spain); Granadino-Roldán, José M.; Fernández-Gómez, Manuel [Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, s/n, 23071 Jaén (Spain)

    2016-04-21

    The effect of fluorine substitution on the molecular structure, crystal packing, and n-type semiconducting properties of a set of poly(arylene-ethynylene) polymers based on alternating thiadiazole and phenyl units linked through ethynylene groups has been studied by means of Density Functional Theory. As a result, an enlargement in the interplanar distance between cofacial polymer chains, as well as a decrease of the electronic coupling and electron mobility is predicted. On the other hand, fluorination could facilitate electron injection into the material. A polymer containing both alkoxy pendant chains and fluorine atoms is proposed as a compromise solution between efficiency of electron injection and charge transport within the material.

  9. High-resolution spectroscopy of deeply-bound pionic atoms in heavy nuclei by pion-transfer reactions of inverse kinematics using the GSI cooler ring ESR

    International Nuclear Information System (INIS)

    Yamazaki, Toshimitsu.

    1991-02-01

    Many studies published in the past are reviewed first in relation to high-resolution spectroscopy of deeply-bound pionic atoms in heavy nuclei. The report then describes a procedure for applying the method of inverse kinematics to the case of (d, 3 He) reactions. The (d, 3 He) reaction in inverse kinematics is feasible from practical viewpoints. Thus a discussion is made of the inverse kinematics in which a heavy-ion beam ( 208 Pb for instance) with a projectile kinetic energy hits a deuteron target and ejected recoil 3 He nuclei are measured in the forward direction. The recoil momentum is calculated as a function of the Q value. Analysis shows that the recoil spectroscopy with inverse kinematics can be applied to the case of (d, 3 He) reaction, which will yield a very high mass resolution. The experimental setup for use in the first stage is then outlined, and a simple detector configuration free of magnetic field is discussed. These investigations demonstrate that the (d, 3 He) reaction in inverse kinematics provides a promising tool for obtaining high-resolution spectra of deeply-bound pionic atoms. (N.K.)

  10. Hirshfeld atom refinement.

    Science.gov (United States)

    Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

    2014-09-01

    Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

  11. A new approach for the determination of sulphur in food samples by high-resolution continuum source flame atomic absorption spectrometer.

    Science.gov (United States)

    Ozbek, N; Baysal, A

    2015-02-01

    The new approach for the determination of sulphur in foods was developed, and the sulphur concentrations of various fresh and dried food samples determined using a high-resolution continuum source flame atomic absorption spectrometer with an air/acetylene flame. The proposed method was optimised and the validated using standard reference materials, and certified values were found to be within the 95% confidence interval. The sulphur content of foods ranged from less than the LOD to 1.5mgg(-1). The method is accurate, fast, simple and sensitive. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Focusing Double Bent Crystal (DBC) diffractometer for medium-resolution small-angle. Neutron scattering (SANS) experiments

    International Nuclear Information System (INIS)

    Mikula, P.; Wagner, V.; Scherm, R.

    1991-01-01

    A new modification of a focusing SANS instrument where at least the first crystal is set for diffraction in the asymmetric transmission geometry is presented. Unlike an earlier version which employed both crystals in the symmetric Bragg-case geometry, the new modification permits one simultaneously to exploit the effects of natural wavelength focusing and space condensation of the diffracted beam due to asymmetric diffraction. This DBC instrument seems to be suitable for use with beams with a large cross section at the first crystal and for SANS experiments on samples with a small width (few mm). (orig.)

  13. Resolution of crystal structures by X-ray and neutrons powder diffraction using global optimisation methods; Resolution des structures cristallines par diffraction des rayons X et neutrons sur poudres en utilisant les methodes d'optimisation globale

    Energy Technology Data Exchange (ETDEWEB)

    Palin, L

    2005-03-15

    We have shown in this work that X-ray diffraction on powder is a powerful tool to analyze crystal structure. The purpose of this thesis is the resolution of crystal structures by X-ray and neutrons diffraction on powder using global optimisation methods. We have studied 3 different topics. The first one is the order-disorder phenomena observed in some globular organic molecular solids. The second is the opiate family of neuropeptides. These neurotransmitters regulate sensory functions including pain and control of respiration in the central nervous system. The aim of our study was to try to determine the crystal structure of Leu-enkephalin and some of its sub-fragments. The determination of the crystal structures has been done performing Monte Carlo simulations. The third one is the location of benzene in a sodium-X zeolite. The zeolite framework was already known and the benzene has been localized by simulated annealing and by the use of maximum entropy maps.

  14. Curve resolution and figures of merit estimation for determination of trace elements in geological materials by inductively coupled plasma atomic emission spectrometry

    International Nuclear Information System (INIS)

    Lorber, A.; Harel, A.; Goldbart, Z.; Brenner, I.B.

    1987-01-01

    In geochemical analysis using inductively coupled plasma atomic emission spectrometry (ICP-AES), spectral interferences and background enhancement in response to sample concomitants are the main cause of deterioration of the limit of detection (LOD) and inaccuracy of the determination at the trace and minor element levels. In this account, the authors describe the chemometric procedure of curve resolution for compensating for these sources of error. A newly developed method for calculating figures of merit is used to evaluate the correction procedure, test the statistical significance of the determined concentration, and determine LODs for each sample. The technique involves scanning the vicinity of the spectral line of the analyte. With prior knowledge of potential spectral interferences, deconvolution of the overlapped response is possible. Analytical data for a wide range of geological standard reference materials demonstrate the effectiveness of the chemometric techniques. Separation of 0.002 nm spectral coincidence, employing a 0.02 nm resolution spectrometer, is demonstrated

  15. A comparison of single knock-on and complete bubble destruction models of the fission induced re-solution of gas atoms from bubbles

    International Nuclear Information System (INIS)

    Wood, M.H.

    1978-03-01

    In previous theoretical studies of the behaviour of the fission gases in nuclear fuel, the Nelson single knock-on model of the fission induced re-solution of gas atoms from fission gas bubbles has been employed. In the present investigation, predictions from this model are compared with those from a complete bubble destruction model of the re-solution process. The main conclusions of the study are that the complete bubble destruction model predicts more gas release after a particular irradiation time than the single knock-on model, for the same choice of the model parameters, and that parameter sets chosen to give the same gas release predict significantly different bubble size distribution functions. (author)

  16. Preparation, crystallization and X-ray diffraction analysis to 1.5 Å resolution of rat cysteine dioxygenase, a mononuclear iron enzyme responsible for cysteine thiol oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Chad R. [Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001 (United States); Hao, Quan [MacCHESS at the Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853-8001 (United States); Stipanuk, Martha H., E-mail: mhs6@cornell.edu [Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001 (United States)

    2005-11-01

    Recombinant rat cysteine dioxygenase (CDO) has been expressed, purified and crystallized and X-ray diffraction data have been collected to 1.5 Å resolution. Cysteine dioxygenase (CDO; EC 1.13.11.20) is an ∼23 kDa non-heme iron metalloenzyme that is responsible for the oxidation of cysteine by O{sub 2}, yielding cysteinesulfinate. CDO catalyzes the first step in the conversion of cysteine to taurine, as well as the first step in the catabolism of cysteine to pyruvate plus sulfate. Recombinant rat CDO was heterologously expressed, purified and crystallized. The protein was expressed as a fusion protein bearing a polyhistidine tag to facilitate purification, a thioredoxin tag to improve solubility and a factor Xa cleavage site to permit removal of the entire N-terminus, leaving only the 200 amino acids inherent to the native protein. A multi-step purification scheme was used to achieve >95% purity of CDO. The optimal CDO crystals diffracted to 1.5 Å resolution and belonged to space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 57.55, c = 123.06 Å, α = β = γ = 90°. CDO shows little homology to any other proteins; therefore, the structure of the enzyme will be determined by ab initio phasing using a selenomethionyl derivative.

  17. Crystal Structure of a Trapped Catalytic Intermediate Suggests that Forced Atomic Proximity Drives the Catalysis of mIPS

    OpenAIRE

    Neelon, Kelly; Roberts, Mary F.; Stec, Boguslaw

    2011-01-01

    1-L-myo-inositol-phosphate synthase (mIPS) catalyzes the first step of the unique, de novo pathway of inositol biosynthesis. However, details about the complex mIPS catalytic mechanism, which requires oxidation, enolization, intramolecular aldol cyclization, and reduction, are not fully known. To gain further insight into this mechanism, we determined the crystal structure of the wild-type mIPS from Archaeoglobus fulgidus at 1.7 Å, as well as the crystal structures of three active-site mutant...

  18. Anisotropic diffusion of point defects in a two-dimensional crystal of streptavidin observed by high-speed atomic force microscopy

    International Nuclear Information System (INIS)

    Yamamoto, Daisuke; Uchihashi, Takayuki; Kodera, Noriyuki; Ando, Toshio

    2008-01-01

    The diffusion of individual point defects in a two-dimensional streptavidin crystal formed on biotin-containing supported lipid bilayers was observed by high-speed atomic force microscopy. The two-dimensional diffusion of monovacancy defects exhibited anisotropy correlated with the two crystallographic axes in the orthorhombic C 222 crystal; in the 2D plane, one axis (the a-axis) is comprised of contiguous biotin-bound subunit pairs whereas the other axis (the b-axis) is comprised of contiguous biotin-unbound subunit pairs. The diffusivity along the b-axis is approximately 2.4 times larger than that along the a-axis. This anisotropy is ascribed to the difference in the association free energy between the biotin-bound subunit-subunit interaction and the biotin-unbound subunit-subunit interaction. The preferred intermolecular contact occurs between the biotin-unbound subunits. The difference in the intermolecular binding energy between the two types of subunit pair is estimated to be approximately 0.52 kcal mol -1 . Another observed dynamic behavior of point defects was fusion of two point defects into a larger defect, which occurred much more frequently than the fission of a point defect into smaller defects. The diffusivity of point defects increased with increasing defect size. The fusion and the higher diffusivity of larger defects are suggested to be involved in the mechanism for the formation of defect-free crystals

  19. The 1.8-Å resolution crystal structure of YDR533Cp from Saccharomyces cerevisiae: A member of the DJ-1/ThiJ/PfpI superfamily

    Science.gov (United States)

    Wilson, Mark A.; Amour, Courtney V. St.; Collins, Jennifer L.; Ringe, Dagmar; Petsko, Gregory A.

    2004-01-01

    The yeast gene YDR533C encodes a protein belonging to the DJ-1/ThiJ/PfpI superfamily. This family includes the human protein DJ-1, which is mutated in autosomal recessive early-onset Parkinson's disease. The function of DJ-1 and its yeast homologue YDR533Cp is unknown. We report here the crystal structure of YDR533Cp at 1.8-Å resolution. The structure indicates that the closest relative to YDR533Cp is the Escherichia coli heat shock protein Hsp31 (YedU), which has both chaperone and protease activity. As expected, the overall fold of the core domain of YDR533Cp is also similar to that of DJ-1 and the bacterial protease PfpI. YDR533Cp contains a possible catalytic triad analogous to that of Hsp31 and an additional domain that is present in Hsp31 but is not seen in DJ-1 and other members of the family. The cysteine in this triad (Cys-138) is oxidized in this crystal structure, similar to modifications seen in the corresponding cysteine in the crystal structure of DJ-1. YDR533Cp appears to be a dimer both in solution and the crystal, but this dimer is formed by a different interface than that found in Hsp31 or other members of the superfamily. PMID:14745011

  20. Calcite biomineralization in coccoliths: Evidence from atomic force microscopy (AFM)

    DEFF Research Database (Denmark)

    Henriksen, Karen; Stipp, S.L.S.

    2002-01-01

    geochemistry, crystal orientation, coccolith function, biomineralization, biological calcite, atomic force microscopy......geochemistry, crystal orientation, coccolith function, biomineralization, biological calcite, atomic force microscopy...

  1. Direct observation of atoms on surfaces by scanning tunnelling microscopy

    International Nuclear Information System (INIS)

    Baldeschwieler, J.D.

    1989-01-01

    The scanning tunnelling microscope is a non-destructive means of achieving atomic level resolution of crystal surfaces in real space to elucidate surface structures, electronic properties and chemical composition. Scanning tunnelling microscope is a powerful, real space surface structure probe complementary to other techniques such as x-ray diffraction. 21 refs., 8 figs

  2. Upgrades of imaging x-ray crystal spectrometers for high-resolution and high-temperature plasma diagnostics on EAST

    Energy Technology Data Exchange (ETDEWEB)

    Lyu, B., E-mail: blu@ipp.ac.cn; Wang, F. D.; Fu, J.; Li, Y. Y. [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Pan, X. Y.; Chen, J.; Wan, B. N. [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); Bitter, M.; Hill, K. W.; Delgado-Aparicio, L. F.; Pablant, N. [Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543-0451 (United States); Lee, S. G. [National Fusion Research Institute, 52 Eoeun-Dong, Yusung-Gu, Daejeon 305-333 (Korea, Republic of); Shi, Y. J. [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); WCI for Fusion Theory, National Fusion Research Institute, 52 Eoeun-Dong, Yusung-Gu, Daejeon 305-333 (Korea, Republic of); Ye, M. Y. [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2014-11-15

    Upgrade of the imaging X-ray crystal spectrometers continues in order to fulfill the high-performance diagnostics requirements on EAST. For the tangential spectrometer, a new large pixelated two-dimensional detector was deployed on tokamaks for time-resolved X-ray imaging. This vacuum-compatible detector has an area of 83.8 × 325.3 mm{sup 2}, a framing rate over 150 Hz, and water-cooling capability for long-pulse discharges. To effectively extend the temperature limit, a double-crystal assembly was designed to replace the previous single crystals for He-like argon line measurement. The tangential spectrometer employed two crystal slices attached to a common substrate and part of He- and H-like Ar spectra could be recorded on the same detector when crystals were chosen to have similar Bragg angles. This setup cannot only extend the measurable Te up to 10 keV in the core region, but also extend the spatial coverage since He-like argon ions will be present in the outer plasma region. Similarly, crystal slices for He-like iron and argon spectra were adopted on the poloidal spectrometer. Wavelength calibration for absolute rotation velocity measurement will be studied using cadmium characteristic L-shell X-ray lines excited by plasma radiation. A Cd foil is placed before the crystal and can be inserted and retracted for in situ wavelength calibration. The Geant4 code was used to estimate X-ray fluorescence yield and optimize the thickness of the foil.

  3. Investigating effects of sample pretreatment on protein stability using size-exclusion chromatography and high-resolution continuum source atomic absorption spectrometry.

    Science.gov (United States)

    Rakow, Tobias; El Deeb, Sami; Hahne, Thomas; El-Hady, Deia Abd; AlBishri, Hassan M; Wätzig, Hermann

    2014-09-01

    In this study, size-exclusion chromatography and high-resolution atomic absorption spectrometry methods have been developed and evaluated to test the stability of proteins during sample pretreatment. This especially includes different storage conditions but also adsorption before or even during the chromatographic process. For the development of the size exclusion method, a Biosep S3000 5 μm column was used for investigating a series of representative model proteins, namely bovine serum albumin, ovalbumin, monoclonal immunoglobulin G antibody, and myoglobin. Ambient temperature storage was found to be harmful to all model proteins, whereas short-term storage up to 14 days could be done in an ordinary refrigerator. Freezing the protein solutions was always complicated and had to be evaluated for each protein in the corresponding solvent. To keep the proteins in their native state a gentle freezing temperature should be chosen, hence liquid nitrogen should be avoided. Furthermore, a high-resolution continuum source atomic absorption spectrometry method was developed to observe the adsorption of proteins on container material and chromatographic columns. Adsorption to any container led to a sample loss and lowered the recovery rates. During the pretreatment and high-performance size-exclusion chromatography, adsorption caused sample losses of up to 33%. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Micro-sampling method based on high-resolution continuum source graphite furnace atomic absorption spectrometry for calcium determination in blood and mitochondrial suspensions.

    Science.gov (United States)

    Gómez-Nieto, Beatriz; Gismera, Mª Jesús; Sevilla, Mª Teresa; Satrústegui, Jorgina; Procopio, Jesús R

    2017-08-01

    A micro-sampling and straightforward method based on high resolution continuum source atomic absorption spectrometry (HR-CS AAS) was developed to determine extracellular and intracellular Ca in samples of interest in clinical and biomedical analysis. Solid sampling platforms were used to introduce the micro-samples into the graphite furnace atomizer. The secondary absorption line for Ca, located at 239.856nm, was selected to carry out the measurements. Experimental parameters such as pyrolysis and atomization temperatures and the amount of sample introduced for the measurements were optimized. Calibration was performed using aqueous standards and the approach to measure at the wings of the absorption lines was employed for the expansion of the linear response range. The limit of detection was of 0.02mgL -1 Ca (0.39ng Ca) and the upper limit of linear range was increased up to 8.0mgL -1 Ca (160ng Ca). The proposed method was used to determine Ca in mitochondrial suspensions and whole blood samples with successful results. Adequate recoveries (within 91-107%) were obtained in the tests performed for validation purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Study of morphology and crystal growth behaviour of nanoclay-containing biodegradable polymer blend thin films using atomic force microscopy

    CSIR Research Space (South Africa)

    Malwela, T

    2012-04-01

    Full Text Available temperatures, were visualized with atomic force microscope (AFM). AFM images showed that the size of the dispersed PBS phase was reduced on the addition of 2 wt% clay to the PLA/PBS blend, and the size of the dispersed phase increases with the further addition...

  6. Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution

    International Nuclear Information System (INIS)

    Azim, N.; Deery, E.; Warren, M. J.; Wolfenden, B. A. A.; Erskine, P.; Cooper, J. B.; Coker, A.; Wood, S. P.; Akhtar, M.

    2014-01-01

    The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step in the biosynthesis of tetrapyrroles in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. Two near-atomic resolution structures of PBGD from B. megaterium are reported that demonstrate the time-dependent accumulation of partially oxidized forms of the cofactor, including one that possesses a tetrahedral C atom in the terminal pyrrole ring. The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form

  7. Atomic diffusion and point defects in crystals. Final report. Progress report, April 1, 1956--August 31, 1972

    International Nuclear Information System (INIS)

    Slifkin, L.M.

    1972-01-01

    Studies were made to elucidate the fundamental mechanisms of point defect transport in simple metals and in crystals of the silver halides. Experiments performed include: (a) effect of composition on diffusion in Ag-Au alloys and Ag-Cd alloys; (b) effect of a vacancy flux on diffusion; (c) diffusion of solutes in aluminum and its dilute alloys; (d) dislocation effects in Cu 3 Au; (e) role of electronic structure and ionic radius in diffusion of cations in AgCl; (f) effects of ionic radius on halide impurity ion diffusion in AgCl and AgBr; (g) production of excess point defects in AgCl by deformation and by quenching; (h) the kinetics of the pinning of dislocations by point defects in AgBr crystals. (auth)

  8. Ductile–brittle behavior at blunted cavities in 3D iron crystals uncovered and covered by copper atoms

    Czech Academy of Sciences Publication Activity Database

    Pelikán, Vladimír; Hora, Petr; Červená, Olga; Spielmannová, Alena; Machová, Anna

    2010-01-01

    Roč. 4, č. 2 (2010), s. 191-200 ISSN 1802-680X R&D Projects: GA ČR(CZ) GA101/07/0789; GA AV ČR KJB200760802 Institutional research plan: CEZ:AV0Z20760514 Keywords : molecular dynamics * bcc iron crystal * blunted cavity * copper cover * ductile –brittle behavior Subject RIV: JG - Metallurgy http://www.kme.zcu.cz/acm/index.php/acm/article/view/48

  9. Raman spectroscopy adds complementary detail to the high-resolution x-ray crystal structure of photosynthetic PsbP from Spinacia oleracea.

    Directory of Open Access Journals (Sweden)

    Vladimir Kopecky

    Full Text Available Raman microscopy permits structural analysis of protein crystals in situ in hanging drops, allowing for comparison with Raman measurements in solution. Nevertheless, the two methods sometimes reveal subtle differences in structure that are often ascribed to the water layer surrounding the protein. The novel method of drop-coating deposition Raman spectropscopy (DCDR exploits an intermediate phase that, although nominally "dry," has been shown to preserve protein structural features present in solution. The potential of this new approach to bridge the structural gap between proteins in solution and in crystals is explored here with extrinsic protein PsbP of photosystem II from Spinacia oleracea. In the high-resolution (1.98 Å x-ray crystal structure of PsbP reported here, several segments of the protein chain are present but unresolved. Analysis of the three kinds of Raman spectra of PsbP suggests that most of the subtle differences can indeed be attributed to the water envelope, which is shown here to have a similar Raman intensity in glassy and crystal states. Using molecular dynamics simulations cross-validated by Raman solution data, two unresolved segments of the PsbP crystal structure were modeled as loops, and the amino terminus was inferred to contain an additional beta segment. The complete PsbP structure was compared with that of the PsbP-like protein CyanoP, which plays a more peripheral role in photosystem II function. The comparison suggests possible interaction surfaces of PsbP with higher-plant photosystem II. This work provides the first complete structural picture of this key protein, and it represents the first systematic comparison of Raman data from solution, glassy, and crystalline states of a protein.

  10. Atomic Resolution Structural and Chemical Imaging Revealing the Sequential Migration of Ni, Co, and Mn upon the Battery Cycling of Layered Cathode

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Pengfei; Zheng, Jianming; Zhang, Ji-Guang; Wang, Chongmin

    2017-05-11

    Layered lithium transition metal oxides (LTMO) are promising candidate cathode materials for next generation high energy density lithium ion battery. The challenge for using this category of cathode is the capacity and voltage fading, which is believed to be associated with the layered structure disordering, a process that is initiated from the surface or solid-electrolyte interface and facilitated by transition metal (TM) reduction and oxygen vacancy formation. However, the atomic level dynamic mechanism of such a layered structure disordering is still not fully clear. In this work, utilizing atomic resolution electron energy loss spectroscopy (EELS), we map, for the first time at atomic scale, the spatial evolution of Ni, Co and Mn in a cycled LiNi1/3M1/3Co1/3O2 layered cathode. In combination with atomic level structural imaging, we discovered the direct correlation of TM ions migration behavior with lattice disordering, featuring the residing of TM ions in the tetrahedral site and a sequential migration of Ni, Co, and Mn upon the increased lattice disordering of the layered structure. This work highlights that Ni ions, though acting as the dominant redox species in many LTMO, are labile to migrate to cause lattice disordering upon battery cycling; while the Mn ions are more stable as compared with Ni and Co and can act as pillar to stabilize layered structure. Direct visualization of the behavior of TM ions during the battery cycling provides insight for designing of cathode with structural stability and correspondingly a superior performance.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors constitute the largest family of eukaryotic signal transduction proteins that communicate across the membrane. We report the crystal structure of a human beta2-adrenergic receptor-T4 lysozyme fusion protein bound to t...

  12. Atom-resolving x-ray holography

    International Nuclear Information System (INIS)

    Adams, B.; Hiort, T.; Materlik, G.; Nishino, Y.; Novikov, D. V.

    2000-01-01

    The current state of atomic resolution x-ray holography is discussed on the basis of theory and experimental results. X-ray holography is theoretically described in quantum theory. Presently-used experimental implementations are shown together with the data analysis used. Reconstructions of experimental and simulated holograms are compared for a Cu 3 Au crystal structure. Rigorous experimental realizations of pure direct and reciprocal x-ray holography methods are demonstrated, and future developments and applications of the method are suggested

  13. Computer simulation on spatial resolution of X-ray bright-field imaging by dynamical diffraction theory for a Laue-case crystal analyzer

    International Nuclear Information System (INIS)

    Suzuki, Yoshifumi; Chikaura, Yoshinori; Ando, Masami

    2011-01-01

    Recently, dark-field imaging (DFI) and bright-field imaging (BFI) have been proposed and applied to visualize X-ray refraction effects yielded in biomedical objects. In order to clarify the spatial resolution due to a crystal analyzer in Laue geometry, a program based on the Takagi-Taupin equation was modified to be used for carrying out simulations to evaluate the spatial resolution of images coming into a Laue angular analyzer (LAA). The calculation was done with a perfect plane wave for diffraction wave-fields, which corresponded to BFI, under the conditions of 35 keV and a diffraction index 440 for a 2100 μm thick LAA. As a result, the spatial resolution along the g-vector direction showed approximately 37.5 μm. 126 μm-thick LAA showed a spatial resolution better than 3.1 μm under the conditions of 13.7 keV and a diffraction index 220.

  14. DFT study of the polarization behaviors of various distorted barium titanate crystals: The role of atomic displacements

    Science.gov (United States)

    Mirseraji, Mojtaba; Shahraki, Mehran Gholipour

    2018-06-01

    A Local Density Approximation (LDA) was employed to investigate the influence of applied strains on valence charge distributions, atomic displacements, Tisbnd O (3) bond distances and the total polarizations in barium titanate (BaTiO3). Four types of various strains were imposed on perfect tetragonal BaTiO3 along the a, c, ab and abc axial directions. Electromechanical properties of BaTiO3 were evaluated in LDA framework and a good agreement with previous results was achieved. The results show that, in the cases of a, ab strains, the values of polarization are almost constant in negative strains and increased by gradual increasing of the positive strains after a sudden enhancement at about +0.1% strain. In the case of c-strain, axial oxygen and Ti atoms underwent the highest displacements and the polarization linearly increased by applied strain. The case of abc-strain, represent the both types of features. In negative abc-strain show a similar polarization behavior like c-strain case and in positive region, polarization behavior is the same as a- and ab-strain cases. In the abc-strains of -0.3% and +0.1%, an abrupt jump in total polarization curve and a small change, are observed due to abnormal atomic displacements. In the most cases a direct relation between polarization and Tisbnd O (3) bond distance was also beheld. Finally, the effects of valence charge distributions on the atomic displacements and total polarizations are studied. It is found that there is a direct relation between polarization and Valence Charge Asymmetry of 3d -orbitals.

  15. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un [Ithaca, NY; Gruner, Sol M [Ithaca, NY

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  16. Study of atomic jumps in quasi-crystals; Etude des sauts atomiques dans les quasi-cristaux

    Energy Technology Data Exchange (ETDEWEB)

    Lyonnard, S

    1997-05-07

    The terminology phason used in quasicrystals to refer to atomic jumps. The study of the hopping process is important for the understanding of many basic issues in quasi-crystallography: structure, stability, diffusion, phase transitions between quasicrystals and approximants, mechanical properties. Quasi-elastic neutron scattering allows to find the characteristics of each elementary jump: chemical species involves, relaxation times, activation energies, jump distances and orientations. We performed a series of experiments in the perfect icosahedral phases AlFeCu and AlMnPd, on both powders and single domain samples, using time-of-flight, backscattering and triple axis spectrometers. We evidenced the existence of very fast phason hopping, and studied about ten different atomic jumps. An unusual temperature dependence has been found systematically: each process is assisted by a thermally activated mechanism. The assistance process has to be determined case by case, but the more plausible explanation invokes assistance by phonons or phason clouds. Moreover, the dependence of the quasi elastic signal as a function of the momentum transfer shows that the jumps are local and do not give rise to any long-range diffusion. Phason hopping mainly corresponds to the atom moving forwards and backwards between two energetically equivalent sites. Finally, we have been able to show that the jumps occur along the various quasi-crystalline symmetry axes. (author) 91 refs.

  17. A novel gamma-ray detector with submillimeter resolutions using a monolithic MPPC array with pixelized Ce:LYSO and Ce:GGAG crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kato, T., E-mail: katou.frme.8180@asagi.waseda.jp [Research Institute for Science and Engineering, Waseda University, 3-4-1, Ohkubo, Shinjuku, Tokyo (Japan); Kataoka, J.; Nakamori, T.; Miura, T.; Matsuda, H.; Kishimoto, A. [Research Institute for Science and Engineering, Waseda University, 3-4-1, Ohkubo, Shinjuku, Tokyo (Japan); Sato, K.; Ishikawa, Y.; Yamamura, K.; Nakamura, S.; Kawabata, N. [Solid State Division, Hamamatsu Photonics K. K., 1126-1, Ichino-cho, Hamamatsu, Shizuoka (Japan); Ikeda, H. [ISAS/JAXA, 3-1-1, Yoshinodai, Chuo-ku, Sagamihara-shi, Kanagawa (Japan); Yamamoto, S. [Kobe City College of Technology, 8-3, Gakuenhigashimati, Nishi-ku, Kobe-shi, Hyougo 651-2194 (Japan); Kamada, K. [Materials Research Laboratory, Furukawa Co., Ltd., 1-25-13, Kannondai, Tsukuba, Ibaraki 305-0856 (Japan)

    2013-01-21

    We have developed a large-area monolithic Multi-Pixel Photon Counter (MPPC) array consisting of 4×4 channels with a three-side buttable package. Each channel has a photosensitive area of 3×3 mm{sup 2} and 3600 Geiger mode avalanche photodiodes (APDs). For typical operational gain of 7.5×10{sup 5} at +20 °C, gain fluctuation over the entire MPPC device is only ±5.6%, and dark count rates (as measured at the 1 p.e. level) amount to ≤400kcps per channel. We first fabricated a gamma-ray camera consisting of the MPPC array with one-to-one coupling to a Ce-doped (Lu,Y){sub 2}(SiO{sub 4})O (Ce:LYSO) crystal array (4×4 array of 3×3×10 mm{sup 3} crystals). Energy and time resolutions of 11.5±0.5% (FWHM at 662 keV) and 493±22ps were obtained, respectively. When using the charge division resistor network, which compiles signals into four position-encoded analog outputs, the ultimate positional resolution is estimated as 0.19 mm in both X and Y directions, while energy resolution of 10.2±0.4% (FWHM) was obtained. Finally, we fabricated submillimeter Ce:LYSO and Ce-doped Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12} (Ce:GGAG) scintillator matrices each consisting of 1.0×1.0, 0.7×0.7 and 0.5×0.5 mm{sup 2} pixels, to further improve the spatial resolution. In all types of Ce:LYSO and Ce:GGAG matrices, each crystal was clearly resolved in the position histograms when irradiated by a {sup 137}Cs source. The energy resolutions for 662 keV gamma-rays for each Ce:LYSO and Ce:GGAG scintillator matrix were ≤14.3%. These results suggest excellent potential for its use as a high spatial medical imaging device, particularly in positron emission tomography (PET). -- Highlights: ► We developed a newly designed large-area monolithic MPPC array. ► We obtained fine gain uniformity, and good energy and time resolutions when coupled to the LYSO scintillator. ► We fabricated gamma-ray camera consisting of the MPPC array and submillimeter pixelized LYSO and GGAG scintillators. ► In

  18. The monomer-to-dimer transition and bimodal growth of Co-salen on NaCl(001): a high resolution atomic force microscopy study

    International Nuclear Information System (INIS)

    Fremy, S; Schwarz, A; Laemmle, K; Wiesendanger, R; Prosenc, M

    2009-01-01

    Molecules of Co-salen, a paramagnetic metal-organic Schiff base complex, self-assemble into two different well ordered morphologies on a NaCl(001) substrate: nanowires, which form networks, and compact nanocrystallites. Their growth can be controlled by adjusting the deposition parameters. It turns out that the nanowires are metastable. Molecular resolution images suggest that the packing in both morphologies is the same as in bulk Co-salen single crystals. Only the orientation of the c-axis with respect to the substrate is different. The origin of this intriguing bimodal growth is associated with a monomer-to-dimer transition, which probably takes place during initial nucleation at step edges.

  19. The monomer-to-dimer transition and bimodal growth of Co-salen on NaCl(001): a high resolution atomic force microscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Fremy, S; Schwarz, A; Laemmle, K; Wiesendanger, R [Institute of Applied Physics and Microstructure Research Center, University of Hamburg, Jungiusstrasse 11, 20355 Hamburg (Germany); Prosenc, M, E-mail: aschwarz@physnet.uni-hamburg.d [Institute of Inorganic and Applied Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg (Germany)

    2009-10-07

    Molecules of Co-salen, a paramagnetic metal-organic Schiff base complex, self-assemble into two different well ordered morphologies on a NaCl(001) substrate: nanowires, which form networks, and compact nanocrystallites. Their growth can be controlled by adjusting the deposition parameters. It turns out that the nanowires are metastable. Molecular resolution images suggest that the packing in both morphologies is the same as in bulk Co-salen single crystals. Only the orientation of the c-axis with respect to the substrate is different. The origin of this intriguing bimodal growth is associated with a monomer-to-dimer transition, which probably takes place during initial nucleation at step edges.

  20. Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations

    DEFF Research Database (Denmark)

    Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit

    2012-01-01

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic...... resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates...

  1. An Overview of Biological Macromolecule Crystallization

    Directory of Open Access Journals (Sweden)

    Irene Russo Krauss

    2013-05-01

    Full Text Available The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.

  2. High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1

    International Nuclear Information System (INIS)

    Peng, Shuxia; Zhou, Ke; Wang, Wenjia; Gao, Zengqiang; Dong, Yuhui; Liu, Quansheng

    2014-01-01

    Highlights: • Crystal structure of the C-terminal (CT) domain of Swt1 was determined at 2.3 Å. • Structure of the CT domain was identified as HEPN domain superfamily member. • Low-resolution envelope of Swt1 full-length in solution was analyzed by SAXS. • The middle and CT domains gave good fit to SAXS structural model. - Abstract: Swt1 is an RNA endonuclease that plays an important role in quality control of nuclear messenger ribonucleoprotein particles (mRNPs) in eukaryotes; however, its structural details remain to be elucidated. Here, we report the crystal structure of the C-terminal (CT) domain of Swt1 from Saccharomyces cerevisiae, which shares common characteristics of higher eukaryotes and prokaryotes nucleotide binding (HEPN) domain superfamily. To study in detail the full-length protein structure, we analyzed the low-resolution architecture of Swt1 in solution using small angle X-ray scattering (SAXS) method. Both the CT domain and middle domain exhibited a good fit upon superimposing onto the molecular envelope of Swt1. Our study provides the necessary structural information for detailed analysis of the functional role of Swt1, and its importance in the process of nuclear mRNP surveillance

  3. High-resolution electron microscopy study of electron-irradiation-induced crystalline-to-amorphous transition in α-SiC single crystals

    International Nuclear Information System (INIS)

    Inui, H.; Mori, H.; Sakata, T.

    1992-01-01

    An electron-irradiation-induced crystalline-to-amorphous (CA) transition in α-SiC has been studied by high-resolution electron microscopy (HREM). The irradiation-produced damage structure was examined as a function of dose of electrons by taking high-resolution maps extending from the unirradiated crystalline region to the completely amorphized region. In the intermediate region between those two regions, that is in the CA transition region, the damage structure was essentially a mixture of crystalline and amorphous phases. The volume fraction of the amorphous phase was found to increase with increasing dose of electrons and no discrete crystalline-amorphous interface was observed in the CA transition region. These facts indicate the heterogeneous and gradual nature of the CA transition. In the transition region close to the unirradiated crystalline region, a sort of fragmentation of the crystal lattice was observed to occur, crystallites with slightly different orientations with respect to the parent crystal were formed owing to the strain around the dispersed local amorphous regions. In the transition region close to the amorphized region, these crystallites were reduced in size and were embedded in an amorphous matrix. This damage structure is the result of the increased volume fraction of the amorphous phase. In the completely amorphized region, no lattice fringes were recognized in the HREM images. The atomistic process of the CA transition is discussed on the basis of the present results and those from previous studies. (Author)

  4. High-resolution digital dosimetric system for spatial characterization of radiation fields using a thermoluminescent CaF2:Dy crystal

    International Nuclear Information System (INIS)

    Atari, N.A.; Svensson, G.K.

    1986-01-01

    A high-resolution digital dosimetric system has been developed for the spatial characterization of radiation fields. The system comprises the following: 0.5-mm-thick, 25-mm-diam CaF2:Dy thermoluminescent crystal; intensified charge coupled device video camera; video cassette recorder; and a computerized image processing subsystem. The optically flat single crystal is used as a radiation imaging device and the subsequent thermally stimulated phosphorescence is viewed by the intensified camera for further processing and analysis. Parameters governing the performance characteristics of the system were measured. A spatial resolution limit of 31 +/- 2 microns (1 sigma) corresponding to 16 +/- 1 line pairs/mm measured at the 4% level of the modulation transfer function has been achieved. The full width at half maximum of the line spread function measured independently by the slit method or derived from the edge response function was found to be 69 +/- 4 microns (1 sigma). The high resolving power, speed of readout, good precision, wide dynamic range, and the large image storage capacity make the system suitable for the digital mapping of the relative distribution of absorbed doses for various small radiation fields and the edges of larger fields

  5. High-resolution digital dosimetric system for spatial characterization of radiation fields using a thermoluminescent CaF2:Dy crystal

    International Nuclear Information System (INIS)

    Atari, N.A.; Svensson, G.K.

    1986-01-01

    A high-resolution digital dosimetric system has been developed for the spatial characterization of radiation fields. The system comprises the following: 0.5-mm-thick, 25-mm-diam CaF 2 :Dy thermoluminescent crystal; intensified charge coupled device video camera; video cassette recorder; and a computerized image processing subsystem. The optically flat single crystal is used as a radiation imaging device and the subsequent thermally stimulated phosphorescence is viewed by the intensified camera for further processing and analysis. Parameters governing the performance characteristics of the system were measured. A spatial resolution limit of 31 +- 2 μm (1sigma) corresponding to 16 +- 1 line pair/mm measured at the 4% level of the modulation transfer function has been achieved. The full width at half maximum of the line spread function measured independently by the slit method or derived from the edge response function was found to be 69 +- 4 μm (1sigma). The high resolving power, speed of readout, good precision, wide dynamic range, and the large image storage capacity make the system suitable for the digital mapping of the relative distribution of absorbed doses for various small radiation fields and the edges of larger fields

  6. Light-Induced Fluorescence Modulation of Quantum Dot-Crystal Violet Conjugates: Stochastic Off-On-Off Cycles for Multicolor Patterning and Super-Resolution.

    Science.gov (United States)

    Jung, Sungwook; Park, Joonhyuck; Bang, Jiwon; Kim, Jae-Yeol; Kim, Cheolhee; Jeon, Yongmoon; Lee, Seung Hwan; Jin, Ho; Choi, Sukyung; Kim, Bomi; Lee, Woo Jin; Pack, Chan-Gi; Lee, Jong-Bong; Lee, Nam Ki; Kim, Sungjee

    2017-06-07

    Photoswitching or modulation of quantum dots (QDs) can be promising for many fields that include display, memory, and super-resolution imaging. However, such modulations have mostly relied on photomodulations of conjugated molecules in QD vicinity, which typically require high power of high energy photons at UV. We report a visible light-induced facile modulation route for QD-dye conjugates. QD crystal violets conjugates (QD-CVs) were prepared and the crystal violet (CV) molecules on QD quenched the fluorescence efficiently. The fluorescence of QD-CVs showed a single cycle of emission burst as they go through three stages of (i) initially quenched "off" to (ii) photoactivated "on" as the result of chemical change of CVs induced by photoelectrons from QD and (iii) back to photodarkened "off" by radical-associated reactions. Multicolor on-demand photopatterning was demonstrated using QD-CV solid films. QD-CVs were introduced into cells, and excitation with visible light yielded photomodulation from "off" to "on" and "off" by nearly ten fold. Individual photoluminescence dynamics of QD-CVs was investigated using fluorescence correlation spectroscopy and single QD emission analysis, which revealed temporally stochastic photoactivations and photodarkenings. Exploiting the stochastic fluorescence burst of QD-CVs, simultaneous multicolor super-resolution localizations were demonstrated.

  7. Processing method for high resolution monochromator

    International Nuclear Information System (INIS)

    Kiriyama, Koji; Mitsui, Takaya

    2006-12-01

    A processing method for high resolution monochromator (HRM) has been developed at Japanese Atomic Energy Agency/Quantum Beam Science Directorate/Synchrotron Radiation Research unit at SPring-8. For manufacturing a HRM, a sophisticated slicing machine and X-ray diffractometer have been installed for shaping a crystal ingot and orienting precisely the surface of a crystal ingot, respectively. The specification of the slicing machine is following; Maximum size of a diamond blade is φ 350mm in diameter, φ 38.1mm in the spindle diameter, and 2mm in thickness. A large crystal such as an ingot with 100mm in diameter, 200mm in length can be cut. Thin crystal samples such as a wafer can be also cut using by another sample holder. Working distance of a main shaft with the direction perpendicular to working table in the machine is 350mm at maximum. Smallest resolution of the main shaft with directions of front-and-back and top-and-bottom are 0.001mm read by a digital encoder. 2mm/min can set for cutting samples in the forward direction. For orienting crystal faces relative to the blade direction adjustment, a one-circle goniometer and 2-circle segment are equipped on the working table in the machine. A rotation and a tilt of the stage can be done by manual operation. Digital encoder in a turn stage is furnished and has angle resolution of less than 0.01 degrees. In addition, a hand drill as a supporting device for detailed processing of crystal is prepared. Then, an ideal crystal face can be cut from crystal samples within an accuracy of about 0.01 degrees. By installation of these devices, a high energy resolution monochromator crystal for inelastic x-ray scattering and a beam collimator are got in hand and are expected to be used for nanotechnology studies. (author)

  8. Second quantization and atomic spontaneous emission inside one-dimensional photonic crystals via a quasinormal-modes approach

    International Nuclear Information System (INIS)

    Severini, S.; Settimi, A.; Sibilia, C.; Bertolotti, M.; Napoli, A.; Messina, A.

    2004-01-01

    An extension of the second quantization scheme based on the quasinormal-modes theory to one-dimensional photonic band gap (PBG) structures is discussed. Such structures, treated as double open optical cavities, are studied as part of a compound closed system including the electromagnetic radiative external bath. The electromagnetic field inside the photonic crystal is successfully represented by a new class of modes called quasinormal modes. Starting from this representation we introduce the Feynman's propagator to calculate the decay rate of a dipole inside a PBG structure, related to the density of modes, in the presence of the vacuum fluctuations outside the one-dimensional cavity

  9. Design of mirror and monochromator crystals for a high-resolution multiwavelength anomalous diffraction beam line on a bending magnet at the ESRF

    International Nuclear Information System (INIS)

    Roth, M.; Ferrer, J.; Simon, J.; Geissler, E.

    1992-01-01

    High intensity for diffraction experiments with high-energy resolution on an intense x-ray beam, like the bending magnet beam lines at the ESRF, requires a strict control of the curvature of the optical elements placed in the beam for geometrical focusing and for wavelength monochromatization. Unwanted curvatures can come from nonuniform and variable heating of the optical elements produced by the absorption of x rays. To design the CRG/D2AM beam line described in the accompanying paper, some new techniques were developed to control these effects based on geometrical, i.e., topological, considerations. (1) Cooling of the entrance mirror: longitudinal curvature can be strongly reduced by cooling the mirror from the sides (and not from the rear) and only near the reflecting surface (i.e., not over the whole lateral surface). The cooling can be achieved for instance with an isothermal liquid Ga eutectic bath. (2) Cooling of the first single-crystal Si monochromator: because of the size of the crystal, only cooling from the rear is conceivable in this case. It can be shown by calculation that the curvature due to the front-to-rear gradient can be exactly compensated by the thermal expansion of a metallic layer at the rear of the crystal, having a larger expansion coefficient than Si

  10. High-resolution mapping of two-dimensional lattice distortions in ion-implanted crystals from X-ray diffractometry data

    International Nuclear Information System (INIS)

    Nikulin, A.Y.; Gureyev, T.E.; Stevenson, A.W.; Wilkins, S.W.; Hashizume, H.; Cookson, D.

    1996-01-01

    The triple-crystal synchrotron X-ray diffractometry data described in Nikulin, Stevenson, Hashizume, Wilkins, Foran, Cookson and Garrett (J. Appl. Cryst. 28, 57-60 (1995)) has been analyzed to map out two-dimensional (2D) lattice distortions in silicon (111) crystals implanted with B + ions of 100 keV energy through a periodic SiO 2 strip pattern. The lateral periodic structure produced a series of satellite reflections associated with the 111 Bragg peak. The 2D reconstruction incorporates the use of the Petrashen-Chukhovskii method, which retrieves the phases of the Bragg waves for these satellite reflections, together with that for the fundamental. The finite Fourier series is then synthesized with the relative phases determined. Localized distortions perpendicular to the surface arising from deposited B + ions in near-surface layers of the crystal are clearly displayed with spatial resolutions of 0.016 and 0.265 μm in the depth and lateral directions respectively. For a sample with the oxide layer removed from the surface, two equally plausible strain maps have been obtained by assigning relative phases to eleven satellites using a sequential trial method and a minimum-energy method. Failed map reconstructions for the oxide-covered sample are discussed in terms of the non-unique solutions of the Petrashen-Chukhovskii phase-recovery algorithm and the ambiguous phases determined for the satellites. 16 refs., 8 figs

  11. BiFeO3 Crystal Structure at Low Temperatures

    International Nuclear Information System (INIS)

    Palewicz, A.; Sosnowska, I.; Przenioslo, R.; Hewat, A.W.

    2010-01-01

    The crystal and magnetic structure of BiFeO 3 have been studied with the use of high resolution neutron diffraction between 5 K and 300 K. The atomic coordinates in BiFeO 3 are almost unchanged between 5 K and 300 K. (authors)

  12. Seeing the atoms more clearly: STEM imaging from the Crewe era to today

    International Nuclear Information System (INIS)

    Pennycook, S.J.

    2012-01-01

    This review covers the development of scanning transmission electron microscopy from the innovations of Albert Crewe to the two-dimensional spectrum imaging in the era of aberration correction. It traces the key events along the path, the first atomic resolution Z-contrast imaging of individual atoms, the realization of incoherent imaging in crystals and the role of dynamical diffraction, simultaneous, atomic resolution electron energy loss spectroscopy, and finally the tremendous impact of the successful correction of lens aberrations, not just in terms of resolution but also in single atom sensitivity. -- Highlights: ► We review the development of scanning transmission electron microscopy. ► We discuss the innovations of Albert Crewe in the first field emission STEM. ► We discuss use of the high angle annular detector for materials science. ► We discuss atomic resolution Z-contrast imaging and EELS. ► We discuss the benefits of aberration correction.

  13. High-resolution crystal structure of Streptococcus pyogenes β-NAD{sup +} glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin [Seoul National University, Seoul 151-747 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Sang Jae [Seoul National University, Seoul 151-742 (Korea, Republic of); Im, Ha Na; Jang, Jun Young [Seoul National University, Seoul 151-747 (Korea, Republic of); Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-747 (Korea, Republic of)

    2013-11-01

    The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD{sup +} glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD{sup +} glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN{sub ct}–IFS complex, which consists of the SPN C-terminal domain (SPN{sub ct}; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN{sub ct} and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

  14. High-resolution crystal structure of Streptococcus pyogenes β-NAD+ glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

    International Nuclear Information System (INIS)

    Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin; Kim, Hyoun Sook; Lee, Sang Jae; Im, Ha Na; Jang, Jun Young; Suh, Se Won

    2013-01-01

    The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD + glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD + glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN ct –IFS complex, which consists of the SPN C-terminal domain (SPN ct ; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN ct and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope

  15. High mobility In{sub 2}O{sub 3}:H transparent conductive oxides prepared by atomic layer deposition and solid phase crystallization

    Energy Technology Data Exchange (ETDEWEB)

    Macco, B.; Wu, Y.; Vanhemel, D. [Department of Applied Physics, Eindhoven University of Technology (Netherlands); Kessels, W.M.M. [Department of Applied Physics, Eindhoven University of Technology (Netherlands); Solliance Solar Research, Eindhoven (Netherlands)

    2014-12-01

    The preparation of high-quality In{sub 2}O{sub 3}:H, as transparent conductive oxide (TCO), is demonstrated at low temperatures. Amorphous In{sub 2}O{sub 3}:H films were deposited by atomic layer deposition at 100 C, after which they underwent solid phase crystallization by a short anneal at 200 C. TEM analysis has shown that this approach can yield films with a lateral grain size of a few hundred nm, resulting in electron mobility values as high as 138 cm{sup 2}/V s at a device-relevant carrier density of 1.8 x 10{sup 20} cm{sup -3}. Due to the extremely high electron mobility, the crystallized films simultaneously exhibit a very low resistivity (0.27 mΩ cm) and a negligible free carrier absorption. In conjunction with the low temperature processing, this renders these films ideal candidates for front TCO layers in for example silicon heterojunction solar cells and other sensitive optoelectronic applications. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  16. Atomic Layer-Deposited Molybdenum Oxide/Carbon Nanotube Hybrid Electrodes: The Influence of Crystal Structure on Lithium-Ion Capacitor Performance.

    Science.gov (United States)

    Fleischmann, Simon; Zeiger, Marco; Quade, Antje; Kruth, Angela; Presser, Volker

    2018-05-25

    Merging of supercapacitors and batteries promises the creation of electrochemical energy storage devices that combine high specific energy, power, and cycling stability. For that purpose, lithium-ion capacitors (LICs) that store energy by lithiation reactions at the negative electrode and double-layer formation at the positive electrode are currently investigated. In this study, we explore the suitability of molybdenum oxide as a negative electrode material in LICs for the first time. Molybdenum oxide-carbon nanotube hybrid materials were synthesized via atomic layer deposition, and different crystal structures and morphologies were obtained by post-deposition annealing. These model materials are first structurally characterized and electrochemically evaluated in half-cells. Benchmarking in LIC full-cells revealed the influences of crystal structure, half-cell capacity, and rate handling on the actual device level performance metrics. The energy efficiency, specific energy, and power are mainly influenced by the overpotential and kinetics of the lithiation reaction during charging. Optimized LIC cells show a maximum specific energy of about 70 W·h·kg -1 and a high specific power of 4 kW·kg -1 at 34 W·h·kg -1 . The longevity of the LIC cells is drastically increased without significantly reducing the energy by preventing a deep cell discharge, hindering the negative electrode from crossing its anodic potential limit.

  17. Joint application of neutron and X-ray scattering for determination of atomic and electronic structures of molecules and crystals

    International Nuclear Information System (INIS)

    Ozerov, R.P.; Tsirel'son, V.G.

    1978-01-01

    The paper deals with the main principles of methods based on the joint neutron and x-ray diffraction studies. The methods allow one to obtain the information on the charge distribution in molecules in detail. Neutron scattering makes it possible to locate very closely the nucleus of atom or, more precisely, the gravity center of the ellipsoid of nuclear thermal oscillations. X-ray diffraction gives the distribution of electronic density at some distance from the shell gravity center. The joint diffraction method holds the promise and importance for solving physical-chemical problems

  18. Preparation and Loading Process of Single Crystalline Samples into a Gas Environmental Cell Holder for In Situ Atomic Resolution Scanning Transmission Electron Microscopic Observation.

    Science.gov (United States)

    Straubinger, Rainer; Beyer, Andreas; Volz, Kerstin

    2016-06-01

    A reproducible way to transfer a single crystalline sample into a gas environmental cell holder for in situ transmission electron microscopic (TEM) analysis is shown in this study. As in situ holders have only single-tilt capability, it is necessary to prepare the sample precisely along a specific zone axis. This can be achieved by a very accurate focused ion beam lift-out preparation. We show a step-by-step procedure to prepare the sample and transfer it into the gas environmental cell. The sample material is a GaP/Ga(NAsP)/GaP multi-quantum well structure on Si. Scanning TEM observations prove that it is possible to achieve atomic resolution at very high temperatures in a nitrogen environment of 100,000 Pa.

  19. Atomic-resolution characterization of the effects of CdCl2 treatment on poly-crystalline CdTe thin films

    Science.gov (United States)

    Paulauskas, T.; Buurma, C.; Colegrove, E.; Guo, Z.; Sivananthan, S.; Chan, M. K. Y.; Klie, R. F.

    2014-08-01

    Poly-crystalline CdTe thin films on glass are used in commercial solar-cell superstrate devices. It is well known that post-deposition annealing of the CdTe thin films in a CdCl2 environment significantly increases the device performance, but a fundamental understanding of the effects of such annealing has not been achieved. In this Letter, we report a change in the stoichiometry across twin boundaries in CdTe and propose that native point defects alone cannot account for this variation. Upon annealing in CdCl2, we find that the stoichiometry is restored. Our experimental measurements using atomic-resolution high-angle annular dark field imaging, electron energy-loss spectroscopy, and energy dispersive X-ray spectroscopy in a scanning transmission electron microscope are supported by first-principles density functional theory calculations.

  20. Determination of gold and cobalt dopants in advanced materials based on tin oxide by slurry sampling high-resolution continuum source graphite furnace atomic absorption spectrometry

    Science.gov (United States)

    Filatova, Daria G.; Eskina, Vasilina V.; Baranovskaya, Vasilisa B.; Vladimirova, Svetlana A.; Gaskov, Alexander M.; Rumyantseva, Marina N.; Karpov, Yuri A.

    2018-02-01

    A novel approach is developed for the determination of Co and Au dopants in advanced materials based on tin oxide using high-resolution continuum source graphite furnace atomic absorption spectrometry (HR CS GFAAS) with direct slurry sampling. Sodium carboxylmethylcellulose (Na-CMC) is an effective stabilizer for diluted suspensions. Use Na-CMC allows to transfer the analytes into graphite furnace completely and reproducibly. The relative standard deviation obtained by HR CS GFAAS was not higher than 4%. Accuracy was proven by means inductively coupled plasma mass spectrometry (ICP-MS) in solutions after decomposition as a comparative technique. To determine Au and Co in the volume of SnO2, the acid decomposition conditions (HCl, HF) of the samples were suggested by means of an autoclave in a microwave oven.