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Sample records for atomic resolution crystal

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

    Science.gov (United States)

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

    2012-11-01

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

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

    Science.gov (United States)

    Dostál, Jiří; Pecina, Adam; Hrušková-Heidingsfeldová, Olga; Marečková, Lucie; Pichová, Iva; Řezáčová, Pavlina; Lepšík, Martin; Brynda, Jiří

    2015-12-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Indian Academy of Sciences (India)

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

    2007-06-01

    We have studied fast ion–atom and electron–atom collision processes using a reconditioned high resolution X-ray spectrometer. The X-rays, generated by the collisions, are dispersed by a curved ADP crystal (Johansson geometry) and detected by a gas proportional counter. A self-written LabVIEW based program has been used to give precise and controlled movement to the crystal and for data acquisition. The performance was tested by detecting the K diagram and satellite lines of several elements. The K satellite lines of Al have been studied in collision with 3–12 keV electrons and 40 MeV C4+ ions. In ion collisions as large as four L-vacancies are created simultaneously with the K-vacancy, compared to two satellites in case of the e-impact. In addition, we have measured the X-rays from H-, He- and Li-like Si ions which arise due to the electron loss/capture process in highly charged 80 MeV Si7+ ions in collision with thin carbon foil. Approximate charge state distribution has been obtained using this new technique.

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Sanchari Banerjee

    2016-07-01

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

  7. Achieving atomic resolution

    Directory of Open Access Journals (Sweden)

    John Spence

    2002-04-01

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

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

    Science.gov (United States)

    Gessmann, Renate; Brückner, Hans; Petratos, Kyriacos

    2003-01-01

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

  9. AFM's path to atomic resolution

    OpenAIRE

    2005-01-01

    We review progress in improving the spatial resolution of atomic force microscopy (AFM) under vacuum. After an introduction to the basic imaging principle and a conceptual comparison to scanning tunneling microscopy (STM), we outline the main challenges of AFM as well as the solutions that have evolved in the first 20 years of its existence. Some crucial steps along AFM's path toward higher resolution are discussed, followed by an outlook on current and future applications.

  10. High-resolution multiphoton laser-induced fluorescence spectroscopy of zinc atoms ejected from laser-irradiated ZnS crystals

    Science.gov (United States)

    Arlinghaus, H. F.; Calaway, W. F.; Young, C. E.; Pellin, M. J.; Gruen, D. M.; Chase, L. L.

    1989-01-01

    Time-of-flight (TOF) measurements employing high-resolution multiphoton laser-induced fluorescence spectroscopy (LFS) have been used as a probe to determine the yield and velocity distributions of Zn atoms ejected from a ZnS single crystal under irradiation by 308-nm photons. For fluences between 20 and 80 mJ/cm2 (irradiated area 2 mm2), the velocity distributions could be fitted by Maxwell-Boltzmann distributions where the characteristic temperature increased from 2000 to 9000 K, respectively. The absolute neutral Zn yield also increased from 108 to 1012 atoms per pulse over this same fluence range. Plots of temperature (T) as a function of fluence (F) and yield as a function of 1/T and 1/F suggest thermal evaporation as the mechanism for the Zn emission.The results indicate that with increasing fluence a critical combination of particle density and laser intensity is reached for formation of a plasma which interacts with the surface to cause catastrophic failure. For consecutive laser shots at constant ablation laser fluences, a nearly exponential increase of the Zn particle density was observed, although the measured kinetic temperature remains approximately constant even beyond the onset of visible damage to the ZnS surface. Doppler-shift techniques have been combined with TOF measurements for the first time in order to separate prompt from delayed emission of ablated atoms as well as to probe possible molecular or cluster ejection and fragmentation. Evidence for the latter phenomena was obtained.

  11. Characterization of Staphylococcus aureus EssB, an integral membrane component of the Type VII secretion system: atomic resolution crystal structure of the cytoplasmic segment.

    Science.gov (United States)

    Zoltner, Martin; Fyfe, Paul K; Palmer, Tracy; Hunter, William N

    2013-01-15

    The Type VII protein translocation/secretion system, unique to Gram-positive bacteria, is a key virulence determinant in Staphylococcus aureus. We aim to characterize the architecture of this secretion machinery and now describe the present study of S. aureus EssB, a 52 kDa bitopic membrane protein essential for secretion of the ESAT-6 (early secretory antigenic target of 6 kDa) family of proteins, the prototypic substrate of Type VII secretion. Full-length EssB was heterologously expressed in Escherichia coli, solubilized from the bacterial membrane, purified to homogeneity and shown to be dimeric. A C-terminal truncation, EssB∆C, and two soluble fragments termed EssB-N and EssB-C, predicted to occur on either side of the cytoplasmic membrane, have been successfully purified in a recombinant form, characterized and, together with the full-length protein, used in crystallization trials. EssB-N, the 25 kDa N-terminal cytoplasmic fragment, gave well-ordered crystals and we report the structure, determined by SAD (single-wavelength anomalous diffraction) targeting an SeMet (selenomethionine) derivative, refined to atomic (1.05 Å; 1 Å=0.1 nm) resolution. EssB-N is dimeric in solution, but crystallizes as a monomer and displays a fold comprised of two globular domains separated by a cleft. The structure is related to that of serine/threonine protein kinases and the present study identifies that the Type VII secretion system exploits and re-uses a stable modular entity and fold that has evolved to participate in protein-protein interactions in a similar fashion to the catalytically inert pseudokinases.

  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. 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.

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

    Science.gov (United States)

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

    2012-02-01

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

  15. HRTEM Imaging of Atoms at Sub-Angstrom Resolution

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-04-06

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

  16. Can Atomic Force Microscopy Achieve Atomic Resolution in Contact Mode?

    Science.gov (United States)

    Jarvis, M. R.; Pérez, Rubén; Payne, M. C.

    2001-02-01

    Atomic force microscopy operating in the contact mode is studied using total-energy pseudopotential calculations. It is shown that, in the case of a diamond tip and a diamond surface, it is possible for a tip terminated by a single atom to sustain forces in excess of 30 nN. It is also shown that imaging at atomic resolution may be limited by blunting of the tip during lateral scanning.

  17. Atomic resolution images of graphite in air

    Energy Technology Data Exchange (ETDEWEB)

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

    1988-12-01

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

  18. An overview of heavy-atom derivatization of protein crystals.

    Science.gov (United States)

    Pike, Ashley C W; Garman, Elspeth F; Krojer, Tobias; von Delft, Frank; Carpenter, Elisabeth P

    2016-03-01

    Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.

  19. Spatial resolution in atom probe tomography

    CERN Document Server

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

    2015-01-01

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

  20. 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.

  1. Modelling the metal atom positions of the Photosystem II water oxidising complex: a density functional theory appraisal of the 1.9 Å resolution crystal structure.

    Science.gov (United States)

    Petrie, Simon; Gatt, Phillip; Stranger, Rob; Pace, Ron J

    2012-08-28

    Density functional theory (DFT) calculations are reported for a set of model compounds intended to represent the structure of the Photosystem II (PSII) water oxidising complex (WOC) as determined by the recent 1.9 Å resolution single crystal X-ray diffraction (XRD) study of Umena et al. In contrast with several other theoretical studies addressing this structure, we find that it is not necessary to invoke photoreduction of the crystalline sample below the S(1)'resting state' in order to rationalise the observed WOC geometry. Our results are consistent with crystallised PSII in the S(1) state, with S(1) corresponding to either (Mn(III))(4) or (Mn(III))(2)(Mn(IV))(2) as required by the two competing paradigms for the WOC oxidation state pattern. Of these two paradigms, the 'low-oxidation-state' paradigm provides a better match for the crystal structure, with the comparatively long Mn(2)-Mn(3) distance in particular proving difficult to reconcile with the 'high-oxidation-state' model. Best agreement with the set of metal-metal distances is obtained with a S(1) model featuring μ-O, μ-OH bridging between Mn(3) and Mn(4) and deprotonation of one water ligand on Mn(4). Theoretical modelling of the 1.9 Å structure is an important step in assessing the validity of this recent crystal structure, with implications for our understanding of the mechanism of water oxidation by PSII.

  2. Atomic Resolution Imaging of Halide Perovskites.

    Science.gov (United States)

    Yu, Yi; Zhang, Dandan; Kisielowski, Christian; Dou, Letian; Kornienko, Nikolay; Bekenstein, Yehonadav; Wong, Andrew B; Alivisatos, A Paul; Yang, Peidong

    2016-12-14

    The radiation-sensitive nature of halide perovskites has hindered structural studies at the atomic scale. We overcome this obstacle by applying low dose-rate in-line holography, which combines aberration-corrected high-resolution transmission electron microscopy with exit-wave reconstruction. This technique successfully yields the genuine atomic structure of ultrathin two-dimensional CsPbBr3 halide perovskites, and a quantitative structure determination was achieved atom column by atom column using the phase information of the reconstructed exit-wave function without causing electron beam-induced sample alterations. An extraordinarily high image quality enables an unambiguous structural analysis of coexisting high-temperature and low-temperature phases of CsPbBr3 in single particles. On a broader level, our approach offers unprecedented opportunities to better understand halide perovskites at the atomic level as well as other radiation-sensitive materials.

  3. Atomic resolution crystal structures, EXAFS, and quantum chemical studies of rusticyanin and its two mutants provide insight into its unusual properties.

    Science.gov (United States)

    Barrett, Mark L; Harvey, Ian; Sundararajan, Mahesh; Surendran, Rajeev; Hall, John F; Ellis, Mark J; Hough, Michael A; Strange, Richard W; Hillier, Ian H; Hasnain, S Samar

    2006-03-07

    Rusticyanin from the extremophile Thiobacillus ferrooxidans is a blue copper protein with unusually high redox potential and acid stability. We present the crystal structures of native rusticyanin and of its Cu site mutant His143Met at 1.27 and 1.10 A, respectively. The very high resolution of these structures allows a direct comparison with EXAFS data and with quantum chemical models of the oxidized and reduced forms of the proteins, based upon both isolated and embedded clusters and density functional theory (DFT) methods. We further predict the structure of the Cu(II) form of the His143Met mutant which has been experimentally inaccessible due to its very high redox potential. We also present metrical EXAFS data and quantum chemical calculations for the oxidized and reduced states of the Met148Gln mutant, this protein having the lowest redox potential of all currently characterized mutants of rusticyanin. These data offer new insights into the structural factors which affect the redox potential in this important class of proteins. Calculations successfully predict the structure and the order of redox potentials for the three proteins. The calculated redox potential of H143M ( approximately 400 mV greater than native rusticyanin) is consistent with the failure of readily available chemical oxidants to restore a Cu(II) species of this mutant. The structural and energetic effects of mutating the equatorial cysteine to serine, yet to be studied experimentally, are predicted to be considerable by our calculations.

  4. 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...

  5. High-resolution noncontact atomic force microscopy.

    Science.gov (United States)

    Pérez, Rubén; García, Ricardo; Schwarz, Udo

    2009-07-01

    Progress in nanoscience and nanotechnology requires tools that enable the imaging and manipulation of matter at the atomic and molecular scale. During the last two decades or so, scanning probe-based techniques have proven to be particularly versatile in this regard. Among the various probe-based approaches, atomic force microscopy (AFM) stands out in many ways, including the total number of citations and the breadth of possible applications, ranging from materials characterization to nanofabrication and biological studies. However, while nanometer scale operation in different environments became routine, atomic resolution imaging remained elusive for a long time. The reason for this initial deficiency was that contact with the sample blunts atomically sharp tips, which are mandatory for successful atomic resolution imaging. This problem was overcome in the mid-1990s with the introduction of noncontact atomic force microscopy (NC-AFM), which represents a version of AFM where the cantilever is oscillated close to the sample surface without actually 'touching' it. This allows the preservation of the atomic sharpness of the tip while interaction-induced changes in the cantilever's resonance frequency are used to quantify the tip-sample distance. Since then, progress has been steady and includes the development of commercial instruments as well as the addition of many new capabilities beyond imaging, such as the identification and manipulation of individual atoms. A series of annual international conferences, starting in Osaka in 1998, have contributed significantly to this outstanding performance. The program of the most recent conference from this series, held in Madrid on 15-19 September 2008, reflects the maturity of this field, with an increasing number of groups developing strong activities that involve novel approaches and applications covering areas well beyond the original vacuum-based imaging. In this special issue of Nanotechnology we present a selection of

  6. 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).

  7. Atom-Light Interactions in Photonic Crystals

    CERN Document Server

    Goban, A; Yu, S -P; Hood, J D; Muniz, J A; Lee, J H; Martin, M J; McClung, A C; Choi, K S; Chang, D E; Painter, O; Kimble, H J

    2013-01-01

    The integration of nanophotonics and atomic physics has been a long-sought goal that would open new frontiers for optical physics. Here, we report the development of the first integrated optical circuit with a photonic crystal capable of both localizing and interfacing atoms with guided photons in the device. By aligning the optical bands of a photonic crystal waveguide (PCW) with selected atomic transitions, our platform provides new opportunities for novel quantum transport and many-body phenomena by way of photon-mediated atomic interactions along the PCW. From reflection spectra measured with average atom number N = 1.1$\\pm$0.4, we infer that atoms are localized within the PCW by Casimir-Polder and optical dipole forces. The fraction of single-atom radiative decay into the PCW is $\\Gamma_{\\rm 1D}/\\Gamma'$ = 0.32$\\pm$0.08, where $\\Gamma_{1D}$ is the rate of emission into the guided mode and $\\Gamma'$ is the decay rate into all other channels. $\\Gamma_{\\rm 1D}/\\Gamma'$ is quoted without enhancement due to a...

  8. Atomic resolution 3D electron diffraction microscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-03-01

    Electron lens aberration is the major barrier limiting the resolution of electron microscopy. Here we describe a novel form of electron microscopy to overcome electron lens aberration. By combining coherent electron diffraction with the oversampling phasing method, we show that the 3D structure of a 2 x 2 x 2 unit cell nano-crystal (framework of LTA [Al12Si12O48]8) can be ab initio determined at the resolution of 1 Angstrom from a series of simulated noisy diffraction pattern projections with rotation angles ranging from -70 degrees to +70 degrees in 5 degrees increments along a single rotation axis. This form of microscopy (which we call 3D electron diffraction microscopy) does not require any reference waves, and can image the 3D structure of nanocrystals, as well as non-crystalline biological and materials science samples, with the resolution limited only by the quality of sample diffraction.

  9. Atomic force microscopy of lead iodide crystal surfaces

    Science.gov (United States)

    George, M. A.; Azoulay, M.; Jayatirtha, H. N.; Biao, Y.; Burger, A.; Collins, W. E.; Silberman, E.

    1994-03-01

    Atomic force microscopy (AFM) was used to characterize the surface of lead iodide crystals. The high vapor pressure of lead iodide prohibits the use of traditional high resolution surface study techniques that require high vacuum conditions. AFM was used to image numerous insulating surface in various ambients, with very little sample preparation techniques needed. Freshly cleaved and modified surfaces, including, chemical and vacuum etched, and air aged surfaces, were examined. Both intrinsic and induced defects were imaged with high resolution. The results were compared to a similar AFM study of mercuric iodide surfaces and it was found that, at ambient conditions, lead iodide is significantly more stable than mercuric iodide.

  10. Spontaneous Crystallization of Light and Ultracold Atoms

    Science.gov (United States)

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

    2016-04-01

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

  11. X-ray holography with atomic resolution

    Science.gov (United States)

    Tegze, Miklós; Faigel, Gyula

    1996-03-01

    DIFFRACTION methods for crystallographic structure determination suffer from the so-called 'phase problem'; a diffraction pattern provides intensity but not phase information for the scattered beams, and therefore cannot be uniquely inverted to obtain the crystal structure of a sample. Holographic methods1, on the other hand, offer a means of extracting both intensity and phase information. To be useful for crystallographic applications, holography must be implemented with radiation of sufficiently small wavelength to resolve atomic-scale features2. One method, electron-emission holography3-9, uses electron waves and is a powerful tool for studying surface structure; but it cannot image the internal structure of solids because of complications arising from the highly anisotropic nature of electron scattering processes. A proposed alternative method uses X-rays2,10-13, which scatter more isotropically than electrons. Here we demonstrate the efficacy of atomic-scale X-ray holography by obtaining direct images of the three-dimensional arrangement of strontium atoms in the cubic perovskite SrTiO3. With more intense synchrotron sources for illumination, and with the development of improved X-ray detectors, X-ray holography should become a powerful general technique for unambiguous structure determination in condensed matter systems.

  12. Fabrication of crystals from single metal atoms.

    Science.gov (United States)

    Barry, Nicolas P E; Pitto-Barry, Anaïs; Sanchez, Ana M; Dove, Andrew P; Procter, Richard J; Soldevila-Barreda, Joan J; Kirby, Nigel; Hands-Portman, Ian; Smith, Corinne J; O'Reilly, Rachel K; Beanland, Richard; Sadler, Peter J

    2014-05-27

    Metal nanocrystals offer new concepts for the design of nanodevices with a range of potential applications. Currently the formation of metal nanocrystals cannot be controlled at the level of individual atoms. Here we describe a new general method for the fabrication of multi-heteroatom-doped graphitic matrices decorated with very small, ångström-sized, three-dimensional (3D)-metal crystals of defined size. We irradiate boron-rich precious-metal-encapsulated self-spreading polymer micelles with electrons and produce, in real time, a doped graphitic support on which individual osmium atoms hop and migrate to form 3D-nanocrystals, as small as 15 Å in diameter, within 1 h. Crystal growth can be observed, quantified and controlled in real time. We also synthesize the first examples of mixed ruthenium-osmium 3D-nanocrystals. This technology not only allows the production of ångström-sized homo- and hetero-crystals, but also provides new experimental insight into the dynamics of nanocrystals and pathways for their assembly from single atoms.

  13. Time amplifying techniques towards atomic time resolution

    Institute of Scientific and Technical Information of China (English)

    LI JingZhen

    2009-01-01

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

  14. Time amplifying techniques towards atomic time resolution

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

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

  15. A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.

    Science.gov (United States)

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

    2016-07-20

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

  16. Determination of absolute configuration using heavy atom based co-crystallization method: Halogen atom effects

    Science.gov (United States)

    Wang, Jian-Rong; Fan, Xiaowu; Ding, Qiaoce; Mei, Xuefeng

    2016-09-01

    Heavy atom (chloride, bromide, and iodide) based co-crystals for determination of absolute configuration (AC) for chiral molecules were synthesized and evaluated. Co-crystals of cholestanol and L-ascorbic acid were analysed and the effects and potential benefits of varying the heavy atom are discussed. Changing the halogen atoms (chloride, bromide, or iodide) affects the co-crystal formation, X-ray absorption, and anomalous dispersion, and hence the ability to determine AC.

  17. 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.

  18. 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.

  19. Statistiscal Experimental Design for Quantitative Atomic Resolution Transmission Electron Microscopy

    NARCIS (Netherlands)

    Van Aert, S.

    2003-01-01

    Statistical experimental design is applied to set up quantitative atomic resolution transmission electron microscopy experiments. In such experiments, observations of the atomic structure of the object under study are always subject to spontaneous fluctuations. As a result of these fluctuations, the

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

    Science.gov (United States)

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

    2015-03-01

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

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

    CERN Document Server

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

    2015-01-01

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

  2. High resolution adaptive imaging of a single atom

    CERN Document Server

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

    2015-01-01

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

  3. Finite atomic lattices and resolutions of monomial ideals

    CERN Document Server

    Mapes, Sonja

    2010-01-01

    In this paper we primarily study monomial ideals and their minimal free resolutions by studying their associated LCM lattices. In particular, we formally define the notion of coordinatizing a finite atomic lattice P to produce a monomial ideal whose LCM lattice is P, and we give a complete characterization of all such coordinatizations. We prove that all relations in the lattice L(n) of all finite atomic lattices with n ordered atoms can be realized as deformations of exponents of monomial ideals. We also give structural results for L(n). Moreover, we prove that the cellular structure of a minimal free resolution of a monomial ideal M can be extended to minimal resolutions of certain monomial ideals whose LCM lattices are greater than that of M in L(n).

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

    Science.gov (United States)

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

    2014-12-01

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

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

    NARCIS (Netherlands)

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

    1994-01-01

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

  6. Atomic resolution images of solid-liquid interfaces

    OpenAIRE

    Giambattista, Brian; McNairy, W. W.; Slough, C. G.; Johnson, A.; Bell, L. D.; Coleman, R. V.; Schneir, J.; Sonnenfeld, R.; Drake, B; Hansma, P K

    1987-01-01

    A scanning tunneling microscope (STM) can provide atomic-resolution images of solids covered with a variety of liquids, including cryogenic fluids, both polar and nonpolar solvents, conductive aqueous solutions, oils, and even greases. This short overview includes images of solids covered with liquid nitrogen, liquid helium, paraffin oil, silicone oil, microscope immersion oil, silicone vacuum grease, fluorocarbon grease, glycerol, and salt water. These images show atoms, charge-density waves...

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

    Science.gov (United States)

    Merano, Michele

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-25

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

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

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

    2016-09-20

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

  11. 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.

  12. Atomic resolution imaging of beryl: an investigation of the nano-channel occupation.

    Science.gov (United States)

    Arivazhagan, V; Schmitz, F D; Vullum, P E; VAN Helvoort, A T J; Holst, B

    2017-02-01

    Beryl in different varieties (emerald, aquamarine, heliodor etc.) displays a wide range of colours that have fascinated humans throughout history. Beryl is a hexagonal cyclo-silicate (ring-silicate) with channels going through the crystal along the c-axis. The channels are about 0.5 nm in diameter and can be occupied by water and alkali ions. Pure beryl (Be3 Al2 Si6 O18 ) is colourless (variety goshenite). The characteristic colours are believed to be mainly generated through substitutions with metal atoms in the lattice. Which atoms that are substituted is still debated it has been proposed that metal ions may also be enclosed in the channels and that this can also contribute to the crystal colouring. So far spectroscopy studies have not been able to fully answer this. Here we present the first experiments using atomic resolution scanning transmission electron microscope imaging (STEM) to investigate the channel occupation in beryl. We present images of a natural beryl crystal (variety heliodor) from the Bin Thuan Province in Vietnam. The channel occupation can be visualized. Based on the image contrast in combination with ex situ element analysis we suggest that some or all of the atoms that are visible in the channels are Fe ions.

  13. Atomic Resolution Images of Solid-Liquid Interfaces

    Science.gov (United States)

    Giambattista, Brian; McNairy, W. W.; Slough, C. G.; Johnson, A.; Bell, L. D.; Coleman, R. V.; Schneir, J.; Sonnenfeld, R.; Drake, B.; Hansma, P. K.

    1987-07-01

    A scanning tunneling microscope (STM) can provide atomic-resolution images of solids covered with a variety of liquids, including cryogenic fluids, both polar and nonpolar solvents, conductive aqueous solutions, oils, and even greases. This short overview includes images of solids covered with liquid nitrogen, liquid helium, paraffin oil, silicone oil, microscope immersion oil, silicone vacuum grease, fluorocarbon grease, glycerol, and salt water. These images show atoms, charge-density waves, grains in an evaporated metal film, and even corrosion processes as they occur in real time. The future includes not only basic research in surface science but also applied research in lithography, lubrication, catalysis, corrosion, electrochemistry, and perhaps even biology.

  14. CO tip functionalization in subatomic resolution atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-19

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

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

    Institute of Scientific and Technical Information of China (English)

    Hong Yong Xie

    2007-01-01

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

  16. Near-atomic-resolution cryo-EM for molecular virology.

    Science.gov (United States)

    Hryc, Corey F; Chen, Dong-Hua; Chiu, Wah

    2011-08-01

    Electron cryo-microscopy (cryo-EM) is a technique in structural biology that is widely used to solve the three-dimensional structures of macromolecular assemblies, close to their biological and solution conditions. Recent improvements in cryo-EM and single-particle reconstruction methodologies have led to the determination of several virus structures at near-atomic resolution (3.3 - 4.6 Å). These cryo-EM structures not only resolve the Cα backbones and side-chain densities of viral capsid proteins, but also suggest functional roles that the protein domains and some key amino acid residues play. This paper reviews the recent advances in near-atomic-resolution cryo-EM for probing the mechanisms of virus assembly and morphogenesis.

  17. Electron microscopy of gold nanoparticles at atomic resolution

    Science.gov (United States)

    Azubel, Maia; Koivisto, Jaakko; Malola, Sami; Bushnell, David; Hura, Greg L.; Koh, Ai Leen; Tsunoyama, Hironori; Tsukuda, Tatsuya; Pettersson, Mika; Häkkinen, Hannu; Kornberg, Roger D.

    2014-01-01

    Structure determination of gold nanoparticles (AuNPs) is necessary for understanding their physical and chemical properties, and only one AuNP larger than 1 nm in diameter, an Au102NP, has been solved to atomic resolution. Whereas the Au102NP structure was determined by X-ray crystallography, other large AuNPs have proved refractory to this approach. Here we report the structure determination of an Au68NP at atomic resolution by aberration-corrected transmission electron microscopy (AC-TEM), performed with the use of a minimal electron dose, an approach that should prove applicable to metal NPs in general. The structure of the Au68NP was supported by small angle X-ray scattering (SAXS) and by comparison of observed infrared (IR) absorption spectra with calculations by density functional theory (DFT). PMID:25146285

  18. Radiation damping in atomic photonic crystals.

    Science.gov (United States)

    Horsley, S A R; Artoni, M; La Rocca, G C

    2011-07-22

    The force exerted on a material by an incident beam of light is dependent upon the material's velocity in the laboratory frame of reference. This velocity dependence is known to be difficult to measure, as it is proportional to the incident optical power multiplied by the ratio of the material velocity to the speed of light. Here we show that this typically tiny effect is greatly amplified in multilayer systems composed of resonantly absorbing atoms exhibiting ultranarrow photonic band gaps. The amplification effect for optically trapped 87Rb is shown to be as much as 3 orders of magnitude greater than for conventional photonic-band-gap materials. For a specific pulsed regime, damping remains observable without destroying the system and significant for material velocities of a few ms(-1).

  19. Radiation 'damping' in atomic photonic crystals

    CERN Document Server

    Horsley, S A R; La Rocca, G C

    2010-01-01

    The force exerted on a material by an incident beam of light is dependent upon the material's velocity in the laboratory frame of reference. This velocity dependence is known to be diffcult to measure, as it is proportional to the incident optical power multiplied by the ratio of the material velocity to the speed of light. Here we show that this typically tiny effect is greatly amplified in multilayer systems composed of resonantly absorbing atoms (e.g. optically trapped 87Rb), which may exhibit ultra-narrow photonic band gaps. The amplification of the effect is shown to be three orders of magnitude greater than previous estimates for conventional photonic-band-gap materials, and significant for material velocities of a few ms/s.

  20. 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.

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

    Science.gov (United States)

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

    2015-03-17

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-15

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

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

    Science.gov (United States)

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

    2015-02-01

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

  4. Is there a Stobbs factor in atomic-resolution STEM-EELS mapping?

    Energy Technology Data Exchange (ETDEWEB)

    Xin, Huolin L., E-mail: hxin@bnl.gov [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Dwyer, Christian, E-mail: c.dwyer@fz-juelich.de [Monash Centre for Electron Microscopy, ARC Centre of Excellence for Design in Light Metals, Monash University, Clayton, 3800 Vic (Australia); Department of Materials Engineering, Monash University, Clayton, 3800 Vic (Australia); Muller, David A., E-mail: dm24@cornell.edu [School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 (United States); Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 (United States)

    2014-04-01

    Recent work has convincingly argued that the Stobbs factor—disagreement in contrast between simulated and experimental atomic-resolution images—in ADF-STEM imaging can be accounted for by including the incoherent source size in simulation. However, less progress has been made for atomic-resolution STEM-EELS mapping. Here we have performed carefully calibrated EELS mapping experiments of a [101] DyScO{sub 3} single-crystal specimen, allowing atomic-resolution EELS signals to be extracted on an absolute scale for a large range of thicknesses. By simultaneously recording the elastic signal, also on an absolute scale, and using it to characterize the source size, sample thickness and inelastic mean free path, we eliminate all free parameters in the simulation of the core-loss signals. Coupled with double channeling simulations that incorporate both core-loss inelastic scattering and dynamical elastic and thermal diffuse scattering, the present work enables a close scrutiny of the scattering physics in the inelastic channel. We found that by taking into account the effective source distribution determined from the ADF images, both the absolute signal and the contrast in atomic-resolution Dy-M{sub 5} maps can be closely reproduced by the double-channeling simulations. At lower energy losses, discrepancies are present in the Sc-L{sub 2,3} and Dy-N{sub 4,5} maps due to the energy-dependent spatial distribution of the background spectrum, core-hole effects, and omitted complexities in the final states. This work has demonstrated the possibility of using quantitative STEM-EELS for element-specific column-by-column atom counting at higher energy losses and for atomic-like final states, and has elucidated several possible improvements for future theoretical work. - Highlights: • This paper present a carefully calibrated experiment, which allows, for the first time, atomic-resolution chemical signals to be extracted on an absolute scale. • By simultaneously recording

  5. Trapped Atoms in One-Dimensional Photonic Crystals

    Science.gov (United States)

    Kimble, H.

    2013-05-01

    I describe one-dimensional photonic crystals that support a guided mode suitable for atom trapping within a unit cell, as well as a second probe mode with strong atom-photon interactions. A new hybrid trap is analyzed that combines optical and Casimir-Polder forces to form stable traps for neutral atoms in dielectric nanostructures. By suitable design of the band structure, the atomic spontaneous emission rate into the probe mode can exceed the rate into all other modes by more than tenfold. The unprecedented single-atom reflectivity r0 ~= 0 . 9 for the guided probe field could create new scientific opportunities, including quantum many-body physics for 1 D atom chains with photon-mediated interactions and high-precision studies of vacuum forces. Towards these goals, my colleagues and I are pursuing numerical simulation, device fabrication, and cold-atom experiments with nanoscopic structures. Funding is provided by by the IQIM, an NSF PFC with support of the Moore Foundation, by the AFOSR QuMPASS MURI, by the DoD NSSEFF program (HJK), and by NSF Grant PHY0652914 (HJK). DEC acknowledges funding from Fundacio Privada Cellex Barcelona.

  6. 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

  7. 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

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

    Science.gov (United States)

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

    2016-06-01

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

  9. Simulation studies of atomic resolution X-ray holography

    Indian Academy of Sciences (India)

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

    2004-02-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-09-01

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

  11. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Devaud, G. (Department of Physics, University of Colorado, Boulder, Colorado 80309 (United States)); Furcinitti, P.S. (Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309 (United States)); Fleming, J.C.; Lyon, M.K.; Douglas, K. (Department of Physics, University of Colorado, Boulder, Colorado 80309 (United States))

    1992-09-01

    We have examined the structure of S-layers isolated from {ital Sulfolobus} {ital acidocaldarius} using atomic force microscopy (AFM) and transmission electron microscopy (TEM). From the AFM images, we were able to directly observe individual dimers of the crystal, defects in the crystal structure, and twin boundaries. We have identified two types of boundaries, one defined by a mirror plane and the other by a glide plane. This work shows that twin boundaries are highly structured regions that are directly related to the organization of units within each crystal domain. Projection maps from TEM images have shown that there are significant differences in the final average maps, depending on which side of the sample is adsorbed to the carbon support film. Comparison of AFM images to TEM projection maps has allowed us to relate high magnification views obtained by AFM to the relatively high resolution information obtained by electron microscopy and image processing.

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

    Science.gov (United States)

    Pavlov, V. V.

    2008-02-01

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

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

    Science.gov (United States)

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

    2014-12-01

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

  15. 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

  16. Statistical Nature of Atomic Disorder in Irradiated Crystals

    Science.gov (United States)

    Boulle, A.; Debelle, A.

    2016-06-01

    Atomic disorder in irradiated materials is investigated by means of x-ray diffraction, using cubic SiC single crystals as a model material. It is shown that, besides the determination of depth-resolved strain and damage profiles, x-ray diffraction can be efficiently used to determine the probability density function (PDF) of the atomic displacements within the crystal. This task is achieved by analyzing the diffraction-order dependence of the damage profiles. We thereby demonstrate that atomic displacements undergo Lévy flights, with a displacement PDF exhibiting heavy tails [with a tail index in the γ =0.73 - 0.37 range, i.e., far from the commonly assumed Gaussian case (γ =2 )]. It is further demonstrated that these heavy tails are crucial to account for the amorphization kinetics in SiC. From the retrieved displacement PDFs we introduce a dimensionless parameter fDXRD to quantify the disordering. fDXRD is found to be consistent with both independent measurements using ion channeling and with molecular dynamics calculations.

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

    CERN Document Server

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

    1999-01-01

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

  18. Advanced double-biprism holography with atomic resolution.

    Science.gov (United States)

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

    2014-12-01

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

  19. Atomic-resolution structures of prion AGAAAAGA amyloid fibrils

    CERN Document Server

    Zhang, Jiapu

    2011-01-01

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

  20. Rydberg atoms in hollow-core photonic crystal fibres

    CERN Document Server

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, A

    2006-02-01

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

  2. Properties of atomic intercalated boron nitride K4 type crystals

    OpenAIRE

    Itoh, Masahiro; Takami, Seiichi; Kawazoe, Yoshiyuki; Adschiri, Tadafumi

    2010-01-01

    The stability of atomic intercalated boron nitride K4 crystal structures, XBN (X=H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, K, Ca, Ga, Ge, As, Se, Br, Rb or Sr) is evaluated by the geometric optimization and frozen phonon calculations based on the first principles calculations. NaBN, MgBN, GaBN, FBN and ClBN are found to be stable. NaBN, GaBN, FBN and ClBN are metallic, whereas MgBN is semiconducting.

  3. Properties of atomic intercalated carbon K4 crystals

    OpenAIRE

    Itoh, Masahiro; Takami, Seiichi; Kawazoe, Yoshiyuki; Adschiri, Tadafumi

    2009-01-01

    The stability of atomic intercalated carbon $K_{4}$ crystals, XC$_{2}$ (X=H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, K, Ca, Ga, Ge, As, Se, Br, Rb or Sr) is evaluated by geometry optimization and frozen phonon analysis based on first principles calculations. Although C $K_{4}$ is unstable, NaC$_{2}$ and MgC$_{2}$ are found to be stable. It is shown that NaC$_{2}$ and MgC$_{2}$ are metallic and semi conducting, respectively.

  4. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo [Yale University

    2014-12-10

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-09-01

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

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

    Science.gov (United States)

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

    2014-06-01

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

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

    CERN Document Server

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

    2014-01-01

    Unlike photons, which are conveniently handled by mirrors and optical fibres without loss of coherence, atoms lose their coherence via atom-atom and atom-wall interactions. This decoherence of atoms deteriorates the performance of atomic clocks and magnetometers, and also hinders their miniaturisation. Here we report a novel platform for precision spectroscopy. Ultracold strontium atoms inside a kKagome-lattice hollow-core photonic crystal fibre (HC-PCF) are transversely confined by an optical lattice to prevent atoms from interacting with the fibre wall. By confining at most one atom in each lattice site, to avoid atom-atom interactions and Doppler effect, a 7.8-kHz-wide spectrum is observed for the $^1 S_0-{}^3P_1$ (m=0) transition. Atoms singly trapped in a magic lattice in hollow-core photonic crystal fibresHC-PCFs improve the optical depth while preserving atomic coherence time.

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-09-01

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

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

    CERN Document Server

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

    2009-01-01

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

  12. 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...

  13. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    Science.gov (United States)

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

    2016-08-03

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

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

    DEFF Research Database (Denmark)

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

    1965-01-01

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

  15. 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.

  16. Atomic Migration Induced Crystal Structure Transformation and Core-Centered Phase Transition in Single Crystal Ge2Sb2Te5 Nanowires.

    Science.gov (United States)

    Lee, Jun-Young; Kim, Jeong-Hyeon; Jeon, Deok-Jin; Han, Jaehyun; Yeo, Jong-Souk

    2016-10-12

    A phase change nanowire holds a promise for nonvolatile memory applications, but its transition mechanism has remained unclear due to the analytical difficulties at atomic resolution. Here we obtain a deeper understanding on the phase transition of a single crystalline Ge2Sb2Te5 nanowire (GST NW) using atomic scale imaging, diffraction, and chemical analysis. Our cross-sectional analysis has shown that the as-grown hexagonal close-packed structure of the single crystal GST NW transforms to a metastable face-centered cubic structure due to the atomic migration to the pre-existing vacancy layers in the hcp structure going through iterative electrical switching. We call this crystal structure transformation "metastabilization", which is also confirmed by the increase of set-resistance during the switching operation. For the set to reset transition between crystalline and amorphous phases, high-resolution imaging indicates that the longitudinal center of the nanowire mainly undergoes phase transition. According to the atomic scale analysis of the GST NW after repeated electrical switching, partial crystallites are distributed around the core-centered amorphous region of the nanowire where atomic migration is mainly induced, thus potentially leading to low power electrical switching. These results provide a novel understanding of phase change nanowires, and can be applied to enhance the design of nanowire phase change memory devices for improved electrical performance.

  17. Feasibility of filter atomization in high-resolution continuum source atomic absorption spectrometry

    Science.gov (United States)

    Heitmann, Uwe; Becker-Ross, Helmut; Katskov, Dmitri

    2006-03-01

    A prototype spectrometer for high-resolution continuum source atomic absorption spectrometry (HR-CS AAS), built at ISAS Berlin, Germany, was combined with a graphite filter atomizer (GFA), earlier developed at TUT, Pretoria, South Africa. The furnace and auto-sampler units from a commercial AA spectrometer, model AAS vario 6 (Analytik Jena AG, Jena, Germany), were employed in the instrument. Instead of conventional platform tube, the GFA was used to provide low measurement susceptibility to interferences and short determination cycle. The GFA was modified according to the design of the furnace unit and optimal physical parameters of its components (filter and collector) found. Afterwards, optimal GFA was replicated and tested to outline analytical performances of the HR-CS GFA AA spectrometer in view of prospects of multi-element analysis. In particular, reproducibility of performances, repeatability of analytical signals, lifetime, temperature limit and duration of the measurement cycle were examined, and elements available for determination justified. The results show that the peak area of the atomic absorption signal is reproduced in various GFA copies within ± 4% deviation range. The GFA can stand temperatures of 2800 °C with 6 s hold time for 55 temperature cycles, and 2700 °C (8 s) for about 200 cycles. Only the external tube is prone to destruction while the filter and collector do not show any sign of erosion caused by temperature or aggressive matrix. Analytical signals are affected insignificantly by tube aging. Repeatability of the peak area remains within 1.1-1.7% RSD over more than hundred determination cycles. Peak areas are proportional to the sample volume of injected organic and inorganic liquids up to at least 50 μL. The drying stage is combined with hot sampling and cut down to 15-20 s. The list of metals available for determination with full vapor release includes Al, Co, Cr, Ni, Pt as well as more volatile metals. Characteristic masses at

  18. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

  20. Separate-type scanner and wideband high-voltage amplifier for atomic-resolution and high-speed atomic force microscopy.

    Science.gov (United States)

    Miyata, Kazuki; Usho, Satoshi; Yamada, Satoshi; Furuya, Shoji; Yoshida, Kiyonori; Asakawa, Hitoshi; Fukuma, Takeshi

    2013-04-01

    We have developed a liquid-environment atomic force microscope with a wideband and low-noise scanning system for atomic-scale imaging of dynamic processes at solid/liquid interfaces. The developed scanning system consists of a separate-type scanner and a wideband high-voltage amplifier (HVA). By separating an XY-sample scanner from a Z-tip scanner, we have enabled to use a relatively large sample without compromising the high resonance frequency. We compared various cantilever- and sample-holding mechanisms by experiments and finite element analyses for optimizing the balance between the usability and frequency response characteristics. We specifically designed the HVA to drive the developed scanners, which enabled to achieve the positioning accuracy of 5.7 and 0.53 pm in the XY and Z axes, respectively. Such an excellent noise performance allowed us to perform atomic-resolution imaging of mica and calcite in liquid. Furthermore, we demonstrate in situ and atomic-resolution imaging of the calcite crystal growth process in water.

  1. One more chiral drug prone to spontaneous resolution: Binary phase diagram, absolute configuration, and crystal packing of bevantolol hydrochloride

    Science.gov (United States)

    Bredikhina, Zemfira A.; Zakharychev, Dmitry V.; Gubaidullin, Aidar T.; Bredikhin, Alexander A.

    2009-11-01

    Spontaneous resolution of cardioselective β1-adrenergic blocker bevantolol hydrochloride1·HCl was established by IR spectroscopy, differential scanning calorimetry, and by single crystal X-ray analysis both for enantiopure and racemic samples. The absolute configuration of 1·HCl was evaluated through Flack parameter method. The molecular structure and crystal packing details were evaluated; the symmetry independent fragment of the P1 unit cell consists of two molecules which have almost identical spatial arrangement, but differ sufficiently in the nature of nitrogen atoms: quaternary form in one case and free amine form in the other.

  2. High-resolution adaptive imaging of a single atom

    Science.gov (United States)

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

    2016-09-01

    Optical imaging systems are used extensively in the life and physical sciences because of their ability to non-invasively capture details on the microscopic and nanoscopic scales. Such systems are often limited by source or detector noise, image distortions and human operator misjudgement. Here, we report a general, quantitative method to analyse and correct these errors. We use this method to identify and correct optical aberrations in an imaging system for single atoms and realize an atomic position sensitivity of ˜0.5 nm Hz-1/2 with a minimum uncertainty of 1.7 nm, allowing the direct imaging of atomic motion. This is the highest position sensitivity ever measured for an isolated atom and opens up the possibility of performing out-of-focus three-dimensional particle tracking, imaging of atoms in three-dimensional optical lattices or sensing forces at the yoctonewton (10-24 N) scale.

  3. Photonic Band Gap Structures with Periodically Arranged Atoms in a Two-Dimensional Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    LI Zhi-Yu; CHEN Fang; ZHOU Jian-Ying

    2005-01-01

    @@ Linear transmission, reflection and absorption spectra for a new two-dimensional photonic crystal with periodically arranged resonant atoms are examined. Numerical results show that a twin-gap structure with forbidden bands displaced from a non-doped bandgap structure can be produced as a result of atomic polarization. The absorption spectrum is also significantly altered compared to the single atom entity.

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

    Science.gov (United States)

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

    2013-04-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Robert S Miyaoka

    2012-03-06

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

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

    CERN Document Server

    Li, Zheng; Chapman, Henry; Shih, Yanhua

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

  8. 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.

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

    Directory of Open Access Journals (Sweden)

    Daniel H Anderson

    2007-11-01

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

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

    Science.gov (United States)

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

    2007-11-01

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

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

    Science.gov (United States)

    Sikorski, Pawel; Hori, Ritsuko; Wada, Masahisa

    2009-05-11

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

  12. Validation methods for low-resolution fitting of atomic structures to electron microscopy data

    OpenAIRE

    Xu, Xiao-Ping; Volkmann, Niels

    2015-01-01

    Fitting of atomic-resolution structures into reconstructions from electron cryo-microscopy is routinely used to understand the structure and function of macromolecular machines. Despite the fact that a plethora of fitting methods has been developed over recent years, standard protocols for quality assessment and validation of these fits have not been established. Here, we present the general concepts underlying current validation ideas as they relate to fitting of atomic-resolution models int...

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

    Science.gov (United States)

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

    2014-02-01

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

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

    NARCIS (Netherlands)

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

    2016-01-01

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

  15. Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution.

    Science.gov (United States)

    Chen, Chien-Chun; Zhu, Chun; White, Edward R; Chiu, Chin-Yi; Scott, M C; Regan, B C; Marks, Laurence D; Huang, Yu; Miao, Jianwei

    2013-04-04

    Dislocations and their interactions strongly influence many material properties, ranging from the strength of metals and alloys to the efficiency of light-emitting diodes and laser diodes. Several experimental methods can be used to visualize dislocations. Transmission electron microscopy (TEM) has long been used to image dislocations in materials, and high-resolution electron microscopy can reveal dislocation core structures in high detail, particularly in annular dark-field mode. A TEM image, however, represents a two-dimensional projection of a three-dimensional (3D) object (although stereo TEM provides limited information about 3D dislocations). X-ray topography can image dislocations in three dimensions, but with reduced resolution. Using weak-beam dark-field TEM and scanning TEM, electron tomography has been used to image 3D dislocations at a resolution of about five nanometres (refs 15, 16). Atom probe tomography can offer higher-resolution 3D characterization of dislocations, but requires needle-shaped samples and can detect only about 60 per cent of the atoms in a sample. Here we report 3D imaging of dislocations in materials at atomic resolution by electron tomography. By applying 3D Fourier filtering together with equal-slope tomographic reconstruction, we observe nearly all the atoms in a multiply twinned platinum nanoparticle. We observed atomic steps at 3D twin boundaries and imaged the 3D core structure of edge and screw dislocations at atomic resolution. These dislocations and the atomic steps at the twin boundaries, which appear to be stress-relief mechanisms, are not visible in conventional two-dimensional projections. The ability to image 3D disordered structures such as dislocations at atomic resolution is expected to find applications in materials science, nanoscience, solid-state physics and chemistry.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-10-11

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

  17. Introductory lecture: Time-resolved chemistry at atomic resolution.

    Science.gov (United States)

    Coppens, Philip; Novozhilova, Irina V

    2003-01-01

    Though time-resolved studies are still at an early stage, the field is rapidly being developed and applied to an increasingly broad spectrum of problems with timescales varying from seconds or more down to femtoseconds. In this overview a number of different techniques are discussed, with emphasis on chemical applications in which information is obtained at the atomic level. The need to correlate with theory, both for calibration of theoretical methods and to obtain related information not accessible experimentally, is stressed.

  18. Crystal structure of lactoperoxidase at 2.4 A resolution.

    Science.gov (United States)

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

    2008-02-29

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

  19. Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".

    Science.gov (United States)

    Belnap, D M; Kumar, A; Folk, J T; Smith, T J; Baker, T S

    1999-01-01

    Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 A), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.

  20. Rydberg atoms inside hollow-core photonic crystal fibres

    Science.gov (United States)

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

    2014-05-01

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

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

    NARCIS (Netherlands)

    van Oosten, D.; Kuipers, L.

    2011-01-01

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

  2. 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.

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

    Science.gov (United States)

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

    2016-01-01

    Calcium binding and dissociation within the cardiac thin filament (CTF) is a fundamental regulator of normal contraction and relaxation. Although the disruption of this complex, allosterically mediated process has long been implicated in human disease, the precise atomic-level mechanisms remain opaque, greatly hampering the development of novel targeted therapies. To address this question, we used a fully atomistic CTF model to test both Ca2+ binding strength and the energy required to remove Ca2+ from the N-lobe binding site in WT and mutant troponin complexes that have been linked to genetic cardiomyopathies. This computational approach is combined with measurements of in vitro Ca2+ dissociation rates in fully reconstituted WT and cardiac troponin T R92L and R92W thin filaments. These human disease mutations represent known substitutions at the same residue, reside at a significant distance from the calcium binding site in cardiac troponin C, and do not affect either the binding pocket affinity or EF-hand structure of the binding domain. Both have been shown to have significantly different effects on cardiac function in vivo. We now show that these mutations independently alter the interaction between the Ca2+ ion and cardiac troponin I subunit. This interaction is a previously unidentified mechanism, in which mutations in one protein of a complex indirectly affect a third via structural and dynamic changes in a second to yield a pathogenic change in thin filament function that results in mutation-specific disease states. We can now provide atom-level insight that is potentially highly actionable in drug design. PMID:26957598

  4. TUNABLE Band Structures of 2d Multi-Atom Archimedean-Like Phononic Crystals

    Science.gov (United States)

    Xu, Y. L.; Chen, C. Q.; Tian, X. G.

    2012-06-01

    Two dimensional multi-atom Archimedean-like phononic crystals (MAPCs) can be obtained by adding "atoms" at suitable positions in primitive cells of traditional simple lattices. Band structures of solid-solid and solid-air MAPCs are computed by the finite element method in conjunction with the Bloch theory. For the solid-solid system, our results show that the MAPCs can be suitably designed to split and shift band gaps of the corresponding traditional simple phononic crystal (i.e., with only one scatterer inside a primitive cell). For the solid-air system, the MAPCs have more and wider band gaps than the corresponding traditional simple phononic crystal. Numerical calculations for both solid-solid and solid-air MAPCs show that the band gap of traditional simple phononic crystal can be tuned by appropriately adding "atoms" into its primitive cell.

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Science.gov (United States)

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

    2011-03-09

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

  7. 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.

  8. Atomic resolution structure of serine protease proteinase K at ambient temperature

    Science.gov (United States)

    Masuda, Tetsuya; Suzuki, Mamoru; Inoue, Shigeyuki; Song, Changyong; Nakane, Takanori; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Mikami, Bunzo; Nureki, Osamu; Numata, Keiji; Iwata, So; Sugahara, Michihiro

    2017-01-01

    Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites. PMID:28361898

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

    Institute of Scientific and Technical Information of China (English)

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

    2015-01-01

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

  10. 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.

  11. 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.

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

    Science.gov (United States)

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

    2016-03-01

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

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

    Institute of Scientific and Technical Information of China (English)

    LI KeYan; XUE DongFeng

    2009-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-15

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

  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. Surface morphology study on CdZnTe crystals by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Azoulay, M.; George, M.A.; Burger, A.; Collins, W.E.; Silberman, E. [Fisk Univ., Nashville, TN (United States)

    1993-03-01

    The study of the crystal surface morphology of CdZnTe is important for the understanding of the fundamentals of crystal growth in order to improve the crystal quality which is essential in applications such as substrates for epitaxy or performance of devices, i.e., room temperature nuclear spectrometers. We present a first atomic force microscopy study on CdZnTe. Cleaved (110) surfaces were imaged in the ambient and an atomic layer step structure was revealed. The effects of thermal annealing on the atomic steps together with Te precipitation along these steps are discussed in terms of deformation due to stress relief and the diffusion of tellurium precipitates. 12 refs., 3 figs.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-09-01

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

  18. Combined low-temperature scanning tunneling/atomic force microscope for atomic resolution imaging and site-specific force spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo; Albers, Boris J.; Liebmann, Marcus; Schwendemann, Todd C.; Baykara, Mehmet Z.; Heyde, Markus; Salmeron, Miquel; Altman, Eric I.; Schwarz, Udo D.

    2008-02-27

    The authors present the design and first results of a low-temperature, ultrahigh vacuum scanning probe microscope enabling atomic resolution imaging in both scanning tunneling microscopy (STM) and noncontact atomic force microscopy (NC-AFM) modes. A tuning-fork-based sensor provides flexibility in selecting probe tip materials, which can be either metallic or nonmetallic. When choosing a conducting tip and sample, simultaneous STM/NC-AFM data acquisition is possible. Noticeable characteristics that distinguish this setup from similar systems providing simultaneous STM/NC-AFM capabilities are its combination of relative compactness (on-top bath cryostat needs no pit), in situ exchange of tip and sample at low temperatures, short turnaround times, modest helium consumption, and unrestricted access from dedicated flanges. The latter permits not only the optical surveillance of the tip during approach but also the direct deposition of molecules or atoms on either tip or sample while they remain cold. Atomic corrugations as low as 1 pm could successfully be resolved. In addition, lateral drifts rates of below 15 pm/h allow long-term data acquisition series and the recording of site-specific spectroscopy maps. Results obtained on Cu(111) and graphite illustrate the microscope's performance.

  19. Combined low-temperature scanning tunneling/atomic force microscope for atomic resolution imaging and site-specific force spectroscopy

    Science.gov (United States)

    Albers, Boris J.; Liebmann, Marcus; Schwendemann, Todd C.; Baykara, Mehmet Z.; Heyde, Markus; Salmeron, Miquel; Altman, Eric I.; Schwarz, Udo D.

    2008-03-01

    We present the design and first results of a low-temperature, ultrahigh vacuum scanning probe microscope enabling atomic resolution imaging in both scanning tunneling microscopy (STM) and noncontact atomic force microscopy (NC-AFM) modes. A tuning-fork-based sensor provides flexibility in selecting probe tip materials, which can be either metallic or nonmetallic. When choosing a conducting tip and sample, simultaneous STM/NC-AFM data acquisition is possible. Noticeable characteristics that distinguish this setup from similar systems providing simultaneous STM/NC-AFM capabilities are its combination of relative compactness (on-top bath cryostat needs no pit), in situ exchange of tip and sample at low temperatures, short turnaround times, modest helium consumption, and unrestricted access from dedicated flanges. The latter permits not only the optical surveillance of the tip during approach but also the direct deposition of molecules or atoms on either tip or sample while they remain cold. Atomic corrugations as low as 1pm could successfully be resolved. In addition, lateral drifts rates of below 15pm/h allow long-term data acquisition series and the recording of site-specific spectroscopy maps. Results obtained on Cu(111) and graphite illustrate the microscope's performance.

  20. High-resolution dynamic atomic force microscopy in liquids with different feedback architectures

    Directory of Open Access Journals (Sweden)

    John Melcher

    2013-02-01

    Full Text Available The recent achievement of atomic resolution with dynamic atomic force microscopy (dAFM [Fukuma et al., Appl. Phys. Lett. 2005, 87, 034101], where quality factors of the oscillating probe are inherently low, challenges some accepted beliefs concerning sensitivity and resolution in dAFM imaging modes. Through analysis and experiment we study the performance metrics for high-resolution imaging with dAFM in liquid media with amplitude modulation (AM, frequency modulation (FM and drive-amplitude modulation (DAM imaging modes. We find that while the quality factors of dAFM probes may deviate by several orders of magnitude between vacuum and liquid media, their sensitivity to tip–sample forces can be remarkable similar. Furthermore, the reduction in noncontact forces and quality factors in liquids diminishes the role of feedback control in achieving high-resolution images. The theoretical findings are supported by atomic-resolution images of mica in water acquired with AM, FM and DAM under similar operating conditions.

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

    Science.gov (United States)

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

    2016-02-01

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

  2. Atomic Resolution Imaging at an Ultralow Accelerating Voltage by a Monochromatic Transmission Electron Microscope

    Science.gov (United States)

    Morishita, Shigeyuki; Mukai, Masaki; Suenaga, Kazu; Sawada, Hidetaka

    2016-10-01

    Transmission electron microscopy using low-energy electrons would be very useful for atomic resolution imaging of specimens that would be damaged at higher energies. However, the resolution at low voltages is degraded because of geometrical and chromatic aberrations. In the present study, we diminish the effect of these aberrations by using a delta-type corrector and a monochromator. The dominant residual aberration in a delta-type corrector, which is the sixth-order three-lobe aberration, is counterbalanced by other threefold aberrations. Defocus spread caused by chromatic aberration is reduced by using a monochromated beam with an energy spread of 0.05 eV. We obtain images of graphene and demonstrate atomic resolution at an ultralow accelerating voltage of 15 kV.

  3. 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.

  4. 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

    2016-10-27

    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.

  5. Probe spectrum of a four-level atom in a double-band photonic crystal

    Institute of Scientific and Technical Information of China (English)

    Wen Qing-Bo; Wang Jian; Zhang Han-Zhuang

    2004-01-01

    In this paper, the probe absorption spectrum of an atom in a double-band photonic crystal have been studied. In the modes, we assume that one of the two atomic transitions in a A-type atomic system is interacting with free vacuum modes, and another transition is interacting with free vacuum modes, isotropic photonic band gap (PBG) modes and anisotropic PBG modes, separately. The effects of the fine structure of the atomic lower levels on the probe absorption spectrum are investigated in detail in the three cases. The most interesting thing is that the two (four) transparencies at one (two) probe absorption peak(s), caused by the fine structure of the lower levels of an atom, are predicted in the case of isotropic PBG modes.

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

    Directory of Open Access Journals (Sweden)

    Robert F. Tournier

    2014-08-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-08-21

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

  8. Synchrotron X-Ray Reciprocal Space Mapping, Topography and Diffraction Resolution Studies of Macromolecular Crystal Quality

    Science.gov (United States)

    Boggon, T. J.; Helliwell, J. R.; Judge, Russell A.; Siddons, D. P.; Snell, Edward H.; Stojanoff, V.

    2000-01-01

    A comprehensive study of microgravity and ground grown chicken egg white lysozyme crystals is presented using synchrotron X-ray reciprocal space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed, on average, reduced intrinsic mosaicities but no differences in terms of stress over their earth grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the earth case at the diffraction peak only a small volume of the crystal contributed to the intensity. The techniques prove to be highly complementary with the reciprocal space mapping providing a quantitative measure of the crystal mosaicity and stress (or variation in lattice spacing) and topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out both at the synchrotron and in the laboratory.

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

    Science.gov (United States)

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

    2016-09-21

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

    Kobayashi, Keita; Koshino, Masanori; Suenaga, Kazu

    2011-05-20

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

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

    Science.gov (United States)

    Elking, Dennis M

    2016-08-15

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

  13. 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

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

    Directory of Open Access Journals (Sweden)

    Daniel J Kuster

    Full Text Available 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

  15. Rydberg atoms in hollow-core photonic crystal fibres

    Science.gov (United States)

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

    2014-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-05-15

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

  17. 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...the capability of a recently adopted high fidelity two phase flow solver in the context of diesel engine sprays. Previous works relating to this

  18. 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.

  19. Towards quantitative, atomic-resolution reconstruction of the electrostatic potential via differential phase contrast using electrons

    Energy Technology Data Exchange (ETDEWEB)

    Close, R.; Chen, Z. [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia); Shibata, N. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Findlay, S.D., E-mail: scott.findlay@monash.edu [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia)

    2015-12-15

    Differential phase contrast images in scanning transmission electron microscopy can be directly and quantitatively related to the gradient of the projected specimen potential provided that (a) the specimen can be treated as a phase object and (b) full 2D diffraction patterns as a function of probe position can be obtained. Both are challenging to achieve in atomic resolution imaging. The former is fundamentally limited by probe spreading and dynamical electron scattering, and we explore its validity domain in the context of atomic resolution differential phase contrast imaging. The latter, for which proof-of-principle experimental data sets exist, is not yet routine. We explore the extent to which more established segmented detector geometries can instead be used to reconstruct a quantitatively good approximation to the projected specimen potential. - Highlights: • Atomic-resolution differential phase contrast (DPC) imaging explored via simulation. • Phase-object approximation limits quantification to specimens a few nanometers thick. • Segmented detectors give good estimates of the diffraction pattern's first moment.

  20. 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

    2016-08-01

    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 Cc/Cs 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.

  1. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-08-01

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

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

    Science.gov (United States)

    Monserrate, Aitor; Casado, Santiago; Flors, Cristina

    2014-03-17

    Hybrid microscopy: A correlative microscopy tool that combines in situ super-resolution fluorescence microscopy based on single-molecule localization and atomic force microscopy is presented. Direct comparison with high- resolution topography allows the authors to improve fluorescence labeling and image analysis in super-resolution imaging.

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

    DEFF Research Database (Denmark)

    Andersen, Hans Henrik; Sigmund, Peter

    1966-01-01

    Presents the solution of a special scattering problem which may be important in the theory of slowing-down of atomic particles in crystals. A projectile moves along the centre axis of a regular ring of n equal atoms which are free and do not interact with each other. The interaction between...... the projectile and each ring atom is described by a Born-Mayer potential, and the scattering is assumed to be elastic and governed by the classical equations of motion. Because of symmetry, the problem can be reduced to plane motion of a particle in a potential of elliptic symmetry. The elliptic force field...... 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...

  5. Spontaneous emission spectrum of a four-level atom in a double-band photonic crystal

    Institute of Scientific and Technical Information of China (English)

    Wang Jian; Yang Dong; Zhang Han-Zhang

    2005-01-01

    The spontaneous emission spectrum from a four-level atom in a double-band photonic crystal has been investigated.We use the model which assumes three atomic transitions. One of the transitions interacts with the free vacuum modes,and the other two transitions couple to the modes of the isotropic photonic band gap (PBG), the anisotropic PBG and another free vacuum. The effects of the fine structure of the lower levels on the spontaneous emission spectrum of an atom are investigated in detail in the three cases. New features of four (two) transparencies with two (one) spontaneous emission peaks, resulting from the fine structure of the lower levels of an atom, are predicted in the case of isotropic PBG modes.

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

    Science.gov (United States)

    Yaqoob, Faisal; Huang, Mengbing

    2016-09-01

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

  7. Quantitative annular dark-field imaging of single-layer graphene-II: atomic-resolution image contrast.

    Science.gov (United States)

    Yamashita, Shunsuke; Koshiya, Shogo; Nagai, Takuro; Kikkawa, Jun; Ishizuka, Kazuo; Kimoto, Koji

    2015-12-01

    We have investigated how accurately atomic-resolution annular dark-field (ADF) images match between experiments and simulations to conduct more reliable crystal structure analyses. Quantitative ADF imaging, in which the ADF intensity at each pixel represents the fraction of the incident probe current, allows us to perform direct comparisons with simulations without the use of fitting parameters. Although the conventional comparison suffers from experimental uncertainties such as an amorphous surface layer and specimen thickness, in this study we eliminated such uncertainties by using a single-layer graphene as a specimen. Furthermore, to reduce image distortion and shot noises in experimental images, multiple acquisitions with drift correction were performed, and the atomic ADF contrast was quantitatively acquired. To reproduce the experimental ADF contrast, we used three distribution functions as the effective source distribution in simulations. The optimum distribution function and its full-width at half-maximum were evaluated by measuring the residuals between the experimental and simulated images. It was found that the experimental images could be explained well by a linear combination of a Gaussian function and a Lorentzian function with a longer tail than the Gaussian function.

  8. LiF crystals as high spatial resolution neutron imaging detectors

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-21

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

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

    CERN Document Server

    Merano, Michele

    2015-01-01

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

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

    CERN Document Server

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

    2010-01-01

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

  11. Depth of interaction resolution of LuAP and LYSO crystals

    CERN Document Server

    Trummer, J; Lecoq, P

    2009-01-01

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

  12. 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 t

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

    Science.gov (United States)

    Smither, Robert K.

    2011-05-17

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-11-15

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

  15. Electronic Properties of Graphene Encapsulated with Different Two-Dimensional Atomic Crystals

    OpenAIRE

    2014-01-01

    Hexagonal boron nitride is the only substrate that has so far allowed graphene devices exhibiting micron-scale ballistic transport. Can other atomically flat crystals be used as substrates for making quality graphene heterostructures? Here we report on our search for alternative substrates. The devices fabricated by encapsulating graphene with molybdenum or tungsten disulphides and hBN are found to exhibit consistently high carrier mobilities of about 60,000 cm$^{2}$V$^{-1}$s$^{-1}$. In contr...

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

    Science.gov (United States)

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

    2016-02-01

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

  17. Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6-a resolution.

    Science.gov (United States)

    Broser, Matthias; Gabdulkhakov, Azat; Kern, Jan; Guskov, Albert; Müh, Frank; Saenger, Wolfram; Zouni, Athina

    2010-08-20

    The membrane-embedded photosystem II core complex (PSIIcc) uses light energy to oxidize water in photosynthesis. Information about the spatial structure of PSIIcc obtained from x-ray crystallography was so far derived from homodimeric PSIIcc of thermophilic cyanobacteria. Here, we report the first crystallization and structural analysis of the monomeric form of PSIIcc with high oxygen evolution capacity, isolated from Thermosynechococcus elongatus. The crystals belong to the space group C222(1), contain one monomer per asymmetric unit, and diffract to a resolution of 3.6 A. The x-ray diffraction pattern of the PSIIcc-monomer crystals exhibit less anisotropy (dependence of resolution on crystal orientation) compared with crystals of dimeric PSIIcc, and the packing of the molecules within the unit cell is different. In the monomer, 19 protein subunits, 35 chlorophylls, two pheophytins, the non-heme iron, the primary plastoquinone Q(A), two heme groups, 11 beta-carotenes, 22 lipids, seven detergent molecules, and the Mn(4)Ca cluster of the water oxidizing complex could be assigned analogous to the dimer. Based on the new structural information, the roles of lipids and protein subunits in dimer formation of PSIIcc are discussed. Due to the lack of non-crystallographic symmetry and the orientation of the membrane normal of PSIIcc perpendicular ( approximately 87 degrees ) to the crystallographic b-axis, further information about the structure of the Mn(4)Ca cluster is expected to become available from orientation-dependent spectroscopy on this new crystal form.

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

    Institute of Scientific and Technical Information of China (English)

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

    2002-01-01

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

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

    CERN Document Server

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

    2012-01-01

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

  20. Improving the energy resolution of bent crystal X-ray spectrometers with position-sensitive detectors.

    Science.gov (United States)

    Honkanen, Ari Pekka; Verbeni, Roberto; Simonelli, Laura; Moretti Sala, Marco; Al-Zein, Ali; Krisch, Michael; Monaco, Giulio; Huotari, Simo

    2014-07-01

    Wavelength-dispersive high-resolution X-ray spectrometers often employ elastically bent crystals for the wavelength analysis. In a preceding paper [Honkanen et al. (2014). J. Synchrotron Rad. 21, 104-110] a theory for quantifying the internal stress of a macroscopically large spherically curved analyser crystal was presented. Here the theory is applied to compensate for the corresponding decrease of the energy resolution. The technique is demonstrated with a Johann-type spectrometer using a spherically bent Si(660) analyser in near-backscattering geometry, where an improvement in the energy resolution from 1.0 eV down to 0.5 eV at 9.7 keV incident photon energy was observed.

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

    Science.gov (United States)

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

    2016-01-01

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

  2. Probing three-dimensional surface force fields with atomic resolution: Measurement strategies, limitations, and artifact reduction

    Directory of Open Access Journals (Sweden)

    Mehmet Z. Baykara

    2012-09-01

    Full Text Available Noncontact atomic force microscopy (NC-AFM is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation.In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2017-03-01

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

  5. 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.

  6. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-03-15

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

  8. Zeeman Effect of Sm Atoms by High-Resolution Diode-Laser Spectroscopy

    Directory of Open Access Journals (Sweden)

    Wei-Guo Jin

    2013-01-01

    Full Text Available High-resolution atomic-beam diode-laser spectroscopy in Sm I has been performed. Zeeman spectra have been measured for the three optical transitions at different external magnetic fields and well resolved at the magnetic fields of stronger than 6.0 mT. Using the known precise Landé -factors of the ground multiplet, the Landé -factors of the upper 4f66s6p   and levels have been determined, and their precision has been improved compared with the reference values.

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

    CERN Document Server

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

    2014-01-01

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

  10. 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.

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    刘国强; 王健; 张汉壮

    2005-01-01

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

  13. Disordered crystal structure of pentamethylcyclopentadienylsodium as seen by high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Tedesco, C; Dinnebier, R E; Olbrich, F; van Smaalen, S

    2001-10-01

    The crystal structure of pentamethylcyclopentadienylsodium, [NaC10H15] (NaCp*), has been determined from high-resolution X-ray powder diffraction. The compound crystallizes in space group Cmcm with lattice parameters a = 4.61030 (3), b = 16.4621 (3), c = 14.6751 (2) A, V = 1113.77 (4) A(3) (Z = 4). NaCp* forms polymeric multidecker chains along the a axis. The Rietveld refinement (R(p) = 0.050 and R(F) = 0.163) shows that the Cp* moieties occupy, with disorder, two different orientations rotated away from the eclipsed conformation by +/-13.8 degrees.

  14. 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.

  15. Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR.

    Science.gov (United States)

    Shi, Chaowei; Fricke, Pascal; Lin, Lin; Chevelkov, Veniamin; Wegstroth, Melanie; Giller, Karin; Becker, Stefan; Thanbichler, Martin; Lange, Adam

    2015-12-01

    Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the species Caulobacter crescentus is not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR-derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-06-19

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

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

    Science.gov (United States)

    Campbellová, Anna; Ondráček, Martin; Pou, Pablo; Pérez, Rubén; Klapetek, Petr; Jelínek, Pavel

    2011-07-22

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

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

    Science.gov (United States)

    Smither, Robert K.

    2008-12-23

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-17

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

  20. 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

  1. High Resolution Triple Axis X-Ray Diffraction Analysis of II-VI Semiconductor Crystals

    Science.gov (United States)

    Volz, H. M.; Matyi, R. J.

    1999-01-01

    The objective of this research program is to develop methods of structural analysis based on high resolution triple axis X-ray diffractometry (HRTXD) and to carry out detailed studies of defect distributions in crystals grown in both microgravity and ground-based environments. HRTXD represents a modification of the widely used double axis X-ray rocking curve method for the characterization of grown-in defects in nearly perfect crystals. In a double axis rocking curve experiment, the sample is illuminated by a monochromatic X-ray beam and the diffracted intensity is recorded by a fixed, wide-open detector. The intensity diffracted by the sample is then monitored as the sample is rotated through the Bragg reflection condition. The breadth of the peak, which is often reported as the full angular width at half the maximum intensity (FWHM), is used as an indicator of the amount of defects in the sample. This work has shown that high resolution triple axis X-ray diffraction is an effective tool for characterizing the defect structure in semiconductor crystals, particularly at high defect densities. Additionally, the technique is complimentary to X-ray topography for defect characterization in crystals.

  2. 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...

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

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

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

    CERN Document Server

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

  7. Local determination of the amount of integration of an atom into a crystal surface

    Science.gov (United States)

    Volgmann, K.; Gawronski, H.; Zaum, Ch; Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.; Morgenstern, K.

    2014-10-01

    Collective vibrational modes of crystal lattices, called phonons, determine fundamental material properties, such as their thermal and electrical conductivities. Bulk phonon spectra are influenced by point defects. More recently, the importance of phonons on nanostructures has come into the focus of attention. Here we show a spatially resolved phonon spectra of point defects that reveal distinctly different signatures for a cavity alone and an impurity atom fully integrated into the surface as opposed to one placed into a cavity. The spectra are indicative for delocalized phonons and localized vibrations, respectively, as confirmed by theory.

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

    Science.gov (United States)

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

    1986-01-01

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

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

    Science.gov (United States)

    Gessmann, Renate; Brückner, Hans; Petratos, Kyriacos

    2016-02-01

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

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

    Indian Academy of Sciences (India)

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

    2012-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-12-04

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

  12. Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution.

    Science.gov (United States)

    von der Ecken, Julian; Heissler, Sarah M; Pathan-Chhatbar, Salma; Manstein, Dietmar J; Raunser, Stefan

    2016-06-30

    The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated during a complex mechanochemical reaction cycle. Crystal structures of myosin in different states have provided important structural insights into the myosin motor cycle when myosin is detached from F-actin. The difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of actomyosin complexes. Thus, although structural models exist of F-actin in complex with various myosins, a high-resolution structure of the F-actin–myosin complex is missing. Here, using electron cryomicroscopy, we present the structure of a human rigor actomyosin complex at an average resolution of 3.9 Å. The structure reveals details of the actomyosin interface, which is mainly stabilized by hydrophobic interactions. The negatively charged amino (N) terminus of actin interacts with a conserved basic motif in loop 2 of myosin, promoting cleft closure in myosin. Surprisingly, the overall structure of myosin is similar to rigor-like myosin structures in the absence of F-actin, indicating that F-actin binding induces only minimal conformational changes in myosin. A comparison with pre-powerstroke and intermediate (Pi-release) states of myosin allows us to discuss the general mechanism of myosin binding to F-actin. Our results serve as a strong foundation for the molecular understanding of cytoskeletal diseases, such as autosomal dominant hearing loss and diseases affecting skeletal and cardiac muscles, in particular nemaline myopathy and hypertrophic cardiomyopathy.

  13. '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.

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

    Science.gov (United States)

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

    2013-04-02

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-12-15

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

  16. Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

    Science.gov (United States)

    West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

    2017-02-09

    A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C2 molecule.

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

    Science.gov (United States)

    Beyer, Andreas; Belz, Jürgen; Knaub, Nikolai; Jandieri, Kakhaber; Volz, Kerstin

    2016-10-01

    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.

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

    CERN Document Server

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

    2014-01-01

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

  19. 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.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Science.gov (United States)

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

    2012-09-11

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

  2. Atoms

    Institute of Scientific and Technical Information of China (English)

    刘洪毓

    2007-01-01

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

  3. High-resolution microdiffraction study of notch-tip deformation in Mo single crystals using x-ray synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Ice, G.; Habenschuss, A. (Oak Ridge National Lab., TN (United States)); Bilello, J.C. (California State Univ., Fullerton, CA (United States)); Rebonato, R. (Oxford Univ. (United Kingdom). Physical Chemistry Lab.)

    1989-01-01

    A new technique is presented for the determination of strain fields in single crystals, based on the simultaneous recording of the energy and position of a diffracted beam, with a resolution of 25 micrometers under current experimental conditions. The technique can be profitably used for perfect to highly deformed crystals, in materials as highly absorbing as Molybdenum, and allows a spatial resolution of one part in 10{sup 4}. Indications are given as to possible refinements and improvements of the method.

  4. High-resolution microdiffraction study of notch-tip deformation in Mo single crystals using x-ray synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Ice, G.; Habenschuss, A. [Oak Ridge National Lab., TN (United States); Bilello, J.C. [California State Univ., Fullerton, CA (United States); Rebonato, R. [Oxford Univ. (United Kingdom). Physical Chemistry Lab.

    1989-12-31

    A new technique is presented for the determination of strain fields in single crystals, based on the simultaneous recording of the energy and position of a diffracted beam, with a resolution of 25 micrometers under current experimental conditions. The technique can be profitably used for perfect to highly deformed crystals, in materials as highly absorbing as Molybdenum, and allows a spatial resolution of one part in 10{sup 4}. Indications are given as to possible refinements and improvements of the method.

  5. Determination of a high spatial resolution geopotential model using atomic clock comparisons

    Science.gov (United States)

    Lion, G.; Panet, I.; Wolf, P.; Guerlin, C.; Bize, S.; Delva, P.

    2017-01-01

    Recent technological advances in optical atomic clocks are opening new perspectives for the direct determination of geopotential differences between any two points at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. We present a first step in that direction with the aim and hope of triggering further work and efforts in this emerging field of chronometric geodesy and geophysics. We specifically focus on evaluating the contribution of this new kind of direct measurements in determining the geopotential at high spatial resolution (≈ 10 km). We studied two test areas, both located in France and corresponding to a middle (Massif Central) and high (Alps) mountainous terrain. These regions are interesting because the gravitational field strength varies greatly from place to place at high spatial resolution due to the complex topography. Our method consists in first generating a synthetic high-resolution geopotential map, then drawing synthetic measurement data (gravimetry and clock data) from it, and finally reconstructing the geopotential map from that data using least squares collocation. The quality of the reconstructed map is then assessed by comparing it to the original one used to generate the data. We show that adding only a few clock data points (less than 1% of the gravimetry data) reduces the bias significantly and improves the standard deviation by a factor 3. The effect of the data coverage and data quality on the results is investigated, and the trade-off between the measurement noise level and the number of data points is discussed.

  6. Spontaneous emission from a microwave-driven four-level atom in an anisotropic photonic crystal

    Science.gov (United States)

    Jiang, Li; Wan, Ren-Gang; Yao, Zhi-Hai

    2016-10-01

    The spontaneous emission from a microwave-driven four-level atom embedded in an anisotropic photonic crystal is studied. Due to the modified density of state (DOS) in the anisotropic photonic band gap (PBG) and the coherent control induced by the coupling fields, spontaneous emission can be significantly enhanced when the position of the spontaneous emission peak gets close to the band gap edge. As a result of the closed-loop interaction between the fields and the atom, the spontaneous emission depends on the dynamically induced Autler-Townes splitting and its position relative to the PBG. Interesting phenomena, such as spectral-line suppression, enhancement and narrowing, and fluorescence quenching, appear in the spontaneous emission spectra, which are modulated by amplitudes and phases of the coherently driven fields and the effect of PBG. This theoretical study can provide us with more efficient methods to manipulate the atomic spontaneous emission. Project supported by the National Natural Science Foundation of China (Grant Nos. 11447232, 11204367, 11447157, and 11305020).

  7. Atomic resolution imaging of YAlO3: Ce in the chromatic and spherical aberration corrected PICO electron microscope.

    Science.gov (United States)

    Jin, Lei; Barthel, Juri; Jia, Chun-Lin; Urban, Knut W

    2017-01-31

    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 200kV. 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.

  8. Fluctuations of tensile strength and hardness of c-BC₂N crystals induced by difference in atomic configuration.

    Science.gov (United States)

    Zhuang, Chunqiang; Li, Xiaoqing; Zhao, Jijun; Samra, H Abu; Jiang, Xin

    2011-11-23

    At the atomistic level, the physical properties of a material are determined by its structure such as atomic arrangements. Here first-principles calculations were performed to investigate the effect of atomic configuration on the tensile strength and Vickers hardness of cubic-BC₂N (c-BC₂N) crystals. Depending on the degree of mixture between diamond and c-BN, the tensile strength of c-BC2N crystals can vary drastically from 27 to 77 GPa. The magnitude of the Vickers hardness fluctuations (~10 GPa) is also comparable to the experimental difference (~14 GPa). Thus, atomic-scale characterization of c-BC₂N crystal structures may unveil the discrepancy of the measured Vickers hardness in experiments, and uncover the obvious differences of tensile strength described in theoretical calculations.

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

    Directory of Open Access Journals (Sweden)

    H Ichinose

    2000-01-01

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

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

    NARCIS (Netherlands)

    Nunez, E.; Vancso, G.J.; Gedde, U.W.

    2008-01-01

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

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

    Science.gov (United States)

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

    2011-11-01

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

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

    Institute of Scientific and Technical Information of China (English)

    LIUYing-Tai; ZHANGQi-Ren; 等

    2002-01-01

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

  13. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-11-01

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

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

    Science.gov (United States)

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

    2016-11-20

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

  16. Atomic resolution transmission electron microscopy of the intergranular structure of a Y{sub 2}O{sub 3}-silicon nitride ceramic

    Energy Technology Data Exchange (ETDEWEB)

    Ziegler, A.; Kisielowski, C.; Hoffmann, M.J.; Ritchie, R.O.

    2002-05-01

    High-resolution transmission electron microscopy (HRTEM) employing focus-variation phase-reconstruction methods is used to image the atomic structure of grain boundaries in a silicon nitride ceramic at a resolution of 0.8 Angstrom

  17. Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations

    DEFF Research Database (Denmark)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano;

    2015-01-01

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulation...

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

    OpenAIRE

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

    2014-01-01

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

  19. Sidewall roughness measurement inside photonic crystal holes by atomic force microscopy

    Science.gov (United States)

    Strasser, P.; Robin, F.; Carlström, C. F.; Wüest, R.; Kappeler, R.; Jäckel, H.

    2007-10-01

    We present a measurement technique to quantify sidewall roughness inside planar photonic crystal (PhC) holes. Atomic force microscopy is used to scan hole cross-section profiles. By fitting a circle onto each scan line and subtracting this circle from the measurement data, a quantitative value for the deviation from the ideal cylindrical hole shape is extracted. We investigate the sidewall roughness of InP-based PhC holes depending on the nitrogen content of the semiconductor etching plasma. The existence of a trade-off between hole undercut and surface roughness by optimizing the flux of nitrogen during the plasma etching of the PhC holes is confirmed. We further quantify with this technique the influence of the direct-writing of octagons instead of circles by electron-beam lithography on the measured roughness.

  20. Topography and Atomic Structure Investigations Of (100 Cleavage Surface of In4Se3 Layered Crystals

    Directory of Open Access Journals (Sweden)

    P.V. Galiy

    2014-06-01

    Full Text Available The atomic microstructure and crystallography of (100 surfaces of In4Se3 layered crystals obtained by cleavage in situ were studied by the methods of scanning tunneling and atomic force microscopies (STM, AFM and low energy electron diffraction (LEED for reflection. The obtained results indicate the existence of periodic corrugated structures on the cleavage surface. It is shown that (100 In4Se3 cleavage surface is structurally stable and doesn't undergo reconstruction in a wide temperature range of 77-295 K. The anisotropy of thermal expansion along the main crystallography directions in the (100 In4Se3 cleavage plane has been shown. The evaluation of the two-dimensional lattice constant in the cleavage (100 surface plane of orthorhombic In4Se3 layered crystal was done. The calculated values of the lattice constants in consequence of LEED study, such as b  11,475 Å and c  3,734 Å, coincide well with those obtained by the AFM and STM (b  13-14 Å and c  4 Å, and correlate, within the errors limits, with the corresponding values obtained by X-ray diffraction (b  12,308(1 Å and c  4,0810(5 Å. Besides, the obtained results of cleavage surface structure studies show the correctness of filtering application concerning topography images and indicate the adequacy of the model used for calculations of the cleavage (100 surfaces lattice constants of In4Se3 in accordance with the LEED results. The influence of the LEED experimental module structure on the results has been considered.

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

    Energy Technology Data Exchange (ETDEWEB)

    De Gerone, M., E-mail: matteo.degerone@ge.infn.it [Istituto Nazionale di Fisica Nucleare, Genova (Italy); Biasotti, M.; Ceriale, V.; Corsini, D.; Gatti, F. [Istituto Nazionale di Fisica Nucleare, Genova (Italy); Dipartimento di Fisica, Università degli Studi di Genova, Genova (Italy); Orlando, A. [Istituto Nazionale di Fisica Nucleare, Genova (Italy); Pizzigoni, G. [Istituto Nazionale di Fisica Nucleare, Genova (Italy); Dipartimento di Fisica, Università degli Studi di Genova, Genova (Italy)

    2016-07-11

    In the last years organic scintillators have been largely investigated in order to achieve high light yield together with good time response. Pure organic compound with high quality crystalline structure can achieve both this goals. Among a large type of organic compound, para-terphenyl (C{sub 18}H{sub 14}) have proven to have practical applications as detector medium for particle physics. In this work, the characterization of different sizes high quality mono-crystal p-terphenyl samples is presented. The optical and scintillation properties (emission spectrum, light yield, attenuation length, and decay time) are investigated. Coupling a Silicon PhotoMultiplier-based readout system to the crystal, a small prototype for a high resolution TOF detector was built; the preliminary results, obtained on a 20×30×3 mm{sup 3} sample, with dual-side read-out (Hamamatsu S10931-050P SiPMs) and irradiated with {sup 90}Sr source, show a time resolution of 35 ps.

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

    Science.gov (United States)

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

    2005-01-01

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

  3. Atomic resolution model of the antibody Fc interaction with the complement C1q component.

    Science.gov (United States)

    Schneider, Sebastian; Zacharias, Martin

    2012-05-01

    The globular C1q heterotrimer is a subunit of the C1 complement factor. Binding of the C1q subunit to the constant (Fc) part of antibody molecules is a first step and key event of complement activation. Although three-dimensional structures of C1q and antibody Fc subunits have been determined experimentally no atomic resolution structure of the C1q-Fc complex is known so far. Based on systematic protein-protein docking searches and Molecular Dynamics simulations a structural model of the C1q-IgG1-Fc-binding geometry has been obtained. The structural model is compatible with available experimental data on the interaction between the two partner proteins. It predicts a binding geometry that involves mainly the B-subunit of the C1q-trimer and both subunits of the IgG1-Fc-dimer with small conformational adjustments with respect to the unbound partners to achieve high surface complementarity. In addition to several charge-charge and polar contacts in the rim region of the interface it also involves nonpolar contacts between the two proteins and is compatible with the carbohydrate moiety of the Fc subunit. The model for the complex structure provides a working model for rationalizing available biochemical data on this important interaction and can form the basis for the design of Fc variants with a greater capacity to activate the complement system for example on binding to cancer cells or other target structures.

  4. Enhanced light element imaging in atomic resolution scanning transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Findlay, S.D., E-mail: scott.findlay@monash.edu [School of Physics, Monash University, Victoria 3800 (Australia); Kohno, Y. [JEOL Ltd., Tokyo 196-8558 (Japan); Cardamone, L.A. [School of Physics, Monash University, Victoria 3800 (Australia); Ikuhara, Y. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Nanostructures Research Laboratory, Japan Fine Ceramics Center, Nagoya 456-8587 (Japan); WPI Advanced Institute for Materials Research, Tohoku University, Sendai 980-8577 (Japan); Shibata, N. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); PRESTO, Japan Science and Technology Agency, Saitama 332-0012 (Japan)

    2014-01-15

    We show that an imaging mode based on taking the difference between signals recorded from the bright field (forward scattering region) in atomic resolution scanning transmission electron microscopy provides an enhancement of the detectability of light elements over existing techniques. In some instances this is an enhancement of the visibility of the light element columns relative to heavy element columns. In all cases explored it is an enhancement in the signal-to-noise ratio of the image at the light column site. The image formation mechanisms are explained and the technique is compared with earlier approaches. Experimental data, supported by simulation, are presented for imaging the oxygen columns in LaAlO{sub 3}. Case studies looking at imaging hydrogen columns in YH{sub 2} and lithium columns in Al{sub 3}Li are also explored through simulation, particularly with respect to the dependence on defocus, probe-forming aperture angle and detector collection aperture angles. - Author-Highlights: • We present a method for enhancing the visibility and reliability of imaging light elements in STEM. • The method involves taking the difference between signals on separate bright field detectors. • Experimental data for LaAlO{sub 3} are presented, and are shown to compare favourably with simulation. • Optimum imaging parameters are explored through simulation.

  5. 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.

  6. Coherence and statistics of a one-atom laser in a photonic crystal microcavity

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Xiaoyong; Ren, Zhongzhou [Department of Physics, Nanjing University, Nanjing 210008 (China); Lue, Shuchen, E-mail: lushuchen63@yahoo.com.c [Province Key Laboratory of Nanosize Functional Materials, School of Physics and Electronic Engineering, Harbin Normal University, Harbin 150080 (China)

    2010-11-28

    Through calculating the quantum degree of second-order coherence and photon number distribution numerically, we investigate the coherence and statistics of a one-atom laser where a coherently driven two-level atom is coupled to a photonic crystal microcavity. By going beyond the previous theoretical studies, we show that in the presence of non-secular terms the cavity field displays a variable degree of second-order coherence as a function of discontinuities in the photonic density of states. The cavity field is characterized by photon antibunching and sub-Poissonian statistics for large discontinuities. In the case of a vanishing photonic density of states on the lower Mollow sideband, we can obtain only weak antibunching. If the jump in the photonic density of states is small, the bunching and super-Poissonian statistics field is generated in the cavity. Consequently, the cavity field exhibits certain non-classical features when non-secular interaction is included into the dynamics of the system. The theoretical analysis and numerical calculations presented here coincide with recent experimental observations.

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

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

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  10. 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.

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

    Science.gov (United States)

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

    2016-12-01

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

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

    Science.gov (United States)

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

    2013-09-01

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

  13. Van der Waals interaction between microparticle and uniaxial crystal with application to hydrogen atoms and multiwall carbon nanotubes

    CERN Document Server

    Blagov, E V; Mostepanenko, V M

    2005-01-01

    The Lifshitz theory of the van der Waals force is extended for the case of an atom (molecule) interacting with a plane surface of an uniaxial crystal or with a long solid cylinder or cylindrical shell made of isotropic material or uniaxial crystal. For a microparticle near a semispace or flat plate made of an uniaxial crystal the exact expressions for the free energy of the van der Waals and Casimir-Polder interaction are presented. An approximate expression for the free energy of microparticle- cylinder interaction is obtained which becomes precise for microparticle-cylinder separations much smaller than cylinder radius. The obtained expressions are used to investigate the van der Waals interaction between hydrogen atoms (molecules) and graphite plates or multiwall carbon nanotubes. To accomplish this the behavior of graphite dielectric permittivities along the imaginary frequency axis is found using the optical data for the complex refractive index of graphite for the ordinary and extraordinary rays. It is ...

  14. Second-harmonic generation in quaternary atomically thin layered AgInP2S6 crystals

    Science.gov (United States)

    Wang, Xingzhi; Du, Kezhao; Liu, Weiwei; Hu, Peng; Lu, Xin; Xu, Weigao; Kloc, Christian; Xiong, Qihua

    2016-09-01

    Nonlinear effects in two-dimensional (2D) atomic layered materials have attracted increasing interest. Here, we report the observation of optical second-harmonic generation (SHG) in two-dimensional atomically thin silver indium phosphorus sulfide (AgInP2S6) crystals, with odd layer thickness. The nonlinear signal facilitates the use of thickness-dependent SHG intensity to investigate the stacking type of this material, while the crystal-orientation dependent SHG intensity of the monolayer sample reveals the rotational symmetry of the AgInP2S6 lattice in plane. Our studies expand the 2D crystal family in nonlinear effect field, which opened considerable promise to the functionalities and potential applications of 2D materials.

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

    Science.gov (United States)

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

    2013-11-14

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

  16. 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.

  17. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models.

    Science.gov (United States)

    Liao, Chenyi; Zhao, Xiaochuan; Liu, Jiyuan; Schneebeli, Severin T; Shelley, John C; Li, Jianing

    2017-03-20

    The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.

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

    Science.gov (United States)

    Passos, Dario Oliveira; Lyumkis, Dmitry

    2015-11-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    Science.gov (United States)

    Malinska, Maura; Dauter, Zbigniew

    2016-06-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

  2. 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

    2016-10-21

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

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

    Science.gov (United States)

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

    2015-08-01

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

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

    OpenAIRE

    2015-01-01

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

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

    Science.gov (United States)

    DiMaio, F; Chiu, W

    2016-01-01

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

  6. A Time-Dependent Approach to High-Resolution Photoabsorption Spectrum of Rydberg Atoms in Magnetic Fields

    Institute of Scientific and Technical Information of China (English)

    BIAN Xue-Bin; LIU Hong-Ping; SHI Ting-Yun

    2008-01-01

    A robust time-dependent approach to the high-resolution photoabsorption spectrum of Rydberg atoms in magnetic fields is presented. Traditionally we have to numerically diagonalize a huge matrix to solve the eigen-problem and then to obtain the spectral information. This matrix operation requires high-speed computers with large memories. Alternatively we present a unitary but very easily parallelized time-evolution method in an inexpensive way, which is very accurate and stable even in long-time scale evolution. With this method, we perform the spectral calculation of hydrogen atom in magnetic field, which agrees well with the experimental observation. It can be extended to study the dynamics of Rydberg atoms in more complicated cases such as in combined electric and magnetic fields.

  7. Mesopore generation by organosilane surfactant during LTA zeolite crystallization, investigated by high-resolution SEM and Monte Carlo simulation

    Science.gov (United States)

    Cho, Kanghee; Ryoo, Ryong; Asahina, Shunsuke; Xiao, Changhong; Klingstedt, Miia; Umemura, Ayako; Anderson, Michael W.; Terasaki, Osamu

    2011-04-01

    The crystallization of LTA zeolite under a hydrothermal synthesis condition that contained a quaternary ammonium-type organosilane surfactant was studied with X-ray powder diffraction (XRD), high-resolution scanning electron microscopy (HRSEM) and Monte Carlo simulation of the crystal growth. The hydrothermal reaction products were collected at various crystallization times, and investigated with XRD and HRSEM. The HRSEM images of the final zeolite products were taken as synthesized and also after cross-sectioning with an argon ion beam. The HRSEM investigation revealed presence of a disordered network of mesoporous channels that penetrated the microporous zeolite crystal. Unless the loading of the surfactant was exceedingly high, the microporous zeolite particles exhibited truncated cubic morphologies that were almost like single crystals, despite penetration by the mesopores. The outline of the zeolite particle became progressively rounded as the mesoporosity was increased according to the surfactant loading. The mesoporosity in the zeolite crystals was well maintained against crystal-ripening processes for 6 d. This result supports the fact that the organosilane surfactant micelles became incorporated inside the zeolite crystal as a mesopore generator during the crystallization process. Data from Monte Carlo simulation agreed with these experimental results.

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

    Science.gov (United States)

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

    2016-10-01

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

  9. Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy

    Science.gov (United States)

    Yehl, Jenna; Kudryashova, Elena; Reisler, Emil; Kudryashov, Dmitri; Polenova, Tatyana

    2017-01-01

    Cellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin’s involvement in these processes is mediated by many actin-binding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin. PMID:28303963

  10. Molecular Resolution of Zeolite Surfaces as Imaged by Atomic Force Microscopy

    Science.gov (United States)

    1992-05-15

    absorption of molecules may for our AFM study. The techniques required to use phenmenaAFM for synthetic crystals that are currently available... clinoptilolite ) single crystal by imaging with an AFM under water, salt solutions, and alcohols. 7 Previously, - AFMs have been used to nondestructively

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-05-20

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

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

    Science.gov (United States)

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

    2012-03-01

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

  13. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    Science.gov (United States)

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  14. A High-resolution Vacuum Ultraviolet Laser Photoionization and Photoelectron Study of the Co Atom

    Science.gov (United States)

    Huang, Huang; Wang, Hailing; Luo, Zhihong; Shi, Xiaoyu; Chang, Yih-Chung; Ng, C. Y.

    2016-12-01

    We have measured the vacuum ultraviolet-photoionization efficiency (VUV-PIE) spectrum of Co in the energy range of 63,500-67,000 cm-1, which covers the photoionization transitions of Co(3d74s2 4F9/2) \\to Co+(3d8 3F4), Co(3d74s2 4F7/2) \\to Co+(3d8 3F3), Co(3d74s2 4F9/2) \\to Co+(3d8 3F3), Co(3d74s2 4F9/2) \\to Co+(3d8 3F2), and Co(3d74s2 4F9/2) \\to Co+(3d74s1 5F5). We have also recorded the pulsed field ionization photoelectron spectrum of Co in the same energy range, allowing accurate determinations of ionization energies (IEs) for the photoionization transitions from the Co(3d74s2 4F9/2) ground neutral state to the Co+(3F J ) (J = 4 and 3) and Co+(5F5) ionic states, as well as from the Co(3d74s2 4F7/2) excited neural state to the Co+(3d8 3F3) ionic state. The high-resolution nature of the VUV laser used has allowed the observation of many well-resolved autoionizing resonances in the VUV-PIE spectrum, among which an autoionizing Rydberg series, 3d74s1(5F5)np (n = 19-38), converging to the Co+(3d74s1 5F5) ionic state from the Co(3d74s2 4F9/2) ground neutral state is identified. The fact that no discernible step-like structures are present at these ionization thresholds in the VUV-PIE spectrum indicates that direct photoionization of Co is minor compared to autoionization in this energy range. The IE values, the autoionizing Rydberg series, and the photoionization cross sections obtained in this experiment are valuable for understanding the VUV opacity and abundance measurement of the Co atom in stars and solar atmospheres, as well as for benchmarking the theoretical results calculated in the Opacity Project and the IRON Project, and thus are of relevance to astrophysics.

  15. Spontaneous resolution upon crystallization of chiral La(III) and Gd(III) MOFs from achiral dihydroxymalonate.

    Science.gov (United States)

    Gil-Hernández, Beatriz; Höppe, Henning A; Vieth, Jana K; Sanchiz, Joaquin; Janiak, Christoph

    2010-11-21

    The achiral chelating and bridging dihydroxymalonato (mesoxalato) ligand is a new enantiopurity enforcer in extended structures by yielding the Λ/Δ-metal configured homochiral MOFs 2D-[Ln(2)(μ-mesoxalato)(3)(H(2)O)(6)] (Ln = La(III), Gd(III)) through self-resolution during crystal growth.

  16. Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy

    Science.gov (United States)

    Malkin, A. J.; Kuznetsov, Yu. G.; McPherson, A.

    2001-11-01

    In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV), cucumber mosaic virus (CMV) and glucose isomerase. Growth of these crystals proceeded by two-dimensional (2D) nucleation. For glucose isomerase, from supersaturation dependencies of tangential step rates and critical step length, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated for different crystallographic directions. The molecular structure of the step edges, the adsorption of individual virus particles and their aggregates, and the initial stages of formation of 2D nuclei on the surfaces of TYMV and CMV crystals were recorded. The surfaces of individual TYMV virions within crystals were visualized, and hexameric and pentameric capsomers of the T=3 capsids were clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the TYMV crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions.

  17. Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite.

    Science.gov (United States)

    Chin, Yiing; Panduwinata, Dwi; Sintic, Maxine; Sum, Tze Jing; Hush, Noel S; Crossley, Maxwell J; Reimers, Jeffrey R

    2011-01-20

    The atomic structure of the chains of an alkyl porphyrin (5,10,15,20-tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for porphyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible. A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and, of the many possible atomic structures modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.

  18. Atomic-resolution chemical mapping of ordered precipitates in Al alloys using energy-dispersive X-ray spectroscopy.

    Science.gov (United States)

    Wenner, Sigurd; Jones, Lewys; Marioara, Calin D; Holmestad, Randi

    2017-05-01

    Scanning transmission electron microscopy (STEM) coupled with energy-dispersive X-ray spectroscopy (EDS) is a common technique for chemical mapping in thin samples. Obtaining high-resolution elemental maps in the STEM is jointly dependent on stepping the sharply focused electron probe in a precise raster, on collecting a significant number of characteristic X-rays over time, and on avoiding damage to the sample. In this work, 80kV aberration-corrected STEM-EDS mapping was performed on ordered precipitates in aluminium alloys. Probe and sample instability problems are handled by acquiring series of annular dark-field (ADF) images and simultaneous EDS volumes, which are aligned and non-rigidly registered after acquisition. The summed EDS volumes yield elemental maps of Al, Mg, Si, and Cu, with sufficient resolution and signal-to-noise ratio to determine the elemental species of each atomic column in a periodic structure, and in some cases the species of single atomic columns. Within the uncertainty of the technique, S and β" phases were found to have pure elemental atomic columns with compositions Al2CuMg and Al2Mg5Si4, respectively. The Q' phase showed some variation in chemistry across a single precipitate, although the majority of unit cells had a composition Al6Mg6Si7.2Cu2.

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

    Science.gov (United States)

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2016-01-26

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

  1. 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.

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

    Science.gov (United States)

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

    2008-10-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2015-08-01

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

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

    Science.gov (United States)

    Waugh, Barnali; Sen, Udayaditya; Banerjee, Rahul

    2016-02-01

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

  6. 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.

  7. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

    Science.gov (United States)

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

    2012-03-07

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-03-14

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

  9. A low noise all-fiber interferometer for high resolution frequency modulated atomic force microscopy imaging in liquids.

    Science.gov (United States)

    Rasool, Haider I; Wilkinson, Paul R; Stieg, Adam Z; Gimzewski, James K

    2010-02-01

    We have developed a low noise all-fiber interferometer for use as the deflection sensor in liquid environment frequency modulated atomic force microscopy (FM-AFM). A detailed description and rationale for the choice of the critical components are provided along with the design of a simple alignment assembly. The optimization of the deflection sensor toward achieving the highest possible sensitivity and lowest deflection noise density is discussed in the context of an ideal interference cavity. Based on the provided analysis we have achieved deflection noise densities of 2 fm/square root(Hz) on commercially available cantilevers in both ambient and liquid environments. The low noise interferometer works without the need for differential detection, special focusing lenses, or polarization sensitive optics, dramatically simplifying measurements. True atomic resolution imaging of muscovite mica by FM-AFM in water is demonstrated using the developed deflection sensor.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-02-02

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

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

    Science.gov (United States)

    Friedman, E.; Okada, S.

    2013-10-01

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

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

    OpenAIRE

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

  14. 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\\.

  15. Protein Crystallization

    Science.gov (United States)

    Chernov, Alexander A.

    2005-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Longxia Li

    2008-03-19

    The spectroscopic performance of current large-volume Cadmium 10% Zinc Telluride, Cd{sub 0.9}Zn{sub 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 < 1 {micro}m) CZT n+-type with resistivity > 10{sup 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Ohno, Yutaka, E-mail: yutakaohno@imr.tohoku.ac.jp; Inoue, Kaihei; Fujiwara, Kozo; Deura, Momoko; Kutsukake, Kentaro; Yonenaga, Ichiro [Institute for Materials Research (IMR), Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577 (Japan); Shimizu, Yasuo; Inoue, Koji; Ebisawa, Naoki; Nagai, Yasuyoshi [The Oarai Center, IMR, Tohoku University, Oarai, Ibaraki 311-1313 (Japan)

    2015-06-22

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-29

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

  20. Determination of a high spatial resolution geopotential model using atomic clock comparisons

    OpenAIRE

    Lion, Guillaume; Panet, Isabelle; Wolf, Peter; Guerlin, Christine; Bize, Sébastien; Delva, Pacôme

    2016-01-01

    Recent technological advances in optical atomic clocks are opening new perspectives for the direct determination of geopotential differences between any two points at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. We present a first step in that direction with the aim and hope of triggering further work and efforts in this emerging ...

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

    Science.gov (United States)

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

    2017-03-21

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

  2. 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

  3. Signatures of distinct impurity configurations in atomic-resolution valence electron-energy-loss spectroscopy: Application to graphene

    Science.gov (United States)

    Kapetanakis, Myron D.; Oxley, Mark P.; Zhou, Wu; Pennycook, Stephen J.; Idrobo, Juan-Carlos; Pantelides, Sokrates T.

    2016-10-01

    The detection and identification of impurities and other point defects in materials is a challenging task. Signatures for point defects are typically obtained using spectroscopies without spatial resolution. Here we demonstrate the power of valence electron-energy-loss spectroscopy (VEELS) in an aberration-corrected scanning transmission-electron microscope (STEM) to provide energy-resolved and atomically resolved maps of electronic excitations of individual impurities which, combined with theoretical simulations, yield unique signatures of distinct bonding configurations of impurities. We report VEELS maps for isolated Si impurities in graphene, which are known to exist in two distinct configurations. We also report simulations of the maps, based on density functional theory and dynamical scattering theory, which agree with and provide direct interpretation of observed features. We show that theoretical VEELS maps exhibit distinct and unambiguous signatures for the threefold- and fourfold-coordinated configurations of Si impurities in different energy-loss windows, corresponding to impurity-induced bound states, resonances, and antiresonances. With the advent of new monochromators and detectors with high energy resolution and low signal-to-noise ratio, the present work ushers an atomically resolved STEM-based spectroscopy of individual impurities as an alternative to conventional spectroscopies for probing impurities and defects.

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

    Directory of Open Access Journals (Sweden)

    Xiaojun Xu

    2015-01-01

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

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

    NARCIS (Netherlands)

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

    2001-01-01

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

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

    NARCIS (Netherlands)

    Radenovic, N.

    2005-01-01

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

  7. Atomic layer deposition of TiO2 photonic crystal waveguide biosensors

    NARCIS (Netherlands)

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

    2009-01-01

    A photonic crystal waveguide biosensor in the visible is presented for biosensing. The sensor is applied to Refractive Index (RI) measurements. The sensitivity at different wavelength is presented for both air holes and air core configurations of photonic crystal waveguide (PCW) made of TiO2. It is

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

    Science.gov (United States)

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

    2015-11-15

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

  9. Old relief printing applied to the current preparation of multi-color and high resolution colloidal photonic crystal patterns.

    Science.gov (United States)

    Yang, Dongpeng; Ye, Siyun; Ge, Jianping

    2015-12-11

    Monodisperse SiO2 colloids are assembled into colloidal crystals in the mixture of monomer and solvent, which is transformed into a mechanochromic photonic crystal paper by polymerization. Following the relief printing strategy, the printing plates are pressed onto the paper to generate letters or images due to the contrast of structural color between the deformed and the undeformed paper, and the images can be permanently retained through UV curing. The wide tunable range of structural color for the current paper under deformation helps to realize multi-color printing. The localized deformation among or even inside the colloidal microcrystals renders the paper with a precise mechanochromic response to the printing plates and leads to the production of high resolution photonic crystal patterns.

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

    Science.gov (United States)

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

    2016-12-01

    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.

  11. High resolution transmission electron microscope Imaging and first-principles simulations of atomic-scale features in graphene membrane

    Science.gov (United States)

    Wang, Wei; Bhandari, Sagar; Yi, Wei; Bell, David; Westervelt, Robert; Kaxiras, Efthimios

    2012-02-01

    Ultra-thin membranes such as graphene[1] are of great importance for basic science and technology applications. Graphene sets the ultimate limit of thinness, demonstrating that a free-standing single atomic layer not only exists but can be extremely stable and strong [2--4]. However, both theory [5, 6] and experiments [3, 7] suggest that the existence of graphene relies on intrinsic ripples that suppress the long-wavelength thermal fluctuations which otherwise spontaneously destroy long range order in a two dimensional system. Here we show direct imaging of the atomic features in graphene including the ripples resolved using monochromatic aberration-corrected transmission electron microscopy (TEM). We compare the images observed in TEM with simulated images based on an accurate first-principles total potential. We show that these atomic scale features can be mapped through accurate first-principles simulations into high resolution TEM contrast. [1] Geim, A. K. & Novoselov, K. S. Nat. Mater. 6, 183-191, (2007). [2] Novoselov, K. S.et al. Science 306, 666-669, (2004). [3] Meyer, J. C. et al. Nature 446, 60-63, (2007). [4] Lee, C., Wei, X. D., Kysar, J. W. & Hone, J. Science 321, 385-388, (2008). [5] Nelson, D. R. & Peliti, L. J Phys-Paris 48, 1085-1092, (1987). [6] Fasolino, A., Los, J. H. & Katsnelson, M. I. Nat. Mater. 6, 858-861, (2007). [7] Meyer, J. C. et al. Solid State Commun. 143, 101-109, (2007).

  12. Real-time, high-resolution x-ray diffraction measurements on shocked crystals at a synchrotron facility.

    Science.gov (United States)

    Gupta, Y M; Turneaure, Stefan J; Perkins, K; Zimmerman, K; Arganbright, N; Shen, G; Chow, P

    2012-12-01

    The Advanced Photon Source (APS) at Argonne National Laboratory was used to obtain real-time, high-resolution x-ray diffraction measurements to determine the microscopic response of shock-compressed single crystals. Disk shaped samples were subjected to plane shock wave compression by impacting them with half-inch diameter, flat-faced projectiles. The projectiles were accelerated to velocities ranging between 300 and 1200 m/s using a compact powder gun designed specifically for use at a synchrotron facility. The experiments were designed to keep the sample probed volume under uniaxial strain and constant stress for a duration longer than the 153.4 ns spacing between x-ray bunches. X-rays from a single pulse (crystals at the APS are presented. Analytic developments to determine the effects of crystal substructure and non-ideal geometry on the diffraction pattern position and shape are presented. Representative real-time x-ray diffraction data, indicating shock-induced microstructural changes, are presented for a shock-compressed Al(111) sample. The experimental developments presented here provided, in part, the impetus for the Dynamic Compression Sector (DCS) currently under development at the APS. Both the synchronization∕x-ray detection methods and the analysis equations for high-resolution single crystal x-ray diffraction can be used at the DCS.

  13. Structural characterization of three crystalline modifications of telmisartan by single crystal and high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Dinnebier, R E; Sieger, P; Nar, H; Shankland, K; David, W I

    2000-11-01

    Three crystalline modifications (A, B, and C) of 4'-[[2-n-propyl-4-methyl-6-(1-methyl-benzimidazol-2-yl)benzi midazol-1-yl]methyl]biphenyl-2-carboxylic acid (INN name, telmisartan) have been detected and their crystal structures have been determined by single-crystal X-ray diffraction (pseudopolymorph C) and the method of simulated annealing from high-resolution X-ray powder diffraction data (polymorphs A and B). The compound is of interest because of its use as an angiotensin II receptor antagonist. Polymorph A crystallizes in space group P2(I)/c, Z = 4, with unit cell parameters a = 18.7798(3), b = 18.1043(2), and c = 8.00578(7) A, beta = 97.066(1) degrees, and V = 2701.31 A(3). Polymorph B crystallizes in space group P2(I)/a, Z = 4, with unit cell parameters a = 16.0646(5), b = 13.0909(3), and c = 13.3231(3) A, beta = 99.402(1) degrees, and V = 2764.2(1) A(3). The solvated form C crystallizes in space group C2/c, Z = 8, with unit cell parameters a = 30.990(5), b = 13.130(3), and c = 16.381(3) A, beta = 95.02(2) degrees, and V = 6639(2) A(3). For the structure solutions of polymorphs A and B, 13 degrees of freedom (3 translational, 3 orientational, 7 torsion angles) were determined in approximately 2 h of computer time, demonstrating that the crystal packing and the molecular conformation of medium-sized (MW approximately 500) pharmaceutical compounds can now be solved quickly and routinely from high-resolution X-ray powder diffraction data.

  14. Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus.

    Science.gov (United States)

    Du, Wen-Ge Han; Noodleman, Louis

    2013-12-16

    Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.

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

    Science.gov (United States)

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

    2016-07-01

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

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

    CERN Document Server

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

  18. Exotic atoms and their electron shell

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-04-01

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

  19. Exotic atoms and their electron shell

    Science.gov (United States)

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

    1994-04-01

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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Science.gov (United States)

    Huang, Jen-Ching; Weng, Yung-Jin

    2014-01-01

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

  2. Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

    Science.gov (United States)

    Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

    2015-11-19

    The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).

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

    OpenAIRE

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

    2007-01-01

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

  4. First-principles study on molecular dissociation under metallization pressure in aromatic monomolecular crystals with iodine atoms

    CERN Document Server

    Tateyama, Y

    2002-01-01

    We have examined the metallization mechanism and possibility of molecular dissociation in iodanil (IA) and hexa-iodobenzene (HIB) under pressure by using first-principles calculations. We found that the metallization in IA is caused by the band overlap in the molecular phase and dissociation does not follow the metallization. In HIB, on the other hand, the band overlap mechanism is found to be less probable, which implies that a structural transformation will occur before the metallization. Both mechanisms are completely different from that for I sub 2 diatomic molecular crystal, and suggest essential roles of C sub 6 rings and O atoms.

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

    Energy Technology Data Exchange (ETDEWEB)

    Monreal, Benjamin

    2014-10-15

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

  6. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-04-12

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

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

    Directory of Open Access Journals (Sweden)

    A. Castellanos-Gómez

    2012-03-01

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

  9. Quantifying Surface Characteristics of Ice Crystals using High-Resolution Imagery and Wavelet-based Image Processing Techniques

    Science.gov (United States)

    Brown, T.

    2015-12-01

    The surface characteristics of ice crystals have a considerable impact on the bulk scattering properties of ice clouds. Here, 2.3 μm-resolution silhouettes of crystals imaged by a Cloud Particle Imager (CPI) obtained from the Tropical Warm Pool - International Cloud and Mixed Phase Arctic Cloud Experiments are combined with wavelet analysis to characterize crystal surfaces. Wavelet analysis is a multiresolution tool that is applied to reveal underlying textural details of crystal images on several spatial scales. Images are defined as matrices in which each pixel corresponds to a gray level intensity value. Wavelet functions are used to decompose crystal images into a set of approximation and detail components by applying high and low-pass filters to the rows and columns of the image matrix. Following each level of decomposition, gray level intensity histograms are produced by calculating the frequency distribution of pixel intensities from the detailed coefficients, which contain artifacts, but also important textural information. First-order statistics are calculated from gray level histograms of the detailed coefficients to estimate variability across crystal surfaces, but lack information on the spatial distribution of pixel intensities. Thus, a second-order statistical measure, the gray level co-occurrence matrix (GLCM), is also extracted from the detailed coefficients to provide a more precise measure of surface texture. GLCMs are calculated by how often pairs of pixels with specific values and in certain spatial relationships occur in an image. Several degrees of texture are defined by first and second-order statistics to investigate how the surface texture of crystals varies with environmental conditions. Estimations of surface roughness using the proposed methods may have implications for improving bulk scattering calculations used in satellite retrieval algorithms and global climate model parameterizations.

  10. 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.

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

    Science.gov (United States)

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

    2016-10-01

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

  12. Electronic and atomic structures of the Sr3Ir4Sn13 single crystal: A possible charge density wave material

    Science.gov (United States)

    Wang, H.-T.; Srivastava, M. K.; Wu, C.-C.; Hsieh, S.-H.; Wang, Y.-F.; Shao, Y.-C.; Liang, Y.-H.; Du, C.-H.; Chiou, J.-W.; Cheng, C.-M.; Chen, J.-L.; Pao, C.-W.; Lee, J.-F.; Kuo, C. N.; Lue, C. S.; Wu, M.-K.; Pong, W.-F.

    2017-01-01

    X-ray scattering (XRS), x-ray absorption near-edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) spectroscopic techniques were used to study the electronic and atomic structures of the high-quality Sr3Ir4Sn13 (SIS) single crystal below and above the transition temperature (T* ≈ 147 K). The evolution of a series of modulated satellite peaks below the transition temperature in the XRS experiment indicated the formation of a possible charge density wave (CDW) in the (110) plane. The EXAFS phase derivative analysis supports the CDW-like formation by revealing different bond distances [Sn1(2)-Sn2] below and above T* in the (110) plane. XANES spectra at the Ir L3-edge and Sn K-edge demonstrated an increase (decrease) in the unoccupied (occupied) density of Ir 5d-derived states and a nearly constant density of Sn 5p-derived states at temperatures T atomic structures and the CDW-like phase in the SIS single crystal. PMID:28106144

  13. 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

  14. 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

    , thus preserving long-term creep strength. This can be done by alloying with Ta instead of Nb and V. Recent investigations have indicated a direct transformation of MN into CrMN to take place, not the traditional nucleation/dissolution process. In this paper atomic resolution microscopy shows how Cr......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...... 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...

  15. 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.

  16. An observation of nanotwin lamellae in Cd 0.6Mn 0.4Te crystal by atomic force microscopy

    Science.gov (United States)

    George, M. A.; Azoulay, M.; Collins, W. E.; Burger, A.; Silberman, E.

    1993-05-01

    Atomic force microscopy (AFM) is used to examine the structure of freshly cleaved Cd 0.6Mn 0.4Te surfaces. The present report complements previous results obtained with X-ray diffraction and optical microscopy which showed the existence of microtwins. The AFM analysis was performed under ambient conditions and yielded nanometer scale resolution images of single twin lamellae that ranged between 20 and 100 nm in width. This is a first observation using AFM of such a substructure, which we interpret as evidence for the presence of nonotwins.

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

    Science.gov (United States)

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

    2006-12-01

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

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

    Science.gov (United States)

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

    2015-02-01

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

  19. High resolution short focal distance Bent Crystal Laue Analyzer for copper K edge x-ray absorption spectroscopy.

    Science.gov (United States)

    Kujala, N G; Karanfil, C; Barrea, R A

    2011-06-01

    We have developed a compact short focal distance Bent Crystal Laue Analyzer (BCLA) for Cu speciation studies of biological systems with specific applications to cancer biology. The system provides high energy resolution and high background rejection. The system is composed of an aluminum block serving as a log spiral bender for a 15 micron thick Silicon 111 crystal and a set of soller slits. The energy resolution of the BCLA-about 14 eV at the Cu Kα line- allows resolution of the Cu Kα(1) and CuKα(2) lines. The system is easily aligned by using a set of motorized XYZ linear stages. Two operation modes are available: incident energy scans (IES) and emission energy scans (EES). IES allows scanning of the incident energy while the BCLA system is maintained at a preselected fixed position--typically CuKα(1) line. EES is used when the incident energy is fixed and the analyzer is scanned to provide the peak profile of the emission lines of Cu.

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

    Science.gov (United States)

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

    2015-10-14

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

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

    Science.gov (United States)

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

    2016-07-13

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

  2. 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.

  3. 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

    , platinum(II) and trimethyllead compounds as being particularly useful. On the other hand, lanthanide and uranyl compounds are poorly represented, which may be a consequence of these compounds having aggressive effects in crystal-soaking procedures. Furthermore, the database highlights the variety...

  4. Crystal structure of intercalated four-stranded d(C3T) at 1.4 angstroms resolution

    Science.gov (United States)

    Kang, C. H.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

    1994-01-01

    The crystal structure of d(C3T), solved at 1.4 angstroms resolution, reveals that the molecule forms a four-stranded intercalated complex. It consists of two parallel-stranded duplexes, each of which is held together by cytosine-protonated cytosine base pairs. The two duplexes are intercalated with each other and have opposite strand orientation. The molecule has a flat, lath-like appearance, and the covalently bonded cytosines have a slow right-handed twist of 17.1 degrees. However, there is considerable asymmetry. On one of the flat sides, the phosphate groups are rotated away from the center of the molecule. They are held in this orientation by bridging water molecules that bind the NH of cytosine and a phosphate group of an opposite chain. There is also considerable microheterogeneity in the structure. The cytosine hemiprotonation occurs even at pH 7 where stable crystals form.

  5. The New High Resolution Crystal Structure of NS2B-NS3 Protease of Zika Virus

    Science.gov (United States)

    Badshah, Syed Lal; Naeem, Abdul; Mabkhot, Yahia

    2017-01-01

    Zika virus (ZIKV) is the cause of a significant viral disease affecting humans, which has spread throughout many South American countries and has also become a threat to Southeastern Asia. This commentary discusses the article “Crystal structure of unlinked NS2B-NS3 protease from Zika virus” published recently in the journal Science by Zhang et al. of Nanyang Technological University, Singapore. They resolved a 1.58 Å resolution structure of the NS2B-NS3 protease of ZIKV and demonstrated how peptide and non-peptide inhibitors interact with this structure, along with the different conformational states that were observed. This protease crystal structure offers new opportunities for the design and development of novel antiviral drugs used for the treatment and control of ZIKV. PMID:28075376

  6. The New High Resolution Crystal Structure of NS2B-NS3 Protease of Zika Virus

    OpenAIRE

    Syed Lal Badshah; Abdul Naeem; Yahia Mabkhot

    2017-01-01

    Zika virus (ZIKV) is the cause of a significant viral disease affecting humans, which has spread throughout many South American countries and has also become a threat to Southeastern Asia. This commentary discusses the article “Crystal structure of unlinked NS2B-NS3 protease from Zika virus” published recently in the journal Science by Zhang et al. of Nanyang Technological University, Singapore. They resolved a 1.58 Å resolution structure of the NS2B-NS3 protease of ZIKV and demonstrated how ...

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

    Science.gov (United States)

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

    2014-12-01

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

  8. GENERAL REGULARITIES OF FORMATION OF CRYSTAL STRUCTURES OF ELEMENTS DEPENDING ON ELECTRON STRUCTURE OF ATOMS (OBSHCHILE ZAKONOMERNOSTI OBRAZOVANIYA KRISTALLICHESKIKH STRUKTUR ELEMENTOV V ZAVISIMOSTI OT ELEKTRONNOGO STROENIYA ATOMOV),

    Science.gov (United States)

    A table is given showing the dependence of crystalline structures of elements on the number of electrons in the incompleted electronic subshells of...its atoms. The conclusion is drawn that the types of crystalline structures of the elements depend on the configuration of the outer electronic...subshells acquired by the atoms prior to crystallization. Crystalline structures of elements not governed by the 8 - N rule are determined by one or both

  9. Temperature effects on the atomic structure and kinetics in single crystal electrochemistry

    Science.gov (United States)

    Gründer, Yvonne; Markovic, Nenad M.; Thompson, Paul; Lucas, Christopher A.

    2015-01-01

    The influence of temperature on the atomic structure at the electrochemical interface has been studied using in-situ surface x-ray scattering (SXS) during the formation of metal monolayers on a Au(111) electrode. For the surface reconstruction of Au(111), higher temperatures increase the mobility of surface atoms in the unreconstructed phase which then determines the surface ordering during the formation of the reconstruction. For the underpotential deposition (UPD) systems, the surface diffusion of the depositing metal adatoms is significantly reduced at low temperatures which results in the frustration of ordered structures in the case of Cu UPD, occurring on a Br-modified surface, and in the formation of a disordered Ag monolayer during Ag UPD. The results indicate that temperature changes affect the mass transport and diffusion of metal adatoms on the electrode surface. This demonstrates the importance of including temperature as a variable in studying surface structure and reactions at the electrochemical interface.

  10. Atomic modelling of crystal/complex fluid/crystal contacts—Part I. The genetic iterative multi-species (GIMS) approach and case of kaolinite/brine/kaolinite

    Science.gov (United States)

    Jouanna, P.; Pèpe, G.; Dweik, J.; Gouze, P.

    2010-11-01

    Predicting the impact of underground engineering on the environment requires the knowledge of natural media at different scales. In particular, understanding basic phenomena controlling the properties of rocks in the presence of complex fluids necessitates a detailed atomic description of the solid/fluid/solid contacts, the subject of Part I of the present study. First, building the solid interspace between two different crystals in a non-periodic situation is achieved using the ab initio and molecular mechanics code GenMol TM. A description of the fluid confined within the interspace is then derived from the original genetic iterative multi-species (GIMS) algorithm implemented in the same code. This approach consists of equilibrating chemical potentials, cycle after cycle and species after species, between the confined fluid and the free natural fluid. An elementary iteration for a species k consists of different steps incrementing the number Nk of particles k, with other numbers Nk' remaining constant. At each step, an optimum fluid composition is obtained by a genetic process distributing the fluid particles on a grid by stochastic shots, followed in fine by a refining process. The effectiveness of the GIMS approach is demonstrated in the case study of a fluid confined between two (0 0 1) kaolinite faces, with apertures h varying between 4 and 10 Å, connected to a 9-species external solution [H 2O, Cl -, N a+, CO 2(aq), NaCl (aq), Ca 2+, Mg 2+, HCO3-, H 3O +] where concentrations are ranging from 55 to 10 -4 mol/L. The results show a drastic variation in the solute/solvent and cations/ions ratios in the confined fluid when aperture h is lowered to less than 1 nm. These results obtained with a very rapid convergence of the iterative algorithm combined with a very competitive genetic optimizer are validated with high precision on a free solution. This description of contacts between crystals is original and unattainable by standard crystal interface approaches

  11. Electromechanical sensing of substrate charge hidden under atomic 2D crystals.

    Science.gov (United States)

    Kay, Nicholas D; Robinson, Benjamin J; Fal'ko, Vladimir I; Novoselov, Konstantin S; Kolosov, Oleg V

    2014-06-11

    The functionality of graphene and other two-dimensional materials in electronic devices is highly influenced by the film-substrate charge transfer affecting local carrier density. We demonstrate that charges buried under the few layer graphene on/in the insulating substrate can be detected using electromechanical actuation of the conductive atomically thin layers, allowing measurements of areal density of film-substrate transferred charges under few layer graphene and MoS2 suspended films.

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

    Science.gov (United States)

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

    2016-09-01

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

  13. Fluid dynamics and convective heat transfer in impinging jets through implementation of a high resolution liquid crystal technique

    Science.gov (United States)

    Kim, K.; Wiedner, B.; Camci, C.

    1993-01-01

    A combined convective heat transfer and fluid dynamics investigation in a turbulent round jet impinging on a flat surface is presented. The experimental study uses a high resolution liquid crystal technique for the determination of the convective heat transfer coefficients on the impingement plate. The heat transfer experiments are performed using a transient heat transfer method. The mean flow and the character of turbulent flow in the free jet is presented through five hole probe and hot wire measurements, respectively. The flow field character of the region near the impingement plate plays an important role in the amount of convective heat transfer. Detailed surveys obtained from five hole probe and hot wire measurements are provided. An extensive validation of the liquid crystal based heat transfer method against a conventional technique is also presented. After a complete documentation of the mean and turbulent flow field, the convective heat transfer coefficient distributions on the impingement plate are presented. The near wall of the impingement plate and the free jet region is treated separately. The current heat transfer distributions are compared to other studies available from the literature. The present paper contains complete sets of information on the three dimensional mean flow, turbulent velocity fluctuations, and convective heat transfer to the plate. The experiments also prove that the present nonintrusive heat transfer method is highly effective in obtaining high resolution heat transfer maps with a heat transfer coefficient uncertainty of 5.7 percent.

  14. 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.

  15. High-resolution crystal structure of the PDZ1 domain of human protein tyrosine phosphatase PTP-Bas.

    Science.gov (United States)

    Lee, Sang-Ok; Lee, Mi-Kyung; Ku, Bonsu; Bae, Kwang-Hee; Lee, Sang Chul; Lim, Heon M; Kim, Seung Jun; Chi, Seung-Wook

    2016-09-23

    Protein tyrosine phosphatase-Basophil (PTP-Bas) is a membrane-associated protein tyrosine phosphatase with five PDZ domains and is involved in apoptosis, tumorigenesis, and insulin signaling. The interaction between PTP-Bas and tandem-PH-domain-containing protein 1/2 (TAPP1/2) plays an essential role in the regulation of insulin signaling. Despite its high sequence homology with the other PDZ domains, only the PDZ1 domain of PTP-Bas showed distinct binding specificity for TAPP1/2. Although the interaction between PTP-Bas PDZ1 and TAPP1/2 is a therapeutic target for diabetes, the structural basis for the interaction has not been elucidated. In the present study, we determined the crystal structure of the PTP-Bas PDZ1 domain at 1.6 Å resolution. In addition, we calculated the structural models of complexes of PTP-Bas PDZ1 and the C-terminal peptides of TAPP1/2 (referred to as TAPP1p/2p). Structural comparison with the PTP-Bas PDZ2/RA-GEF2 peptide complex revealed a structural basis for distinct binding specificity of PTP-Bas PDZ1 for TAPP1p/2p peptides. Our high-resolution crystal structure of PTP-Bas PDZ1 will serve as a useful template for rational structure-based design of novel anti-diabetes therapeutics.

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

    Science.gov (United States)

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

    2008-03-01

    The thermophilic bacterium Moorella thermoacetica possesses an rsb operon that is related to the genetic locus common to many Gram-positive bacteria that regulates the activity of the stress-responsive sigma factor sigma(B). One of the gene products of this operon is RsbS, a single STAS-domain protein that is a component of higher order assemblies in Bacillus subtilis known as 'stressosomes'. It is expected that similar complexes are found in M. thermoacetica, but in this instance regulating the biosynthesis of cyclic di-GMP, a ubiquitous secondary messenger. Selenomethionine-labelled MtRsbS protein was crystallized at room temperature using the hanging-drop vapour-diffusion method. Crystals belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.07, b = 60.52, c = 89.28 A, diffracted to 2.5 A resolution on beamline I04 of the Diamond Light Source. The selenium substructure was solved using SHELX and it is believed that this represents the first reported ab initio crystal structure to be solved using diffraction data collected at DLS.

  17. Multi-scale characterization of lyotropic liquid crystals using 2H and diffusion MRI with spatial resolution in three dimensions.

    Directory of Open Access Journals (Sweden)

    Diana Bernin

    Full Text Available The ability of lyotropic liquid crystals to form intricate structures on a range of length scales can be utilized for the synthesis of structurally complex inorganic materials, as well as in devices for controlled drug delivery. Here we employ magnetic resonance imaging (MRI for non-invasive characterization of nano-, micro-, and millimeter scale structures in liquid crystals. The structure is mirrored in the translational and rotational motion of the water, which we assess by measuring spatially resolved self-diffusion tensors and 2H spectra. Our approach differs from previous works in that the MRI parameters are mapped with spatial resolution in all three dimensions, thus allowing for detailed studies of liquid crystals with complex millimeter-scale morphologies that are stable on the measurement time-scale of 10 hours. The 2H data conveys information on the nanometer-scale structure of the liquid crystalline phase, while the combination of diffusion and 2H data permits an estimate of the orientational distribution of micrometer-scale anisotropic domains. We study lamellar phases consisting of the nonionic surfactant C10E3 in 2H2O, and follow their structural equilibration after a temperature jump and the cessation of shear. Our experimental approach may be useful for detailed characterization of liquid crystalline materials with structures on multiple length scales, as well as for studying the mechanisms of phase transitions.

  18. Optical and atomic force microscopic study on step bunching in BaB2O4 crystal growth

    Institute of Scientific and Technical Information of China (English)

    Pan Xiu-Hong; Jin Wei-Qing; Liu Yan; Ai Fei; Jin Fei; Xie Jun-Jie

    2011-01-01

    The formation of macrostep during high-temperature phase of barium meta-borate (α-BaB2O4) single crystal growth has been investigated by both optical in-situ observation system and atomic force microscopy (AFM). The in-situ observation results demonstrate that the critical linear size of growing facet exceeding the size that the macrostep generates is significantly anisotropic. The critical linear sizes are around 280 μm and 620 μm for {10(1)0} and {(1)010} planes, respectively. AFM study illustrates that macrostep train with a height of 150 nm~200 nm is one typical morphological feature of the as-grown crystal surface. The riser of each macrostep consists of several straight and parallel sub-steps, indicating the occurrence of step bunching. Additionally, triangular sub-steps with heights of several nanometers on the treads of the macrosteps are found to be another typical feature of surface morphology, which implies a microscopically competitive bunching of sub-steps between various crystallographic orientations.

  19. Emergence of Zeolite Analogs and other Microporous Crystals in an Atomic Lattice Model of Silica and Related Materials.

    Science.gov (United States)

    Jin, Lin; Auerbach, Scott M; Monson, Peter A

    2012-03-15

    The potential of tailored nanopores to transform technologies such as drug delivery, biofuel production, and optical-electronic devices depends on fundamental knowledge of the self-assembly of ordered nanoporous solids. Atomic-level geometries of critical nuclei that lead to such solids have remained hidden in the nanoscale blind spot between local (5 nm) probes of structure. Heroic efforts at molecular simulation of nanopore formation have provided massive libraries of hypothetical structures; (1-5) however, to date no statistical simulation has generated a crystallization pathway from random initial condition to ordered nanoporous solid, until now. In this work, we show that a recently developed atomic lattice model of silica and related materials can form ordered nanoporous solids with a rich variety of structures including known chalcogenides, zeolite analogs, and layered materials. We find that whereas canonical Monte Carlo simulations of the model consistently produce the amorphous solids studied in our previous work, parallel tempering Monte Carlo gives rise to ordered nanoporous solids. The utility of parallel tempering highlights the existence of barriers between amorphous and crystalline phases of our model. Moreover, the self-assembly or nanoporous crystalline phases in the model open the door to detailed understanding of nanopore nucleation.

  20. 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).

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

    Institute of Scientific and Technical Information of China (English)

    XUE Ping; James G FUJIMOTO

    2008-01-01

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

  2. 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.

  3. Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin.

    Science.gov (United States)

    Hagiwara, Yoshinori; Wada, Kei; Irikawa, Teppei; Sato, Hideaki; Unno, Masaki; Yamamoto, Ken; Fukuyama, Keiichi; Sugishima, Masakazu

    2016-10-01

    Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the reduction of biliverdin (BV) to produce phycocyanobilin, a linear tetrapyrrole pigment used for light harvesting and light sensing. Spectroscopic and HPLC analyses inidicate that BV bound to the I86D mutant of PcyA is fully protonated (BVH(+) ) and can accept an electron, but I86D is unable to donate protons for the reduction; therefore, compared to the wild-type PcyA, the I86D mutant stabilizes BVH(+) . To elucidate the structural basis of the I86D mutation, we determined the atomic-resolution structure of the I86D-BVH(+) complex and the protonation states of the essential residues Asp105 and Glu76 in PcyA. Our study revealed that Asp105 adopted a fixed conformation in the I86D mutant, although it had dual conformations in wild-type PcyA which reflected the protonation states of BV. Taken together with biochemical/spectroscopic results, our analysis of the I86D-BVH(+) structure supports the hypothesis that flexibility of Asp105 is essential for the catalytic activity of PcyA.

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

    Energy Technology Data Exchange (ETDEWEB)

    Welz, Bernhard, E-mail: w.bernardo@terra.com.b [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis-SC (Brazil); Instituto Nacional de Ciencia e Tecnologia do CMPq-INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador-BA (Brazil); Santos, Lisia M.G. dos [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis-SC (Brazil); Instituto Nacional de Controle de Qualidade em Saude-INCQS-Fiocruz, 21040-900 Rio de Janeiro-RJ (Brazil); Araujo, Rennan G.O. [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis-SC (Brazil); Departamento de Quimica, Universidade Federal de Sergipe, 49100-000 Sao Cristovao-SE (Brazil); Jacob, Silvana do C. [Instituto Nacional de Controle de Qualidade em Saude-INCQS-Fiocruz, 21040-900 Rio de Janeiro-RJ (Brazil); Vale, Maria Goreti R. [Instituto Nacional de Ciencia e Tecnologia do CMPq-INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador-BA (Brazil); Instituto de Quimica, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre-RS (Brazil); Okruss, Michael; Becker-Ross, Helmut [Leibniz-Institut fuer Analytische Wissenschaften-ISAS-Department Berlin, 12489 Berlin (Germany)

    2010-03-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Czarnota, M.; Banas, D.; Pajek, M. [Jan Kochanowski Univ., Institute of Physics, Kielce (Poland); Berset, M.; Dousse, J.C.; Hoszowska, J.; Maillard, Y.P.; Mauron, O.; Raboud, P.A. [Fribourg Univ., Dept. of Physics (Switzerland); Chmielewska, D.; Rzadkiewicz, J.; Sujkowski, Z. [Soltan Institute for Nuclear Studies, Otwock-Swierk (Poland); Polasik, M.; Slabkowska, K. [Nicholas Copernicus Univ., Faculty of Chemistry, Torun (Poland)

    2010-04-15

    The multiple ionization of the L- and M-shells of Pd by fast oxygen ions has been studied by measuring with high-resolution the satellite structures of the Lalpha{sub 1,2} X-ray transitions. Relativistic multi-configuration Dirac-Fock (MCDF) calculations were used to interpret the complex X-ray spectrum, allowing to derive the number of L- and M-shell spectator vacancies at the moment of the X-ray emission. After correcting these numbers for the atomic vacancy rearrangement processes that take place prior to the X-ray emission, the ionization probabilities corresponding to the collision time were obtained. The latter were compared to predictions of the semiclassical approximation (SCA) and the geometrical model. The SCA calculations were performed using relativistic hydrogenic and self-consistent Dirac-Hartree-Fock (DHF) electronic wave functions. It was found that the use of the more realistic DHF wave functions in the SCA calculations leads to a much better description of the measured ionization probabilities for both the L- and M-shells. (authors)

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

    Energy Technology Data Exchange (ETDEWEB)

    Hau-Riege, S

    2010-10-07

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2000-01-01

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

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

    Science.gov (United States)

    Damljanović, V; Gajić, R

    2016-03-02

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

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

    Science.gov (United States)

    Damljanović, V.; Gajić, R.

    2016-03-01

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

  10. Velocity tuning of friction with two trapped atoms

    CERN Document Server

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-01

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

  12. Crystal structure of human adenovirus at 3.5 Å resolution*

    OpenAIRE

    Reddy, Vijay S.; Natchiar, S. Kundhavai; Phoebe L Stewart; Nemerow, Glen R.

    2010-01-01

    Rational development of adenovirus vectors for therapeutic gene transfer is hampered by the lack of accurate structural information. Here we report the X-ray structure at 3.5 Å resolution of the 150 megadalton adenovirus capsid containing nearly 1 million amino acids. We describe interactions between the major capsid protein (hexon) and several accessory molecules that stabilize the capsid. The virus structure also reveals an altered association between the penton base and the trimeric fiber ...

  13. 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.

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

    Science.gov (United States)

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

    2016-06-28

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

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

    Directory of Open Access Journals (Sweden)

    Stephan Ratzsch

    2015-11-01

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

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

    Institute of Scientific and Technical Information of China (English)

    焦志伟; 陈西园

    2001-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Tatsuaki Tsuruyama

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

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

    Science.gov (United States)

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

    2013-01-01

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

  19. Enzymatic degradation processes of lamellar crystals in thin films for poly[(R)-3-hydroxybutyric acid] and its copolymers revealed by real-time atomic force microscopy.

    Science.gov (United States)

    Numata, Keiji; Hirota, Takuya; Kikkawa, Yoshihiro; Tsuge, Takeharu; Iwata, Tadahisa; Abe, Hideki; Doi, Yoshiharu

    2004-01-01

    Enzymatic degradation processes of flat-on lamellar crystals in melt-crystallized thin films of poly[(R)-3-hydroxybutyric acid] (P(3HB)) and its copolymers were characterized by real-time atomic force microscopy (AFM) in a phosphate buffer solution containing PHB depolymerase from Ralstonia pickettii T1. Fiberlike crystals with regular intervals were generated along the crystallographic a axis at the end of lamellar crystals during the enzymatic degradation. The morphologies and sizes of the fiberlike crystals were markedly dependent on the compositions of comonomer units in the polyesters. Length, width, interval, and thickness of the fiberlike crystals after the enzymatic degradation for 2 h were measured by AFM, and the dimensions were related to the solid-state structures of P(3HB) and its copolymers. The width and thickness decreased at the tip of fiberlike crystals, indicating that the enzymatic degradation of crystals takes place not only along the a axis but also along the b and c axes. These results from AFM measurement were compared with the data on crystal size by wide-angle X-ray diffraction, and on lamellar thickness and long period by small-angle X-ray scattering. In addition, the enzymatic erosion rate of flat-on lamellar crystals along the a axis was measured from real-time AFM height images. A schematic glacier model for the enzymatic degradation of flat-on lamellar crystals of P(3HB) by PHB depolymerase has been proposed on the basis of the AFM observations.

  20. High resolution time-to-space conversion of sub-picosecond pulses at 1.55µm by non-degenerate SFG in PPLN crystal.

    Science.gov (United States)

    Shayovitz, Dror; Herrmann, Harald; Sohler, Wolfgang; Ricken, Raimund; Silberhorn, Christine; Marom, Dan M

    2012-11-19

    We demonstrate high resolution and increased efficiency background-free time-to-space conversion using spectrally resolved non-degenerate and collinear SFG in a bulk PPLN crystal. A serial-to-parallel resolution factor of 95 and a time window of 42 ps were achieved. A 60-fold increase in conversion efficiency slope compared with our previous work using a BBO crystal [D. Shayovitz and D. M. Marom, Opt. Lett. 36, 1957 (2011)] was recorded. Finally the measured 40 GHz narrow linewidth of the output SFG signal implies the possibility to extract phase information by employing coherent detection techniques.

  1. High resolution x-ray investigation of periodically poled lithium tantalate crystals with short periodicity

    CERN Document Server

    Bazzan, Marco; Argiolas, Nicola; Busacca, Alessandro C; Oliveri, Roberto L; Stivala, Salvatore; Curcio, Luciano; Sanseverino, Stefano Riva; 10.1063/1.3264620

    2012-01-01

    Domain engineering technology in lithium tantalate is a well studied approach for nonlinear optical applications. However, for several cases of interest, the realization of short period structures (< 2 \\mu m) is required, which make their characterization difficult with standard techniques. In this work, we show that high resolution x-ray diffraction is a convenient approach for the characterization of such structures, allowing us to obtain in a nondestructive fashion information such as the average domain period, the domain wall inclination, and the overall structure quality.

  2. Water Structure in Trichosanthin Crystal at 1.73 Resolution

    Institute of Scientific and Technical Information of China (English)

    高奔; 马星奇; 王耀萍; 陈世芝; 吴伸; 董贻诚

    1994-01-01

    The water-structure model in Trichosanthin crystal is presented,and 133 water moleculesare included and 118 water molecules are hydrogen-bonded to protein.In the interior of Trichosanthin,thereare four discrete internal water molecules,among which two water molecules W251 and W252 are separated-ly hydrogen-bonded to the side-chain groupsof 156Gln and 157Ser in the distorted segment of A5 helix andplay a role in maintaining the conformation of the active site.The comparative result of water structures incrystals indicates that when approaching the protein,the ribosome induces a conformational change in theresidues of the active site,which leads to an appropriate alignment of catalytic groups as well as the optimalconformation for the catalysis,and activates a water molecule (W257) to participate in the ribosome inactiva-tion.

  3. Crystal and Molecular Structure of a Collagen-Like Peptide at 1.9 overset{circ}{A} Resolution

    Science.gov (United States)

    Bella, Jordi; Eaton, Mark; Brodsky, Barbara; Berman, Helen M.

    1994-10-01

    The structure of a protein triple helix has been determined at 1.9 angstrom resolution by x-ray crystallographic studies of a collagen-like peptide containing a single substitution of the consensus sequence. This peptide adopts a triple-helical structure that confirms the basic features determined from fiber diffraction studies on collagen: supercoiling of polyproline II helices and interchain hydrogen bonding that follows the model II of Rich and Crick. In addition, the structure provides new information concerning the nature of this protein fold. Each triple helix is surrounded by a cylinder of hydration, with an extensive hydrogen bonding network between water molecules and peptide acceptor groups. Hydroxyproline residues have a critical role in this water network. The interaxial spacing of triple helices in the crystal is similar to that in collagen fibrils, and the water networks linking adjacent triple helices in the crystal structure are likely to be present in connective tissues. The breaking of the repeating (X-Y-Gly)_n pattern by a Gly-->Ala substitution results in a subtle alteration of the conformation, with a local untwisting of the triple helix. At the substitution site, direct interchain hydrogen bonds are replaced with interstitial water bridges between the peptide groups. Similar conformational changes may occur in Gly-->X mutated collagens responsible for the diseases osteogenesis imperfecta, chondrodysplasias, and Ehlers-Danlos syndrome IV.

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

    Science.gov (United States)

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

    2015-01-01

    The hepatitis B virus (HBV) core protein is essential for HBV replication and an important target for antiviral drug discovery. We report the first, to our knowledge, high-resolution crystal structure of an antiviral compound bound to the HBV core protein. The compound NVR-010–001-E2 can induce assembly of the HBV core wild-type and Y132A mutant proteins and thermostabilize the proteins with a Tm increase of more than 10 °C. NVR-010–001-E2 binds at the dimer–dimer interface of the core proteins, forms a new interaction surface promoting protein–protein interaction, induces protein assembly, and increases stability. The impact of naturally occurring core protein mutations on antiviral activity correlates with NVR-010–001-E2 binding interactions determined by crystallography. The crystal structure provides understanding of a drug efficacy mechanism related to the induction and stabilization of protein–protein interactions and enables structure-guided design to improve antiviral potency and drug-like properties. PMID:26598693

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

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    沈大可; 韩高荣; 杜丕一; 阙端麟; SOUI.K

    2004-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

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

    2016-11-01

    We report the calibration of the Orion High-Resolution X-ray (OHREX) imaging crystal spectrometer at the EBIT-I electron beam ion trap at Livermore. Two such instruments, dubbed OHREX-1 and OHREX-2, are fielded for plasma diagnostics at the Orion laser facility in the United Kingdom. The OHREX spectrometer can simultaneously house two spherically bent crystals with a radius of curvature of r = 67.2 cm. The focusing properties of the spectrometer allow both for larger distance to the source due to the increase in collected light and for observation of extended sources. OHREX is designed to cover a 2.5°-3° spectral range at Bragg angles around 51.3°. The typically high resolving powers at these large Bragg angles are ideally suited for line shape diagnostics. For instance, the nominal resolving power of the instrument (>10 000) is much higher than the effective resolving power associated with the Doppler broadening due to the temperature of the trapped ions in EBIT-I. The effective resolving power is only around 3000 at typical EBIT-I conditions, which nevertheless is sufficient to set up and test the instrument's spectral characteristics. We have calibrated the spectral range for a number of crystals using well known reference lines in the first and second order and derived the ion temperatures from these lines. We have also made use of the 50 μm size of the EBIT-I source width to characterize the spatial focusing of the spectrometer.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-12-01

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

  10. Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations

    Science.gov (United States)

    Peng, Junhui; Zhang, Zhiyong

    2016-07-01

    Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1-3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.

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

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, T; Manz, TA; Sholl, DS

    2011-03-24

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-02-28

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

  13. PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

    Science.gov (United States)

    Tang, Yat T; Marshall, Garland R

    2011-02-28

    scoring function was an objective of this study, the main focus was evaluation of the use of high-resolution X-ray crystal structures with high-quality thermodynamic parameters from isothermal titration calorimetry for scoring function development. With the increasing application of structure-based methods in molecular design, this study suggests that using high-resolution crystal structures, separating enthalpy and entropy contributions to binding free energy, and including descriptors to better capture entropic contributions may prove to be effective strategies toward rapid and accurate calculation of binding affinity.

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

    Science.gov (United States)

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

    2016-04-01

    The norepinephrine pathway is believed to modulate behavioral and physiological processes, such as mood, overall arousal, and attention. Furthermore, abnormalities in the pathway have been linked to numerous diseases, for example hypertension, depression, anxiety, Parkinson's disease, schizophrenia, Alzheimer's disease, attention deficit hyperactivity disorder, and cocaine dependence. We report the crystal structure of human dopamine β-hydroxylase, which is the enzyme converting dopamine to norepinephrine. The structure of the DOMON (dopamine β-monooxygenase N-terminal) domain, also found in >1600 other proteins, reveals a possible metal-binding site and a ligand-binding pocket. The catalytic core structure shows two different conformations: an open active site, as also seen in another member of this enzyme family [the peptidylglycine α-hydroxylating (and α-amidating) monooxygenase], and a closed active site structure, in which the two copper-binding sites are only 4 to 5 Å apart, in what might be a coupled binuclear copper site. The dimerization domain adopts a conformation that bears no resemblance to any other known protein structure. The structure provides new molecular insights into the numerous devastating disorders of both physiological and neurological origins associated with the dopamine system.

  15. Deterministic tuning of slow-light in photonic-crystal waveguides through the C and L bands by atomic layer deposition

    CERN Document Server

    Chen, Charlton J; Meric, Inanc; Shepard, Ken L; Wong, Chee Wei; Green, William M J; Vlasov, Yurii A; Assefa, Solomon

    2009-01-01

    We demonstrate digital tuning of the slow-light regime in silicon photonic-crystal waveguides by performing atomic layer deposition of hafnium oxide. The high group-index regime was deterministically controlled (red-shift of 140 +/- 10 pm per atomic layer) without affecting the group-velocity dispersion and third-order dispersion. Additionally, differential tuning of 110 +/- 30 pm per monolayer of the slow-light TE-like and TM-like modes was observed. This passive post-fabrication process has potential applications including the tuning of chip-scale optical interconnects, as well as Raman and parametric amplification.

  16. 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...

  17. CRYSTAL-STRUCTURE OF RECOMBINANT HUMAN TRIOSEPHOSPHATE ISOMERASE AT 2.8 ANGSTROM RESOLUTION - TRIOSEPHOSPHATE ISOMERASE-RELATED HUMAN GENETIC-DISORDERS AND COMPARISON WITH THE TRYPANOSOMAL ENZYME

    NARCIS (Netherlands)

    MANDE, SC; MAINFROID, [No Value; KALK, KH; GORAJ, K; MARTIAL, JA; HOL, WGJ

    1994-01-01

    The crystal structure of recombinant human triosephosphate isomerase (hTIM) has been determined complexed with the transition-state analogue 2-phosphoglycolate at a resolution of 2.8 Angstrom. After refinement, the R-factor is 16.7% with good geometry. The asymmetric unit contains 1 complete dimer o

  18. CRYSTAL-STRUCTURE OF DEOXYGENATED LIMULUS-POLYPHEMUS SUBUNIT-II HEMOCYANIN AT 2.18-ANGSTROM RESOLUTION - CLUES FOR A MECHANISM FOR ALLOSTERIC REGULATION

    NARCIS (Netherlands)

    HAZES, B; MAGNUS, KA; BONAVENTURA, C; BONAVENTURA, J; DAUTER, Z; KALK, KH; HOL, WGJ

    1993-01-01

    The crystal structure of Limulus polyphemus subunit type II hemocyanin in the deoxygenated state has been determined to a resolution of 2.18 angstrom. Phase information for this first structure of a cheliceratan hemocyanin was obtained by molecular replacement using the crustacean hemocyanin structu

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

    CERN Document Server

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

    2016-01-01

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

  20. [Connection of magnetic antisense probe with SK-Br-3 oncocyte mRNA nucleotide detected by high resolution atomic force microscope].

    Science.gov (United States)

    Tan, Shude; Ouyang, Yu; Li, Xinyou; Wen, Ming; Li, Shaolin

    2011-06-01

    The present paper is aimed to detect superparamagnetic iron oxide labeled c-erbB2 oncogene antisense oligonucleotide probe (magnetic antisense probe) connected with SK-Br-3 oncocyte mRNA nucleotide by high resolution atomic force microscope (AFM). We transfected SK-Br-3 oncocyte with magnetic antisense probe, then observed the cells by AFM with high resolution and detected protein expression and magnetic resonance imagine (MRI). The high resolution AFM clearly showed the connection of the oligonucleotide remote end of magnetic antisense probe with the mRNA nucleotide of oncocyte. The expression of e-erbB2 protein in SK-Br3 cells were highly inhibited by using magnetic antisense probe. We then obtained the lowest signal to noise ratio (SNR) of SK-Br-3 oncocyte transfected with magnetic antisense probe by MRI (PSK-Br-3 mRNA of tumor cell nuclear.

  1. Crystal structure of raw pure Mysore silk fibre based on (Ala-Gly)2-Ser-Gly peptide sequence using Linked-Atom-Least-Squares method

    Indian Academy of Sciences (India)

    Sangappa; S S Mahesh; R Somashekar

    2005-03-01

    We have carried out crystal structure analysis of raw pure Mysore silk fibers belonging to Bombyx mori on the basis of model parameters of Marsh et al using Linked-Atom-Least-Squares technique. The intensity of all the reflections were computed employing CCP13 software. We observe that the molecular modification is essentially same as -pleated structure with antipolar-antiparallel arrangements formed by hydrogen bonds. The essential differences observed in the structure are highlighted and discussed.

  2. 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

  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 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.

  5. Two-dimensional folded chain crystals composed of a single isotactic poly(methyl methacrylate) chain observed by atomic force microscopy

    Science.gov (United States)

    Kumaki, Jiro; Anzai, Takahiro

    2014-03-01

    We successfully visualized crystallization behavior of a single isolated polymer chain at a molecular level by atomic force microscopy (AFM). Previously, we found that isotactic poly(methyl methacrylate) (it-PMMA) formed two-dimensional folded chain crystals upon compression of its Langmuir monolayer on a water surface, and the molecular images of the crystals deposited on mica were clearly visualized by AFM (Kumaki, et al. JACS 2005, 127, 5788; J. Phys. Chem. B 2013, 117, 5594). In the present study, a high-molecular-weight it-PMMA was diluted in a monolayer of an it-PMMA oligomer which cannot crystallize due to the low molecular weight. At a low surface pressure, isolated amorphous chains of the high-molecular-weight it-PMMA solubilized in the oligomer monolayer were observed. On compression, the isolated chains converted to crystals composed of a single chain. Detailed AFM observations of the crystals indicated that the crystalline nuclei preferably formed at the ends of the chains, and the size of the nuclei was almost independent on the molecular weight of the it-PMMA in a wide range.

  6. 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

  7. STUDIES ON PRIMARY CRYSTALLIZATION OF RAPIDLY QUENCHED Al-Ni-Cu-Nd METALLIC GLASS BY USING HIGH RESOLUTION TRASMISSION ELECTRON MICROSCOPY

    Institute of Scientific and Technical Information of China (English)

    Y.D. Xiao; W.X. Li; D. Jacovkis; N. Clavaguera; M.T. Clavaguera-Mora; J. Rodriguez- Viejo

    2003-01-01

    Rapidly solidified Al87Ni7Cu3Nd3 metallic glasses, prepared by using melt spinning,were treated under both isothermal and non-isothermal regime. The amorphous ribbon and the annealed samples were closely examined by means of differential scanning calorimetric, conventional X-ray diffraction and high resolution transmission electron microscopy with selected-area electron diffraction, with special interest in primary crystallization into α-Al nanocrystalline particles, in order to understand structural characteristics of Al-based amorphous/nanocrystalline alloys, and nucleation and grain growth mechanism on the nanometer scale during primary crystallization.The results show that, the as-prepared ribbons are fully amorphous and homogeneous in the micron scale, but contain high density of quenched-in clusters or crystallite embryos. Primary crystallization mainly leads to formation of two-phase mixture of α-Al crystal and residual amorphous phase. The annealed ribbons exposed isothermally at 110℃f or 5, 130 minutes and heated continuously up to less than 310℃ at 40℃/min consist of large amount of α-Al fcc crystal nanoparticles dispersed uniformly in an amorphous matrix. However, a very little amount of finer orthorhombie Al3Ni intermetalics particles exist in the annealed ribbons heated up to 310℃. During primary crystallization, the leading kinetic mechanics to impede growth of the α-Al crystal is soft impingement, instead of geometrie impingement.

  8. Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of C(alpha atoms.

    Directory of Open Access Journals (Sweden)

    Rupali A Gadkari

    Full Text Available BACKGROUND: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C(alpha atoms which are modeled with modest accuracy. METHODOLOGY/PRINCIPAL FINDINGS: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C(alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C(alpha. We extend the method further to recognize potential protein-protein interface residues. CONCLUSION/ SIGNIFICANCE: Our approach to identify buried and exposed residues solely from the positions of C(alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C(alpha positions and all-atom models suggested that, recognition of interfacial residues using C(alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only (alpha positions are available as, for example, in the cases of integration of cryo

  9. Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca 2+ -calmodulin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jiusheng; van den Bedem, Henry; Brunger, Axel T.; Wilson, Mark A.

    2016-01-01

    Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca2+-CaM, but no assignment of these features has been made. In addition, Ca2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca2+-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.

  10. 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.

  11. Detection of high energy muons with sub-20 ps timing resolution using L(Y)SO crystals and SiPM readout

    Science.gov (United States)

    Benaglia, A.; Gundacker, S.; Lecoq, P.; Lucchini, M. T.; Para, A.; Pauwels, K.; Auffray, E.

    2016-09-01

    Precise timing capability will be a key aspect of particle detectors at future high energy colliders, as the time information can help in the reconstruction of physics events at the high collision rate expected there. Other than being used in detectors for PET, fast scintillating crystals coupled to compact Silicon Photomultipliers (SiPMs) constitute a versatile system that can be exploited to realize an ad-hoc timing device to be hosted in a larger high energy physics detector. In this paper, we present the timing performance of LYSO:Ce and LSO:Ce codoped 0.4% Ca crystals coupled to SiPMs, as measured with 150 GeV muons at the CERN SPS H2 extraction line. Small crystals, with lengths ranging from 5 mm up to 30 mm and transverse size of 2 × 2mm2 or 3 × 3mm2 , were exposed to a 150 GeV muon beam. SiPMs from two different companies (Hamamatsu and FBK) were used to detect the light produced in the crystals. The best coincidence time resolution value of (14.5 ± 0.5) ps , corresponding to a single-detector time resolution of about 10 ps, is demonstrated for 5 mm long LSO:Ce,Ca crystals coupled to FBK SiPMs, when time walk corrections are applied.

  12. Organometallic Bonding in an Ullmann-Type On-Surface Chemical Reaction Studied by High-Resolution Atomic Force Microscopy.

    Science.gov (United States)

    Kawai, Shigeki; Sadeghi, Ali; Okamoto, Toshihiro; Mitsui, Chikahiko; Pawlak, Rémy; Meier, Tobias; Takeya, Jun; Goedecker, Stefan; Meyer, Ernst

    2016-10-01

    The on-surface Ullmann-type chemical reaction synthesizes polymers by linking carbons of adjacent molecules on solid surfaces. Although an organometallic compound is recently identified as the reaction intermediate, little is known about the detailed structure of the bonded organometallic species and its influence on the molecule and the reaction. Herein atomic force microscopy at low temperature is used to study the reaction with 3,9-diiododinaphtho[2,3-b:2',3'-d]thiophene (I-DNT-VW), which is polymerized on Ag(111) in vacuum. Thermally sublimated I-DNT-VW picks up a Ag surface atom, forming a CAg bond at one end after removing an iodine. The CAg bond is usually short-lived, and a CAgC organometallic bond immediately forms with an adjacent molecule. The existence of the bonded Ag atoms strongly affects the bending angle and adsorption height of the molecular unit. Density functional theory calculations reveal the bending mechanism, which reveals that charge from the terminus of the molecule is transferred via the Ag atom into the organometallic bond and strengths the local adsorption to the substrate. Such deformations vanish when the Ag atoms are removed by annealing and CC bonds are established.

  13. 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.)

  14. Phase-modulated electronic wave-packet interferometry reveals high resolution vibronic spectra of free Rb atoms and Rb*He molecules

    CERN Document Server

    Bruder, Lukas; Stienkemeier, Frank

    2015-01-01

    Phase-modulated wave-packet interferometry is combined with mass-resolved photoion detection to investigate rubidium atoms attached to helium nanodroplets in a molecular beam experiment. The spectra of atomic Rb electronic states show a vastly enhanced sensitivity and spectral resolution when compared to conventional pump-probe wave-packet interferometry. Furthermore, the formation of Rb*He exciplex molecules is probed and for the first time a fully resolved vibrational spectrum for transitions between the lowest excited $5\\Pi_{3/2}$ and the high-lying electronic states $2^2\\Pi$, $4^2\\Delta$, $6^2\\Sigma$ is obtained and compared to theory. The feasibility of applying coherent multidimensional spectroscopy to dilute cold gas phase samples is demonstrated in these experiments.

  15. Theoretical and experimental study of the Stark effect in the ground state of alkali atoms in helium crystals

    OpenAIRE

    2007-01-01

    This thesis work describes a detailed study of the Stark interaction in the ground state of cesium atoms trapped in a solid helium matrix. The motivation for the investigation of electric field effects on alkali species implanted in solid helium is related to the original main goal of our experimental activities, i.e., the measurement of a permanent atomic electric dipole moment (EDM). The existence of an atomic EDM simultaneously violates the discrete symmetries of time reversal (T) and pari...

  16. 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.

  17. A dead-zone free ⁴He atomic magnetometer with intensity-modulated linearly polarized light and a liquid crystal polarization rotator.

    Science.gov (United States)

    Wu, T; Peng, X; Lin, Z; Guo, H

    2015-10-01

    We demonstrate an all-optical (4)He atomic magnetometer experimental scheme based on an original Bell-Bloom configuration. A single intensity-modulated linearly polarized laser beam is used both for generating spin polarization within a single (4)He vapor and probing the spin precessing under a static magnetic field. The transmitted light signal from the vapor is then phase-sensitively detected at the modulation frequency and its harmonics, which lead to the atomic magnetic resonance signals. Based on this structure, a liquid crystal is added in our magnetometer system and constitutes a polarization rotator. By controlling the voltage applied on the liquid crystal, the light linear polarization vector can be kept perpendicular with the ambient magnetic field direction, which in turn provides the maximum resonance signal amplitude. Moreover, the system exhibits a magnetic-field noise floor of about 2pT/√Hz, which is not degraded due to the presence of the liquid crystal and varying magnetic field direction. The experiment results prove that our method can eliminate the dead-zone effect, improve the system spatial isotropy, and thus be suitable in mobile applications.

  18. IN-SITU AFM OF POLYMER CRYSTALLIZATION

    Institute of Scientific and Technical Information of China (English)

    J.K.Hobbs

    2003-01-01

    Atomic force microscopy images taken during the crystallization of polyethylene both from processed and quiescent melts are presented. Crystallization from processed melts provides further evidence of a region in front of a growing lamella that is influenced by the crystallization process, but extending only 40 nm into the melt. High-resolution images of the growing crystal tip, taken during crystallization, show no direct evidence of the existence of intermediate phases. The growing tip is shown to be slightly rounded. In-filling crystallization, occurring after the initial flush of growth,is imaged in polyethylene for the first time, and shown to continue to a temperature 8℃ below the initial crystallization temperature.

  19. IN—SITU AFM OF POLYMER CRYSTALLIZATION

    Institute of Scientific and Technical Information of China (English)

    J.K.Hobbs

    2003-01-01

    Atomic force microscopy images taken during the crystallization of polyethylene both from processed and quiescent melts are presented.Crystallization from processed melts provides further evidence of a region in front of a growing lamella that is influenced by the crystallization process,but extending only 40nm into the melt.High-resolution images of the growing crystal tip,taken during crystallization,show no direct evidence of the existence of intermediate phases.The growing tip is shown to be slightly rounded.In-filling crystallization,occurring after the initial flush of growth,is imaged in polyethylene for the first time,and shown to continue to a temperature 8℃ below the initial crystallization temperature.

  20. Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.

    Science.gov (United States)

    Zhang, H; Huang, K; Li, Z; Banerjei, L; Fisher, K E; Grishin, N V; Eisenstein, E; Herzberg, O

    2000-07-01

    Structural genomics of proteins of unknown function most straightforwardly assists with assignment of biochemical activity when the new structure resembles that of proteins whose functions are known. When a new fold is revealed, the universe of known folds is enriched, and once the function is determined by other means, novel structure-function relationships are established. The previously unannotated protein HI1434 from H. influenzae provides a hybrid example of these two paradigms. It is a member of a microbial protein family, labeled in SwissProt as YbaK and ebsC. The crystal structure at 1.8 A resolution reported here reveals a fold that is only remotely related to the C-lectin fold, in particular to endostatin, and thus is not sufficiently similar to imply that YbaK proteins are saccharide binding proteins. However, a crevice that may accommodate a small ligand is evident. The putative binding site contains only one invariant residue, Lys46, which carries a functional group that could play a role in catalysis, indicating that YbaK is probably not an enzyme. Detailed sequence analysis, including a number of newly sequenced microbial organisms, highlights sequence homology to an insertion domain in prolyl-tRNA synthetases (proRS) from prokaryote, a domain whose function is unknown. A HI1434-based model of the insertion domain shows that it should also contain the putative binding site. Being part of a tRNA synthetases, the insertion domain is likely to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. By analogy, YbaK may also play a role in nucleotide or oligonucleotide binding, the nature of which is yet to be determined.

  1. Crystal structure determination of an acidic neurotoxin (BmK M8) from scorpion Buthm martensii Karsch at 0.25nm resolution

    Institute of Scientific and Technical Information of China (English)

    李宏民; 金雷; 曾宗浩; 王淼; 张英; 王大成

    1996-01-01

    The crystal structure of an acidic neurotoxin, BmK M8, from Chinese scorpion Buthus martensii Karsch was determined at 0.25 nm resolution. The X-ray diffraction data of BmK M8 crystals at 0.25nm resolution were collected on a Siemens area detector. Using molecular replacement method with a basic scorpion toxin AaH II in a search model, the cross-rotation function, PC-refinement and translation function were calculated by X-PLOR program package. The correct orientation and position of BmK M8 molecule in crystal were determined in a resolution range of 1.5 - 0.35nm, The oystallographic refinement was further performed by stereo-chemical restrict least-square technique, followed by simulated annealing, slow-cooling protocols. The final crystallographic R-factor at 0.8-0.25 nm is 0.171. The standard deviations of bond length and bond angle from ideality are 0.001 7nm and 2.24° , respectively. The final model of BmK M8 structure is composed of a dense core of secondary structure elements by a stretch of α-

  2. Position Dependent Spontaneous Emission Spectra of a A-Type Atomic System Embedded in a Defective Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    S. Roshan Entezar

    2012-01-01

    We investigate the position dependent spontaneous emission spectra of a A-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.

  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%.

  4. A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

    Science.gov (United States)

    Salmon, Loïc; Bascom, Gavin; Andricioaei, Ioan; Al-Hashimi, Hashim M

    2013-04-10

    The ability to modulate alignment and measure multiple independent sets of NMR residual dipolar couplings (RDCs) has made it possible to characterize internal motions in proteins at atomic resolution and with time scale sensitivity ranging from picoseconds up to milliseconds. The application of such methods to the study of RNA dynamics, however, remains fundamentally limited by the inability to modulate alignment and by strong couplings between internal and overall motions that complicate the quantitative interpretation of RDCs. Here, we address this problem by showing that RNA alignment can be generally modulated, in a controlled manner, by variable elongation of A-form helices and that the information contained within the measured RDCs can be extracted even in the presence of strong couplings between motions and overall alignment via structure-based prediction of alignment. Using this approach, four RDC data sets, and a broad conformational pool obtained from a 8.2 μs molecular dynamics simulation, we successfully construct and validate an atomic resolution ensemble of human immunodeficiency virus type I transactivation response element RNA. This ensemble reveals local motions in and around the bulge involving changes in stacking and hydrogen-bonding interactions, which are undetectable by traditional spin relaxation and drive global changes in interhelical orientation. This new approach broadens the scope of using RDCs in characterizing the dynamics of nucleic acids.

  5. Absolute configuration and crystal packing for three chiral drugs prone to spontaneous resolution: Guaifenesin, methocarbamol and mephenesin

    Science.gov (United States)

    Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Krivolapov, Dmitry B.; Pashagin, Alexander V.; Litvinov, Igor A.

    2009-02-01

    Popular chiral drugs, guaifenesin, methocarbamol, and mephenesin were investigated by single-crystal X-ray analysis both for enantiopure and racemic samples. The absolute configurations for all substances were established through Flack parameter method. The conglomerate-forming nature for the compounds was confirmed by equivalence of crystal characteristics of enantiopure and racemic samples. The molecular structures and crystal packing details were evaluated and compared with one another for all three investigated substances.

  6. Atom probe tomography of secondary γ′ precipitation in a single crystal Ni-based superalloy after isothermal aging at 1100 °C

    Energy Technology Data Exchange (ETDEWEB)

    Tan, X.P., E-mail: xptan1985@gmail.com [IM 2NP, UMR 7334 CNRS, Université Aix-Marseille, 13397 Marseille Cedex 20 (France); Mangelinck, D.; Perrin-Pellegrino, C. [IM 2NP, UMR 7334 CNRS, Université Aix-Marseille, 13397 Marseille Cedex 20 (France); Rougier, L. [LSMX, MXG, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland); Gandin, Ch.-A. [CEMEF, UMR 7635 CNRS, MINES ParisTech, 06904 Sophia Antipolis (France); Jacot, A. [LSMX, MXG, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland); Ponsen, D.; Jaquet, V. [Snecma-SAFRAN Group, Service YQGC, 92702 Colombes (France)

    2014-10-25

    Highlights: • Bimodal size distribution of γ′ precipitates occurs after isothermal aging at 1100 °C. • Characterization of secondary γ′ by atom probe tomography. • It is proposed that the secondary γ′ occurs via a non-classical nucleation. • The coarsening of secondary γ′ precipitates well obeys the classical LSW theory. - Abstract: Secondary γ′ precipitation in a commercial single crystal Ni-based superalloy after the 1100 °C isothermal aging has been investigated by atom probe tomography. After the isothermal aging for 300 s, 1800 s and 3600 s, a bimodal size distribution of larger primary γ′ precipitates and numerous smaller secondary γ′ precipitates was obtained. It is proposed that the secondary γ′ precipitated via a non-classical nucleation mode. The coarsening of secondary γ′ precipitates well obeys the classical LSW theory.

  7. Crack nucleation using combined crystal plasticity modelling, high-resolution digital image correlation and high-resolution electron backscatter diffraction in a superalloy containing non-metallic inclusions under fatigue

    Science.gov (United States)

    Zhang, Tiantian; Jiang, Jun; Britton, Ben; Shollock, Barbara; Dunne, Fionn

    2016-05-01

    A crystal plasticity finite-element model, which explicitly and directly represents the complex microstructures of a non-metallic agglomerate inclusion within polycrystal nickel alloy, has been developed to study the mechanistic basis of fatigue crack nucleation. The methodology is to use the crystal plasticity model in conjunction with direct measurement at the microscale using high (angular) resolution-electron backscatter diffraction (HR-EBSD) and high (spatial) resolution-digital image correlation (HR-DIC) strain measurement techniques. Experimentally, this sample has been subjected to heat treatment leading to the establishment of residual (elastic) strains local to the agglomerate and subsequently loaded under conditions of low cyclic fatigue. The full thermal and mechanical loading history was reproduced within the model. HR-EBSD and HR-DIC elastic and total strain measurements demonstrate qualitative and quantitative agreement with crystal plasticity results. Crack nucleation by interfacial decohesion at the nickel matrix/agglomerate inclusion boundaries is observed experimentally, and systematic modelling studies enable the mechanistic basis of the nucleation to be established. A number of fatigue crack nucleation indicators are also assessed against the experimental results. Decohesion was found to be driven by interface tensile normal stress alone, and the interfacial strength was determined to be in the range of 1270-1480 MPa.

  8. X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.

    Science.gov (United States)

    Peters, J W; Lanzilotta, W N; Lemon, B J; Seefeldt, L C

    1998-12-01

    A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by x-ray crystallography using multiwavelength anomalous dispersion (MAD) phasing. CpI, an enzyme that catalyzes the two-electron reduction of two protons to yield dihydrogen, was found to contain 20 gram atoms of iron per mole of protein, arranged into five distinct [Fe-S] clusters. The probable active-site cluster, previously termed the H-cluster, was found to be an unexpected arrangement of six iron atoms existing as a [4Fe-4S] cubane subcluster covalently bridged by a cysteinate thiol to a [2Fe] subcluster. The iron atoms of the [2Fe] subcluster both exist with an octahedral coordination geometry and are bridged to each other by three non-protein atoms, assigned as two sulfide atoms and one carbonyl or cyanide molecule. This structure provides insights into the mechanism of biological hydrogen activation and has broader implications for [Fe-S] cluster structure and function in biological systems.

  9. 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...

  10. 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.

  11. Incorporating two different chromophores onto a silicon atom: the crystal structure and photophysical properties of 9-{4-[(9,9-dimethyl-9H-fluoren-2-yl)dimethylsilyl]phenyl}-9H-carbazole.

    Science.gov (United States)

    Lee, Ah-Rang; Han, Won-Sik

    2015-03-01

    The crystal structure of the title bifunctional silicon-bridged compound, C(35)H(31)NSi, (I), has been determined. The compound crystallizes in the centrosymmetric space group P2(1)/c. In the crystal structure, the pairs of aryl rings in the two different chromophores, i.e. 9-phenyl-9H-carbazole and 9,9-dimethyl-9H-fluorene, are positioned orthogonally. In the crystal packing, no classical hydrogen bonding is observed. UV-Vis absorption and fluorescence emission spectra show that the central Si atom successfully breaks the electronic conjugation between the two different chromophores, and this was further analysed by density functional theory (DFT) calculations.

  12. Reactive-Atom Scattering from Liquid Crystals at the Liquid-Vacuum Interface: [C12mim][BF4] and 4-Cyano-4'-Octylbiphenyl (8CB).

    Science.gov (United States)

    Purcell, Simon M; Tesa-Serrate, Maria A; Marshall, Brooks C; Bruce, Duncan W; D'Andrea, Lucía; Costen, Matthew L; Slattery, John M; Smoll, Eric J; Minton, Timothy K; McKendrick, Kenneth G

    2016-10-04

    Two complementary approaches were used to study the liquid-vacuum interface of the liquid-crystalline ionic liquid 1-dodecyl-3-methylimidazolium tetrafluoroborate ([C12mim][BF4]) in the smectic A (SmA) and isotropic phases. O atoms with two distinct incident translational energies were scattered from the surface of [C12mim][BF4]. Angle-dependent time-of-flight distributions and OH yields, respectively, were recorded from high- and low-energy O atoms. There were no significant changes in the measurements using either approach, nor the properties derived from them, accompanying the transition from the SmA to the isotropic phase. This indicates that the surface structure of [C12mim][BF4] remains essentially unchanged across the phase boundary, implying that the bulk order and surface structure are not strongly correlated for this material. This effect is ascribed to the strong propensity for the outer surfaces of ionic liquids to be dominated by alkyl chains, over an underlying layer rich in anions and cation head groups, whether or not the bulk material is a liquid crystal. In a comparative study, the OH yield from the surface of the liquid crystal, 8CB, was found to be affected by the bulk order, showing a surprising step increase at the SmA-nematic transition temperature, whose origin is the subject of speculation.

  13. Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.

    Science.gov (United States)

    Sun, Lei; Zhang, Xinzheng; Gao, Song; Rao, Prashant A; Padilla-Sanchez, Victor; Chen, Zhenguo; Sun, Siyang; Xiang, Ye; Subramaniam, Sriram; Rao, Venigalla B; Rossmann, Michael G

    2015-07-06

    The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.

  14. External Heavy-Atom Effect via Orbital Interactions Revealed by Single-Crystal X-ray Diffraction.

    Science.gov (United States)

    Sun, Xingxing; Zhang, Baicheng; Li, Xinyang; Trindle, Carl O; Zhang, Guoqing

    2016-07-28

    Enhanced spin-orbit coupling through external heavy-atom effect (EHE) has been routinely used to induce room-temperature phosphorescence (RTP) for purely organic molecular materials. Therefore, understanding the nature of EHE, i.e., the specific orbital interactions between the external heavy atom and the luminophore, is of essential importance in molecular design. For organic systems, halogens (e.g., Cl, Br, and I) are the most commonly seen heavy atoms serving to realize the EHE-related RTP. In this report, we conduct an investigation on how heavy-atom perturbers and aromatic luminophores interact on the basis of data obtained from crystallography. We synthesized two classes of molecular systems including N-haloalkyl-substituted carbazoles and quinolinium halides, where the luminescent molecules are considered as "base" or "acid" relative to the heavy-atom perturbers, respectively. We propose that electron donation from a π molecular orbital (MO) of the carbazole to the σ* MO of the C-X bond (π/σ*) and n electron donation to a π* MO of the quinolinium moiety (n/π*) are responsible for the EHE (RTP) in the solid state, respectively.

  15. High-resolution X-ray focusing concave (elliptical) curved crystal spectrograph for laser-produced plasma

    Institute of Scientific and Technical Information of China (English)

    Shali xiao(肖沙里); Yingjun Pan(潘英俊); Xianxin Zhong(钟先信); Xiancai Xiong(熊先才); Guohong Yang(杨国洪); Zongli Liu(刘宗礼); Yongkun Ding(丁永坤)

    2004-01-01

    The X-ray spectrum emitted from laser-produced plasma contains plentiful information.X-ray spectrometer is a powerful tool for plasma diagnosis and studying the information and evolution of the plasma.X-ray concave(elliptical)curved crystals analyzer was designed and manufactured to investigate the properties of laser-produced plasma.The experiment was carried out on Mianyang Xingguang-ⅡFacility and aimed at investigating the characteristics of a high density iron plasma.Experimental results using KAP,LIF,PET,and MICA curved crystal analyzers are described,and the spectra of Au,Ti laser-produced plasma are shown.The focusing crystal analyzer clearly gave an increase in sensitivity over a flat crystal.

  16. Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy

    Science.gov (United States)

    Cartagena, Alexander; Hernando-Pérez, Mercedes; Carrascosa, José L.; de Pablo, Pedro J.; Raman, Arvind

    2013-05-01

    Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the study of structure-property-function relationships. We present an in vitro dynamic AFM technique operating in the intermittent contact regime which synthesizes anharmonic Lorentz-force excited AFM cantilevers to map quantitatively at nanometer resolution the local electro-mechanical force gradient, adhesion, and hydration layer viscosity within individual φ29 virions. Furthermore, the changes in material properties over the entire φ29 virion provoked by the local disruption of its shell are studied, providing evidence of bacteriophage depressurization. The technique significantly generalizes recent multi-harmonic theory (A. Raman, et al., Nat. Nanotechnol., 2011, 6, 809-814) and enables high-resolution in vitro quantitative mapping of multiple material properties within weakly bonded viruses and nanoparticles with complex structure that otherwise cannot be observed using standard AFM techniques.Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the

  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. The role of symmetry in the theory of inelastic high-energy electron scattering and its application to atomic-resolution core-loss imaging.

    Science.gov (United States)

    Dwyer, C

    2015-04-01

    The inelastic scattering of a high-energy electron in a solid constitutes a bipartite quantum system with an intrinsically large number of excitations, posing a considerable challenge for theorists. It is demonstrated how and why the utilization of symmetries, or approximate symmetries, can lead to significant improvements in both the description of the scattering physics and the efficiency of numerical computations. These ideas are explored thoroughly for the case of core-loss excitations, where it is shown that the coupled angular momentum basis leads to dramatic improvements over the bases employed in previous work. The resulting gains in efficiency are demonstrated explicitly for K-, L- and M-shell excitations, including such excitations in the context of atomic-resolution imaging in the scanning transmission electron microscope. The utilization of other symmetries is also discussed.

  19. Atomic-resolution characterization of the effects of CdCl{sub 2} treatment on poly-crystalline CdTe thin films

    Energy Technology Data Exchange (ETDEWEB)

    Paulauskas, T., E-mail: tpaula2@uic.edu; Buurma, C.; Colegrove, E.; Guo, Z.; Sivananthan, S.; Klie, R. F. [Department of Physics, University of Illinois at Chicago, 845 W. Taylor St. M/C 273, Chicago, Illinois 60607-7059 (United States); Chan, M. K. Y. [Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Building 440, Argonne, Illinois 60439 (United States)

    2014-08-18

    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 CdCl{sub 2} 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 CdCl{sub 2}, 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. Morphological stability of the atomically clean surface of silicon (100) crystals after microwave plasma-chemical processing

    Energy Technology Data Exchange (ETDEWEB)

    Yafarov, R. K., E-mail: pirpc@yandex.ru; Shanygin, V. Ya. [Russian Academy of Sciences, Saratov Branch of the Kotel’nikov Institute of Radio Engineering and Electronics (Russian Federation)

    2016-01-15

    The morphological stability of atomically clean silicon (100) surface after low-energy microwave plasma-chemical etching in various plasma-forming media is studied. It is found that relaxation changes in the surface density and atomic bump heights after plasma processing in inert and chemically active media are multidirectional in character. After processing in a freon-14 medium, the free energy is minimized due to a decrease in the surface density of microbumps and an increase in their height. After argon-plasma processing, an insignificant increase in the bump density with a simultaneous decrease in bump heights is observed. The physicochemical processes causing these changes are considered.

  1. Preparation of the Crystal Complex of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis with Coenzyme A and Investigation of Its Three-Dimensional Structure at 2.1-Å Resolution

    Science.gov (United States)

    Timofeev, V. I.; Smirnova, E. A.; Chupova, L. A.; Esipov, R. S.; Kuranova, I. P.

    2010-11-01

    Recombinant phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPAT Mt), which was produced by a high-producing strain and purified to 99%, was used for the crystal growth of the complex of the enzyme with coenzyme A (CoA). Crystals suitable for X-ray diffraction study were obtained by cocrystallization. The crystals belong to sp. gr. R32 and have the unit-cell parameters a = b = 98.840 Å, c = 112.880 Å, α = β = 90.00°, and γ = 120.00°. The three-dimensional structure of the complex was determined based on X-ray diffraction data collected from the crystals to 2.1 Å resolution and refined to Rf = 22.7% and Rfree = 25.93%. Active-site bound coenzyme A was found, and its nearest environment was described. The conformational changes of the enzyme due to ligand binding were revealed. The binding of CoA by tuberculosis phosphopantetheine adenylyltransferase was characterized by comparing the structures of the title complex to a similar complex of PPAT from E. coli (PPAT Ec).

  2. Preparation of the Crystal Complex of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis with Coenzyme A and Investigation of Its Three-Dimensional Structure at 2.1-A Resolution

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, V. I.; Smirnova, E. A., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Chupova, L. A.; Esipov, R. S. [Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-11-15

    Recombinant phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPAT Mt), which was produced by a high-producing strain and purified to 99%, was used for the crystal growth of the complex of the enzyme with coenzyme A (CoA). Crystals suitable for X-ray diffraction study were obtained by cocrystallization. The crystals belong to sp. gr. R32 and have the unit-cell parameters a = b = 98.840 A, c = 112.880 A, {alpha} = {beta} = 90.00{sup o}, and {gamma} = 120.00{sup o}. The three-dimensional structure of the complex was determined based on X-ray diffraction data collected from the crystals to 2.1 A resolution and refined to Rf = 22.7% and Rfree = 25.93%. Active-site bound coenzyme A was found, and its nearest environment was described. The conformational changes of the enzyme due to ligand binding were revealed. The binding of CoA by tuberculosis phosphopantetheine adenylyltransferase was characterized by comparing the structures of the title complex to a similar complex of PPAT from E. coli (PPAT Ec).

  3. Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole.

    Science.gov (United States)

    Asztalos, Peter; Müller, Astrid; Hölke, Werner; Sobek, Harald; Rudolph, Markus G

    2014-07-01

    Lysobacter enzymogenes lysyl endoproteinase (LysC) is a trypsin-type serine protease with a high pH optimum that hydrolyses all Lys-Xaa peptide bonds. The high specificity of LysC renders it useful for biotechnological purposes. The K30R variant of a related lysyl endoproteinase from Achromobacter lyticus has favourable enzymatic properties that might be transferrable to LysC. To visualize structural differences in the substrate-binding sites, the crystal structures of wild-type and the K30R variant of LysC were determined. The mutation is located at a distance of 12 Å from the catalytic triad and subtly changes the surface properties of the substrate-binding site. The high pH optimum of LysC can be attributed to electrostatic effects of an aromatic Tyr/His stack on the catalytic aspartate and is a general feature of this enzyme subfamily. LysC crystals in complex with the covalent inhibitor N(α)-p-tosyl-lysyl chloromethylketone yielded data to 1.1 and 0.9 Å resolution, resulting in unprecedented precision of the active and substrate-binding sites for this enzyme subfamily. Error estimates on bond lengths and difference electron density indicate that instead of the expected oxyanion a hydroxyl group binds to the partially solvent-exposed oxyanion hole. Protonation of the alkoxide catalytic intermediate might be a recurring feature during serine protease catalysis.

  4. Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift.

    Science.gov (United States)

    Fenn, Timothy D; Ringe, Dagmar; Petsko, Gregory A

    2004-06-01

    Xylose isomerase (E.C. 5.3.1.5) catalyzes the interconversion of aldose and ketose sugars and has an absolute requirement for two divalent cations at its active site to drive the hydride transfer rates of sugar isomerization. Evidence suggests some degree of metal movement at the second metal site, although how this movement may affect catalysis is unknown. The 0.95 A resolution structure of the xylitol-inhibited enzyme presented here suggests three alternative positions for the second metal ion, only one of which appears positioned in a catalytically competent manner. To complete the reaction, an active site hydroxyl species appears appropriately positioned for hydrogen transfer, as evidenced by precise bonding distances. Conversely, the 0.98 A resolution structure of the enzyme with glucose bound in the alpha-pyranose state only shows one of the metal ion conformations at the second metal ion binding site, suggesting that the linear form of the sugar is required to promote the second and third metal ion conformations. The two structures suggest a strong degree of conformational flexibility at the active site, which seems required for catalysis and may explain the poor rate of turnover for this enzyme. Further, the pyranose structure implies that His53 may act as the initial acid responsible for ring opening of the sugar to the aldose form, an observation that has been difficult to establish in previous studies. The glucose ring also appears to display significant segmented disorder in a manner suggestive of ring opening, perhaps lending insight into means of enzyme destabilization of the ground state to promote catalysis. On the basis of these results, we propose a modified version of the bridged bimetallic mechanism for hydride transfer in the case of Streptomyces olivochromogenes xylose isomerase.

  5. High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand

    DEFF Research Database (Denmark)

    Taskinen, Jukka P; van Aalten, Daan M; Knudsen, Jens;

    2007-01-01

    The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described....... The binding of the acyl-CoA molecule induces only few structural differences near the binding pocket. The crystal form of the liganded ACBP, which has two ACBP molecules in the asymmetric unit, shows that in human ACBP the same acyl-CoA binding pocket is present as previously described for the bovine...... and Plasmodium falciparum ACBP and the mode of binding of the 3'-phosphate-AMP moiety is conserved. Unexpectedly, in one of the acyl-CoA binding pockets the acyl moiety is bound in a reversed mode as compared with the bovine and P. falciparum structures. In this binding mode, the myristoyl-CoA molecule is fully...

  6. Characterization of x-ray imaging crystal spectrometer for high-resolution spatially-resolved x-ray Thomson scattering measurements in shock-compressed experiments

    Science.gov (United States)

    Lu, J.; Hill, K. W.; Bitter, M.; Pablant, N. A.; Delgado-Aparicio, L. F.; Efthimion, P. C.; Lee, H. J.; Zastrau, U.

    2017-01-01

    We have proposed, designed and built a dual-channel x-ray imaging crystal spectrometer (XICS) for spectrally- and spatially-resolved x-ray Thomson scattering (XRTS) measurements in the Matter in Extreme Conditions (MEC) end station at the Linac Coherent Light Source (LCLS). This spectrometer employs two spherically-bent germanium (Ge) 220 crystals, which are combined to form a large aperture dispersive element with a spectral bandwidth of 300 eV that enables both the elastic and inelastic x-ray scattering peaks to be simultaneously measured. The apparatus and its characterization are described. A resolving power of 1900 was demonstrated and a spatial resolution of 12 μm was achieved in calibration tests. For XRTS measurements, a narrow-bandwidth (ΔE/Ecarbon plasma produced in shock-compressed samples of different forms of carbon. Preliminary results of the scattering experiments from Pyrolytic Graphite samples that illustrate the utility of the instrument are presented.

  7. Deformable elastic network refinement for low-resolution macromolecular crystallography.

    Science.gov (United States)

    Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

    2014-09-01

    Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  8. Achieving error-free translation; the mechanism of proofreading of threonyl-tRNA synthetase at atomic resolution.

    Science.gov (United States)

    Dock-Bregeon, Anne-Catherine; Rees, Bernard; Torres-Larios, Alfredo; Bey, Gilbert; Caillet, Joel; Moras, Dino

    2004-11-05

    The fidelity of aminoacylation of tRNA(Thr) by the threonyl-tRNA synthetase (ThrRS) requires the discrimination of the cognate substrate threonine from the noncognate serine. Misacylation by serine is corrected in a proofreading or editing step. An editing site has been located 39 A away from the aminoacylation site. We report the crystal structures of this editing domain in its apo form and in complex with the serine product, and with two nonhydrolyzable analogs of potential substrates: the terminal tRNA adenosine charged with serine, and seryl adenylate. The structures show how serine is recognized, and threonine rejected, and provide the structural basis for the editing mechanism, a water-mediated hydrolysis of the mischarged tRNA. When the adenylate analog binds in the editing site, a phosphate oxygen takes the place of one of the catalytic water molecules, thereby blocking the reaction. This rules out a correction mechanism that would occur before the binding of the amino acid on the tRNA.

  9. Mapping chemical/structural order in double perovskite Sr2-xGdxMnTiO6 by atomic resolution electron microscopy

    Science.gov (United States)

    Alvarez, Inmaculada; Biskup, Neven; Lopez, Maria; Garcia-Hernandez, Mar; Veiga, Luisa; Varela, Maria; UCM Collaboration; ORNL Collaboration; CSIC Collaboration

    2013-03-01

    We report on visualizing the chemical and structural order of double perovskite Sr2-xGdxMnTiO6. The antisite disorder of Mn and Ti is detected even at atomic scale at all x, resulting in Mn-rich and Ti-rich regions. For x ?0.75, the majority of manganese ions are in Mn3+ state and are centered in Jahn-Teller distorted MnO6octahedra. The Fourier transformation of atomic resolution images along the [110] zone axis reveals a superstructure that corresponds to the tilting of oxygen octahedra and that doubles the unit cell along [001]c. This superstructure is spatially inhomogeneous and coincides with the regions where B-site ion (Mn/Ti) is displaced along the [110] direction. We discuss these findings in the frame of possible local ferroelectricity and in the light of strong electroresistance observed in Sr1.25Gd0.75MnTiO6. Research at ORNL supported by the U.S. DOE-BES, Materials Sciences and Engineering Division, and also by ORNL's ShaRE User Program (sponsored by DOE-BES). Research at UCM supported by the ERC Starting Investigator Award and MAT2010-20117.

  10. Evaluation of solid sampling for determination of Mo, Ni, Co, and V in soil by high-resolution continuum source graphite furnace atomic absorption spectrometry

    Science.gov (United States)

    Babos, Diego Victor; Barros, Ariane Isis; Ferreira, Edilene Cristina; Neto, José Anchieta Gomes

    2017-04-01

    New methods are proposed for the determination of Mo, Ni, Co, and V in soils using high-resolution continuum source graphite furnace atomic absorption spectrometry with direct solid sampling. Cobalt and V were simultaneously determined, and different analytical lines of Ni and V were monitored to adjust sensitivity for each sample. Accuracy was checked by means of soil certified reference materials, and also by flame atomic absorption spectrometry as comparative technique. The results for Mo, Ni, Co, and V found by proposed methods were in agreement with certified values and with those obtained by the comparative technique at 95% confidence level. The concentrations found in different soil samples were in the ranges 0.19-1.84 mg kg- 1 (Mo), 9.2-22.7 mg kg- 1 (Ni), 1.1-10.7 mg kg- 1 (Co), and 35.6-426.1 mg kg- 1 (V). The relative standard deviations were in the ranges 3.2-10% (Mo), 2.8-9.8% (Ni), 4.0-9.2% (Co), and 1.2-8.0% (V). The limits of quantification for Mo, Ni, Co, and V were 0.027, 0.071, 0.15, and 1.43 ng, respectively.

  11. Evaluation of solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry for direct determination of chromium in medicinal plants

    Energy Technology Data Exchange (ETDEWEB)

    Virgilio, Alex; Nobrega, Joaquim A. [Department of Chemistry, Federal University of Sao Carlos, Post Office Box 676, 13560-970, Sao Carlos-SP (Brazil); Rego, Jardes F. [Department of Analytical Chemistry, Institute of Chemistry, Sao Paulo State University-UNESP, Post Office Box 355, 14801-970, Araraquara-SP (Brazil); Neto, Jose A. Gomes, E-mail: anchieta@iq.unesp.br [Department of Analytical Chemistry, Institute of Chemistry, Sao Paulo State University-UNESP, Post Office Box 355, 14801-970, Araraquara-SP (Brazil)

    2012-12-01

    A method for Cr determination in medicinal plants using direct solid sampling graphite furnace high-resolution continuum source atomic absorption spectrometry was developed. Modifiers were dispensable. Pyrolysis and atomization temperatures were 1500 Degree-Sign C and 2400 Degree-Sign C, respectively. Slopes of calibration curves (50-750 pg Cr, R{sup 2} > 0.999) using aqueous and solid standards coincides in 96%, indicated feasibility of aqueous calibration for solid sampling of medicinal plants. Accuracy was checked by analysis of four plant certified reference materials. Results were in agreement at 95% confidence level with certified and non-certified values. Ten samples of medicinal plants were analyzed and Cr contents were in the 1.3-17.7 {mu}g g{sup -1} Cr range. The highest RSD (n = 5) was 15.4% for the sample Melissa officinalis containing 13.9 {+-} 2.1 {mu}g g{sup -1} Cr. The limit of detection was 3.3 ng g{sup -1} Cr. - Highlights: Black-Right-Pointing-Pointer Direct solid sampling is first time employed for Cr in plant materials. Black-Right-Pointing-Pointer Calibration curves with liquids and solids are coincident. Black-Right-Pointing-Pointer Microanalysis of plants for Cr is validated by reference materials. Black-Right-Pointing-Pointer The proposed HR-CS GF AAS method is environmental friendly.

  12. Evaluation of solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry for direct determination of chromium in medicinal plants

    Science.gov (United States)

    Virgilio, Alex; Nóbrega, Joaquim A.; Rêgo, Jardes F.; Neto, José A. Gomes

    2012-12-01

    A method for Cr determination in medicinal plants using direct solid sampling graphite furnace high-resolution continuum source atomic absorption spectrometry was developed. Modifiers were dispensable. Pyrolysis and atomization temperatures were 1500 °C and 2400 °C, respectively. Slopes of calibration curves (50-750 pg Cr, R2 > 0.999) using aqueous and solid standards coincides in 96%, indicated feasibility of aqueous calibration for solid sampling of medicinal plants. Accuracy was checked by analysis of four plant certified reference materials. Results were in agreement at 95% confidence level with certified and non-certified values. Ten samples of medicinal plants were analyzed and Cr contents were in the 1.3-17.7 μg g- 1 Cr range. The highest RSD (n = 5) was 15.4% for the sample Melissa officinalis containing 13.9 ± 2.1 μg g- 1 Cr. The limit of detection was 3.3 ng g- 1 Cr.

  13. Simultaneous determination of iron and nickel in fluoropolymers by solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry.

    Science.gov (United States)

    Soares, Bruno M; Santos, Rafael F; Bolzan, Rodrigo C; Muller, Edson I; Primel, Ednei G; Duarte, Fabio A

    2016-11-01

    This paper reports the development of a method of simultaneous determination of iron and nickel in fluoropolymers by high-resolution continuum source graphite furnace atomic absorption spectrometry (HR-CS GF AAS) with direct solid sampling. In order to carry out simultaneous measurements, both the main resonance line of nickel (232.003nm) and the adjacent secondary line of iron (232.036nm) were monitored in the same spectral window. The proposed method was optimized with a perfluoroalkoxy (PFA) sample and was applied to the determination of iron and nickel in fluorinated ethylene propylene (FEP) and modified polytetrafluoroethylene (PTFE-TFM) samples. Pyrolysis and atomization temperatures, as well as the use of Pd and H2 (during pyrolysis) as chemical modifiers, were carefully investigated. Compromise temperatures for pyrolysis and atomization of both analytes were achieved at 800 and 2300°C, respectively, using only 0.5Lmin(-1) H2 as chemical modifier during pyrolysis. Calibration curves were performed with aqueous standards by using a single solution which contained both analytes. Limits of detection were 221 and 9.6ngg(-1) for iron and nickel, respectively. Analyte concentrations in all samples ranged from 3.53 to 12.4µgg(-1) for iron and from 37 to 78ngg(-1) for nickel, with relative standard deviation less than 19%. Accuracy was evaluated by comparing these results with those obtained by inductively coupled plasma mass spectrometry after sample digestion by microwave-induced combustion and no significant statistical difference was observed.

  14. Monitoring and Method development of Hg in Istanbul Airborne Particulates by Solid Sampling Continuum Source-High Resolution Electrothermal Atomic Absorption Spectromerty

    Directory of Open Access Journals (Sweden)

    Soydemir E.

    2014-07-01

    Full Text Available In this work, a method has been developed and monitoring for the determination of mercury in PM2.5 airborne particulates by solid sampling high-resolution continuum source electrothermal atomic absorption spectrometry. The PM2.5 airborne particulates were collected on quartz filters using high volume samplers (500 L/min in Istanbul (Turkey for 96 hours every month in one year. At first, experimental conditions as well as the validation tests were optimized using collected filter. For this purpose, the effects of atomization temperature, amount of sample intoduced in to the furnace, addition of acids and/or KMnO4 on the sample, covering of graphite tube and platform or using of Ag nanoparticulates, Au nanoparticulates, and Pd solutions on the accuracy and precision were investigated. After optimization of the experimental conditions, the mercury concentrations were determined in the collected filter. The filters with PM2.5 airborne particulates were dried, divided into small fine particles and then Hg concentrations were determined directly. In order to eliminate any error due to the sensitivity difference between aqueous standards and solid samples, the quantification was performed using solid calibrants. The limit of detection, based on three times the standard deviations for ten atomizations of an unused filter, was 30 ng/g. The Hg content was dependent on the sampling site, season etc, ranging from

  15. The atomic geometries of GaP(110) and ZnS(110) revisited - A structural ambiguity and its resolution

    Science.gov (United States)

    Duke, C. B.; Paton, A.; Kahn, A.

    1984-01-01

    The atomic geometries of GaP(110) and ZnS(110) are reexamined using the R-factor minimization procedure, developed for GaAs(110) and previously applied to GaSb(110), ZnTe(110), InAs(110), and AlP(110), to analyze experimental elastic low-energy electron diffraction intensities. Unlike most of the earlier cases, both GaP(110) and ZnS(110) exhibit two distinct minimum-Rx structures which cannot be distinguished by analysis of the shapes of the intensity profiles alone. One region of best-fit structures exhibits top-layer displacements normal to the surface characterized by a small bond-length-conserving, top-layer rotation (omega aproximately 2-3 deg), a small relaxation of the top layer away from the surface, and a 10 percent expansion of the top-layer bond length. The other region of best-fit structures is the conventional one: nearly bond-length-conserving rotations of omega = 26-28 deg in the top layer and a small (approximately 0.1 A) contraction of the uppermost layer spacing. This ambiguity may be removed, however, by consideration of the integrated beam intensities. The conventional region of structural parameters provides a decisively better description of the relative magnitudes of the integrated beam intensities and hence is the preferred structure.

  16. OZSPEC-2: an improved broadband high-resolution elliptical crystal x-ray spectrometer for high-energy density physics experiments (invited).

    Science.gov (United States)

    Heeter, R F; Anderson, S G; Booth, R; Brown, G V; Emig, J; Fulkerson, S; McCarville, T; Norman, D; Schneider, M B; Young, B K F

    2008-10-01

    A novel time, space, and energy-resolved x-ray spectrometer has been developed which produces, in a single snapshot, a broadband and relatively calibrated spectrum of the x-ray emission from a high-energy density laboratory plasma. The opacity zipper spectrometer (OZSPEC-1) records a nearly continuous spectrum for x-ray energies from 240 to 5800 eV in a single shot. The second-generation OZSPEC-2, detailed in this work, records fully continuous spectra on a single shot from any two of these three bands: 270-650, 660-1580, and 1960-4720 eV. These instruments thus record thermal and line radiation from a wide range of plasmas. These instruments' single-shot bandwidth is unmatched in a time-gated spectrometer; conversely, other broadband instruments are either time-integrated (using crystals or gratings), lack spectral resolution (diode arrays), or cover a lower energy band (gratings). The OZSPECs are based on the zipper detector, a large-format (100x35 mm) gated microchannel plate detector, with spectra dispersed along the 100 mm dimension. OZSPEC-1 and -2 both use elliptically bent crystals of OHM, RAP, and/or PET. Individual spectra are gated in 100 ps. OZSPEC-2 provides one-dimensional spatial imaging with 30-50 microm resolution over a 1500 microm field of view at the source. The elliptical crystal design yields broad spectral coverage with resolution E/DeltaE>500, strong rejection of hard x-ray backgrounds, and negligible source broadening for extended sources. Near-term applications include plasma opacity measurements, detailed spectra of inertial fusion Hohlraums, and laboratory astrophysics experiments.

  17. Local symmetry breaking of a thin crystal structure of β-Si3N4 as revealed by spherical aberration corrected high-resolution transmission electron microscopy images.

    Science.gov (United States)

    Kim, Hwang Su; Zhang, Zaoli; Kaiser, Ute

    2012-06-01

    This report is an extension of the study for structural imaging of 5-6 nm thick β-Si(3)N(4) [0001] crystal with a spherical aberration corrected transmission electron microscope by Zhang and Kaiser [2009. Structure imaging of β-Si(3)N(4) by spherical aberration-corrected high-resolution transmission electron microscopy. Ultramicroscopy 109, 1114-1120]. In this work, a local symmetry breaking with an uneven resolution of dumbbells in the six-membered rings revealed in the reported images in the study of Zhang and Kaiser has been analyzed in detail. It is found that this local asymmetry in the image basically is not relevant to a slight mistilt of the specimen and/or a beam tilt (coma). Rather the certain variation of the tetrahedral bond length of Si-N(4) in the crystal structure is found to be responsible for the uneven resolution with a local structural variation from region to region. This characteristic of the variation is also supposed to give a distorted lattice of apparently 2°-2.5° deviations from the perfect hexagonal unit cell as observed in the reported image in the work of Zhang and Kaiser. It is discussed that this variation may prevail only in a thin specimen with a thickness ranging ~≤ 5-6 nm. At the same time, it is noted that the average of the bond length variation is close to the fixed length known in a bulk crystal of β-Si(3)N(4).

  18. Crystal structures at 2.5 Angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate

    DEFF Research Database (Denmark)

    Belrhali, H.; Yaremchuk, A.; Tukalo, M.;

    1994-01-01

    Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 Angstrom resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically...... in a deep hydrophilic cleft formed by the antiparallel beta sheet and surrounding loops of the synthetase catalytic domain. Four regions in the primary sequence are involved in the interactions, including the motif 2 and 3 regions of class 2 synthetases. Apart from the specific recognition of the serine...

  19. New protein fold revealed by a 1.65 Å resolution crystal structure of Francisella tularensis pathogenicity island protein IglC

    Science.gov (United States)

    Sun, Ping; Austin, Brian P.; Schubot, Florian D.; Waugh, David S.

    2007-01-01

    Francisella tularensis is a highly infectious Gram-negative intracellular pathogen that causes the fulminating disease tularemia and is considered to be a potential bioweapon. F. tularensis pathogenicity island proteins play a key role in modulating phagosome biogenesis and subsequent bacterial escape into the cytoplasm of macrophages. The 23 kDa pathogenicity island protein IglC is essential for the survival and proliferation of F. tularensis in macrophages. Seeking to gain some insight into its function, we determined the crystal structure of IglC at 1.65 Å resolution. IglC adopts a β-sandwich conformation that exhibits no similarity with any known protein structure. PMID:17905833

  20. Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0.

    Science.gov (United States)

    Chiu, Po-Lin; Li, Xueming; Li, Zongli; Beckett, Brian; Brilot, Axel F; Grigorieff, Nikolaus; Agard, David A; Cheng, Yifan; Walz, Thomas

    2015-11-01

    The K2 Summit camera was initially the only commercially available direct electron detection camera that was optimized for high-speed counting of primary electrons and was also the only one that implemented centroiding so that the resolution of the camera can be extended beyond the Nyquist limit set by the physical pixel size. In this study, we used well-characterized two-dimensional crystals of the membrane protein aquaporin-0 to characterize the performance of the camera below and beyond the physical Nyquist limit and to measure the influence of electron dose rate on image amplitudes and phases.

  1. High-resolution high-speed dynamic mechanical spectroscopy of cells and other soft materials with the help of atomic force microscopy.

    Science.gov (United States)

    Dokukin, M; Sokolov, I

    2015-07-28

    Dynamic mechanical spectroscopy (DMS), which allows measuring frequency-dependent viscoelastic properties, is important to study soft materials, tissues, biomaterials, polymers. However, the existing DMS techniques (nanoindentation) have limited resolution when used on soft materials, preventing them from being used to study mechanics at the nanoscale. The nanoindenters are not capable of measuring cells, nanointerfaces of composite materials. Here we present a highly accurate DMS modality, which is a combination of three different methods: quantitative nanoindentation (nanoDMA), gentle force and fast response of atomic force microscopy (AFM), and Fourier transform (FT) spectroscopy. This new spectroscopy (which we suggest to call FT-nanoDMA) is fast and sensitive enough to allow DMS imaging of nanointerfaces, single cells, while attaining about 100x improvements on polymers in both spatial (to 10-70 nm) and temporal resolution (to 0.7 s/pixel) compared to the current art. Multiple frequencies are measured simultaneously. The use of 10 frequencies are demonstrated here (up to 300 Hz which is a rather relevant range for biological materials and polymers, in both ambient conditions and liquid). The method is quantitatively verified on known polymers and demonstrated on cells and polymers blends. Analysis shows that FT-nanoDMA is highly quantitative. The FT-nanoDMA spectroscopy can easily be implemented in the existing AFMs.

  2. High-resolution high-speed dynamic mechanical spectroscopy of cells and other soft materials with the help of atomic force microscopy

    Science.gov (United States)

    Dokukin, M.; Sokolov, I.

    2015-01-01

    Dynamic mechanical spectroscopy (DMS), which allows measuring frequency-dependent viscoelastic properties, is important to study soft materials, tissues, biomaterials, polymers. However, the existing DMS techniques (nanoindentation) have limited resolution when used on soft materials, preventing them from being used to study mechanics at the nanoscale. The nanoindenters are not capable of measuring cells, nanointerfaces of composite materials. Here we present a highly accurate DMS modality, which is a combination of three different methods: quantitative nanoindentation (nanoDMA), gentle force and fast response of atomic force microscopy (AFM), and Fourier transform (FT) spectroscopy. This new spectroscopy (which we suggest to call FT-nanoDMA) is fast and sensitive enough to allow DMS imaging of nanointerfaces, single cells, while attaining about 100x improvements on polymers in both spatial (to 10–70 nm) and temporal resolution (to 0.7s/pixel) compared to the current art. Multiple frequencies are measured simultaneously. The use of 10 frequencies are demonstrated here (up to 300 Hz which is a rather relevant range for biological materials and polymers, in both ambient conditions and liquid). The method is quantitatively verified on known polymers and demonstrated on cells and polymers blends. Analysis shows that FT-nanoDMA is highly quantitative. The FT-nanoDMA spectroscopy can easily be implemented in the existing AFMs. PMID:26218346

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-05-19

    A high-resolution X-ray imaging crystal spectrometer, whose instrumental concept was thoroughly tested on NSTX and Alcator C-Mod, is presently being designed for LHD. The instrument will record spatially resolved spectra of helium-like Ar16+ and provide ion temperature profiles with spatial and temporal resolutions of 1 cm and > 10 ms which are obtained by a tomographic inversion of the spectral data, using the stellarator equilibrium reconstruction codes, STELLOPT and PIES. Since the spectrometer will be equipped with radiation hardened, high count rate, PILATUS detectors,, it is expected to be operational for all experimental conditions on LHD, which include plasmas of high density and plasmas with auxiliary RF and neutral beam heating. The special design features required by the magnetic field structure at LHD will be described.

  4. Atomic resolution view into the structure-function relationships of the human myelin peripheral membrane protein P2.

    Science.gov (United States)

    Ruskamo, Salla; Yadav, Ravi P; Sharma, Satyan; Lehtimäki, Mari; Laulumaa, Saara; Aggarwal, Shweta; Simons, Mikael; Bürck, Jochen; Ulrich, Anne S; Juffer, André H; Kursula, Inari; Kursula, Petri

    2014-01-01

    P2 is a fatty acid-binding protein expressed in vertebrate peripheral nerve myelin, where it may function in bilayer stacking and lipid transport. P2 binds to phospholipid membranes through its positively charged surface and a hydrophobic tip, and accommodates fatty acids inside its barrel structure. The structure of human P2 refined at the ultrahigh resolution of 0.93 Å allows detailed structural analyses, including the full organization of an internal hydrogen-bonding network. The orientation of the bound fatty-acid carboxyl group is linked to the protonation states of two coordinating arginine residues. An anion-binding site in the portal region is suggested to be relevant for membrane interactions and conformational changes. When bound to membrane multilayers, P2 has a preferred orientation and is stabilized, and the repeat distance indicates a single layer of P2 between membranes. Simulations show the formation of a double bilayer in the presence of P2, and in cultured cells wild-type P2 induces membrane-domain formation. Here, the most accurate structural and functional view to date on P2, a major component of peripheral nerve myelin, is presented, showing how it can interact with two membranes simultaneously while going through conformational changes at its portal region enabling ligand transfer.

  5. Efficient phase contrast imaging in STEM using a pixelated detector. Part 1: Experimental demonstration at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Pennycook, Timothy J., E-mail: tpennycook@gmail.com [EPSRC SuperSTEM Facility, Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Lupini, Andrew R. [Oak Ridge National Laboratory, Materials Science and Technology Division, Oak Ridge, TN 37830 (United States); Yang, Hao [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Murfitt, Matthew F. [Nion Co., 1102 8th St., Kirkland, WA 98033 (United States); Jones, Lewys [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Nellist, Peter D. [EPSRC SuperSTEM Facility, Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom)

    2015-04-15

    We demonstrate a method to achieve high efficiency phase contrast imaging in aberration corrected scanning transmission electron microscopy (STEM) with a pixelated detector. The pixelated detector is used to record the Ronchigram as a function of probe position which is then analyzed with ptychography. Ptychography has previously been used to provide super-resolution beyond the diffraction limit of the optics, alongside numerically correcting for spherical aberration. Here we rely on a hardware aberration corrector to eliminate aberrations, but use the pixelated detector data set to utilize the largest possible volume of Fourier space to create high efficiency phase contrast images. The use of ptychography to diagnose the effects of chromatic aberration is also demonstrated. Finally, the four dimensional dataset is used to compare different bright field detector configurations from the same scan for a sample of bilayer graphene. Our method of high efficiency ptychography produces the clearest images, while annular bright field produces almost no contrast for an in-focus aberration-corrected probe. - Highlights: • Ptychographic high efficiency phase contrast imaging is demonstrated in STEM. • We rely on a hardware aberration corrector to eliminate aberrations. • High efficiency is achieved by collecting all the relevant interference. • Use of a pixelated detector allows comparison of bright field modes post acquisition. • Ptychography provides the clearest images among the STEM bright field modes tested.

  6. Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations.

    Science.gov (United States)

    Kraft, Johan F; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea

    2012-05-08

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A. Kukol fails to maintain stable micelles, whereas the most recent CHARMM36 lipid parameters and GROMOS96 with the so-called Berger lipid parameters both succeed in this regard.

  7. Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

    Science.gov (United States)

    Croll, Tristan Ian; Andersen, Gregers Rom

    2016-09-01

    While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement.

  8. Crystal Dislocations

    Directory of Open Access Journals (Sweden)

    Ronald W. Armstrong

    2016-01-01

    Full Text Available Crystal dislocations were invisible until the mid-20th century although their presence had been inferred; the atomic and molecular scale dimensions had prevented earlier discovery. Now they are normally known to be just about everywhere, for example, in the softest molecularly-bonded crystals as well as within the hardest covalently-bonded diamonds. The advent of advanced techniques of atomic-scale probing has facilitated modern observations of dislocations in every crystal structure-type, particularly by X-ray diffraction topography and transmission electron microscopy. The present Special Issue provides a flavor of their ubiquitous presences, their characterizations and, especially, their influence on mechanical and electrical properties.

  9. Spectral aspects of the determination of Si in organic and aqueous solutions using high-resolution continuum source or line source flame atomic absorption spectrometry

    Science.gov (United States)

    Kowalewska, Zofia; Pilarczyk, Janusz; Gościniak, Łukasz

    2016-06-01

    High-resolution continuum source flame atomic absorption spectrometry (HR-CS FAAS) was applied to reveal and investigate spectral interference in the determination of Si. An intensive structured background was observed in the analysis of both aqueous and xylene solutions containing S compounds. This background was attributed to absorption by the CS molecule formed in the N2O-C2H2 flame. The lines of the CS spectrum at least partially overlap all five of the most sensitive Si lines investigated. The 251.611 nm Si line was demonstrated to be the most advantageous. The intensity of the structured background caused by the CS molecule significantly depends on the chemical form of S in the solution and is the highest for the most-volatile CS2. The presence of O atoms in an initial S molecule can diminish the formation of CS. To overcome this S effect, various modes of baseline fitting and background correction were evaluated, including iterative background correction (IBC) and utilization of correction pixels (WRC). These modes were used either independently or in conjunction with least squares background correction (LSBC). The IBC + LSBC mode can correct the extremely strong interference caused by CS2 at an S concentration of 5% w:w in the investigated solution. However, the efficiency of this mode depends on the similarity of the processed spectra and the correction spectra in terms of intensity and in additional effects, such as a sloping baseline. In the vicinity of the Si line, three lines of V were recorded. These lines are well-separated in the HR-CS FAAS spectrum, but they could be a potential source of overcorrection when using line source flame atomic absorption spectrometry (LS FAAS). The expected signal for the 251.625 nm Fe line was not registered at 200 mg L- 1 Fe concentration in the solution, probably due to the diminished population of Fe atoms in the high-temperature flame used. The observations made using HR-CS FAAS helped to establish a "safe" level

  10. Crystal Growth and Characterization of Ca3NbGa3Si2O14 Single Crystal

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Single crystals of Ca3NbGa3Si2O14 (CNGS) with ordered Ca3Ga2Ge4O14 (CGG) structure were successfully grown from stoichiometric melts by conventional Czochralski technique along the a-axis and two large (001) facets and two small (100) facets appear in every crystal. An arrangement of parallel steps and a clear height change were observed in (001) facet by atomic force microscopy (AFM). High-resolution X-ray diffraction (HRXRD) results indicate that CNGS crystals have good quality and free low-angle boundaries. The crystals also exhibit good optical quality and high optical transmittance in c-direction.

  11. 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.

  12. 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

  13. High-resolution insights into episodes of crystallization, hydrothermal alteration and remelting in the Skaergaard intrusive complex

    Science.gov (United States)

    Wotzlaw, Jörn-Frederik; Bindeman, Ilya N.; Schaltegger, Urs; Brooks, C. Kent; Naslund, H. Richard

    2012-11-01

    This paper presents a new high-precision zircon U-Pb geochronological view on the crystallization and assembly process of one of the most important and intensely studied intrusive bodies on Earth—the Skaergaard intrusion in East Greenland. With analytical uncertainties of a few tens of thousands of years, we were able to resolve several important events during cooling of this intrusion. Initial cooling of the shallowly intruded ˜300 km3 of tholeiitic basaltic magma from liquidus to zircon saturation at ˜1000 °C is recorded by a precise zircon crystallization age of 55.960±0.018 Ma of an intercumulus gabbroic pegmatite in the lower portion of the intrusion. Based on this zircon crystallization age and a published cooling model we estimate the "true" age of emplacement to be ˜56.02 Ma. The last portions of Skaergaard appear to crystallize completely ˜100 ka after emplacement as recorded by abundant ˜55.91-55.93 Ma zircons in the Sandwich Horizon (SH), where lower and upper solidification fronts met. Intrusion of an isotopically distinct new magma batch, the ˜600 m thick Basistoppen Sill, into the solidified upper portion of Skaergaard, happened at 55.895±0.018 Ma, suggesting close timing between crystallization of evolved rocks around the SH and intrusion of the Basistoppen Sill. The novel result of this work is the demonstration that zircons in the SH, >100 m below the Basistoppen contact, have a bimodal age distribution, with the youngest population of 55.838±0.019 Ma postdating intrusion of the Basistoppen Sill by 57±37 ka. Oxygen isotope analyses reveal that SH zircons are low and heterogeneous with respect to δ18O. These results support the proposed conclusion that the SH crystallized twice: it was fully crystalline, then hydrothermally-altered by low-δ18O surface waters and subsequently partially remelted, triggered by heat of the Basistoppen Sill. The low-degree partial melt generated during remelting partially migrated upward by intergranular

  14. Determination of Iron in Layered Crystal Sodium Disilicate and Sodium Silicate by Flame Atomic Absorption Spectrometry with Boric Acid as a Matrix Modifier

    Institute of Scientific and Technical Information of China (English)

    Zhi Hua WANG; Min CAI; Shu Jun WANG

    2006-01-01

    The effects of matrix silicate and experimental conditions on the determination of iron in flame atomic absorption spectrometry (FAAS) were investigated. It was found that boric acid as a matrix modifier obviously eliminated silicate interference. Under the optimum operating conditions, the determination results of iron in layered crystal sodium disilicate and sodium silicate samples by FAAS were satisfactory. The linear range of calibration curve is 0-10.5 μg.mL-1, the relative standard deviation of method is 1.2%-2.2%, the recovery of added iron is 96.0%-101%, the of iron of the standard curve method, standard addition calibration and colorimetry method was the same, but the first has the merits of rapid sample preparation, reduced contamination risks and fast analysis.

  15. Interface Properties of Atomic-Layer-Deposited Al2O3 Thin Films on Ultraviolet/Ozone-Treated Multilayer MoS2 Crystals.

    Science.gov (United States)

    Park, Seonyoung; Kim, Seong Yeoul; Choi, Yura; Kim, Myungjun; Shin, Hyunjung; Kim, Jiyoung; Choi, Woong

    2016-05-11

    We report the interface properties of atomic-layer-deposited Al2O3 thin films on ultraviolet/ozone (UV/O3)-treated multilayer MoS2 crystals. The formation of S-O bonds on MoS2 after low-power UV/O3 treatment increased the surface energy, allowing the subsequent deposition of uniform Al2O3 thin films. The capacitance-voltage measurement of Au-Al2O3-MoS2 metal oxide semiconductor capacitors indicated n-type MoS2 with an electron density of ∼10(17) cm(-3) and a minimum interface trap density of ∼10(11) cm(-2) eV(-1). These results demonstrate the possibility of forming a high-quality Al2O3-MoS2 interface by proper UV/O3 treatment, providing important implications for their integration into field-effect transistors.

  16. On the lipid-bacterial protein interaction studied by quartz crystal microbalance with dissipation, transmission electron microscopy and atomic force microscopy

    CERN Document Server

    Delcea, Mihaela; Pum, Dietmar; Sleytr, Uwe Bernd; Toca-Herrera, Jose Luis

    2009-01-01

    The interaction between the bacterial S-protein SbpA on different types of lipid membranes has been studied using atomic force microscopy, transmission electron microscopy, and quartz crystal microbalance with dissipation. On one hand, It has been found that the bacterial forms two dimensional nanocrystals on zwitterionic DOPC bilayers and negatively charged DMPG vesicles adsorbed on mica, on zwitterionic DPPC and charged DPPC/DMPG (1:1) monolayers adsorbed on carbon grids. On the other hand, SbpA protein adsorption took place on zwitterionic DOPC bilayers and DOPC/DOPS (4:1) bilayers, previously adsorbed on silicon supports. SbpA adsorption also took place on DPPC/DOPS (1:1) monolayers adsorbed on carbon grids. Finally, neither SbpA adsorption, nor recrystallization was observed on zwitterionic DMPC vesicles (previously adsorbed on polyelectrolyte multilayers), and on DPPC vesicles supported on silicon.

  17. High resolution crystal structure of Clostridium propionicum β-alanyl-CoA:ammonia lyase, a new member of the "hot dog fold" protein superfamily.

    Science.gov (United States)

    Heine, Andreas; Herrmann, Gloria; Selmer, Thorsten; Terwesten, Felix; Buckel, Wolfgang; Reuter, Klaus

    2014-09-01

    Clostridium propionicum is the only organism known to ferment β-alanine, a constituent of coenzyme A (CoA) and the phosphopantetheinyl prosthetic group of holo-acyl carrier protein. The first step in the fermentation is a CoA-transfer to β-alanine. Subsequently, the resulting β-alanyl-CoA is deaminated by the enzyme β-alanyl-CoA:ammonia lyase (Acl) to reversibly form ammonia and acrylyl-CoA. We have determined the crystal structure of Acl in its apo-form at a resolution of 0.97 Å as well as in complex with CoA at a resolution of 1.59 Å. The structures reveal that the enyzme belongs to a superfamily of proteins exhibiting a so called "hot dog fold" which is characterized by a five-stranded antiparallel β-sheet with a long α-helix packed against it. The functional unit of all "hot dog fold" proteins is a homodimer containing two equivalent substrate binding sites which are established by the dimer interface. In the case of Acl, three functional dimers combine to a homohexamer strongly resembling the homohexamer formed by YciA-like acyl-CoA thioesterases. Here, we propose an enzymatic mechanism based on the crystal structure of the Acl·CoA complex and molecular docking.

  18. Focusing bent perfect-crystal neutron monochromator a key to high-resolution stress/strain measurement studies of polycrystalline materials

    CERN Document Server

    Ono, M; Harjo, S; Saroun, J; Yoneda, K; Sawano, J; Sakurai, Y; Kobayashi, T

    2000-01-01

    A new neutron focusing device with bent Si-single crystal has been installed at high-resolution neutron diffractometer dedicated to strain/stress investigations in polycrystalline materials and introduced into routine operation as a neutron strain scanner using reactor neutrons from supermirror guider at Kyoto University Research Reactor (KUR). Properties of the diffractometer are described on the basis of experimental results when one slab or two slabs of curved Si single crystals are employed as monochromator:i.e. 1) the luminosity 2) the absolute value of monochromatic neutrons with the Au-foil activation method, 3) beam profiles with the imaging plate method, 4) characterization of the diffractometer with alpha Fe (211) peak and its comparison with the Bragg optical prediction. It is confirmed that the FWHM of the instrumental delta d/d-profile of the peak can be less than 3*10/sup -3/ at d=1.17 A and the resolution permits us to investigate both the macro- and microstrains with good luminosity. The lumin...

  19. High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Shuxia, E-mail: pengsx@ihep.ac.cn; Zhou, Ke; Wang, Wenjia; Gao, Zengqiang; Dong, Yuhui; Liu, Quansheng

    2014-10-31

    Highlights: • Crystal structure of the C-terminal (CT) domain of Swt1 was determined at 2.3 Å. • Structure of the CT domain was identified as HEPN domain superfamily member. • Low-resolution envelope of Swt1 full-length in solution was analyzed by SAXS. • The middle and CT domains gave good fit to SAXS structural model. - Abstract: Swt1 is an RNA endonuclease that plays an important role in quality control of nuclear messenger ribonucleoprotein particles (mRNPs) in eukaryotes; however, its structural details remain to be elucidated. Here, we report the crystal structure of the C-terminal (CT) domain of Swt1 from Saccharomyces cerevisiae, which shares common characteristics of higher eukaryotes and prokaryotes nucleotide binding (HEPN) domain superfamily. To study in detail the full-length protein structure, we analyzed the low-resolution architecture of Swt1 in solution using small angle X-ray scattering (SAXS) method. Both the CT domain and middle domain exhibited a good fit upon superimposing onto the molecular envelope of Swt1. Our study provides the necessary structural information for detailed analysis of the functional role of Swt1, and its importance in the process of nuclear mRNP surveillance.

  20. Determination of crystal growth rates during rapid solidification of polycrystalline aluminum by nano-scale spatio-temporal resolution in situ transmission electron microscopy

    Science.gov (United States)

    Zweiacker, K.; McKeown, J. T.; Liu, C.; LaGrange, T.; Reed, B. W.; Campbell, G. H.; Wiezorek, J. M. K.

    2016-08-01

    In situ investigations of rapid solidification in polycrystalline Al thin films were conducted using nano-scale spatio-temporal resolution dynamic transmission electron microscopy. Differences in crystal growth rates and asymmetries in melt pool development were observed as the heat extraction geometry was varied by controlling the proximity of the laser-pulse irradiation and the associated induced melt pools to the edge of the transmission electron microscopy support grid, which acts as a large heat sink. Experimental parameters have been established to maximize the reproducibility of the material response to the laser-pulse-related heating and to ensure that observations of the dynamical behavior of the metal are free from artifacts, leading to accurate interpretations and quantifiable measurements with improved precision. Interface migration rate measurements revealed solidification velocities that increased consistently from ˜1.3 m s-1 to ˜2.5 m s-1 during the rapid solidification process of the Al thin films. Under the influence of an additional large heat sink, increased crystal growth rates as high as 3.3 m s-1 have been measured. The in situ experiments also provided evidence for development of a partially melted, two-phase region prior to the onset of rapid solidification facilitated crystal growth. Using the experimental observations and associated measurements as benchmarks, finite-element modeling based calculations of the melt pool evolution after pulsed laser irradiation have been performed to obtain estimates of the temperature evolution in the thin films.

  1. 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.

  2. SINGLE CRYSTAL NEUTRON DIFFRACTION.

    Energy Technology Data Exchange (ETDEWEB)

    KOETZLE,T.F.

    2001-03-13

    Single-crystal neutron diffraction measures the elastic Bragg reflection intensities from crystals of a material, the structure of which is the subject of investigation. A single crystal is placed in a beam of neutrons produced at a nuclear reactor or at a proton accelerator-based spallation source. Single-crystal diffraction measurements are commonly made at thermal neutron beam energies, which correspond to neutron wavelengths in the neighborhood of 1 Angstrom. For high-resolution studies requiring shorter wavelengths (ca. 0.3-0.8 Angstroms), a pulsed spallation source or a high-temperature moderator (a ''hot source'') at a reactor may be used. When complex structures with large unit-cell repeats are under investigation, as is the case in structural biology, a cryogenic-temperature moderator (a ''cold source'') may be employed to obtain longer neutron wavelengths (ca. 4-10 Angstroms). A single-crystal neutron diffraction analysis will determine the crystal structure of the material, typically including its unit cell and space group, the positions of the atomic nuclei and their mean-square displacements, and relevant site occupancies. Because the neutron possesses a magnetic moment, the magnetic structure of the material can be determined as well, from the magnetic contribution to the Bragg intensities. This latter aspect falls beyond the scope of the present unit; for information on magnetic scattering of neutrons see Unit 14.3. Instruments for single-crystal diffraction (single-crystal diffractometers or SCDs) are generally available at the major neutron scattering center facilities. Beam time on many of these instruments is available through a proposal mechanism. A listing of neutron SCD instruments and their corresponding facility contacts is included in an appendix accompanying this unit.

  3. Damage creation in silicon single crystals irradiated with 200 keV/atom Au{sub n}{sup +} clusters

    Energy Technology Data Exchange (ETDEWEB)

    Canut, B. E-mail: bruno.canut@dpmsun1.univ-lyon1.fr; Fallavier, M.; Marty, O.; Ramos, S.M.M

    2000-04-01

    Silicon wafers of (1 0 0) orientation were irradiated with Au{sub n} cluster beams (1{<=}n{<=}7) produced by the 2.5 MV Van de Graaff accelerator of the Institut de Physique Nucleaire de Lyon equipped with a liquid metal source. The incident energy was of 200 keV per gold atom, which corresponds to a slowing-down mainly governed by elastic processes (nuclear energy loss of Au{sup +} ions: 3 keV nm{sup -1}). All the irradiations were performed at room temperature with fluences up to 5x10{sup 14} Au (at. cm{sup -2}). The typical beam currents varied from 1.5 nA for Au{sup +} down to 20 pA for Au{sub 7}{sup +}. The radiation-induced disorder was measured by means of Rutherford backscattering spectrometry in channeling geometry (RBS-C), using a {sup 4}He{sup +} beam accelerated at 2 MV. From the fluence evolution of the lattice disorder at the target surface, we evidence that polyatomic projectiles produce more defects per incident atom than single Au{sup +} ions. As an example we measured damage cross-sections per incident Au atom of 12.5 and 2.7 nm{sup 2} for Au{sub 7}{sup +} and Au{sup +} projectiles, respectively. This cluster effect was ascribed to the high density of nuclear energy deposited within the cascade. Transmission electron microscopy (TEM) was performed on samples irradiated at low fluences (10{sup 9} at. cm{sup -2}) in order to visualize each projectile impact.

  4. 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.)

  5. Potential and piezoelectric response imaging of 180^o domain of atomically ordered clean surfaces of BaTiO3 single crystals in UHV

    Science.gov (United States)

    Watanabe, Yukio; Kaku, S.; Matsumoto, D.; Cheong, S. W.

    2009-03-01

    We report the electrostatic and piezoelectric properties of the clean, free surface of BaTiO3 single crystal in ultra high vacuum (UHV) The topographic imaging by AFM confirmed that the surface is atomically wellordered exhibiting clear one-lattice-height atomic steps. The amplitude and the phase image of piezoelectric response microscopy (PFM) identified 180^o domains. The electrostatic potential mapping by Kelvin force microscopy (KFM) of these domains revealed that the shapes of the domains agreed exactly with the PFM images, which confirms the correctness of the standard 180^o domain theory and disagrees with closure domains. However, the potential difference of upward and downward domain is approx. 0.1V, which is 100 times smaller than the value estimated by the standard theory. Similar measurements with changing temperature across Curie temperature show that this result cannot be explained by the compensation of the spontaneous polarization by contamination or oxygen deficiency or ionic conduction). The present results suggest that an intrinsic electrostatic shielding mechanism exists for 180^o domains, which is consistent with the reports of surface electron/hole layers [1]. [4pt] [1] Watanabe et al. PRL86332(2001);Ferroelectr.367, 23(2008) We acknowledge JSPS No.19340084.

  6. Synthesis of Mixed Tail Triphenylene Discotic Liquid Crystals:Molecular Symmetry and Oxygen-Atom Effect on the Stabilization of Columnar Mesophases

    Institute of Scientific and Technical Information of China (English)

    ZHAO Ke-Qing; HU Ping; WANG Bi-Qin; YU Wen-Hao; CHEN Hong-Mei; WANG Xin-Ling; SHIMIZU Yo

    2007-01-01

    Small change in chemical structure of discotic liquid crystals can cause big difference in their mesomorphism.Replacing of the alkoxy peripheral chains of triphenylene by oxygen-atom containing ester chains would result in novel mesomorphism. A series of mixed tail triphenylenes containing propoxyacetyloxy and alkoxy, abbreviated as C18H6(OCnH2n+1)3(OCOCH2OC3H7)3, n=4-8, and hexa(propyloxyacetyloxy)triphenylene, C18H6(OCOCH2OC3H7)6 were synthesized. Thermal gravimetry analysis (TGA) of three discogens showed that they had good thermal stability till 350℃. The mesomorphism was investigated through differential scanning calorimetry (DSC)and polarized optical microscopy (POM). The preliminary X-ray diffraction (XRD) results of one compound showed that it exhibited ordered hexagonal columnar (Colho) mesophase. These mixed tail triphenylene derivatives possessed much stable Colho mesophase and wider mesophase ranges than their hexaalkoxytriphenylene C18H6(OR)6 and hexaalkanoyloxytriphenylene C18H6(OCOR')6 analogues. The asymmetrical compounds 2,6,11-trialkoxy-3,7,10-tri(2-propyloxyacetyloxy)triphenylenes with n=5-8 displayed higher clearing points and wider temperature ranges than their symmetrical isomers 2,6,10-trialkoxy-3,7,11-tri(2-propyloxyacetyloxy)triphenylenes, while C18H6(OCOCH2OC3H7)6 had the highest clearing point due to the β-oxygen-atom effect.

  7. DHS Internship Summary-Crystal Assembly at Different Length Scales

    Energy Technology Data Exchange (ETDEWEB)

    Mishchenko, L

    2009-08-06

    I was part of a project in which in situ atomic force microscopy (AFM) was used to monitor growth and dissolution of atomic and colloidal crystals. At both length scales, the chemical environment of the system greatly altered crystal growth and dissolution. Calcium phosphate was used as a model system for atomic crystals. A dissolution-reprecipitation reaction was observed in this first system, involving the conversion of brushite (DCPD) to octacalcium phosphate (OCP). In the second system, polymeric colloidal crystals were dissolved in an ionic solvent, revealing the underlying structure of the crystal. The dissolved crystal was then regrown through an evaporative step method. Recently, we have also found that colloids can be reversibly deposited in situ onto an ITO (indium tin oxide) substrate via an electrochemistry setup. The overall goal of this project was to develop an understanding of the mechanisms that control crystallization and order, so that these might be controlled during material synthesis. Controlled assembly of materials over a range of length scales from molecules to nanoparticles to colloids is critical for designing new materials. In particular, developing materials for sensor applications with tailorable properties and long range order is important. In this work, we examine two of these length scales: small molecule crystallization of calcium phosphate (whose crystal phases include DCPD, OCP, and HAP) and colloidal crystallization of Poly(methyl methacrylate) beads. Atomic Force Microscopy is ideal for this line of work because it allows for the possibility of observing non-conducting samples in fluid during growth with high resolution ({approx} 10 nm). In fact, during atomic crystal growth one can observe changes in atomic steps, and with colloidal crystals, one can monitor the individual building blocks of the crystal. Colloids and atoms crystallize under the influence of different forces acting at different length scales as seen in Table 1

  8. Determination of mercury in airborne particulate matter collected on glass fiber filters using high-resolution continuum source graphite furnace atomic absorption spectrometry and direct solid sampling

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Rennan G.O., E-mail: rgoa01@terra.com.br [Laboratorio de Quimica Analitica Ambiental, Departamento de Quimica, Universidade Federal de Sergipe, Campus Sao Cristovao, 49.100-000, Sao Cristovao, SE (Brazil); Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900, Florianopolis, SC (Brazil); Vignola, Fabiola; Castilho, Ivan N.B. [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900, Florianopolis, SC (Brazil); Borges, Daniel L.G.; Welz, Bernhard [Departamento de Quimica, Universidade Federal de Santa Catarina, 88040-900, Florianopolis, SC (Brazil); Instituto Nacional de Ciencia e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador, BA (Brazil); Vale, Maria Goreti R. [Instituto Nacional de Ciencia e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador, BA (Brazil); Instituto de Quimica, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS (Brazil); Smichowski, Patricia [Comision Nacional de Energia Atomica (CNEA) and Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires (Argentina); Ferreira, Sergio L.C. [Instituto Nacional de Ciencia e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador, BA (Brazil); Instituto de Quimica, Universidade Federal da Bahia, 40170-290, Salvador, BA (Brazil); Becker-Ross, Helmut [Leibniz-Institut fuer Analytische Wissenschaften-ISAS-e.V., Department Berlin, 12489 Berlin (Germany)

    2011-05-15

    A study has been undertaken to assess the capability of high-resolution continuum source graphite furnace atomic absorption spectrometry for the determination of mercury in airborne particulate matter (APM) collected on glass fiber filters using direct solid sampling. The main Hg absorption line at 253.652 nm was used for all determinations. The certified reference material NIST SRM 1648 (Urban Particulate Matter) was used to check the accuracy of the method, and good agreement was obtained between published and determined values. The characteristic mass was 22 pg Hg. The limit of detection (3{sigma}), based on ten atomizations of an unexposed filter, was 40 ng g{sup -1}, corresponding to 0.12 ng m{sup -3} in the air for a typical air volume of 1440 m{sup 3} collected within 24 h. The limit of quantification was 150 ng g{sup -1}, equivalent to 0.41 ng m{sup -3} in the air. The repeatability of measurements was better than 17% RSD (n = 5). Mercury concentrations found in filter samples loaded with APM collected in Buenos Aires, Argentina, were between < 40 ng g{sup -1} and 381 {+-} 24 ng g{sup -1}. These values correspond to a mercury concentration in the air between < 0.12 ng m{sup -3} and 1.47 {+-} 0.09 ng m{sup -3}. The proposed procedure was found to be simple, fast and reliable, and suitable as a screening procedure for the determination of mercury in APM samples.

  9. Determinations of Sb and Mo in Cairo's dust using high-resolution continuum source graphite furnace atomic absorption spectrometry and direct solid sample analysis

    Science.gov (United States)

    Shaltout, Abdallah A.; Welz, Bernhard; Castilho, Ivan N. B.

    2013-12-01

    The present work describes the determination of Sb and Mo in dust deposited on tree leaves using direct solid sample analysis. Nineteen air particulate samples were collected from different districts of Cairo and surrounding cities. Since some samples have been taken from places less exposed to the pollution factors, the present study allows the comparison of air quality between high and low polluted areas. High-resolution continuum source graphite furnace atomic absorption spectrometry has been investigated, using direct solid sample analysis. The optimum pyrolysis and atomization temperatures for Sb were found to be 800 °C and 1900 °C, and 1200 °C and 2650 °C, respectively for Mo. The limits of detection and quantification for both, Sb and Mo, were 15 μg g-1 and 50 ng g-1, respectively. The characteristic mass at was found to be m0 = 38 pg for Sb (217.582 nm) and m0 = 28 pg for Mo (313.259 nm). The results obtained for three certified reference materials of urban particulate matter confirmed the validity of the investigated method. The content of Sb varied between 213 ± 1.3 μg g-1 and 1117 ± 230 μg g-1 with an average of 667 ± 339 μg g-1. On the other hand, the Mo content varied from 113 ± 2.3 μg g-1 to 361 ± 51 μg g-1 and its average value equals 190 ± 62 μg g-1.

  10. Direct and simultaneous determination of Cr and Fe in crude oil using high-resolution continuum source graphite furnace atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Dittert, Ingrid M. [Departamento de Quimica, Universidade Federal de Santa Catarina, Campus Universitario, Trindade, 88040-900, Florianopolis, SC (Brazil); Silva, Jessee S.A. [Centro Federal de Educacao Tecnologica de Santa Catarina, Florianopolis, SC (Brazil); Araujo, Rennan G.O. [Departamento de Quimica, Universidade Federal de Santa Catarina, Campus Universitario, Trindade, 88040-900, Florianopolis, SC (Brazil)], E-mail: rgoa01@terra.com.br; Curtius, Adilson J.; Welz, Bernhard [Departamento de Quimica, Universidade Federal de Santa Catarina, Campus Universitario, Trindade, 88040-900, Florianopolis, SC (Brazil); Becker-Ross, Helmut [ISAS, Institute for Analytical Sciences, Department of Interface Spectroscopy, Albert-Einstein-Str. 9, 12489 Berlin (Germany)

    2009-06-15

    A simple, fast and sensitive direct method for the simultaneous determination of Cr and Fe in crude oil samples is proposed using high-resolution continuum source graphite furnace atomic absorption spectrometry. No sample preparation is used except for a 10-minute homogenization in an ultrasonic bath. Aliquots of 0.1-4 mg of the samples are weighed onto solid sampling platforms and analyzed directly using aqueous standards for calibration. The simultaneous determination was possible because there is a secondary Fe line at 358.120 nm in the vicinity of the most sensitive Cr line at 357.868 nm, and both absorption lines were within the wavelength interval covered by the linear charge-coupled device array detector. It has also been of advantage that the sensitivity ratio between the two analytical lines corresponded roughly to the concentration ratio of the two elements found in crude oil, and that both analytes have very similar volatility, so that no compromises had to be made regarding pyrolysis and atomization temperatures. Two oil reference materials have been analyzed and the results were in agreement with the certified or reported values. Characteristic masses of 3.6 pg and 0.5 ng were obtained for Cr and Fe, respectively. The limits of detection (3{sigma}, n = 10) were 1 {mu}g kg{sup - 1} for Cr and 0.6 mg kg{sup - 1} for Fe, and the precision, expressed as the relative standard deviation, ranged from 4 to 20%, which is often acceptable for a rapid direct analytical procedure. Five crude oils samples were analyzed.

  11. Direct and simultaneous determination of Cr and Fe in crude oil using high-resolution continuum source graphite furnace atomic absorption spectrometry

    Science.gov (United States)

    Dittert, Ingrid M.; Silva, Jessee S. A.; Araujo, Rennan G. O.; Curtius, Adilson J.; Welz, Bernhard; Becker-Ross, Helmut

    2009-06-01

    A simple, fast and sensitive direct method for the simultaneous determination of Cr and Fe in crude oil samples is proposed using high-resolution continuum source graphite furnace atomic absorption spectrometry. No sample preparation is used except for a 10-minute homogenization in an ultrasonic bath. Aliquots of 0.1-4 mg of the samples are weighed onto solid sampling platforms and analyzed directly using aqueous standards for calibration. The simultaneous determination was possible because there is a secondary Fe line at 358.120 nm in the vicinity of the most sensitive Cr line at 357.868 nm, and both absorption lines were within the wavelength interval covered by the linear charge-coupled device array detector. It has also been of advantage that the sensitivity ratio between the two analytical lines corresponded roughly to the concentration ratio of the two elements found in crude oil, and that both analytes have very similar volatility, so that no compromises had to be made regarding pyrolysis and atomization temperatures. Two oil reference materials have been analyzed and the results were in agreement with the certified or reported values. Characteristic masses of 3.6 pg and 0.5 ng were obtained for Cr and Fe, respectively. The limits of detection (3 σ, n = 10) were 1 µg kg - 1 for Cr and 0.6 mg kg - 1 for Fe, and the precision, expressed as the relative standard deviation, ranged from 4 to 20%, which is often acceptable for a rapid direct analytical procedure. Five crude oils samples were analyzed.

  12. A simple and fast method for assessment of the nitrogen–phosphorus–potassium rating of fertilizers using high-resolution continuum source atomic and molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Bechlin, Marcos André; Fortunato, Felipe Manfroi; Moutinho da Silva, Ricardo; Ferreira, Edilene Cristina; Gomes Neto, José Anchieta, E-mail: anchieta@iq.unesp.br

    2014-11-01

    The determination of N, P, and K in fertilizers by high-resolution continuum source flame atomic and molecular absorption spectrometry is proposed. Under optimized conditions, measurements of the diatomic molecules NO and PO at 215.360 and 247.620 nm, respectively, and K using the wing of the alternative line at 404.722 nm allowed calibration curves to be constructed in the ranges 500–5000 mg L{sup −1} N (r = 0.9994), 100–2000 mg L{sup −1} P (r = 0.9946), and 100–2500 mg L{sup −1} K (r = 0.9995). Commercial fertilizers were analyzed by the proposed method and the concentrations of N, P, and K were found to be in agreement with those obtained by Kjeldahl, spectrophotometric, and flame atomic emission spectrometry methods, respectively, at a 95% confidence level (paired t-test). A phosphate rock certified reference material (CRM) was analyzed and the results for P and K were in agreement with the reference values. Recoveries from spiked CRM were in the ranges 97–105% (NO{sub 3}{sup −}-N), 95–103% (NH{sub 4}{sup +}-N), 93–103% (urea-N), 99–108% (P), and 99–102% (K). The relative standard deviations (n = 12) for N, P, and K were 6, 4, and 2%, respectively. - Highlights: • A single technique is proposed to analyze NPK fertilizer. • HR-CS FAAS is proposed for the first time for N, P and K determination in fertilizers. • The method employs the same sample preparation and dilution for the three analytes. • Addition of H{sub 2}O{sub 2} allows analysis of fertilizers with different nitrogen species. • Proposal provides advantages over traditional methods in terms of cost and time.

  13. Direct determination of chromium in infant formulas employing high-resolution continuum source electrothermal atomic absorption spectrometry and solid sample analysis.

    Science.gov (United States)

    Silva, Arlene S; Brandao, Geovani C; Matos, Geraldo D; Ferreira, Sergio L C

    2015-11-01

    The present work proposed an analytical method for the direct determination of chromium in infant formulas employing the high-resolution continuum source electrothermal atomic absorption spectrometry combined with the solid sample analysis (SS-HR-CS ET AAS). Sample masses up to 2.0mg were directly weighted on a solid sampling platform and introduced into the graphite tube. In order to minimize the formation of carbonaceous residues and to improve the contact of the modifier solution with the solid sample, a volume of 10 µL of a solution containing 6% (v/v) H2O2, 20% (v/v) ethanol and 1% (v/v) HNO3 was added. The pyrolysis and atomization temperatures established were 1600 and 2400 °C, respectively, using magnesium as chemical modifier. The calibration technique was evaluated by comparing the slopes of calibration curves established using aqueous and solid standards. This test revealed that chromium can be determined employing the external calibration technique using aqueous standards. Under these conditions, the method developed allows the direct determination of chromium with limit of quantification of 11.5 ng g(-1), precision expressed as relative standard deviation (RSD) in the range of 4.0-17.9% (n=3) and a characteristic mass of 1.2 pg of chromium. The accuracy was confirmed by analysis of a certified reference material of tomato leaves furnished by National Institute of Standards and Technology. The method proposed was applied for the determination of chromium in five different infant formula samples. The chromium content found varied in the range of 33.9-58.1 ng g(-1) (n=3). These samples were also analyzed employing ICP-MS. A statistical test demonstrated that there is no significant difference between the results found by two methods. The chromium concentrations achieved are lower than the maximum limit permissible for chromium in foods by Brazilian Legislation.

  14. Extensive simulation studies on the reconstructed image resolution of a position sensitive detector based on pixelated CdTe crystals

    CERN Document Server

    Zachariadou, K; Kaissas, I; Seferlis, S; Lambropoulos, C; Loukas, D; Potiriadis, C

    2011-01-01

    We present results on the reconstructed image resolution of a position sensitive radiation instrument (COCAE) based on extensive simulation studies. The reconstructed image resolution has been investigated in a wide range of incident photon energies emitted by point-like sources located at different source-to-detector distances on and off the detector's symmetry axis. The ability of the detector to distinguish multiple radioactive sources observed simultaneously is investigating by simulating point-like sources of different energies located on and off the detector's symmetry axis and at different positions

  15. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

    Science.gov (United States)

    Das, Debanu; Kozbial, Piotr; Axelrod, Herbert L; Miller, Mitchell D; McMullan, Daniel; Krishna, S Sri; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Burra, Prasad; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C; Duan, Lian; Elias, Ylva; Elsliger, Marc-André; Ernst, Dustin; Farr, Carol; Feuerhelm, Julie; Grzechnik, Anna; Grzechnik, Slawomir K; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K; Johnson, Hope A; Klock, Heath E; Knuth, Mark W; Kumar, Abhinav; Marciano, David; Morse, Andrew T; Murphy, Kevin D; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L; Sefcovic, Natasha; Sudek, Sebastian; Tien, Henry; Trame, Christine; Trout, Christina V; van den Bedem, Henry; Weekes, Dana; White, Aprilfawn; Xu, Qingping; Hodgson, Keith O; Wooley, John; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wilson, Ian A

    2009-05-01

    ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.

  16. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution

    Energy Technology Data Exchange (ETDEWEB)

    Das, Debanu; Kozbial, Piotr; Axelrod, Herbert L.; Miller, Mitchell D.; McMullan, Daniel; Krishna, S. Sri; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Burra, Prasad; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Elias, Ylva; Elsliger, Marc-André; Ernst, Dustin; Farr, Carol; Feuerhelm, Julie; Grzechnik, Anna; Grzechnik, Slawomir K.; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Murphy, Kevin D.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Sudek, Sebastian; Tien, Henry; Trame, Christine; Trout, Christina V.; van den Bedem, Henry; Weekes, Dana; White, Aprilfawn; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.; (SLAC); (Scripps); (SSRL); (JCSG); (SSRl); (UCSD); (Burnham)

    2009-08-28

    ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.

  17. Image quality performance of liquid crystal display systems: influence of display resolution, magnification and window settings on contrast-detail detection.

    Science.gov (United States)

    Bacher, Klaus; Smeets, Peter; De Hauwere, An; Voet, Tony; Duyck, Philippe; Verstraete, Koenraad; Thierens, Hubert

    2006-06-01

    The aim of this study was to investigate the combined effects of liquid crystal display (LCD) resolution, image magnification and window/level adjustment on the low-contrast performance in soft-copy image interpretation in digital radiography and digital mammography. In addition, the effect of a new LCD noise reduction mechanism on the low-contrast detectability was studied. Digital radiographs and mammograms of two dedicated contrast-detail phantoms (CDRAD 2.0 and CDMAM 3.4) were scored on five LCD devices with varying resolutions (1-3- and 5-megapixel) and one dedicated 5-megapixel cathode ray tube monitor. Two 5-megapixel LCDs were included. The first one was a standard 5-megapixel LCD and the second had a new (Per Pixel Uniformity) noise reduction mechanism. A multi-variate analysis of variance revealed a significant influence of LCD resolution, image magnification and window/level adjustment on the image quality performance assessed with both the CDRAD 2.0 and the CDMAM 3.4 phantoms. The interactive adjustment of brightness and contrast of digital images did not affect the reading time, whereas magnification to full resolution resulted in a significantly slower soft-copy interpretation. For digital radiography applications, a 3-megapixel LCD is comparable with a 5-megapixel CRT monitor in terms of low-contrast performance as well as in reading time. The use of a 2-megapixel LCD is only warranted when radiographs are analysed in full resolution and when using the interactive window/level adjustment. In digital mammography, a 5-megapixel monitor should be the first choice. In addition, the new PPU noise reduction system in the 5-megapixel LCD devices provides significantly better results for mammography reading as compared to a standard 5-magapixel LCD or CRT. If a 3-megapixel LCD is used in mammography setting, a very time-consuming magnification of the digital mammograms would be necessary.

  18. Image quality performance of liquid crystal display systems: Influence of display resolution, magnification and window settings on contrast-detail detection

    Energy Technology Data Exchange (ETDEWEB)

    Bacher, Klaus [Department of Medical Physics and Radiation Protection, Ghent University, Proeftuinstraat 86, B-9000 Gent (Belgium)]. E-mail: klaus.bacher@ugent.be; Smeets, Peter [Department of Radiology, Ghent University Hospital, De Pintelaan 185, B-9000 Gent (Belgium); De Hauwere, An [Department of Medical Physics and Radiation Protection, Ghent University, Proeftuinstraat 86, B-9000 Gent (Belgium); Voet, Tony [Department of Radiology, Ghent University Hospital, De Pintelaan 185, B-9000 Gent (Belgium); Duyck, Philippe [Department of Radiology, Ghent University Hospital, De Pintelaan 185, B-9000 Gent (Belgium); Verstraete, Koenraad [Department of Radiology, Ghent University Hospital, De Pintelaan 185, B-9000 Gent (Belgium); Thierens, Hubert [Department of Medical Physics and Radiation Protection, Ghent University, Proeftuinstraat 86, B-9000 Gent (Belgium)

    2006-06-15

    The aim of this study was to investigate the combined effects of liquid crystal display (LCD) resolution, image magnification and window/level adjustment on the low-contrast performance in soft-copy image interpretation in digital radiography and digital mammography. In addition, the effect of a new LCD noise reduction mechanism on the low-contrast detectability was studied. Digital radiographs and mammograms of two dedicated contrast-detail phantoms (CDRAD 2.0 and CDMAM 3.4) were scored on five LCD devices with varying resolutions (1-3- and 5-megapixel) and one dedicated 5-megapixel cathode ray tube monitor. Two 5-megapixel LCDs were included. The first one was a standard 5-megapixel LCD and the second had a new (Per Pixel Uniformity) noise reduction mechanism. A multi-variate analysis of variance revealed a significant influence of LCD resolution, image magnification and window/level adjustment on the image quality performance assessed with both the CDRAD 2.0 and the CDMAM 3.4 phantoms. The interactive adjustment of brightness and contrast of digital images did not affect the reading time, whereas magnification to full resolution resulted in a significantly slower soft-copy interpretation. For digital radiography applications, a 3-megapixel LCD is comparable with a 5-megapixel CRT monitor in terms of low-contrast performance as well as in reading time. The use of a 2-megapixel LCD is only warranted when radiographs are analysed in full resolution and when using the interactive window/level adjustment. In digital mammography, a 5-megapixel monitor should be the first choice. In addition, the new PPU noise reduction system in the 5-megapixel LCD devices provides significantly better results for mammography reading as compared to a standard 5-magapixel LCD or CRT. If a 3-megapixel LCD is used in mammography setting, a very time-consuming magnification of the digital mammograms would be necessary.

  19. He atom-surface scattering: Surface dynamics of insulators, overlayers and crystal growth. Progress report, May 1, 1991--April 30, 1992

    Energy Technology Data Exchange (ETDEWEB)

    1992-05-01

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

  20. Macroscopic scattering of cracks initiated at single impurity atoms

    Science.gov (United States)

    Kermode, J. R.; Ben-Bashat, L.; Atrash, F.; Cilliers, J. J.; Sherman, D.; de Vita, A.

    2013-09-01

    Brittle crystals, such as coloured gems, have long been known to cleave with atomically smooth fracture surfaces, despite being impurity laden, suggesting that isolated atomic impurities do not generally cause cracks to deflect. Whether cracks can ever deviate when hitting an atomic defect, and if so how they can go straight in real brittle crystals, which always contain many such defects, is still an open question. Here we carry out multiscale molecular dynamics simulations and high-resolution experiments on boron-doped silicon, revealing that cracks can be deflected by individual boron atoms. The process, however, requires a characteristic minimum time, which must be less than the time spent by the crack front at the impurity site. Deflection therefore occurs at low crack speeds, leading to surface ridges which intensify when the boron-dopage level is increased, whereas fast-moving cracks are dynamically steered away from being deflected, yielding smooth cleavage surfaces.