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Sample records for pr combined crystallographic

  1. Nickel deficiency in RENi2-xP2 (RE=La, Ce, Pr). Combined crystallographic and physical property studies

    SciTech Connect

    Bauer, Eric D; Ronning, Filip; Thompson, Joe D; Sarrao, John L; Bobev, S; Xia, S

    2008-01-01

    Large single crystals from RENi{sub 2-x}P{sub 2} (RE = La, Ce, Pr) were synthesized from the pure elements using Sn as a metal flux, and their structures were established by X-ray crystallography. The title compounds were confirmed to crystallize in the body-centered tetragonal ThCr{sub 2}Si{sub 2} structure type (space group I4/mmm (No. 139); Pearson's symbol tI10), but with a significant stoichiometry breadth with respect to the transition metal. Systematic synthetic work, coupled with accurate structure refinements indicated strong correlation between the degree of Ni-deficiency and the reaction conditions. For four different PrNi{sub 2-x}P{sub 2} (x {le} 0.5) samples, temperature dependent dc magnetization measurements indicated typical local moment 4f-magnetism and a stable Pr{sup 3+} ground state. Field-dependent heat capacity data confirmed a ferromagnetic order at low temperature, and the variations of T{sub c} with the concentration of Ni defects are discussed. LaNi{sub 2-x}P{sub 2}, as expected was found to be Pauli-like paramagnetic in the studied temperature regime, while the Ce-analog CeNi{sub 2-x}P{sub 2} (x = 0.28(1)) showed the characteristics of a mixed valent Ce{sup 3+}/Ce{sup 4+} system with a possible Kondo temperature on the order of 230 K.

  2. Nickel deficiency in RENi{sub 2-x}P{sub 2} (RE=La, Ce, Pr). Combined crystallographic and physical property studies

    SciTech Connect

    Bobev, Svilen; Xia, Sheng-qing; Bauer, Eric D.; Ronning, Filip; Thompson, Joe D.; Sarrao, John L.

    2009-06-15

    Large single crystals from RENi{sub 2-x}P{sub 2} (RE=La, Ce, Pr) were synthesized from the pure elements using Sn as a metal flux, and their structures were established by X-ray crystallography. The title compounds were confirmed to crystallize in the body-centered tetragonal ThCr{sub 2}Si{sub 2} structure type (space group I4/mmm (No. 139); Pearson's symbol tI10), but with a significant homogeneity range with respect to the transition metal. Systematic synthetic work, coupled with accurate structure refinements indicated strong correlation between the degree of Ni-deficiency and the reaction conditions. According to the temperature dependent dc magnetization measurements, LaNi{sub 2-x}P{sub 2} (x=0.30(1)), as expected, is Pauli-like paramagnetic in the studied temperature regime, while the Ce-analog CeNi{sub 2-x}P{sub 2} (x=0.28(1)) shows the characteristics of a mixed valent Ce{sup 3+}/Ce{sup 4+} system with a possible Kondo temperature scale on the order of 1000 K. For three different PrNi{sub 2-x}P{sub 2} (x<=0.5) samples, the temperature and field dependence of the magnetization indicated typical local moment 4f-magnetism and a stable Pr{sup 3+} ground state, with subtle variations of T{sub C} as a function of the concentration of Ni defects. Field-dependent heat capacity data for CeNi{sub 2-x}P{sub 2} (x=0.28(1)) and PrNi{sub 2-x}P{sub 2} (x=0.53(1)) are discussed as well. - Graphical abstract: The non-stoichiometric RENi{sub 2-x}P{sub 2} phases (RE=La, Ce, Pr), whose average structure belongs to the ThCr{sub 2}Si{sub 2} type, are shown to exist with a wide range of defects on the transition metal site. The changes in the Ni-underoccupancy affect the magnetism of the synthesized materials.

  3. Purification, characterization and preliminary crystallographic studies of a PR-10 protein from Pachyrrhizus erosus seeds.

    PubMed

    Wu, Fang; Li, Yikun; Chang, Shaojie; Zhou, Zhaocai; Wang, Fang; Song, Xiaomin; Lin, Yujuan; Gong, Weimin

    2002-12-01

    A 16 kDa protein SPE16 was purified from the seeds of Pachyrrhizus erosus. Its N-terminal amino-acid sequence showed significant sequence homology to pathogenesis-related proteins from the PR-10 family. An activity assay indicated that SPE16 possesses ribonuclease activity as do some other PR-10 proteins. SPE16 crystals were obtained by the hanging-drop vapour-diffusion method. The space group is P2(1)2(1)2(1), with unit-cell parameters a = 53.36, b = 63.70, c = 72.96 A. PMID:12454488

  4. Single crystalline Pr{sub 2-x}Y{sub x}O{sub 3} (x=0-2) dielectrics on Si with tailored electronic and crystallographic structure

    SciTech Connect

    Seifarth, O.; Schubert, M. A.; Giussani, A.; Schroeder, T.; Klenov, D. O.; Schmeisser, D.

    2010-11-15

    Crystalline oxides on Si with tailored electronic and crystallographic properties are of importance for the integration of functional oxides or alternative semiconductors to enable novel device concepts in Si microelectronics. We present an electronic band gap study of single crystalline Pr{sub 2-x}Y{sub x}O{sub 3} (0{<=}x{<=}2) heterostructures on Si(111). The perfect solubility of the isomorphic bixbyites Pr{sub 2}O{sub 3} and Y{sub 2}O{sub 3} during molecular beam epitaxy thin film growth on Si enables a linear band gap tuning. Special focus is devoted to the determination of the electronic band offsets across the dielectric/Si interface. In addition, the composition x allows to control the crystallographic lattice parameter where, for example, Pr{sub 0.8}Y{sub 1.2}O{sub 3} enables the growth of fully lattice matched oxide heterostructures on Si.

  5. Application of combined EBSD and 3D-SEM technique on crystallographic facet analysis of steel at low temperature.

    PubMed

    Mohseni, P; Solberg, J K; Karlsen, M; Akselsen, O M; Ostby, E

    2013-07-01

    Electron backscatter diffraction has been increasingly used to identify the crystallographic planes and orientation of cleavage facets with respect to the rolling direction in fracture surfaces. The crystallographic indices of cleavage planes can be determined either directly from the fracture surface or indirectly from metallographic sections perpendicular to the plane of the fracture surface. A combination of electron backscatter diffraction and 3D scanning electron microscopy imaging technique has been modified to determine crystallographic facet orientations. The main purpose of this work has been to identify the macroscopic crystallographic orientations of cleavage facets in the fracture surfaces of weld heat affected zones in a well-known steel fractured at low temperatures. The material used for the work was an American Petroleum Institute (API) X80 grade steel developed for applications at low temperatures, and typical heat affected zone microstructures were obtained by carrying out weld thermal simulation. The fracture toughness was measured at different temperatures (0°C, -30°C, -60°C and -90°C) by using Crack Tip Opening Displacement testing. Fracture surfaces and changes in microstructure were analyzed by scanning electron microscopy and light microscopy. Crystallographic orientations were identified by electron backscatter diffraction, indirectly from a polished section perpendicular to the major fracture surface of the samples. Computer assisted 3D imaging was used to measure the angles between the cleavage facets and the adjacent polished surface, and then these angles were combined with electron backscatter diffraction measurements to determine the macroscopic crystallographic planes of the facets. The crystallographic indices of the macroscopic cleavage facet planes were identified to be {100}, {110}, {211} and {310} at all temperatures. PMID:23692572

  6. Crystallographic alignment evolution and magnetic properties of anisotropic Sm0.6Pr0.4Co5 nanoflakes prepared by surfactant-assisted ball milling

    NASA Astrophysics Data System (ADS)

    Xu, M. L.; Wu, Q.; Li, Y. Q.; Liu, W. Q.; Lu, Q. M.; Yue, M.

    2015-08-01

    The microstructure, crystal structure and magnetic properties were studied for Sm0.6Pr0.4Co5 nanoflakes prepared by surfactant-assisted high-energy ball milling (SAHEBM). Effect of ball-milling time on the c-axis crystallographic alignment, morphology and magnetic properties of Sm0.6Pr0.4Co5 nanoflakes was systematically investigated. With increasing milling time from 1 h to 7 h, the intensity ratio between (002) and (111) reflection peaks indicating degree of c-axis crystal texture of the (Sm, Pr)Co5 phase increases first, peaks at 3 h, then drops again, revealing that the strongest c-axis crystal texture was obtained in the nanoflakes milled for 3 h. On the other hand, the coercivity (Hci) of the flakes increases gradually from 1.71 to 14.65 kOe with the increase of ball milling time. As a result, an optimal magnetic properties of Mr of 10.23 kGs, Hci of 11.45 kOe and (BH)max of 24.40 MGOe was obtained in Sm0.6Pr0.4Co5 nanoflakes milled for 3 h, which also displayed a high aspect ratio, small in-plane size, pronounced (001) out-of-plane texture.

  7. Aurophilicity under pressure: a combined crystallographic and in situ spectroscopic study.

    PubMed

    O'Connor, Alice E; Mirzadeh, Nedaossadat; Bhargava, Suresh K; Easun, Timothy L; Schröder, Martin; Blake, Alexander J

    2016-05-21

    High pressure crystallographic studies on [1,4-C6H4{PPh2(AuCl)}2] (1) reveal the largest pressure-induced contraction of an aurophilic interaction observed for any Au(i) complex; Hirshfeld surface analysis and Raman spectroscopy reveal the presence of several types of intermolecular interaction, which play an important role in the behaviour of 1 as a function of pressure. PMID:27009745

  8. Tailored combination prevention packages and PrEP for young key populations

    PubMed Central

    Pettifor, Audrey; Nguyen, Nadia L; Celum, Connie; Cowan, Frances M; Go, Vivian; Hightow-Weidman, Lisa

    2015-01-01

    Introduction Young key populations, defined in this article as men who have sex with men, transgender persons, people who sell sex and people who inject drugs, are at particularly high risk for HIV. Due to the often marginalized and sometimes criminalized status of young people who identify as members of key populations, there is a need for HIV prevention packages that account for the unique and challenging circumstances they face. Pre-exposure prophylaxis (PrEP) is likely to become an important element of combination prevention for many young key populations. Objective In this paper, we discuss important challenges to HIV prevention among young key populations, identify key components of a tailored combination prevention package for this population and examine the role of PrEP in these prevention packages. Methods We conducted a comprehensive review of the evidence to date on prevention strategies, challenges to prevention and combination prevention packages for young key populations. We focused specifically on the role of PrEP in these prevention packages and on young people under the age of 24, and 18 in particular. Results and discussion Combination prevention packages that include effective, acceptable and scalable behavioural, structural and biologic interventions are needed for all key populations to prevent new HIV infections. Interventions in these packages should meaningfully involve beneficiaries in the design and implementation of the intervention, and take into account the context in which the intervention is being delivered to thoughtfully address issues of stigma and discrimination. These interventions will likely be most effective if implemented in conjunction with strategies to facilitate an enabling environment, including increasing access to HIV testing and health services for PrEP and other prevention strategies, decriminalizing key populations’ practices, increasing access to prevention and care, reducing stigma and discrimination, and

  9. Crystallographic Studies of Prion Protein (PrP) Segments Suggest How Structural Changes Encoded by Polymorphism at Residue 129 Modulate Susceptibility to Human Prion Disease

    SciTech Connect

    Apostol, Marcin I.; Sawaya, Michael R.; Cascio, Duilio; Eisenberg, David

    2010-09-23

    A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the molecular basis of this effect remains unexplained. In the current study, we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are 'steric zippers,' pairs of interacting {beta}-sheets. Both structures of these 'homozygous steric zippers' reveal direct intermolecular interactions between Met or Val in one sheet and the identical residue in the mating sheet. These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression.

  10. Crystallographic topology and its applications

    SciTech Connect

    Johnson, C.K.; Burnett, M.N.; Dunbar, W.D.

    1996-10-01

    Geometric topology and structural crystallography concepts are combined to define a new area we call Structural Crystallographic Topology, which may be of interest to both crystallographers and mathematicians. In this paper, we represent crystallographic symmetry groups by orbifolds and crystal structures by Morse - functions. The Morse function uses mildly overlapping Gaussian thermal-motion probability density functions centered on atomic sites to form a critical net with peak, pass, pale, and pit critical points joined into a graph by density gradient-flow separatrices. Critical net crystal structure drawings can be made with the ORTEP-III graphics pro- An orbifold consists of an underlying topological space with an embedded singular set that represents the Wyckoff sites of the crystallographic group. An orbifold for a point group, plane group, or space group is derived by gluing together equivalent edges or faces of a crystallographic asymmetric unit. The critical-net-on-orbifold model incorporates the classical invariant lattice complexes of crystallography and allows concise quotient-space topological illustrations to be drawn without the repetition that is characteristic of normal crystal structure drawings.

  11. Crystallographic properties of fertilizer compounds

    SciTech Connect

    Frazier, A.W.; Dillard, E.F.; Thrasher, R.D.; Waerstad, K.R.; Hunter, S.R.; Kohler, J.J.; Scheib, R.M.

    1991-02-01

    This bulletin is a compilation of crystallographic data collected at NFERC on 450 fertilizer-related compounds. In TVA's fertilizer R and D program, petrographic examination, XRD, and infrared spectroscopy are combined with conventional chemical analysis methods in identifying the individual compounds that occur in fertilizer materials. This handbook brings together the results of these characterization studies and supplemental crystallographic data from the literature. It is in one-compound-per-page, loose-leaf format, ordered alphabetically by IUPAC name. Indexes provided include IUPAC name, formula, group, alternate formula, synonyms, x-ray data, optical data. Tables are given for solids, compounds in commercial MAP and DAP, and matrix materials in phosphate rock.

  12. Crystallographic properties of fertilizer compounds

    SciTech Connect

    Frazier, A.W.; Dillard, E.F.; Thrasher, R.D.; Waerstad, K.R.; Hunter, S.R.; Kohler, J.J.; Scheib, R.M.

    1991-02-01

    This bulletin is a compilation of crystallographic data collected at NFERC on 450 fertilizer-related compounds. In TVA`s fertilizer R and D program, petrographic examination, XRD, and infrared spectroscopy are combined with conventional chemical analysis methods in identifying the individual compounds that occur in fertilizer materials. This handbook brings together the results of these characterization studies and supplemental crystallographic data from the literature. It is in one-compound-per-page, loose-leaf format, ordered alphabetically by IUPAC name. Indexes provided include IUPAC name, formula, group, alternate formula, synonyms, x-ray data, optical data. Tables are given for solids, compounds in commercial MAP and DAP, and matrix materials in phosphate rock.

  13. Crystallographic Information Resources

    ERIC Educational Resources Information Center

    Glasser, Leslie

    2016-01-01

    Crystallographic information provides the fundamental basis for understanding the properties and behavior of materials. This data, such as chemical composition, unit cell dimensions, space group, and atomic positions, derives from the primary literature--that is, from published experimental measurement or theoretical calculation. Although the…

  14. Combined local-density and dynamical mean field theory calculations for the compressed lanthanides Ce, Pr, and Nd

    SciTech Connect

    McMahan, A K

    2005-03-30

    This paper reports calculations for compressed Ce (4f{sup 1}), Pr (4f{sup 2}), and Nd (4f{sup 3}) using a combination of the local-density approximation (LDA) and dynamical mean field theory (DMFT), or LDA+DMFT. The 4f moment, spectra, and the total energy among other properties are examined as functions of volume and atomic number for an assumed face-centered cubic (fcc) structure. These materials are seen to be strongly localized at ambient pressure and for compressions up through the experimentally observed fcc phases ({gamma} phase for Ce), in the sense of having fully formed Hund's rules moments and little 4f spectral weight at the Fermi level. Subsequent compression for all three lanthanides brings about significant deviation of the moments from their Hund's rules values, a growing Kondo resonance at the fermi level, an associated softening in the total energy, and quenching of the spin orbit since the Kondo resonance is of mixed spin-orbit character while the lower Hubbard band is predominantly j = 5/2. while the most dramatic changes for Ce occur within the two-phase region of the {gamma}-{alpha} volume collapse transition, as found in earlier work, those for Pr and Nd occur within the volume range of the experimentally observed distorted fcc (dfcc) phase, which is therefore seen here as transitional and not part of the localized trivalent lanthanide sequence. The experimentally observed collapse to the {alpha}-U structure in Pr occurs only on further compression, and no such collapse is found in Nd. These lanthanides start closer to the localized limit for increasing atomic number, and so the theoretical signatures noted above are also offset to smaller volume as well, which is possibly related to the measured systematics of the size of the volume collapse being 15%, 9%, and none for Ce, Pr, and Nd, respectively.

  15. Knockout of the prion protein (PrP)-like Sprn gene does not produce embryonic lethality in combination with PrP(C)-deficiency.

    PubMed

    Daude, Nathalie; Wohlgemuth, Serene; Brown, Rebecca; Pitstick, Rose; Gapeshina, Hristina; Yang, Jing; Carlson, George A; Westaway, David

    2012-06-01

    The Sprn gene encodes Shadoo (Sho), a glycoprotein with biochemical properties similar to the unstructured region of cellular prion protein (PrP(C)). Sho has been considered a candidate for the hypothetical π protein that supplies a PrP(C)-like function to maintain the viability of Prnp(0/0) mice lacking the PrP(C) protein. To understand these relationships more clearly we probed the cell biology of Sho and created knockout mice. Besides full-length and a "C1" C-terminal fragment, we describe a 6-kDa N-terminal Sho neuropeptide, "N1," which is present in membrane-enriched subcellular fractions of wild-type mice. Sprn null alleles were produced that delete all protein coding sequences yet spare the Mtg1 gene transcription unit that overlaps the Sprn 3' UTR; the resulting mice bred to homozygosity were viable and fertile, although Sprn(0/0) mice maintained in two genetic backgrounds weighed less than wild-type mice. Lack of Sho protein did not affect prion incubation time. Contrasting with lethality reported for knockdown of expression in Prnp(0/0) embryos using lentiviruses targeted against the Sprn 3' UTR, we established that double-knockout mice deficient in both Sho and PrP(C) are fertile and viable up to 690 d of age. Our data reduce the impetus for equating Sho with the notional π protein and are not readily reconciled with hypotheses wherein expression of PrP(C) and Sho are both required for completion of embryogenesis. Alternatively, and in accord with some reports for PrP(C), we infer that Sho's activity will prove germane to the maintenance of neuronal viability in postnatal life. PMID:22619325

  16. Ultrawide-band near-infrared light source over 1 mW by Sm3+,Pr3+-codoped glass phosphor combined with LED

    NASA Astrophysics Data System (ADS)

    Fuchi, Shingo; Shimizu, Yusuke; Watanabe, Keita; Uemura, Hiroki; Takeda, Yoshikazu

    2014-07-01

    We have synthesized 0.3Sm2O3-0.12Pr2O3-10Bi2O3-45Sb2O3-45B2O3 glass as an ultrawide-band near-infrared phosphor for LED-based light sources. We have achieved an ultrawide-band luminescence from 760 to 1100 nm with an output power of over 1 mW by combining a blue LED with Sm3+,Pr3+-codoped borate glass in one package. Absorption bands corresponding to C-H and O-H stretchings in aqueous solutions of glucose have been observed using this light source and a multichannel spectrometer. These results indicate that the Sm3+,Pr3+-codoped borate glass combined with the blue LED is a useful novel light source for absorption spectrometry.

  17. Access to Basic HIV-Related Services and PrEP Acceptability among Men Who Have sex with Men Worldwide: Barriers, Facilitators, and Implications for Combination Prevention

    PubMed Central

    Makofane, Keletso; Santos, Glenn-Milo; Beck, Jack; Do, Tri D.; Wilson, Patrick A.; Pyun, Thomas; Arreola, Sonya

    2013-01-01

    Introduction. Men who have sex with men (MSM) are disproportionately impacted by HIV globally. Easily accessible combination HIV prevention strategies, tailored to the needs of MSM, are needed to effectively address the AIDS pandemic. Methods and Materials. We conducted a cross-sectional study among MSM (n = 3748) from 145 countries from April to August 2012. Using multivariable random effects models, we examined factors associated with acceptability of preexposure prophylaxis (PrEP) and access to condoms, lubricants, HIV testing, and HIV treatment. Results. Condoms and lubricants were accessible to 35% and 22% of all respondents, respectively. HIV testing was accessible to 35% of HIV-negative respondents. Forty-three percent of all HIV-positive respondents reported that antiretroviral therapy was easily accessible. Homophobia, outness, and service provider stigma were significantly associated with reduced access to services. Conversely, community engagement, connection to gay community, and comfort with service providers were associated with increased access. PrEP acceptability was associated with lower PrEP-related stigma, less knowledge about PrEP, less outness, higher service provider stigma, and having experienced violence for being MSM. Conclusions. Ensuring HIV service access among MSM will be critical in maximizing the potential effectiveness of combination approaches, especially given the interdependence of both basic and newer interventions like PrEP. Barriers and facilitators of HIV service access for MSM should be better understood and addressed. PMID:26316968

  18. Crystallographic and Spectroscopic Symmetry Notations.

    ERIC Educational Resources Information Center

    Sharma, B. D.

    1982-01-01

    Compares Schoenflies and Hermann-Mauguin notations of symmetry. Although the former (used by spectroscopists) and latter (used by crystallographers) both describe the same symmetry, there are distinct differences in the manner of description which may lead to confusion in correlating the two notations. (Author/JN)

  19. Triboluminescence dominated by crystallographic orientation

    PubMed Central

    Wang, Kuifang; Ma, Liran; Xu, Xuefeng; Wen, Shizhu; Luo, Jianbin

    2016-01-01

    Triboluminescence (TL) is an optical phenomenon that has a long and varied history with broad applications, such as damage detection, X-ray source, and mass health monitoring sensor. So far, the properties and mechanisms of TL remain not completely understood. The TL properties emitted during the sliding contact between Al2O3 and SiO2 surfaces were studied along different crystallographic orientations. In this study, the TL intensity of Al2O3 was significantly enhanced as Al2O3 surface was along a particular crystallographic orientation, which is an unconventional phenomenon. TL enhancement of Al2O3 was not affected by air atmosphere and atomic stocking mode of Al2O3. The enhancement mechanism of Al2O3 may be influenced by the surface state of Al2O3. This work provides a new method to control the intensity of TL and novel ideas to elucidate the TL mechanism. PMID:27193511

  20. Triboluminescence dominated by crystallographic orientation

    NASA Astrophysics Data System (ADS)

    Wang, Kuifang; Ma, Liran; Xu, Xuefeng; Wen, Shizhu; Luo, Jianbin

    2016-05-01

    Triboluminescence (TL) is an optical phenomenon that has a long and varied history with broad applications, such as damage detection, X-ray source, and mass health monitoring sensor. So far, the properties and mechanisms of TL remain not completely understood. The TL properties emitted during the sliding contact between Al2O3 and SiO2 surfaces were studied along different crystallographic orientations. In this study, the TL intensity of Al2O3 was significantly enhanced as Al2O3 surface was along a particular crystallographic orientation, which is an unconventional phenomenon. TL enhancement of Al2O3 was not affected by air atmosphere and atomic stocking mode of Al2O3. The enhancement mechanism of Al2O3 may be influenced by the surface state of Al2O3. This work provides a new method to control the intensity of TL and novel ideas to elucidate the TL mechanism.

  1. Triboluminescence dominated by crystallographic orientation.

    PubMed

    Wang, Kuifang; Ma, Liran; Xu, Xuefeng; Wen, Shizhu; Luo, Jianbin

    2016-01-01

    Triboluminescence (TL) is an optical phenomenon that has a long and varied history with broad applications, such as damage detection, X-ray source, and mass health monitoring sensor. So far, the properties and mechanisms of TL remain not completely understood. The TL properties emitted during the sliding contact between Al2O3 and SiO2 surfaces were studied along different crystallographic orientations. In this study, the TL intensity of Al2O3 was significantly enhanced as Al2O3 surface was along a particular crystallographic orientation, which is an unconventional phenomenon. TL enhancement of Al2O3 was not affected by air atmosphere and atomic stocking mode of Al2O3. The enhancement mechanism of Al2O3 may be influenced by the surface state of Al2O3. This work provides a new method to control the intensity of TL and novel ideas to elucidate the TL mechanism. PMID:27193511

  2. The coordination chemistry of perfluorovinyl substituted phosphine ligands, a crystallographic and spectroscopic study. Co-crystallisation of both cis- and trans-isomers of [PtCl2{P(i)pr2(CF=CF2)}2] within the same unit cell.

    PubMed

    Barnes, Nicholas A; Brisdon, Alan K; Brown, F R William; Cross, Wendy I; Herbert, Christopher J; Pritchard, Robin G; Sadiq, Ghazala

    2008-01-01

    The coordination chemistry of the perfluorovinyl phosphines PEt2(CF=CF2), P(i)Pr2(CF=CF2), PCy,(CF=CF2) and PPh(CF=CF2)2 to rhodium(I), palladium(II), and platinum(II) centres has been investigated. The electronic properties of the ligands are estimated based on v(CO) and 1J(Rh-P) values. X-Ray diffraction data for the square-planar Pd(II) and Pt(II) perfluorovinyl-phosphine containing complexes allow estimates of the steric demand for the series of ligands PPh2(CF=CF2), PEt2(CF=CF2), P(i)Pr2(CF=CF2), PCy2(CF=CF2) and PPh(CF=CF2)2 to be determined. The (CF=CF2) fragment is found to be more electron withdrawing than (C6F5) yet sterically less demanding. These ligands therefore provide a range of electron-neutral to phosphite-like electronic properties combined with a range of steric demands. This study also reveals that short intramolecular interactions from the metal centre to the beta-fluorine atom cis to phosphorus of the CF=CF2 groups are observed in all-trans square planar complexes of the ligands. Unusually, the complex [PtCl2{P(i)Pr2(CF=CF2)}2] crystallises with both cis- and trans-isomers present in the unit cell. It appears that co-crystallisation of both isomers occurs in order to maximise fluorous regions in the crystal packing, and the extended structure displays short fluorine-fluorine contacts. The generation of mixed geometries seems to be a phenomenon of crystallisation, as solution phase NMR studies reveal the presence of only the trans-isomer. PMID:18399236

  3. Seeking Augmented Information Content Concerning Diurnal Precipitation Achieved by Combining TRMM-PR and CloudSat-CPR Radar Data Sets

    NASA Technical Reports Server (NTRS)

    Smith, Eric A.; Kuo, Kwo-Sen; Carty, Hezekiah

    2008-01-01

    The CloudSat satellite's Cloud Profiling Radar (CPR) is a highly sensitive 94 GHz (W-band) nadir viewing radar system flown in retrograde sun synchronous orbit useful for determining the vertical structure of cloud hydrometeors down to sensitivity of approx. -30 dBZ reflectivity factor. Given this sensitivity, it is possible to unambiguously measure precipitation rates in clouds over a spectrum extending from approx. 0.08 - 3.0 mm hr (sup -1) down to altitudes of 0.5 km with approx.0.25 km vertical binning. This enables an effective means to measure a great deal of the drizzle and light rain spectrum. However, because of its near-polar sunsynchronous orbit, CloudSat cannot sample the diurnal cycle of precipitation, nor with its nadir-only CPR view can it obtain a high duty cycle in sampling precipitation at fixed local times over fixed positions. On the other hand, the TRMM satellite, which is flown in a non-sunsynchronous 35-degree inclined orbit carrying the 13.8 GHz KU-band Precipitation Radar (PR) scanning through nadir over an approx. 225 km swath, can sample both the diurnal cycle and with a much improved duty cycle relative to CloudSat. Moreover, the PR and CPR have the same 0.25 km vertical binning capability. The PR's greatest shortcoming is its approx. +17 dBZ sensitivity, which eliminates the possibility of measuring rain rates below -0.3-0.5 mm hr(sup -1), which can involve rainfall accumulations of up to 50% of the total over some regions. This begs the question of whether by combining CPR and PR data sets, whether it is possible to obtain an augmented measurement of the diurnal precipitation cycle. By collecting complimentary datasets during CloudSat and TRMM satellite orbit crossings within a delta t = 45-min proximity window, it is possible to demonstrate that whenever TRMM detects a precipitation signal, the correlations along the vertical axis between the reflectivities acquired from the CPR and PR are in inverse proportion to the magnitude of the

  4. ANS complex of St John’s wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning

    SciTech Connect

    Sliwiak, Joanna; Dauter, Zbigniew; Kowiel, Marcin; McCoy, Airlie J.; Read, Randy J.; Jaskolski, Mariusz

    2015-04-01

    Hyp-1, a pathogenesis-related class 10 (PR-10) protein from H. perforatum, was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The asymmetric unit of the tetartohedrally twinned crystal contains 28 copies of the protein arranged in columns with noncrystallographic sevenfold translational symmetry and with additional pseudotetragonal rotational NCS. Hyp-1, a pathogenesis-related class 10 (PR-10) protein from St John’s wort (Hypericum perforatum), was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The highly pseudosymmetric crystal has 28 unique protein molecules arranged in columns with sevenfold translational noncrystallographic symmetry (tNCS) along c and modulated X-ray diffraction with intensity crests at l = 7n and l = 7n ± 3. The translational NCS is combined with pseudotetragonal rotational NCS. The crystal was a perfect tetartohedral twin, although detection of twinning was severely hindered by the pseudosymmetry. The structure determined at 2.4 Å resolution reveals that the Hyp-1 molecules (packed as β-sheet dimers) have three novel ligand-binding sites (two internal and one in a surface pocket), which was confirmed by solution studies. In addition to 60 Hyp-1-docked ligands, there are 29 interstitial ANS molecules distributed in a pattern that violates the arrangement of the protein molecules and is likely to be the generator of the structural modulation. In particular, whenever the stacked Hyp-1 molecules are found closer together there is an ANS molecule bridging them.

  5. Recovery of Crystallographic Texture in Remineralized Dental Enamel

    PubMed Central

    Siddiqui, Samera; Anderson, Paul; Al-Jawad, Maisoon

    2014-01-01

    Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture) and position of the (002) Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected enamel to regain

  6. An alternative to the crystallographic reconstruction of austenite in steels

    SciTech Connect

    Bernier, Nicolas; Bracke, Lieven; Malet, Loïc; Godet, Stéphane

    2014-03-01

    An alternative crystallographic austenite reconstruction programme written in Matlab is developed by combining the best features of the existing models: the orientation relationship refinement, the local pixel-by-pixel analysis and the nuclei identification and spreading strategy. This programme can be directly applied to experimental electron backscatter diffraction mappings. Its applicability is demonstrated on both quenching and partitioning and as-quenched lath-martensite steels. - Highlights: • An alternative crystallographic austenite reconstruction program is developed. • The method combines a local analysis and a nuclei identification/spreading strategy. • The validity of the calculated orientation relationship is verified on a Q and P steel. • The accuracy of the reconstructed microtexture is investigated on a martensite steel.

  7. Estimating 13.8-GHz path-integrated attenuation from 10.7-GHz brightness temperatures for the TRMM combined PR-TMI precipitation algorithm

    SciTech Connect

    Smith, E.A.; Farrar, M.R.; Xiang, X.; Turk, F.J.; Mugnai, A.

    1997-04-01

    This study presents research in support of the design and implementation of a combined radar-radiometer algorithm to be used for precipitation retrieval during the Tropical Rainfall Measuring Mission (TRMM). The combined algorithm approach is expected to overcome various difficulties that arise with a radar-only approach, particularly related to estimates of path-integrated attenuation (PIA)along the TRMM radar beam. A technique is described for estimating PIA at the 13.8-GHz frequency of the TRMM precipitation radar (PR) from 10.7-GHz brightness temperature T{sub B} measurements obtained from the TRMM microwave imager. Through the use of variational or probabilistic techniques, the independent PIA calculations provide a means to adjust for errors that accumulate in estimates of range-dependent rain rates at progressively increasing range positions from radar reflectivity vectors. The accepted radar approach for obtaining PIA from ocean-viewing radar reflectivity measurements is called the surface reference technique, a scheme based on the difference in ocean surface cross sections between cloud-free and raining radar pixels. This technique has encountered problems, which are discussed and analyzed with the aid of coordinated aircraft radar (Airborne Rain Mapping Radar) and radiometer (Advanced Microwave Precipitation Radiometer) measurements obtained during the west Pacific Tropical Ocean Global Atmosphere Coupled Ocean-Atmosphere Response Experiment in 1993. 97 refs., 12 figs., 5 tabs.

  8. The New NRL Crystallographic Database

    NASA Astrophysics Data System (ADS)

    Mehl, Michael; Curtarolo, Stefano; Hicks, David; Toher, Cormac; Levy, Ohad; Hart, Gus

    For many years the Naval Research Laboratory maintained an online graphical database of crystal structures for a wide variety of materials. This database has now been redesigned, updated and integrated with the AFLOW framework for high throughput computational materials discovery (http://materials.duke.edu/aflow.html). For each structure we provide an image showing the atomic positions; the primitive vectors of the lattice and the basis vectors of every atom in the unit cell; the space group and Wyckoff positions; Pearson symbols; common names; and Strukturbericht designations, where available. References for each structure are provided, as well as a Crystallographic Information File (CIF). The database currently includes almost 300 entries and will be continuously updated and expanded. It enables easy search of the various structures based on their underlying symmetries, either by Bravais lattice, Pearson symbol, Strukturbericht designation or commonly used prototypes. The talk will describe the features of the database, and highlight its utility for high throughput computational materials design. Work at NRL is funded by a Contract with the Duke University Department of Mechanical Engineering.

  9. Crystallographic Control in Ilmenite Reduction

    NASA Astrophysics Data System (ADS)

    de Vries, M. L.; Grey, I. E.; Fitz Gerald, J. D.

    2007-04-01

    Scanning electron microscopy and transmission electron microscopy techniques were used to characterize the products from hydrogen reduction of polygranular synthetic ilmenite discs at temperatures in the range 823 to 1173 K and pressures in the range 1 to 13 atm. Reduction commences at grain boundaries and cracks and advances progressively to grain interiors. Within individual grains, the morphology of the reduction products was found to be crystallographically controlled. Near parallel bands of metallic iron (Fe m ) form within each grain, aligned with the basal plane of ilmenite (il) (0001) il . The separation between bands is of the order of 1 μm and is relatively constant with change of pressure and temperature. In the interband region, conversion of ilmenite to rutile occurs preferentially parallel to \\{ 11ifmmodeexpandafterbarelseexpandafter\\=fi{2}0\\} _{{il}} ilmenite planes, generating platelets of rutile that grow normal to the Fe m bands. The intergrain duplex morphology of the reduction products closely resembles cellular precipitation in alloys. At reduction temperatures above ˜1000 K, the interband region comprises dense, nonporous oriented intergrowths of rutile platelets and residual ilmenite, whereas below ˜900 K, the interband region contains a fine, filamentary network of pores. In the intermediate temperature regime, a change from dense to porous interband region occurs with increasing pressure. The observations have been interpreted in terms of the relative rates of interfacial chemical reaction and solid-state diffusion, with the latter having a controlling influence at lower temperatures or higher pressures.

  10. ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: A fiendish combination of pseudosymmetry with tetartohedral twinning

    SciTech Connect

    Sliwiak, Joanna; Dauter, Zbigniew; Kowiel, Marcin; McCoy, Airlie J.; Read, Randy J.; Jaskolski, Mariusz

    2015-03-26

    Hyp-1, a pathogenesis-related class 10 (PR-10) protein from St John's wort (Hypericum perforatum), was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The highly pseudosymmetric crystal has 28 unique protein molecules arranged in columns with sevenfold translational noncrystallographic symmetry (tNCS) along c and modulated X-ray diffraction with intensity crests at l = 7n and l = 7n ± 3. The translational NCS is combined with pseudotetragonal rotational NCS. The crystal was a perfect tetartohedral twin, although detection of twinning was severely hindered by the pseudosymmetry. The structure determined at 2.4 Å resolution reveals that the Hyp-1 molecules (packed as β-sheet dimers) have three novel ligand-binding sites (two internal and one in a surface pocket), which was confirmed by solution studies. In addition to 60 Hyp-1-docked ligands, there are 29 interstitial ANS molecules distributed in a pattern that violates the arrangement of the protein molecules and is likely to be the generator of the structural modulation. In particular, whenever the stacked Hyp-1 molecules are found closer together there is an ANS molecule bridging them.

  11. ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: A fiendish combination of pseudosymmetry with tetartohedral twinning

    DOE PAGESBeta

    Sliwiak, Joanna; Dauter, Zbigniew; Kowiel, Marcin; McCoy, Airlie J.; Read, Randy J.; Jaskolski, Mariusz

    2015-03-26

    Hyp-1, a pathogenesis-related class 10 (PR-10) protein from St John's wort (Hypericum perforatum), was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The highly pseudosymmetric crystal has 28 unique protein molecules arranged in columns with sevenfold translational noncrystallographic symmetry (tNCS) along c and modulated X-ray diffraction with intensity crests at l = 7n and l = 7n ± 3. The translational NCS is combined with pseudotetragonal rotational NCS. The crystal was a perfect tetartohedral twin, although detection of twinning was severely hindered by the pseudosymmetry. The structure determined at 2.4 Å resolution reveals that the Hyp-1 molecules (packedmore » as β-sheet dimers) have three novel ligand-binding sites (two internal and one in a surface pocket), which was confirmed by solution studies. In addition to 60 Hyp-1-docked ligands, there are 29 interstitial ANS molecules distributed in a pattern that violates the arrangement of the protein molecules and is likely to be the generator of the structural modulation. In particular, whenever the stacked Hyp-1 molecules are found closer together there is an ANS molecule bridging them.« less

  12. ANS complex of St John’s wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning

    PubMed Central

    Sliwiak, Joanna; Dauter, Zbigniew; Kowiel, Marcin; McCoy, Airlie J.; Read, Randy J.; Jaskolski, Mariusz

    2015-01-01

    Hyp-1, a pathogenesis-related class 10 (PR-10) protein from St John’s wort (Hypericum perforatum), was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The highly pseudosymmetric crystal has 28 unique protein molecules arranged in columns with sevenfold translational noncrystallographic symmetry (tNCS) along c and modulated X-ray diffraction with intensity crests at l = 7n and l = 7n ± 3. The translational NCS is combined with pseudotetragonal rotational NCS. The crystal was a perfect tetartohedral twin, although detection of twinning was severely hindered by the pseudosymmetry. The structure determined at 2.4 Å resolution reveals that the Hyp-1 molecules (packed as β-sheet dimers) have three novel ligand-binding sites (two internal and one in a surface pocket), which was confirmed by solution studies. In addition to 60 Hyp-1-docked ligands, there are 29 interstitial ANS molecules distributed in a pattern that violates the arrangement of the protein molecules and is likely to be the generator of the structural modulation. In particular, whenever the stacked Hyp-1 molecules are found closer together there is an ANS molecule bridging them. PMID:25849394

  13. Metrics for comparison of crystallographic maps

    SciTech Connect

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-10-01

    Numerical comparison of crystallographic contour maps is used extensively in structure solution and model refinement, analysis and validation. However, traditional metrics such as the map correlation coefficient (map CC, real-space CC or RSCC) sometimes contradict the results of visual assessment of the corresponding maps. This article explains such apparent contradictions and suggests new metrics and tools to compare crystallographic contour maps. The key to the new methods is rank scaling of the Fourier syntheses. The new metrics are complementary to the usual map CC and can be more helpful in map comparison, in particular when only some of their aspects, such as regions of high density, are of interest.

  14. Confessions of an icosahedral virus crystallographer

    PubMed Central

    Johnson, John E.

    2013-01-01

    This is a personal history of my structural studies of icosahedral viruses that evolved from crystallographic studies, to hybrid methods with electron cryo-microscopy and image reconstruction (cryoEM) and then developed further by incorporating a variety of physical methods to augment the high resolution crystallographic studies. It is not meant to be comprehensive, even for my own work, but hopefully provides some perspective on the growth of our understanding of these remarkable biologic assemblies. The goal is to provide a historical perspective for those new to the field and to emphasize the limitations of any one method, even those that provide atomic resolution information about viruses. PMID:23291268

  15. Probing PrPSc structure using chemical cross-linking and mass spectrometry: evidence of the proximity of Gly90 amino termini in the PrP 27-30 aggregate.

    PubMed

    Onisko, Bruce; Fernández, Esteban Guitián; Freire, María Louro; Schwarz, Anja; Baier, Michael; Camiña, Félix; García, Javier Rodríguez; Rodríguez-Segade Villamarín, Santiago; Requena, Jesús R

    2005-08-01

    Elucidation of the structure of PrP(Sc) continues to be one of the most important and difficult challenges in prion research. This task, essential for gaining an understanding of the basis of prion infectivity, has been hampered by the insoluble, aggregated nature of this molecule. We used a combination of chemical cross-linking, proteolytic digestion, and mass spectrometry (MALDI-TOF and nanoLC-ESI-QqTOF), in an attempt to gain structural information about PrP 27-30 purified from the brains of Syrian hamsters infected with scrapie. The rationale of this approach is to identify pairs of specific amino acid residues that are close enough to each other to react with a bifunctional reagent of a given chain length. We cross-linked PrP 27-30 with the amino-specific reagent bis(sulfosuccinimidyl) suberate (BS(3)), obtaining dimers, trimers, and higher-order oligomers that were separated by SDS-PAGE. In-gel digestion followed by mass spectrometric analysis showed that BS(3) reacted preferentially with Gly90. A cross-link involving two Gly90 amino termini was found in cross-linked PrP 27-30 dimers, but not in intramolecularly cross-linked monomers or control samples. This observation indicates the spatial proximity of Gly90 amino termini in PrP 27-30 fibrils. The Gly90-Gly90 cross-link is consistent with a recent model of PrP 27-30, based on electron crystallographic data, featuring a fiber composed of stacked trimers of PrP monomers; specifically, it is compatible with cross-linking of monomers stacked vertically along the fiber axis but not those adjacent to each other horizontally in the trimeric building block. Our results constitute the first measured distance constraint in PrP(Sc). PMID:16042387

  16. Crystallographic Data Centre Services and Publications.

    ERIC Educational Resources Information Center

    Cambridge Univ. (England). Chemical Lab.

    The Cambridge Crystallographic Data Centre is concerned with the retrieval, evaluation, synthesis, and dissemination of structural data based on diffraction methods. The source of input is almost entirely primary journals. Bibliographic information and numeric data on crystal and molecular structures are on magnetic tapes. The bibliographic file…

  17. The use of Fourier reverse transforms in crystallographic phase refinement

    SciTech Connect

    Ringrose, S.

    1997-10-08

    Often a crystallographer obtains an electron density map which shows only part of the structure. In such cases, the phasing of the trial model is poor enough that the electron density map may show peaks in some of the atomic positions, but other atomic positions are not visible. There may also be extraneous peaks present which are not due to atomic positions. A method for determination of crystal structures that have resisted solution through normal crystallographic methods has been developed. PHASER is a series of FORTRAN programs which aids in the structure solution of poorly phased electron density maps by refining the crystallographic phases. It facilitates the refinement of such poorly phased electron density maps for difficult structures which might otherwise not be solvable. The trial model, which serves as the starting point for the phase refinement, may be acquired by several routes such as direct methods or Patterson methods. Modifications are made to the reverse transform process based on several assumptions. First, the starting electron density map is modified based on the fact that physically the electron density map must be non-negative at all points. In practice a small positive cutoff is used. A reverse Fourier transform is computed based on the modified electron density map. Secondly, the authors assume that a better electron density map will result by using the observed magnitudes of the structure factors combined with the phases calculated in the reverse transform. After convergence has been reached, more atomic positions and less extraneous peaks are observed in the refined electron density map. The starting model need not be very large to achieve success with PHASER; successful phase refinement has been achieved with a starting model that consists of only 5% of the total scattering power of the full molecule. The second part of the thesis discusses three crystal structure determinations.

  18. Metrics for comparison of crystallographic maps

    DOE PAGESBeta

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-10-01

    Numerical comparison of crystallographic contour maps is used extensively in structure solution and model refinement, analysis and validation. However, traditional metrics such as the map correlation coefficient (map CC, real-space CC or RSCC) sometimes contradict the results of visual assessment of the corresponding maps. This article explains such apparent contradictions and suggests new metrics and tools to compare crystallographic contour maps. The key to the new methods is rank scaling of the Fourier syntheses. The new metrics are complementary to the usual map CC and can be more helpful in map comparison, in particular when only some of their aspects,more » such as regions of high density, are of interest.« less

  19. Quantum crystallographic charge density of urea.

    PubMed

    Wall, Michael E

    2016-07-01

    Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. The results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement. PMID:27437111

  20. Quantum crystallographic charge density of urea

    DOE PAGESBeta

    Wall, Michael E.

    2016-07-01

    Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

  1. Quantum crystallographic charge density of urea

    PubMed Central

    Wall, Michael E.

    2016-01-01

    Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. The results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement. PMID:27437111

  2. A preliminary neutron crystallographic study of thaumatin

    SciTech Connect

    Teixeira, Susana C. M.; Blakeley, Matthew P.; Leal, Ricardo M. F.; Mitchell, Edward P.; Forsyth, V. Trevor

    2008-05-01

    Preliminary neutron crystallographic data from the sweet protein thaumatin have been recorded using the LADI-III diffractometer at the Institut Laue Langevin (ILL). The results illustrate the feasibility of a full neutron structural analysis aimed at further understanding the molecular basis of the perception of sweet taste. Such an analysis will exploit the use of perdeuterated thaumatin. A preliminary neutron crystallographic study of the sweet protein thaumatin is presented. Large hydrogenated crystals were prepared in deuterated crystallization buffer using the gel-acupuncture method. Data were collected to a resolution of 2 Å on the LADI-III diffractometer at the Institut Laue Langevin (ILL). The results demonstrate the feasibility of a full neutron crystallographic analysis of this structure aimed at providing relevant information on the location of H atoms, the distribution of charge on the protein surface and localized water in the structure. This information will be of interest for understanding the specificity of thaumatin–receptor interactions and will contribute to further understanding of the molecular mechanisms underlying the perception of taste.

  3. Predicting Lymph Node Metastasis in Endometrial Cancer Using Serum CA125 Combined with Immunohistochemical Markers PR and Ki67, and a Comparison with Other Prediction Models

    PubMed Central

    Xue, Xiaohong; Wang, Huaying; Shan, Weiwei; Ning, Chengcheng; Zhou, Qiongjie; Chen, Xiaojun; Luo, Xuezhen

    2016-01-01

    We aimed to evaluate the value of immunohistochemical markers and serum CA125 in predicting the risk of lymph node metastasis (LNM) in women with endometrial cancer and to identify a low-risk group of LNM. The medical records of 370 patients with endometrial endometrioid adenocarcinoma who underwent surgical staging in the Obstetrics & Gynecology Hospital of Fudan University were collected and retrospectively reviewed. Immunohistochemical markers were screened. A model using serum cancer antigen 125 (CA125) level, the immunohistochemical markers progesterone receptor (PR) and Ki67 was created for prediction of LNM. A predicted probability of 4% among these patients was defined as low risk. The developed model was externally validated in 200 patients from Shanghai Cancer Center. The efficiency of the model was compared with three other reported prediction models. Patients with serum CA125 < 30.0 IU/mL, either or both of positive PR staining > 50% and Ki67 < 40% in cancer lesion were defined as low risk for LNM. The model showed good discrimination with an area under the receiver operating characteristic curve of 0.82. The model classified 61.9% (229/370) of patients as being at low risk for LNM. Among these 229 patients, 6 patients (2.6%) had LNM and the negative predictive value was 97.4% (223/229). The sensitivity and specificity of the model were 84.6% and 67.4% respectively. In the validation cohort, the model classified 59.5% (119/200) of patients as low-risk, 3 out of these 119 patients (2.5%) has LNM. Our model showed a predictive power similar to those of two previously reported prediction models. The prediction model using serum CA125 and the immunohistochemical markers PR and Ki67 is useful to predict patients with a low risk of LNM and has the potential to provide valuable guidance to clinicians in the treatment of patients with endometrioid endometrial cancer. PMID:27163153

  4. Bilbao Crystallographic Server. II. Representations of crystallographic point groups and space groups.

    PubMed

    Aroyo, Mois I; Kirov, Asen; Capillas, Cesar; Perez-Mato, J M; Wondratschek, Hans

    2006-03-01

    The Bilbao Crystallographic Server is a web site with crystallographic programs and databases freely available on-line (http://www.cryst.ehu.es). The server gives access to general information related to crystallographic symmetry groups (generators, general and special positions, maximal subgroups, Brillouin zones etc.). Apart from the simple tools for retrieving the stored data, there are programs for the analysis of group-subgroup relations between space groups (subgroups and supergroups, Wyckoff-position splitting schemes etc.). There are also software packages studying specific problems of solid-state physics, structural chemistry and crystallography. This article reports on the programs treating representations of point and space groups. There are tools for the construction of irreducible representations, for the study of the correlations between representations of group-subgroup pairs of space groups and for the decompositions of Kronecker products of representations. PMID:16489249

  5. Crystallographic Texture in Ceramics and Metals.

    PubMed

    Vaudin, M D

    2001-01-01

    Preferred crystallographic orientation, or texture, occurs almost universally, both in natural and man-made systems. Many components and devices in electronic and magnetic systems are fabricated from materials that have crystallographic texture. With the rapidly increasing use of thin film technology, where sharp axisymmetric crystallographic texture normal to the film plane is frequently observed, the occurrence and impact of texture are rising. Thin film applications in which the texture of the material plays a key role in determining properties and performance are broad: complex oxides in random access memory devices, ZnO thin film resonators for cell phone applications, metallic alloys in magnetic recording media, and Al and Cu interconnects in integrated circuits are but a few examples. Texture is established during the synthesis or post-synthesis heat treatment of a material and thus has a strong dependence upon processing history. Accurate measurement of texture is not simple and a variety of tools and approaches are being actively employed in texture studies. X-ray, neutron and electron diffraction based techniques are practiced around the world at varying levels of complexity with regard to equipment and analysis methods. Despite the well-documented existence of these varied approaches, many reported texture measurements on electronic materials are based solely on the relative intensities of conventional θ-2θ x-ray diffraction peaks, which typically yield inaccurate results. NIST has developed quantitative texture measurement techniques that employ equipment commonly available in most industrial and academic settings. A number of examples of texture measurement in ceramic and metal systems will be presented, taken from the historical development and application of these techniques at NIST over the past 7 years. PMID:27500066

  6. Crystallographic Texture in Ceramics and Metals

    PubMed Central

    Vaudin, Mark D.

    2001-01-01

    Preferred crystallographic orientation, or texture, occurs almost universally, both in natural and man-made systems. Many components and devices in electronic and magnetic systems are fabricated from materials that have crystallographic texture. With the rapidly increasing use of thin film technology, where sharp axisymmetric crystallographic texture normal to the film plane is frequently observed, the occurrence and impact of texture are rising. Thin film applications in which the texture of the material plays a key role in determining properties and performance are broad: complex oxides in random access memory devices, ZnO thin film resonators for cell phone applications, metallic alloys in magnetic recording media, and Al and Cu interconnects in integrated circuits are but a few examples. Texture is established during the synthesis or post-synthesis heat treatment of a material and thus has a strong dependence upon processing history. Accurate measurement of texture is not simple and a variety of tools and approaches are being actively employed in texture studies. X-ray, neutron and electron diffraction based techniques are practiced around the world at varying levels of complexity with regard to equipment and analysis methods. Despite the well-documented existence of these varied approaches, many reported texture measurements on electronic materials are based solely on the relative intensities of conventional θ-2θ x-ray diffraction peaks, which typically yield inaccurate results. NIST has developed quantitative texture measurement techniques that employ equipment commonly available in most industrial and academic settings. A number of examples of texture measurement in ceramic and metal systems will be presented, taken from the historical development and application of these techniques at NIST over the past 7 years.

  7. Orbits of crystallographic embedding of non-crystallographic groups and applications to virology.

    PubMed

    Twarock, Reidun; Valiunas, Motiejus; Zappa, Emilio

    2015-11-01

    The architecture of infinite structures with non-crystallographic symmetries can be modelled via aperiodic tilings, but a systematic construction method for finite structures with non-crystallographic symmetry at different radial levels is still lacking. This paper presents a group theoretical method for the construction of finite nested point sets with non-crystallographic symmetry. Akin to the construction of quasicrystals, a non-crystallographic group G is embedded into the point group P of a higher-dimensional lattice and the chains of all G-containing subgroups are constructed. The orbits of lattice points under such subgroups are determined, and it is shown that their projection into a lower-dimensional G-invariant subspace consists of nested point sets with G-symmetry at each radial level. The number of different radial levels is bounded by the index of G in the subgroup of P. In the case of icosahedral symmetry, all subgroup chains are determined explicitly and it is illustrated that these point sets in projection provide blueprints that approximate the organization of simple viral capsids, encoding information on the structural organization of capsid proteins and the genomic material collectively, based on two case studies. Contrary to the affine extensions previously introduced, these orbits endow virus architecture with an underlying finite group structure, which lends itself better to the modelling of dynamic properties than its infinite-dimensional counterpart. PMID:26522406

  8. Thermal stability of mullite RMn₂O₅ (R  =  Bi, Y, Pr, Sm or Gd): combined density functional theory and experimental study.

    PubMed

    Li, Chenzhe; Thampy, Sampreetha; Zheng, Yongping; Kweun, Joshua M; Ren, Yixin; Chan, Julia Y; Kim, Hanchul; Cho, Maenghyo; Kim, Yoon Young; Hsu, Julia W P; Cho, Kyeongjae

    2016-03-31

    Understanding and effectively predicting the thermal stability of ternary transition metal oxides with heavy elements using first principle simulations are vital for understanding performance of advanced materials. In this work, we have investigated the thermal stability of mullite RMn2O5 (R  =  Bi, Pr, Sm, or Gd) structures by constructing temperature phase diagrams using an efficient mixed generalized gradient approximation (GGA) and the GGA  +  U method. Simulation predicted stability regions without corrections on heavy elements show a 4-200 K underestimation compared to our experimental results. We have found the number of d/f electrons in the heavy elements shows a linear relationship with the prediction deviation. Further correction on the strongly correlated electrons in heavy elements could significantly reduce the prediction deviations. Our corrected simulation results demonstrate that further correction of R-site elements in RMn2O5 could effectively reduce the underestimation of the density functional theory-predicted decomposition temperature to within 30 K. Therefore, it could produce an accurate thermal stability prediction for complex ternary transition metal oxide compounds with heavy elements. PMID:26932942

  9. Thermal stability of mullite RMn2O5 (R  =  Bi, Y, Pr, Sm or Gd): combined density functional theory and experimental study

    NASA Astrophysics Data System (ADS)

    Li, Chenzhe; Thampy, Sampreetha; Zheng, Yongping; Kweun, Joshua M.; Ren, Yixin; Chan, Julia Y.; Kim, Hanchul; Cho, Maenghyo; Kim, Yoon Young; Hsu, Julia W. P.; Cho, Kyeongjae

    2016-03-01

    Understanding and effectively predicting the thermal stability of ternary transition metal oxides with heavy elements using first principle simulations are vital for understanding performance of advanced materials. In this work, we have investigated the thermal stability of mullite RMn2O5 (R  =  Bi, Pr, Sm, or Gd) structures by constructing temperature phase diagrams using an efficient mixed generalized gradient approximation (GGA) and the GGA  +  U method. Simulation predicted stability regions without corrections on heavy elements show a 4-200 K underestimation compared to our experimental results. We have found the number of d/f electrons in the heavy elements shows a linear relationship with the prediction deviation. Further correction on the strongly correlated electrons in heavy elements could significantly reduce the prediction deviations. Our corrected simulation results demonstrate that further correction of R-site elements in RMn2O5 could effectively reduce the underestimation of the density functional theory-predicted decomposition temperature to within 30 K. Therefore, it could produce an accurate thermal stability prediction for complex ternary transition metal oxide compounds with heavy elements.

  10. Teaching Biochemists and Pharmacologists How to Use Crystallographic Data.

    ERIC Educational Resources Information Center

    Duax, William L.

    1988-01-01

    Describes a one-semester course designed to teach first year graduate students how to extract, interpret, evaluate, and use the information provided by an X-ray crystallographic crystal structure determination. Presents a course outline and discusses the treatment of crystal composition, crystallographic parameters, molecular geometry and…

  11. Morphological and crystallographic evolution of bainite transformation in Fe-0.15C binary alloy.

    PubMed

    Zhang, Di; Terasaki, Hidenori; Komizo, Yuichi

    2010-01-01

    In this article, an in situ observation method, combining laser scanning confocal microscopy and electron backscattering diffraction, was used to investigate the morphological and crystallographic evolution of bainite transformation in a Fe-0.15C binary alloy. The nucleation at a grain boundary and inclusions, sympathetic nucleation, and impingement event of bainitic ferrite were directly shown in real time. The variant evolution during bainite transformation and misorientation between bainitic ferrites were clarified. Strong variant selection was observed during sympathetic nucleation. PMID:19588518

  12. XTAL system of crystallographic programs: programmer's manual

    SciTech Connect

    Hall, S.R.; Stewart, J.M.; Norden, A.P.; Munn, R.J.; Freer, S.T.

    1980-02-01

    This document establishes the basis for collaborative writing of transportable computer programs for x-ray crystallography. The concepts and general-purpose utility subroutines described here can be readily adapted to other scientific calculations. The complete system of crystallographic programs and subroutines is called XTAL and replaces the XRAY (6,7,8) system of programs. The coding language for the XTAL system is RATMAC (5). The XTAL system of programs contains routines for controlling execution of application programs. In this sense it forms a suboperating system that presents the same computational environment to the user and programmer irrespective of the operating system in use at a particular installation. These control routines replace all FORTRAN I/O code, supply character reading and writing, supply binary file reading and writing, serve as a support library for applications programs, and provide for interprogram communication.

  13. Preliminary neutron crystallographic study of human transthyretin

    PubMed Central

    Haupt, Melina; Blakeley, Matthew P.; Teixeira, Susana C. M.; Mason, Sax A.; Mitchell, Edward P.; Cooper, Jonathan B.; Forsyth, V. Trevor

    2011-01-01

    Preliminary studies of perdeuterated crystals of human transthyretin (TTR) have been carried out using the LADI-III and D19 diffractometers at the Institut Laue–Langevin in Grenoble. The results demonstrate the feasibility of a full crystallographic analysis to a resolution of 2.0 Å using Laue diffraction and also illustrate the potential of using monochromatic instruments such as D19 for higher resolution studies where larger crystals having smaller unit cells are available. This study will yield important information on hydrogen bonding, amino-acid protonation states and hydration in the protein. Such information will be of general interest for an understanding of the factors that stabilize/destabilize TTR and for the design of ligands that may be used to counter TTR amyloid fibrillogenesis. PMID:22102249

  14. Combined first-principles and model Hamiltonian study of the perovskite series R MnO 3 (R =La ,Pr ,Nd ,Sm ,Eu , and Gd )

    NASA Astrophysics Data System (ADS)

    Kováčik, Roman; Murthy, Sowmya Sathyanarayana; Quiroga, Carmen E.; Ederer, Claude; Franchini, Cesare

    2016-02-01

    We merge advanced ab initio schemes (standard density functional theory, hybrid functionals, and the G W approximation) with model Hamiltonian approaches (tight-binding and Heisenberg Hamiltonian) to study the evolution of the electronic, magnetic, and dielectric properties of the manganite family R MnO3 (R =La,Pr,Nd,Sm,Eu, and Gd) . The link between first principles and tight binding is established by downfolding the physically relevant subset of 3 d bands with eg character by means of maximally localized Wannier functions (MLWFs) using the VASP2WANNIER90 interface. The MLWFs are then used to construct a general tight-binding Hamiltonian written as a sum of the kinetic term, the Hund's rule coupling, the JT coupling, and the electron-electron interaction. The dispersion of the tight-binding (TB) eg bands at all levels are found to match closely the MLWFs. We provide a complete set of TB parameters which can serve as guidance for the interpretation of future studies based on many-body Hamiltonian approaches. In particular, we find that the Hund's rule coupling strength, the Jahn-Teller coupling strength, and the Hubbard interaction parameter U remain nearly constant for all the members of the R MnO3 series, whereas the nearest-neighbor hopping amplitudes show a monotonic attenuation as expected from the trend of the tolerance factor. Magnetic exchange interactions, computed by mapping a large set of hybrid functional total energies onto an Heisenberg Hamiltonian, clarify the origin of the A-type magnetic ordering observed in the early rare-earth manganite series as arising from a net negative out-of-plane interaction energy. The obtained exchange parameters are used to estimate the Néel temperature by means of Monte Carlo simulations. The resulting data capture well the monotonic decrease of the ordering temperature down the series from R =La to Gd, in agreement with experiments. This trend correlates well with the modulation of structural properties, in

  15. Crystallographic education in the 21st century

    PubMed Central

    Gražulis, Saulius; Sarjeant, Amy Alexis; Moeck, Peter; Stone-Sundberg, Jennifer; Snyder, Trevor J.; Kaminsky, Werner; Oliver, Allen G.; Stern, Charlotte L.; Dawe, Louise N.; Rychkov, Denis A.; Losev, Evgeniy A.; Boldyreva, Elena V.; Tanski, Joseph M.; Bernstein, Joel; Rabeh, Wael M.; Kantardjieff, Katherine A.

    2015-01-01

    There are many methods that can be used to incorporate concepts of crystallography into the learning experiences of students, whether they are in elementary school, at university or part of the public at large. It is not always critical that those who teach crystallography have immediate access to diffraction equipment to be able to introduce the concepts of symmetry, packing or molecular structure in an age- and audience-appropriate manner. Crystallography can be used as a tool for teaching general chemistry concepts as well as general research techniques without ever having a student determine a crystal structure. Thus, methods for younger students to perform crystal growth experiments of simple inorganic salts, organic compounds and even metals are presented. For settings where crystallographic instrumentation is accessible (proximally or remotely), students can be involved in all steps of the process, from crystal growth, to data collection, through structure solution and refinement, to final publication. Several approaches based on the presentations in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly are reported. The topics cover methods for introducing crystallography to undergraduate students as part of a core chemistry curriculum; a successful short-course workshop intended to bootstrap researchers who rely on crystallography for their work; and efforts to bring crystallography to secondary school children and non-science majors. In addition to these workshops, demonstrations and long-format courses, open-format crystallographic databases and three-dimensional printed models as tools that can be used to excite target audiences and inspire them to pursue a deeper understanding of crystallography are described. PMID:26664347

  16. Crystallographic Tool Box (CrysTBox): automated tools for transmission electron microscopists and crystallographers

    PubMed Central

    Klinger, Miloslav; Jäger, Aleš

    2015-01-01

    Three tools for an automated analysis of electron diffraction pattern and crystallographic visualization are presented. Firstly, diffractGUI determines the zone axis from selected area diffraction, convergent beam diffraction or nanodiffraction patterns and allows for indexing of individual reflections. Secondly, ringGUI identifies crystallographic planes corresponding to the depicted rings in the ring diffraction pattern and can select the sample material from a list of candidates. Both diffractGUI and ringGUI employ methods of computer vision for a fast, robust and accurate analysis. Thirdly, cellViewer is an intuitive visualization tool which is also helpful for crystallographic calculations or educational purposes. diffractGUI and cellViewer can be used together during a transmission electron microscopy session to determine the sample holder tilts required to reach a desired zone axis. All the tools offer a graphical user interface. The toolbox is distributed as a standalone application, so it can be installed on the microscope computer and launched directly from DigitalMicrograph (Gatan Inc.). PMID:26664349

  17. Combined effect of chemical pressure and valence electron concentration through the electron-deficient Li substitution on the RE{sub 4}LiGe{sub 4} (RE=La, Ce, Pr, and Sm) system

    SciTech Connect

    Nam, Gnu; Jeon, Jieun; Kim, Youngjo; Kwon Kang, Sung; Ahn, Kyunghan; You, Tae-Soo

    2013-09-15

    Four members of the RE{sub 4}LiGe{sub 4} (RE=La, Ce, Pr, and Sm) system have been prepared by high-temperature reaction method and characterized by X-ray diffractions. All compounds crystallize in the orthorhombic Gd{sub 5}Si{sub 4}-type structure (space group Pnma, Pearson code oP16) with bonding interactions for interslab Ge{sub 2} dimers. The Li substitution for rare-earth elements in the RE{sub 4}LiGe{sub 4} system leads to a combined effect of the increased chemical pressure and the decreased valance electron concentration (VEC), which eventually results in the structure transformation from the Sm{sub 5}Ge{sub 4}-type with all broken interslab Ge–Ge bond for the parental RE{sub 5}Ge{sub 4} to the Gd{sub 5}Si{sub 4}-type structure for the ternary RE{sub 4}LiGe{sub 4} (RE=La, Ce, Pr, and Sm) system. Site-preference between rare-earth metals and Li is proven to generate energetically the most favorable atomic arrangements according to coloring-problem, and the rationale is provided using both the size-factor and the electronic-factor related, respectively, to site-volume and electronegativity as well as QVAL values. Tight-binding, linear-muffin-tin-orbital (TB-LMTO) calculations are performed to investigate electronic densities of states (DOS) and crystal orbital Hamilton population (COHP) curves. The influence of reduced VEC for chemical bonding including the formation of interslab Ge{sub 2} dimers is also discussed. The magnetic property measurements prove that the non-magnetic Li substitution leads to the ferromagnetic (FM)-like ground state for Ce{sub 4}LiGe{sub 4} and the co-existence of antiferromagntic (AFM) and FM ground states for Sm{sub 4}LiGe{sub 4}. - Graphical abstract: Reported is a combined effect of the chemical pressure and the reduced VEC caused by the smaller monovalent non-magnetic Li substitution for the larger trivalent magnetic rare-earth metals in the RE{sub 4}LiGe{sub 4} (RE=La, Ce, Pr, and Sm) system. This results in the structure

  18. Combined effect of chemical pressure and valence electron concentration through the electron-deficient Li substitution on the RE4LiGe4 (RE=La, Ce, Pr, and Sm) system

    NASA Astrophysics Data System (ADS)

    Nam, Gnu; Jeon, Jieun; Kim, Youngjo; Kwon Kang, Sung; Ahn, Kyunghan; You, Tae-Soo

    2013-09-01

    Four members of the RE4LiGe4 (RE=La, Ce, Pr, and Sm) system have been prepared by high-temperature reaction method and characterized by X-ray diffractions. All compounds crystallize in the orthorhombic Gd5Si4-type structure (space group Pnma, Pearson code oP16) with bonding interactions for interslab Ge2 dimers. The Li substitution for rare-earth elements in the RE4LiGe4 system leads to a combined effect of the increased chemical pressure and the decreased valance electron concentration (VEC), which eventually results in the structure transformation from the Sm5Ge4-type with all broken interslab Ge-Ge bond for the parental RE5Ge4 to the Gd5Si4-type structure for the ternary RE4LiGe4 (RE=La, Ce, Pr, and Sm) system. Site-preference between rare-earth metals and Li is proven to generate energetically the most favorable atomic arrangements according to coloring-problem, and the rationale is provided using both the size-factor and the electronic-factor related, respectively, to site-volume and electronegativity as well as QVAL values. Tight-binding, linear-muffin-tin-orbital (TB-LMTO) calculations are performed to investigate electronic densities of states (DOS) and crystal orbital Hamilton population (COHP) curves. The influence of reduced VEC for chemical bonding including the formation of interslab Ge2 dimers is also discussed. The magnetic property measurements prove that the non-magnetic Li substitution leads to the ferromagnetic (FM)-like ground state for Ce4LiGe4 and the co-existence of antiferromagntic (AFM) and FM ground states for Sm4LiGe4.

  19. Crystallographic model quality at a glance

    PubMed Central

    Urzhumtseva, Ludmila; Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre

    2009-01-01

    A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from ‘ideal values’ is shown graphically as a point on a ‘ruler’. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in ‘red zones’ indicate parameters which lie outside typical values. PMID:19237753

  20. Crystallographic model quality at a glance.

    PubMed

    Urzhumtseva, Ludmila; Afonine, Pavel V; Adams, Paul D; Urzhumtsev, Alexandre

    2009-03-01

    A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from ;ideal values' is shown graphically as a point on a ;ruler'. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in ;red zones' indicate parameters which lie outside typical values. PMID:19237753

  1. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.

    PubMed

    Janowski, Pawel A; Moriarty, Nigel W; Kelley, Brian P; Case, David A; York, Darrin M; Adams, Paul D; Warren, Gregory L

    2016-09-01

    Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX-AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX-AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein-ligand PDB structures are presented. Refinements using PHENIX-AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented, PHENIX-AFITT refinements result in more chemically accurate models for small-molecule ligands. PMID:27599738

  2. A crystallographic model for nickel base single crystal alloys

    NASA Technical Reports Server (NTRS)

    Dame, L. T.; Stouffer, D. C.

    1988-01-01

    The purpose of this research is to develop a tool for the mechanical analysis of nickel-base single-crystal superalloys, specifically Rene N4, used in gas turbine engine components. This objective is achieved by developing a rate-dependent anisotropic constitutive model and implementing it in a nonlinear three-dimensional finite-element code. The constitutive model is developed from metallurgical concepts utilizing a crystallographic approach. An extension of Schmid's law is combined with the Bodner-Partom equations to model the inelastic tension/compression asymmetry and orientation-dependence in octahedral slip. Schmid's law is used to approximate the inelastic response of the material in cube slip. The constitutive equations model the tensile behavior, creep response and strain-rate sensitivity of the single-crystal superalloys. Methods for deriving the material constants from standard tests are also discussed. The model is implemented in a finite-element code, and the computed and experimental results are compared for several orientations and loading conditions.

  3. Correlation between crystallographic orientation and surface faceting in UO2

    NASA Astrophysics Data System (ADS)

    Miao, Yinbin; Mo, Kun; Yao, Tiankai; Lian, Jie; Fortner, Jeffrey; Jamison, Laura; Xu, Ruqing; Yacout, Abdellatif M.

    2016-09-01

    Here coordinated experimental efforts to quantitatively correlate crystallographic orientation and surface faceting features in UO2 are reported upon. A sintered polycrystalline UO2 sample was thermally etched to induce the formation of surface faceting features. Synchrotron Laue microdiffraction was used to obtain a precise crystallographic orientation map for the UO2 surface grains. Scanning electron microscopy (SEM) was utilized to collect the detailed information on the surface morphology of the sample. The surface faceting features were found to be highly dependent on the crystallographic orientation. In most cases, Triple-plane structures containing one {100} plane and two {111} planes were found to dominate the surface of UO2. The orientation-faceting relationship established in this study revealed a practical and efficient method of determining crystallographic orientation based on the surface features captured by SEM images.

  4. Correlated crystallographic etching of graphene and nanoribbon formation

    NASA Astrophysics Data System (ADS)

    Johnson, Stephen; Hunley, D. Patrick; Stieha, Joseph; Sundararajan, Abhishek; Kar, Arunita; Johnson, A. T. Charlie; Strachan, Douglas

    2011-03-01

    Catalytic etching is a promising method for constructing crystallographically defined graphene structures such as nanoribbons. Catalytic etching experiments are performed and shown to contain significant correlation yielding crystallographic graphene nanoribbons. This correlation is investigated as a function of etching conditions and compared to simulations with possible sources discussed. Supported in part by NSF Award No. DMR-0805136, the Kentucky NSF EPSCoR program, the University of Kentucky Center for Advanced Materials, and the University of Kentucky Center for Nanoscale Science and Engineering.

  5. Butene oxidation by molybdenum crystallographic shear compounds

    SciTech Connect

    McCormick, R.L.

    1984-06-01

    The reduced molybdenum oxides Mo/sub 4/O/sub 11/-orh, Mo/sub 4/O/sub 11/-mon, Mo/sub 8/O/sub 23/, and Mo/sub 18/O/sub 52/ were synthesized. These compounds, as well as MoO/sub 3/, were characterized by x-ray diffraction, x-ray photoelectron spectroscopy, Raman and FT-IR spectroscopies, and BET surface area measurements. The oxides were then studied in a pulsed reactor at 500/sup 0/C in the selective oxidation of butene and butadiene. The data suggested a process in which the surface site must become more oxidized in parallel with the oxidation of the adsorbed hydrocarbon. Evidence supporting this idea included the high selectivity to maleic anhydride observed over a completely oxidized surface and differences in the reactivity of butene and butadiende. In particular, oxygen insertion into butadiene to form furan occurred in the absence of gas phase O/sub 2/ over the reduced phases, while oxygen insertion into butene required the presence of molecular oxygen. Maleic anhydride formation required the presence of molecular oxygen except in the case of butadiene oxidation over MoO/sub 3/. The long range ordering of defects, known as crystallographic shear, was not shown to have any influence on the initial interaction of reactant and solid. However, the unusual coordination geometries and surface structures that are thought to be caused by the presence of shear planes may be related to the differences in catalytic selectivity observed for these oxides.

  6. Some algebraic properties of crystallographic sublattices.

    PubMed

    Rutherford, John S

    2006-03-01

    In this article, a number of the results relevant to the concept of sublattices of a basic crystallographic lattice are reviewed, emphasizing particularly previously unpublished work on the algebraic aspects. A three-dimensional geometric lattice L can be considered as an infinite Abelian group under addition. A sublattice S of L, which is also three-dimensional, is a subgroup of L such that the finite quotient group, G approximately equals L/S, is an Abelian group of order the index of S in L. The sublattice itself in its standard form is represented by an upper triangular matrix. The index of the sublattice is given by the determinant of this matrix. It is first noted that a sublattice described by an arbitrary basis set in L may be converted to this standard form. Next the sublattice is expressed as the intersection of a set of sublattices of individual index a power of a distinct prime, i.e. S(n = p(a)(1)p(b)(2)...) = S(1)(p(a)(1)[cap]S(2)(p(b)(2)...[cap]... = [bigcap](i)S(i)(p(alpha(i)), where p(1), p(2) etc. are prime numbers and n = Pi(i)p(alpha)(i) is the Euclidean factorization of n. This decomposition is important because it corresponds to the Sylow decomposition of the corresponding quotient group G approximately equals (i)[sign: see text] A(p)(i). It is also useful to be able to carry out two commutative binary operations on sublattices of L; these are to find their common sublattice of lowest index in L, which is their intersection S(cap) = S(a)(m)[cap]S(b)(n) and their common superlattice of highest index in L, given by S(< >) = , where < > indicates the span of the sublattices. PMID:16489245

  7. ESO PR Highlights in 2006

    NASA Astrophysics Data System (ADS)

    2007-01-01

    Last year proved to be another exceptional year for the European organisation for ground-based astronomy. ESO should begin the New Year with two new member states: Spain (PR 05/06) and the Czech Republic (PR 52/06). ESO PR Highlights 2006 2006 was a year of renovation and revolution in the world of planets. A new Earth-like exoplanet has been discovered (PR 03/06) using a network of telescopes from all over the world (including the Danish 1.54-m one at ESO La Silla). It is not the only child of this fruitful year: thanks to the combined use of ESO's Very Large Telescope (VLT) and La Silla instruments, a surprising system of twin giant exoplanets was found (PR 29/06), and a trio of Neptune-like planets hosted by a nearby star were identified (PR 18/06). These results open new perspectives on the search for habitable zones and on the understanding of the mechanism of planet formation. The VISIR instrument on the VLT has been providing unique information to answer this last question, by supplying a high resolution view of a planet-forming disc (PR 36/06). There are not only new members in the planets' register: during the General Assembly of the International Astronomical Union held in Prague (Czech Republic), it was decided that Pluto is not a planet anymore but a 'dwarf planet'. Whatever its status, Pluto still has a satellite, Charon, whose radius and density have been measured more accurately by observing a rare occultation from different sites, including Cerro Paranal (PR 02/06). The scientific community dedicated 2006 to the great physicist James Clerk Maxwell (it was the 175th anniversary of the birth): without his electromagnetic theory of light, none of the astonishing discoveries of modern physics could have been achieved. Nowadays we can look at distant galaxies in great detail: the GIRAFFE spectrograph on the VLT revealed that galaxies 6 billion years ago had the same amount of dark matter relative to stars than nowadays (PR 10/06), while SINFONI gave an

  8. ESO PR Highlights in 2005

    NASA Astrophysics Data System (ADS)

    2006-01-01

    very close collaboration with the space mission' scientific team, in what was perhaps the most comprehensive ground-observing campaign of a celestial object. On this occasion, a dedicated Deep Impact at ESO web site was created, reporting on all the developments. This was not the sole contribution of ESO to the study of the solar system . The NACO SDI instrument was used to obtain outstanding images of Titan, the satellite of Saturn ( PHOT 04/05) and NACO also allowed astronomers to discover the first triple asteroid - two small asteroids orbiting a larger one known since 1866 as 87 Sylvia ( PR 21/05). 2005 was also a very important year for sub-millimetric astronomy at ESO. In July, APEX , the 12-m Atacama Pathfinder Experiment's telescope had first light ( PR 18/05) and since then, has been performing regular science observations ( PR 25/05). Moreover, two major contracts have been signed for ALMA , the Atacama Large Millimeter Array project, among which the largest-ever European industrial contract for a ground-based astronomy project ( PR 31/05 and 34/05). ESO's Very Large Telescope (VLT) proves to be a very efficient science machine that reached in April 2005, the count of more than 1000 scientific papers (see ESO PR 11/05) and the trend does not seem to change, as about 350 papers were published in 2005 based on data collected with the VLT. This efficiency was also recognised worldwide as ESO received the ComputerWorld Honors Program 21st Century Achievement Award in the Science Category ( PR 16/05). The interferometric mode of the VLT (VLTI) was able to observe with unprecedented detail the environment of two stars ( PR 29/05). The VLTI has also seen another extension of its already impressive capabilities by combining interferometrically the light from two relocatable 1.8-m Auxiliary Telescopes ( PR 06/05). ESO PR Highlights 2005 In 2005 again, many nice, amazing astronomical images have been obtained with ESO's telescopes: the super star cluster Westerlund 1

  9. Crystallographic effects during micromachining — A finite-element model

    NASA Astrophysics Data System (ADS)

    Song, Shin-Hyung; Choi, Woo Chun

    2015-07-01

    Mechanical micromachining is a powerful and effective way for manufacturing small sized machine parts. Even though the micromachining process is similar to the traditional machining, the material behavior during the process is much different. In particular, many researchers report that the basic mechanics of the work material is affected by microstructures and their crystallographic orientations. For example, crystallographic orientations of the work material have significant influence on force response, chip formation and surface finish. In order to thoroughly understand the effect of crystallographic orientations on the micromachining process, finite-element model (FEM) simulating orthogonal cutting process of single crystallographic material was presented. For modeling the work material, rate sensitive single crystal plasticity of face-centered cubic (FCC) crystal was implemented. For the chip formation during the simulation, element deletion technique was used. The simulation model is developed using ABAQUS/explicit with user material subroutine via user material subroutine (VUMAT). Simulations showed that variation of the specific cutting energy at different crystallographic orientations of work material shows significant anisotropy. The developed FEM model can be a useful prediction tool of micromachining of crystalline materials.

  10. Fission gas bubble percolation on crystallographically consistent grain boundary networks

    NASA Astrophysics Data System (ADS)

    Sabogal-Suárez, Daniel; David Alzate-Cardona, Juan; Restrepo-Parra, Elisabeth

    2016-07-01

    Fission gas release in nuclear fuels can be modeled in the framework of percolation theory, where each grain boundary is classified as open or closed to the release of the fission gas. In the present work, two-dimensional grain boundary networks were assembled both at random and in a crystallographically consistent manner resembling a general textured microstructure. In the crystallographically consistent networks, grain boundaries were classified according to its misorientation. The percolation behavior of the grain boundary networks was evaluated as a function of radial cracks and radial thermal gradients in the fuel pellet. Percolation thresholds tend to shift to the left with increasing length and number of cracks, especially in the presence of thermal gradients. In general, the topology and percolation behavior of the crystallographically consistent networks differs from those of the random network.

  11. Experimental Investigation of the Cd-Pr Phase Diagram

    PubMed Central

    Reichmann, Thomas L.; Effenberger, Herta S.; Ipser, Herbert

    2014-01-01

    The complete Cd-Pr equilibrium phase diagram was investigated with a combination of powder-XRD, SEM and DTA. All intermetallic compounds within this system, already reported in literature, could be confirmed: CdPr, Cd2Pr, Cd3Pr, Cd45Pr11, Cd58Pr13, Cd6Pr and Cd11Pr. The corresponding phase boundaries were determined at distinct temperatures. The homogeneity range of the high-temperature allotropic modification of Pr could be determined precisely and a limited solubility of 22.1 at.% Cd was derived. Additionally, single-crystal X-ray diffraction was employed to investigate structural details of Cd2Pr; it is isotypic to the AlB2-type structure with a z value of the Cd site of 0.5. DTA results of alloys located in the adjacent two-phase fields of Cd2Pr suggested a phase transformation between 893 and 930°C. For the phase Cd3Pr it was found that the lattice parameter a changes linearly with increasing Cd content, following Vegard’s rule. The corresponding defect mechanism could be evaluated from structural data collected with single-crystal XRD. Introduction of a significant amount of vacancies on the Pr site and the reduction in symmetry of one Cd position (8c to 32f) resulted in a noticeable decrease of all R-values. PMID:24718502

  12. Experimental investigation of the Cd-Pr phase diagram.

    PubMed

    Reichmann, Thomas L; Effenberger, Herta S; Ipser, Herbert

    2014-01-01

    The complete Cd-Pr equilibrium phase diagram was investigated with a combination of powder-XRD, SEM and DTA. All intermetallic compounds within this system, already reported in literature, could be confirmed: CdPr, Cd2Pr, Cd3Pr, Cd45Pr11, Cd58Pr13, Cd6Pr and Cd11Pr. The corresponding phase boundaries were determined at distinct temperatures. The homogeneity range of the high-temperature allotropic modification of Pr could be determined precisely and a limited solubility of 22.1 at.% Cd was derived. Additionally, single-crystal X-ray diffraction was employed to investigate structural details of Cd2Pr; it is isotypic to the AlB2-type structure with a z value of the Cd site of 0.5. DTA results of alloys located in the adjacent two-phase fields of Cd2Pr suggested a phase transformation between 893 and 930°C. For the phase Cd3Pr it was found that the lattice parameter a changes linearly with increasing Cd content, following Vegard's rule. The corresponding defect mechanism could be evaluated from structural data collected with single-crystal XRD. Introduction of a significant amount of vacancies on the Pr site and the reduction in symmetry of one Cd position (8c to 32f) resulted in a noticeable decrease of all R-values. PMID:24718502

  13. Crystallographic Topology 2: Overview and Work in Progress

    SciTech Connect

    Johnson, C.K.

    1999-08-01

    This overview describes an application of contemporary geometric topology and stochastic process concepts to structural crystallography. In this application, crystallographic groups become orbifolds, crystal structures become Morse functions on orbifolds, and vibrating atoms in a crystal become vector valued Gaussian measures with the Radon-Nikodym property. Intended crystallographic benefits include new methods for visualization of space groups and crystal structures, analysis of the thermal motion patterns seen in ORTEP drawings, and a classification scheme for crystal structures based on their Heegaard splitting properties.

  14. Crystallographic variant selection in {alpha}-{beta} brass

    SciTech Connect

    Stanford, N.; Bate, P.S. . E-mail: pete.bate@man.ac.uk

    2005-02-01

    The transformation texture of {alpha}/{beta} brass with a diffusional Widmanstaetten {alpha} growth morphology has been investigated. Electron micrographs and electron backscattered diffraction was used to determine that the orientation relationship between the {beta} phase and the {alpha} associated with nucleation at {beta} grain boundaries was 44.3 deg <1 1 6>. Crystallographic variant selection was observed across those prior {beta}/{beta} grain boundaries, but this has little effect on the transformation texture due to the crystal symmetry. The effect of the crystallographic variant selection on texture is further weakened by nucleation of diffusional transformed {alpha} in the grain interior.

  15. Self-Assembled Monolayers: Star-Shaped Crystallographic Cracking of Localized Nanoporous Defects (Adv. Mater. 33/2015).

    PubMed

    Renner, Frank Uwe; Ankah, Genesis Ngwa; Bashir, Asif; Ma, Duancheng; Biedermann, P Ulrich; Shrestha, Buddha Ratna; Nellessen, Monika; Khorashadizadeh, Anahita; Losada-Pérez, Patricia; Duarte, Maria Jazmin; Raabe, Dierk; Valtiner, Markus

    2015-09-01

    On page 4877, F. U. Renner, A. Bashir, M. Valtiner, and co-workers describe a star-like dealloying corrosion morphology that appears during the localized attack of smooth well-prepared Cu-Au surfaces. The surfaces are initially protected by thiol or selenol inhibitior films. Localized dealloying of Cu-Au produces nanoporous gold under stress and crystallographic cracks - thereby opening a new approach combining surface science with nanoscale mechanical testing. PMID:26332115

  16. Pr16Mo21O56

    PubMed Central

    Gougeon, Patrick; Gall, Philippe

    2011-01-01

    The structure of hexa­deca­praseodymium henicosa­molybden­um hexa­penta­contaoxide, Pr16Mo21O56, is isotypic with other rare earth representatives of formula type RE 16Mo21O56 (RE = La, Ce, Nd). It is characterized by Mo10O18 iO8 a units (where i = inner and a = apical O atoms) containing biocta­hedral Mo10 clusters and octa­hedral MoO6 units that share some of their O atoms to form the Mo–O framework. The two independent Mo10 cluster units are centred at Wyckoff positions 2b and 2c and have point-group symmetry . The Mo atom of the MoO6 unit is likewise situated at an inversion centre (2d). The eight crystallographically different Pr3+ cations occupy irregular voids in the framework with coordination numbers to the O atoms varying between 8 and 11. PMID:21754260

  17. X-ray Crystallographic Computations Using a Programmable Calculator.

    ERIC Educational Resources Information Center

    Attard, Alfred E.; Lee, Henry C.

    1979-01-01

    Describes six crystallographic programs which have been developed to illustrate the range of usefulness of programmable calculators in providing computational assistance in chemical analysis. These programs are suitable for the analysis of x-ray diffraction data in the laboratory by students. (HM)

  18. ``Crystallographic'' holes: new insights for a beneficial structural feature for photocatalytic applications

    NASA Astrophysics Data System (ADS)

    Vajda, Krisztina; Kása, Zsolt; Dombi, András; Németh, Zoltán; Kovács, Gábor; Danciu, Virginia; Radu, Teodora; Ghica, Corneliu; Baia, Lucian; Hernádi, Klára; Pap, Zsolt

    2015-03-01

    One of the most fundamental aspects of the heterogeneous catalysis field is the manipulation of the catalysts' activity. In photocatalysis this is carried out by maximizing the right crystal plane of a semiconductor oxide. Until now, most of the papers have achieved this by a combination of different oxides, with noble metals and sometimes with carbon nanomaterials. In this work MWCNTs (multiwalled carbon nanotubes) were applied as ``crystallization promoters'' in a very simple, safe, one-step hydrothermal method. By this method TiO2 nano/micro crystals with exposed {001} facets were obtained in the first step. The next episode in the crystal manipulation ``saga'' was the modification of the (001) crystallographic plane's structure by creating ordered/own faceted ``crystallographic holes''. These elements are capable of further enhancing the obtained activity of titania microcrystals to a higher extent, as shown by the UV driven photocatalytic phenol degradation experiments. The appearance of the holes was ``provoked'' by simple calcination and their presence and influence were demonstrated by XPS and HRTEM.One of the most fundamental aspects of the heterogeneous catalysis field is the manipulation of the catalysts' activity. In photocatalysis this is carried out by maximizing the right crystal plane of a semiconductor oxide. Until now, most of the papers have achieved this by a combination of different oxides, with noble metals and sometimes with carbon nanomaterials. In this work MWCNTs (multiwalled carbon nanotubes) were applied as ``crystallization promoters'' in a very simple, safe, one-step hydrothermal method. By this method TiO2 nano/micro crystals with exposed {001} facets were obtained in the first step. The next episode in the crystal manipulation ``saga'' was the modification of the (001) crystallographic plane's structure by creating ordered/own faceted ``crystallographic holes''. These elements are capable of further enhancing the obtained activity of

  19. Structural changes that occur upon photolysis of the Fe(II)a3 - CO complex in the cytochrome ba3-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to CuB

    PubMed Central

    Liu, Bin; Zhang, Yang; Sage, J. Timothy; Soltis, S. Michael; Doukov, Tzanko; Chen, Ying; Stout, C. David; Fee, James A.

    2012-01-01

    The purpose of the work was to provide a crystallographic demonstration of the venerable idea that CO photolyzed from ferrous heme-a3 moves to the nearby cuprous ion in the cytochrome c oxidases. Crystal structures of CO-bound cytochrome ba3-oxidase from Thermus thermophilus, determined at ~ 2.8 – 3.2 Å resolution, reveal a Fe-C distance of ~2.0 Å, a Cu-O distance of 2.4 Å and a Fe-C-O angle of ~126°. Upon photodissociation at 100 K, X-ray structures indicate loss of Fea3-CO and appearance of CuB-CO having a Cu-C distance of ~1.9 Å and an O-Fe distance of ~2.3 Å. Absolute FTIR spectra recorded from single crystals of reduced ba3–CO that had not been exposed to X-ray radiation, showed several peaks around 1975 cm−1; after photolysis at 100 K, the absolute FTIR spectra also showed a significant peak at 2050 cm−1. Analysis of the “light’ minus ‘dark’ difference spectra showed four very sharp CO stretching bands at 1970 cm−1, 1977 cm−1, 1981 cm−1, and 1985 cm−1, previously assigned to the Fea3-CO complex, and a significantly broader CO stretching band centered at ~2050 cm−1, previously assigned to the CO stretching frequency of CuB bound CO. As expected for light propagating along the tetragonal axis of the P43212 space group, the single crystal spectra exhibit negligible dichroism. Absolute FTIR spectrometry of a CO-laden ba3 crystal, exposed to an amount of X-ray radiation required to obtain structural data sets before FTIR characterization, showed a significant signal due to photogenerated CO2 at 2337 cm−1 and one from traces of CO at 2133 cm−1; while bands associated with CO bound to either Fea3 or to CuB in “light” minus “dark” FTIR difference spectra shifted and broadened in response to X-ray exposure. In spite of considerable radiation damage to the crystals, both X-ray analysis at 2.8 and 3.2 Å and FTIR spectra support the long-held position that photolysis of Fea3-CO in cytochrome c oxidases leads to significant

  20. {sup 203,205}Tl NMR Studies of Crystallographically Characterized Thallium Alkoxides. X-Ray Structures of [Tl(OCH{sub 2}CH{sub 3})]4 and [Tl(OAr)]{sub infinity} where OAr = OC{sub 6}H{sub 3}(Me){sub 2}-2,6 and OC{sub 6}H{sub 3}(Pr{sup i}){sub 2}-2,6

    SciTech Connect

    ZECHMANN,CECILIA A.; BOYLE,TIMOTHY J.; PEDROTTY,DAWN M.; ALAM,TODD M.; LANG,DAVID P.; SCOTT,BRIAN L.

    2000-07-25

    [Tl(OCH{sub 2}CH{sub 3})]{sub 4}, (1) was reacted with excess HOR to prepare a series of [Tl(OR)]{sub n} where OR= OCHMe{sub 2} (2, n = 4), OCMe{sub 3} (3, n = 4), OCH{sub 2}CMe{sub 3} (4, n = 4), OC{sub 6}H{sub 3}(Me){sub 2}-2,6 (5, n = {infinity}), and OC{sub 6}H{sub 3}(Pr{sup i}){sub 2}-2,6 (6, n = {infinity}). Single crystal X-ray diffraction was used to determine the structure of compounds ligated by more sterically demanding ligands. Compound 4 was found to adopt a cubane structure, while 5 and 6 formed linear polymeric structures. These compounds were additionally characterized by {sup 203,205}Tl solution and {sup 205}Tl solid state NMR. Compounds 1--4 were found to remain intact in solution while the polymeric species, 5 and 6, appeared to be fluxional. While variations in the solution and solid state structures for the tetrameric [Tl(OR)]{sub 4} and polymeric [Tl(OAr)]{sub {infinity}} may be influenced by the steric hindrance of their respective ligands, the covalency of the species is believed to be more an effect of the parent alcohol acidity.

  1. Effect of tungsten crystallographic orientation on He-ion-induced surface morphology changes

    SciTech Connect

    Parish, Chad M; Hijazi, Hussein Dib; Meyer III, Harry M; Meyer, Fred W

    2014-01-01

    In order to study the early stages of nanofuzz growth in fusion-plasma-facing tungsten, mirror-polished high-purity tungsten was exposed to 80 eV helium at 1130 C to a fluence of 4 1024 He/m2. The previously smooth surface shows morphology changes, and grains form one of four qualitatively different morphologies: smooth, wavy, pyramidal, or terraced/wide waves. Combining high-resolution scanning electron microscopy (SEM) observations to determine the morphology of each grain with quantitative measurement of the grain's orientation via electron backscatter diffraction (EBSD) in SEM shows that the normal-direction crystallographic orientation of the underlying grain controls the growth morphology. Specifically, near-<001> || normal direction (ND) grains formed pyramids, near-<114> to <112> || ND grains formed wavy and stepped structures, and near-<103> || ND grains remained smooth. Comparisons to control specimens indicate no changes to underlying bulk crystallographic texture, and the effects are attributed to surface energy anisotropy, although, surprisingly, the expected {101} low-energy planes were not the most stable. Future developments to control tungsten texture via thermomechanical processing, ideally obtaining a sharp near- <103> || ND processing texture, may delay the formation of nanofuzz.

  2. "Crystallographic" holes: new insights for a beneficial structural feature for photocatalytic applications.

    PubMed

    Vajda, Krisztina; Kása, Zsolt; Dombi, András; Németh, Zoltán; Kovács, Gábor; Danciu, Virginia; Radu, Teodora; Ghica, Corneliu; Baia, Lucian; Hernádi, Klára; Pap, Zsolt

    2015-03-19

    One of the most fundamental aspects of the heterogeneous catalysis field is the manipulation of the catalysts' activity. In photocatalysis this is carried out by maximizing the right crystal plane of a semiconductor oxide. Until now, most of the papers have achieved this by a combination of different oxides, with noble metals and sometimes with carbon nanomaterials. In this work MWCNTs (multiwalled carbon nanotubes) were applied as "crystallization promoters" in a very simple, safe, one-step hydrothermal method. By this method TiO₂ nano/micro crystals with exposed {001} facets were obtained in the first step. The next episode in the crystal manipulation "saga" was the modification of the (001) crystallographic plane's structure by creating ordered/own faceted "crystallographic holes". These elements are capable of further enhancing the obtained activity of titania microcrystals to a higher extent, as shown by the UV driven photocatalytic phenol degradation experiments. The appearance of the holes was "provoked" by simple calcination and their presence and influence were demonstrated by XPS and HRTEM. PMID:25757557

  3. Crystallographic changes in lead zirconate titanate due to neutron irradiation

    DOE PAGESBeta

    Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; Ihlefeld, Jon F.; Brennecka, Geoff L.; Brown, Donald W.; Forrester, Jennifer S.; Jones, Jacob L.

    2014-11-17

    Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method) is used to quantify the type and extent of structural changes in PbZr0.5Ti0.5O3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 1015 neutrons/cm2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. Lastly, the results demonstrate a method by which the effects of radiation on crystallographic structuremore » may be investigated.« less

  4. Crystallographic changes in lead zirconate titanate due to neutron irradiation

    SciTech Connect

    Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; Ihlefeld, Jon F.; Brennecka, Geoff L.; Brown, Donald W.; Forrester, Jennifer S.; Jones, Jacob L.

    2014-11-17

    Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method) is used to quantify the type and extent of structural changes in PbZr0.5Ti0.5O3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 1015 neutrons/cm2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. Lastly, the results demonstrate a method by which the effects of radiation on crystallographic structure may be investigated.

  5. Crystallographic changes in lead zirconate titanate due to neutron irradiation

    SciTech Connect

    Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; Ihlefeld, Jon F.; Brennecka, Geoff L.; Brown, Donald W.; Forrester, Jennifer S.; Jones, Jacob L.

    2014-11-15

    Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method) is used to quantify the type and extent of structural changes in PbZr{sub 0.5}Ti{sub 0.5}O{sub 3} after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 10{sup 15} neutrons/cm{sup 2}. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. The results demonstrate a method by which the effects of radiation on crystallographic structure may be investigated.

  6. Automated identification of crystallographic ligands using sparse-density representations

    SciTech Connect

    Carolan, C. G.; Lamzin, V. S.

    2014-07-01

    A novel procedure for identifying ligands in macromolecular crystallographic electron-density maps is introduced. Density clusters in such maps can be rapidly attributed to one of 82 different ligands in an automated manner. A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the method for the identification of binding entities in fragment-based drug screening and in model completion in macromolecular structure determination.

  7. A crystallographic perspective on sharing data and knowledge.

    PubMed

    Bruno, Ian J; Groom, Colin R

    2014-10-01

    The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices. PMID:25091065

  8. Crystallographic changes in lead zirconate titanate due to neutron irradiation

    DOE PAGESBeta

    Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; Ihlefeld, Jon F.; Brennecka, Geoff L.; Brown, Donald W.; Forrester, Jennifer S.; Jones, Jacob L.

    2014-11-17

    Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method) is used to quantify the type and extent of structural changes in PbZr0.5Ti0.5O3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 1015 neutrons/cm2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. The results demonstrate a method by which the effects of radiation on crystallographic structure maymore » be investigated.« less

  9. Crystallographic changes in lead zirconate titanate due to neutron irradiation

    SciTech Connect

    Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; Ihlefeld, Jon F.; Brennecka, Geoff L.; Brown, Donald W.; Forrester, Jennifer S.; Jones, Jacob L.

    2014-11-17

    Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method) is used to quantify the type and extent of structural changes in PbZr0.5Ti0.5O3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 1015 neutrons/cm2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. The results demonstrate a method by which the effects of radiation on crystallographic structure may be investigated.

  10. Crystallographic data processing for free-electron laser sources

    SciTech Connect

    White, Thomas A. Barty, Anton; Stellato, Francesco; Holton, James M.; Kirian, Richard A.; Zatsepin, Nadia A.; Chapman, Henry N.

    2013-07-01

    A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam.

  11. A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere.

    PubMed

    Rutenber, E E; McPhee, F; Kaplan, A P; Gallion, S L; Hogan, J C; Craik, C S; Stroud, R M

    1996-09-01

    The essential role of HIV-1 protease (HIV-1 PR) in the viral life cycle makes it an attractive target for the development of substrate-based inhibitors that may find efficacy as anti-AIDS drugs. However, resistance has arisen to potent peptidomimetic drugs necessitating the further development of novel chemical backbones for diversity based chemistry focused on probing the active site for inhibitor interactions and binding modes that evade protease resistance. AQ148 is a potent inhibitor of HIV-1 PR and represents a new class of transition state analogues incorporating an aminimide peptide isostere. A 3-D crystallographic structure of AQ148, a tetrapeptide isostere, has been determined in complex with its target HIV-1 PR to a resolution of 2.5 A and used to evaluate the specific structural determinants of AQ148 potency and to correlate structure-activity relationships within the class of related compounds. AQ148 is a competitive inhibitor of HIV-1 PR with a Ki value of 137 nM. Twenty-nine derivatives have been synthesized and chemical modifications have been made at the P1, P2, P1', and P2' sites. The atomic resolution structure of AQ148 bound to HIV-1 PR reveals both an inhibitor binding mode that closely resembles that of other peptidomimetic inhibitors and specific protein/inhibitor interactions that correlate with structure-activity relationships. The structure provides the basis for the design, synthesis and evaluation of the next generation of hydroxyethyl aminimide inhibitors. The aminimide peptide isostere is a scaffold with favorable biological properties well suited to both the combinatorial methods of peptidomimesis and the rational design of potent and specific substrate-based analogues. PMID:8894111

  12. Crystallographic texture of light tinplate coatings made in various electrolytes

    NASA Astrophysics Data System (ADS)

    Gburík, R.; Černík, M.; Leggat, R.; Vranec, P.

    2015-04-01

    Two electrolytic tinplating processes are currently used in Europe: PSA (based on phenolsulfonic acid) and MSA (based on methanesulfonic acid). The Halogen Process is used in other parts of the world. The electrolyte composition and process parameters affect the electrodeposit and ultimately the tinplate appearance and performance. In order to better understand the impact of electrolyte composition on the crystallographic texture of tin coating tinplate, light tin coatings on single reduced, continuously annealed (CA) tinplate produced in three electrolytes: Halogen, PSA and MSA were analyzed. The crystallographic texture of thin tin coating (<2.8gm-2) was analyzed by X-ray Diffraction and Electron Backscatter Diffraction. The effect of reflow (melting of the tin followed by rapid solidification) and ironing during drawn and wall ironed (DWI) can forming on the tin crystallography were evaluated. Both texture analysis by XRD and EBSD confirmed that all un-melted tin coatings, made in three different electrolytes, contain texture fibers. The effect of steel sheet crystallographic texture was investigated by comparing the tin crystallographic orientation on continuously annealed steel substrate (with α and γ fiber texture) versus batch annealed (BA) steel with a strong γ fiber texture. The main electrolytic parameters, current density and line speed, did not affect the texture formation of tin coating produced in MSA-based electrolyte within the commercial ranges. Un-melted tin coatings produced in the MSA-based electrolyte showed sharper texture than those produced in PSA and Halogen electrolytes. The FeSn2 alloy structure was not observed in un-melted tin coatings; however, it was detected after ironing in the DWI process.

  13. Atoms.inp Archive: Crystallographic Data from GSECARS

    DOE Data Explorer

    Newville, Matthew

    The Atoms.inp Archive is a collection of crystallographic data for use in XAFS analysis. The crystallographic data is stored as atoms.inp files, which contain all the information necessary to describe the crystal, and can be used by the program ATOMS to generate feff.inp files. These files can then be used by the FEFF program [See http://leonardo.phys.washington.edu/feff/] to calculate a theoretical XAFS spectrum for the crystal. This archive exists because it can take a considerable amount of time to locate a suitable reference for a model structure to use for making theoretical XAFS standards. Even then, references sometimes give non-standard or incomplete crystallographic notation that ATOMS has difficulty interpreting. All of this means that getting a reliable atoms.inp file can take quite a bit of effort. It is hoped that this collection of well-documented and well-tested atoms.inp files will eliminate much of the work in creating theoretical XAFS standards from FEFF. [Taken from http://cars9.uchicago.edu/~newville/adb/]. The collection currently has more than 200 crystal structures, 2748 data files, and it continues to expand. The collection is related to the UWXAFS Project [http://depts.washington.edu/uwxafs/] and to the work of the Consortium for Advanced Radiation Sources (CARS). After searching the Archive, a user may also choose to run the web version of ATOMS software.

  14. Crystallographic variant selection of martensite during fatigue deformation

    NASA Astrophysics Data System (ADS)

    Das, Arpan

    2015-03-01

    Metastable austenitic stainless steels are prone to form deformation-induced martensite under the influence of externally applied stress. Crystallographic variant selection during martensitic transformation of metastable austenite has been investigated thoroughly with respect to the interaction between the applied uniaxial cyclic stress and the resulting accumulated plastic strain during cyclic plastic deformation. The orientation of all the Kurdjomov-Sachs (K-S) variants has been evaluated extensively and compared with the measured orientation of martensite with their corresponding interaction energies by applying the elegant transformation texture model recently developed by Kundu and Bhadeshia. Encouraging correlation between model prediction and experimental data generation for martensite pole figures at many deformed austenite grains has been observed. It has been found that both the applied uniaxial cyclic stress and the accumulated plastic strain are having strong influence on crystallographic variant selection during cyclic plastic deformation. Patel and Cohen's classical theory can be utilized to predict the crystallographic variant selection, if it is correctly used along with the phenomenological theory of martensite crystallography.

  15. Crystallographically uniform arrays of ordered (In)GaN nanocolumns

    SciTech Connect

    Gačević, Ž. Bengoechea-Encabo, A.; Albert, S.; Calleja, E.

    2015-01-21

    In this work, through a comparative study of self-assembled (SA) and selective area grown (SAG) (In)GaN nanocolumn (NC) ensembles, we first give a detailed insight into improved crystallographic uniformity (homogeneity of crystallographic tilts and twists) of the latter ones. The study, performed making use of: reflective high energy electron diffraction, X-ray diffraction and scanning electron microscopy, reveals that unlike their SA counterparts, the ensembles of SAG NCs show single epitaxial relationship to both sapphire(0001) and Si(111) underlying substrates. In the second part of the article, making use of X-ray diffraction, we directly show that the selective area growth leads to improved compositional uniformity of InGaN NC ensembles. This further leads to improved spectral purity of their luminescence, as confirmed by comparative macro-photoluminescence measurements performed on SA and SAG InGaN NC ensembles. An improved crystallographic uniformity of NC ensembles facilitates their integration into optoelectronic devices, whereas their improved compositional uniformity allows for their employment in single-color optoelectronic applications.

  16. Crystallographically uniform arrays of ordered (In)GaN nanocolumns

    NASA Astrophysics Data System (ADS)

    Gačević, Ž.; Bengoechea-Encabo, A.; Albert, S.; Torres-Pardo, A.; González-Calbet, J. M.; Calleja, E.

    2015-01-01

    In this work, through a comparative study of self-assembled (SA) and selective area grown (SAG) (In)GaN nanocolumn (NC) ensembles, we first give a detailed insight into improved crystallographic uniformity (homogeneity of crystallographic tilts and twists) of the latter ones. The study, performed making use of: reflective high energy electron diffraction, X-ray diffraction and scanning electron microscopy, reveals that unlike their SA counterparts, the ensembles of SAG NCs show single epitaxial relationship to both sapphire(0001) and Si(111) underlying substrates. In the second part of the article, making use of X-ray diffraction, we directly show that the selective area growth leads to improved compositional uniformity of InGaN NC ensembles. This further leads to improved spectral purity of their luminescence, as confirmed by comparative macro-photoluminescence measurements performed on SA and SAG InGaN NC ensembles. An improved crystallographic uniformity of NC ensembles facilitates their integration into optoelectronic devices, whereas their improved compositional uniformity allows for their employment in single-color optoelectronic applications.

  17. PR-PR: Cross-Platform Laboratory Automation System

    SciTech Connect

    Linshiz, G; Stawski, N; Goyal, G; Bi, CH; Poust, S; Sharma, M; Mutalik, V; Keasling, JD; Hillson, NJ

    2014-08-01

    To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.

  18. Purification, identification and preliminary crystallographic studies of a 2S albumin seed protein from Lens culinaris

    SciTech Connect

    Gupta, Pankaj; Gaur, Vineet; Salunke, Dinakar M.

    2008-08-01

    A 2S albumin from L. culinaris was purified and crystallized and preliminary crystallographic studies were carried out. Lens culinaris (lentil) is a widely consumed high-protein-content leguminous crop. A 2S albumin protein (26.5 kDa) has been identified using NH{sub 2}-terminal sequencing from a 90% ammonium sulfate saturation fraction of total L. culinaris seed protein extract. The NH{sub 2}-terminal sequence shows very high homology to PA2, an allergy-related protein from Pisum sativum. The 2S albumin protein was purified using a combination of size-exclusion and ion-exchange chromatography. Crystals of the 2S seed albumin obtained using the hanging-drop vapour-diffusion method diffracted to 2.5 Å resolution and were indexed in space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 78.6, c = 135.2 Å.

  19. Ge/SrTiO{sub 3}(001): Correlation between interface chemistry and crystallographic orientation

    SciTech Connect

    Gobaut, B.; Penuelas, J.; Grenet, G.; Ferrah, D.; Benamrouche, A.; Chettaoui, A.; Robach, Y.; Botella, C.; Saint-Girons, G.; El Kazzi, M.; Silly, M. G.; Sirotti, F.

    2012-11-01

    In this work, the desorption of a submonolayer deposit of Ge on SrTiO{sub 3}(001) is studied by reflection high energy electron diffraction. The results are compared to those of a previous experiment done using soft x-ray photoelectron spectroscopy. Combining these techniques allows for correlating interface chemistry and crystal orientation, and for bringing clarifying elements concerning the competition between (111) and (001) crystal orientation typical for the semiconductor/perovskite epitaxial systems. Despite poor interface matching, (111)-oriented islands are stabilized at the expense of (001)-oriented islands due to the relatively low energy of their free facets. Such 'surface energy driven' crystallographic orientation of the deposit is enhanced by the low adhesion energy characteristic of the Ge/SrTiO{sub 3} system.

  20. Anomalous polarization dependence of Raman scattering and crystallographic orientation of black phosphorus.

    PubMed

    Kim, Jungcheol; Lee, Jae-Ung; Lee, Jinhwan; Park, Hyo Ju; Lee, Zonghoon; Lee, Changgu; Cheong, Hyeonsik

    2015-11-28

    We investigated polarization dependence of the Raman modes in black phosphorus (BP) using five different excitation wavelengths. The crystallographic orientation was determined by comparing polarized optical microscopy with high-resolution transmission electron microscopy analysis. In polarized Raman spectroscopy, the B2g mode shows the same polarization dependence regardless of the excitation wavelength or the sample thickness. On the other hand, the Ag(1) and Ag(2) modes show a peculiar polarization behavior that depends on the excitation wavelength and the sample thickness. The thickness dependence can be explained by considering the anisotropic interference effect due to the birefringence and dichroism of the BP crystal, but the wavelength dependence cannot be explained. We propose a simple and fail-proof procedure to determine the orientation of a BP crystal by combining polarized Raman scattering with polarized optical microscopy. PMID:26503032

  1. Bacteriological and crystallographical analysis of urinary calculi: aid to patient management.

    PubMed

    Rosenstein, I; Osborn, R S; Hopewell, J P; Hamilton-Miller, J M; Brumfitt, W

    1984-06-01

    In an analysis, by both crystallographic and microbiological methods, of 50 urinary calculi recently removed by surgical operation, 33 proved to be of metabolic origin (mostly calcium oxalate and some uric acid or urate) and 17 of 'infective' origin (struvite, apatite or a mixture of the two). Metabolic stones were usually bacteriologically sterile or contained only small numbers (less than 10(3)/g of stone) of bacteria which did not produce urease, while infective stones always contained urease-producing organisms, usually Proteus mirabilis, in large numbers (greater than 10(5)/g). The combined approach of stone analysis by crystallography and microbiological culture yields more information than conventional techniques on which to base the treatment of urinary calculi and the prevention of their recurrence. PMID:6737406

  2. A Novel c.554+5C>T Mutation in the DUOXA2 Gene Combined with p.R885Q Mutation in the DUOX2 Gene Causing Congenital Hypothyroidism.

    PubMed

    Zheng, Xiao; Ma, Shao Gang; Qiu, Ya Li; Guo, Man Li; Shao, Xiao Juan

    2016-06-01

    The coexistence of mutations in the dual oxidase maturation factor 2 (DUOXA2) and dual oxidase 2 (DUOX2) genes is rarely identified in congenital hypothyroidism (CH). This study reports a boy with CH due to a novel splice-site mutation in the DUOXA2 gene and a missense mutation in the DUOX2 gene. A four-year-old boy was diagnosed with CH at neonatal screening and was enrolled in this study. The DUOXA2, DUOX2, thyroid peroxidase (TPO), and thyrotropin receptor (TSHR) genes were considered for genetic defects screening. Genomic DNA was extracted from peripheral blood leukocytes, and Sanger sequencing was used to screen the mutations in the exon fragments. Family members of the patient and the controls were also enrolled and evaluated. The boy harbored compound heterozygous mutations including a novel splice-site mutation c.554+5C>T in the maternal DUOXA2 allele and c.2654G>A (p.R885Q) in the paternal DUOX2 allele. The germline mutations from his parents were consistent with an autosomal recessive inheritance pattern. No mutations in the TPO and TSHR genes were detected. A novel splice-site mutation c.554+5C>T in the DUOXA2 gene and a mutation p.R885Q in the DUOX2 gene were identified in a 4-year-old patient with goitrous CH. PMID:26758695

  3. Polyhedra with noncrystallographic symmetry as the orbits of crystallographic point symmetry groups

    NASA Astrophysics Data System (ADS)

    Ovsetsina, T. I.; Chuprunov, E. V.

    2015-11-01

    Polyhedra with noncrystallographic symmetry are analyzed as the orbits of crystallographic point symmetry groups on a set of smooth or structured ("hatched") planes. Polyhedra with symmetrically equivalent faces, obtained using crystallographic point groups but having noncrystallographic symmetry, and polyhedra, the symmetry group T of which is crystallographic but can be implemented only on the assumption of a noncrystallographic character of the internal structure of polyhedron, are studied. The results of the analysis for all 32 point symmetry groups are listed in table.

  4. Crystallographic investigation of grain selection during initial solidification

    NASA Astrophysics Data System (ADS)

    Esaka, H.; Kataoka, Y.; Shinozuka, K.

    2016-03-01

    Normally, macroscopic solidified structure consists of chill, columnar and equiaxed zones. In a chill zone, many fine grains nucleate on the mold surface and grow their own preferred growth direction. Only a few of them continue to grow because of grain selection. In order to understand the grain selection process, crystallographic investigation has been carried out in the zone of initial solidification in this study. 10 g of Al-6 wt%Si alloy was melted at 850 °C and poured on the thick copper plate. Longitudinal cross section of the solidified shell was observed by a SEM and analyzed by EBSD. The result of EBSD mapping reveals that crystallographic orientation was random in the range of initial solidification. Further, some grains are elongated along their <100> direction. Columnar grains, whose growth directions are almost parallel to the heat flow direction, develop via grain selection. Here, a dendrite whose growth direction is close to the heat flow direction overgrows the other dendrite whose growth direction is far from the heat flow direction. However, sometimes we observed that dendrite, whose zenith angle is large, overgrew the other dendrite. It can be deduced that the time of nucleation on the mold surface is not constant.

  5. International summer school on macromolecular crystallographic computing. Final report

    SciTech Connect

    1998-08-01

    The School was the seventh in a series of International Union of Crystallography (IUCr) Crystallographic Symposia. The format of the School was formal lectures in the morning, tutorials in the afternoon, and software demonstrations and more lectures in the evening. The full program which left both the organizers and attendees exhausted, reflects the current state of excitement in the field of macromolecular structure determination using the technique of X-ray crystallography. The new and improved technologies and techniques described in these Proceedings are contributing to that growth and at the same time, as pointed out in the paper given by Sussman, creating challenges for the Protein Data Bank (PDB). As the School progressed, the authors were struck by the similarities to events which took place in small molecule crystallography beginning some 20 to 25 years ago. Growth then was fueled by the advent of new algorithms, affordable computer hardware, and good software. So it is today for macromolecular crystallography, but with the added bonus of the Internet which is changing how scientist conduct their research. Flack presented this view as part of his on-going contribution to how crystallographers use the Internet. After presentations discussing structures en masse they returned to the more traditional mode of presentation which parallels the determination of a single macromolecular structure: data collection -- phasing -- model building and visualization -- refinement.

  6. Crystallographic studies of gas sorption in metal–organic frameworks

    PubMed Central

    Carrington, Elliot J.; Vitórica-Yrezábal, Iñigo J.; Brammer, Lee

    2014-01-01

    Metal–organic frameworks (MOFs) are a class of porous crystalline materials of modular design. One of the primary applications of these materials is in the adsorption and separation of gases, with potential benefits to the energy, transport and medical sectors. In situ crystallography of MOFs under gas atmospheres has enabled the behaviour of the frameworks under gas loading to be investigated and has established the precise location of adsorbed gas molecules in a significant number of MOFs. This article reviews progress in such crystallographic studies, which has taken place over the past decade, but has its origins in earlier studies of zeolites, clathrates etc. The review considers studies by single-crystal or powder diffraction using either X-rays or neutrons. Features of MOFs that strongly affect gas sorption behaviour are discussed in the context of in situ crystallographic studies, specifically framework flexibility, and the presence of (organic) functional groups and unsaturated (open) metal sites within pores that can form specific interactions with gas molecules. PMID:24892587

  7. Effects of microstructure and crystallographic texture on yield behavior of aluminum-copper-lithium 2195 plate

    NASA Astrophysics Data System (ADS)

    Crosby, Karen Elizabeth

    2000-10-01

    The focus of this research is to study the effects of deformation and aging on the yield behavior of precipitation-hardened Al-Cu-Li alloys, specifically AI-Cu-Li 2195 plate. Al-Cu-Li 2195 is a relatively new and exceptionally strong, yet lightweight aluminum alloy. Experimental methods applicable to mechanical/structural engineering and materials science problems provide the means for understanding the interrelation of deformation, microstructure, and crystal orientation (texture) as they affect the mechanical properties of crystalline materials. Yield strength is a vital mechanical property in that it defines the boundary of stress that may be applied to a part before a permanent, in some cases, detrimental shape change occurs. The values of yield strength often have directional characteristics, such that the values assessed depend on the direction of measurement. The major elements affecting yield and anisotropic nature of Al-Cu-Li materials are induced crystallographic texture from prior deformation such as rolling, elongated grain structure, and the presence of microscopic precipitates. In order to complete the understanding of how these aspects relate, it is intended to characterize the material and model the yield behavior of the material using theoretical techniques based on polycrystal plasticity. Numerous phenomenological yield expressions exist that describe 2- or 3-dimensional yield behavior (i.e., yield surface or yield locus) and recent advances in computational methods and computer resources have enabled the application of polycrystal yield definitions. Meanwhile, whereas the cumulative effects of precipitate state and crystallographic texture on mechanical behavior have been acknowledged, they have not been widely studied in a quantitative manner. Therefore the intent of this research is to determine the influence of the combination of microstructural effects such as texture (arising from prior deformation) and precipitates (formed during the

  8. Effects of the η(5)-C5H4(i)Pr Ligand on the Properties Exhibited by Its Tungsten Nitrosyl Complexes.

    PubMed

    Fabulyak, Diana; Baillie, Rhett A; Patrick, Brian O; Legzdins, Peter; Rosenfeld, Devon C

    2016-02-15

    Reaction of Na[η(5)-C5H4(i)Pr] with W(CO)6 in refluxing THF for 4 days generates a solution of Na[(η(5)-C5H4(i)Pr)W(CO)3] that when treated with N-methyl-N-nitroso-p-toluenesulfonamide at ambient temperatures affords (η(5)-C5H4(i)Pr)W(NO)(CO)2 (1) that is isolable in good yield as an analytically pure orange oil. Treatment of 1 with an equimolar amount of I2 in Et2O at ambient temperatures affords (η(5)-C5H4(i)Pr)W(NO)I2 (2) as a dark brown solid in excellent yield. Sequential treatment at low temperatures of 2 with 0.5 equiv of Mg(CH2CMe3)2 and Mg(CH2CH═CMe2)2 in Et2O produces the alkyl allyl complex, (η(5)-C5H4(i)Pr)W(NO)(CH2CMe3)(η(3)-CH2CHCMe2) (3), as a thermally sensitive yellow liquid. Complex 3 may also be synthesized, albeit in low yield, in one vessel at low temperatures by reacting 1 first with 1 equiv of PCl5 and then with the binary magnesium reagents specified above. Interestingly, similar treatment of 1 in Et2O with PCl5 and only 0.5 equiv of Mg(CH2CH═CMe2)2 results in the formation of the unusual complex (η(5)-C5H4(i)Pr)W(NO)(PCl2CMe2CH═CH2)Cl2 (4), which probably is formed via a metathesis reaction of the binary magnesium reagent with (η(5)-C5H4(i)Pr)W(NO)(PCl3)Cl2. The C-D activation of C6D6 by complex 3 has been investigated and compared to that exhibited by its η(5)-C5Me5, η(5)-C5Me4H, and η(5)-C5Me4(n)Pr analogues. Kinetic analyses of the various activations have established that the presence of the η(5)-C5H4(i)Pr ligand significantly increases the rate of the reaction, an outcome that can be attributed to a combination of steric and electronic factors. In addition, mechanistic studies have established that in solution 3 loses neopentane under ambient conditions to generate exclusively the 16e η(2)-diene intermediate complex (η(5)-C5H4(i)Pr)W(NO)(η(2)-CH2═CMeCH═CH2), which then effects the subsequent C-D activations. This behavior contrasts with that exhibited by the η(5)-C5Me5 analogue of 3 which forms both η(2

  9. Préface

    NASA Astrophysics Data System (ADS)

    Chardonnet, Christian; Millot, Guy

    2006-10-01

    COLOQ, réunion nationale biennale initiée en 1988 par la communauté française des lasers, de l'optique non linéaire et de l'optique quantique atteint sa neuvième édition. Depuis sa création, les objectifs poursuivis sont les suivants : - réunir la communauté française des lasers, de l'optique non linéaire et de l'optique quantique, en dépassant les clivages fondamental/appliqué, recherche publique/industrielle, - faire le point sur les avancées récentes, - permettre aux jeunes chercheurs de se rencontrer, de s'exprimer et de s'aguerrir au plan national. Le but est que tout thésard du domaine de l'optique puisse participer à COLOQ une fois durant sa thèse, présenter son travail et de se confronter à la communauté de l'optique. COLOQ9 s'est tenu, pour sa 9e édition, sur le campus universitaire de Dijon, du 7 au 9 septembre 2005. Il a été une grande réussite : nombre de participants (255) et de présentations scientifiques record (148 affiches), forte représentation des industriels (15) et participation d'environ 200 lycéens aux conférences grand public. Le nombre plus élevé que prévu d'affiches a rendu un peu serrée leur présentation : une attention particulière sera portée à cet aspect lors des prochaines éditions. Ces journées ont été consacrées à des conférences invitées données par des scientifiques de haut niveau et à des présentations sous forme d'affiches. Une plage de temps importante a été réservée pour des discussions autour des affiches. À proximité immédiate de la salle de conférence, l'exposition de matériels spécialisés pour les lasers, l'optique et l'optoélectronique a été une occasion pour les jeunes participants de découvrir et contacter les industriels et les autres grands acteurs de l'optique. L'année 2005 ayant été l'année mondiale de la physique, COLOQ9 a retenu comme thème central ”1905-2005 : à propos d'Einstein". Plusieurs grandes conférences ont été dédiées à ce th

  10. ESO PR Highlights in 2001

    NASA Astrophysics Data System (ADS)

    2002-01-01

    The year 2001 brought further success to European Astronomy and ESO. All of the four 8.2-m Unit Telescopes of the Very Large Telescope (VLT) are now in regular use and the VLT Interferometer (VLTI) had "first fringes" early in the year. The first tests were made with two small telescopes and later the light beams from two of the large telescopes were combined. The first scientific observations proved the extraordinary stability of the complex VLTI system and already produced excellent results. The Adaptive Optics technique was introduced at the VLT when the new NAOS-CONICA instrument had "First Light" in November. The sharpest-ever VLT images were obtained and immediately demonstrated the enormous potential for exciting front-line research programmes with this new facility. An extraordinary amount of first-class data were obtained by the astronomical communities in the ESO member countries and beyond from the VLT and other ESO telescopes. They resulted in numerous new discoveries and hundreds of articles in the professional literature - some of them were also presented to the public in ESO Press Releases. Portugal became the ninth ESO member country. The UK decided to join ESO by mid-2002 and other countries expressed interest. Japan moved closer to the intercontinental ALMA project and ESO continued its concept studies for a future 100-metre optical/IR telescope (OWL). The ESO Educational Office was established in July 2001. The aim is to provide support for astronomical and astrophysical education, especially at the secondary level. The Europe-wide, EU-sponsored "Life in the Universe" educational project was successfully accomplished, in collaboration with CERN, ESA and other international research organisations. At the end of a hectic and fruitful year, ESO and its staff in Europe and Chile can be optimistic about the future. New state-of-the-art astronomical instruments will be mounted on the ESO telescopes at La Silla and Paranal in 2002, further enhancing the

  11. Synthesis and Crystallographic Analysis of 5-Se-Thymidine DNAs

    SciTech Connect

    Hassan, A.; Sheng, J; Jiang, J; Zhanbg, W; Huang, Z

    2009-01-01

    We investigated the possibility of the interaction of 5-CH3 of thymidine and its 5?-phosphate backbone (C-H O-PO3 interaction) in DNA via the insertion of the atomic probe (a selenium atom) into the exo-5-position of thymidine (5-Se-T). 5-Se-T was synthesized for the first time, via Mn(OAc)3 assisted electrophilic addition of CH3SeSeCH3 to 3?,5?-di-O-benzoyl-2?-deoxyuridine. The 5-Se-T phosphoramidite was subsequently synthesized and incorporated into DNA in over 99% coupling yield. Biophysical and structural investigations of the 5-Se-T DNAs revealed that the Se-modified and nonmodified DNAs are virtually identical. In addition, the crystallographic analysis of a 5-Se-T DNA strongly suggests a hydrogen-bond formation between the 5-CH3 and 5?-phosphate groups (CH3 PO4- interaction).

  12. Catalytic, Enantioselective Sulfenofunctionalisation of Alkenes: Mechanistic, Crystallographic, and Computational Studies

    PubMed Central

    Denmark, Scott E.; Hartmann, Eduard; Kornfilt, David J. P.; Wang, Hao

    2015-01-01

    The stereocontrolled introduction of vicinal heteroatomic substituents into organic molecules is one of the most powerful ways of adding value and function. Whereas many methods exist for the introduction of oxygen- and nitrogen-containing substituents, the number stereocontrolled methods for the introduction of sulfur-containing substituents pales by comparison. Previous reports from these laboratories have described the sulfenofunctionalization of alkenes that construct vicinal carbon-sulfur and carbon-oxygen, carbon-nitrogen as well as carbon-carbon bonds with high levels of diastereospecificity and enantioselectivity. This process is enabled by the concept of Lewis base activation of Lewis acids that provides activation of Group 16 electrophiles. To provide a foundation for expansion of substrate scope and improved selectivities, we have undertaken a comprehensive study of the catalytically active species. Insights gleaned from kinetic, crystallographic and computational methods have led to the introduction of a new family of sulfenylating agents that provide significantly enhanced selectivities. PMID:25411883

  13. Crystallographic variant selection in Ti-6Al-4V

    SciTech Connect

    Stanford, N.; Bate, P.S. . E-mail: pete.bate@man.ac.uk

    2004-10-04

    Transformation textures in the two-phase alloy Ti-6Al-4V have been studied. Samples were heated into the fully {beta} phase condition and then slow cooled to allow diffusional transformation to {alpha}. This produced a microstructure of grain boundary {alpha} encircling colonies of Widmanstaetten {alpha}. Electron backscattered diffraction (EBSD) texture measurements showed that the {alpha} texture was markedly sharper than that calculated on a basis of equal variant probability, indicating that significant variant selection was occurring during diffusional transformation. Investigation of the {alpha} variants produced across prior {beta} grain boundaries has shown that the selection of variants during transformation is highly dependant on the crystallography of those boundaries. The effect of this crystallographic variant selection on the transformation texture has been modelled.

  14. Crystallographic data processing for free-electron laser sources.

    PubMed

    White, Thomas A; Barty, Anton; Stellato, Francesco; Holton, James M; Kirian, Richard A; Zatsepin, Nadia A; Chapman, Henry N

    2013-07-01

    A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam. PMID:23793149

  15. Expression, purification and preliminary X-ray crystallographic studies of the human immunodeficiency virus 1 subtype C protease

    SciTech Connect

    Coman, Roxana M.; Robbins, Arthur; Goodenow, Maureen M.; McKenna, Robert; Dunn, Ben M.

    2007-04-01

    Crystals of the human immunodeficiency virus 1 subtype C protease complexed with indinavir and nelfinavir have been grown in the monoclinic space group P2{sub 1} and shown to diffract X-rays to 2.3 Å resolution. Crystals of the human immunodeficiency virus 1 (HIV-1) subtype C protease (PR) complexed with the clinically used inhibitors indinavir (IDV) and nelfinavir (NFV) have been grown in the monoclinic space group P2{sub 1}, with mean unit-cell parameters a = 46.7 (±0.1), b = 59.8 (±0.3), c = 87.0 (±0.4) Å, β = 95.2 (±0.5)°. The crystals of both complexes have been shown to diffract X-rays to 2.3 Å resolution. The diffraction data for the subtype C PR complexes with IDV and NFV were subsequently processed and reduced, with overall R{sub sym} values of 8.4 and 11.4%, respectively. Based on the unit-cell volumes, molecular-replacement results and packing considerations, there are two protease homodimers per crystallographic asymmetric unit in each of the complexes. The data were initially phased using a model based on the crystal structure of HIV-1 subtype B PR; the structures have been determined and further refinement and analysis are in progress. These structures and subsequent studies with other inhibitors will greatly aid in correlating the amino-acid variation between the different HIV PRs and understanding their differential sensitivity and resistance to current drug therapy.

  16. Microfocus/Polycapillary-Optic Crystallographic X-Ray System

    NASA Technical Reports Server (NTRS)

    Joy, Marshall; Gubarev, Mikhail; Ciszak, Ewa

    2005-01-01

    A system that generates an intense, nearly collimated, nearly monochromatic, small-diameter x-ray beam has been developed for use in macromolecular crystallography. A conventional x-ray system for macromolecular crystallography includes a rotating-anode x-ray source, which is massive (.500 kg), large (approximately 2 by 2 by 1 m), and power-hungry (between 2 and 18 kW). In contrast, the present system generates a beam of the required brightness from a microfocus source, which is small and light enough to be mounted on a laboratory bench, and operates at a power level of only tens of watts. The figure schematically depicts the system as configured for observing x-ray diffraction from a macromolecular crystal. In addition to the microfocus x-ray source, the system includes a polycapillary optic . a monolithic block (typically a bundle of fused glass tubes) that contains thousands of straight or gently curved capillary channels, along which x-rays propagate with multiple reflections. This particular polycapillary optic is configured to act as a collimator; the x-ray beam that emerges from its output face consists of quasi-parallel subbeams with a small angular divergence and a diameter comparable to the size of a crystal to be studied. The gap between the microfocus x-ray source and the input face of the polycapillary optic is chosen consistently with the focal length of the polycapillary optic and the need to maximize the solid angle subtended by the optic in order to maximize the collimated x-ray flux. The spectrum from the source contains a significant component of Cu K (photon energy is 8.08 keV) radiation. The beam is monochromatized (for Cu K ) by a nickel filter 10 m thick. In a test, this system was operated at a power of 40 W (current of 897 A at an accelerating potential of 45 kV), with an anode x-ray spot size of 41+/-2 microns. Also tested, in order to provide a standard for comparison, was a commercial rotating-anode x-ray crystallographic system with a

  17. The PR Officer's Survival Kit.

    ERIC Educational Resources Information Center

    Woodrum, Robert L.

    1996-01-01

    A former corporate public relations (PR) professional shares strategies for communicating and cooperating with the chief executive officer, and particularly for coping with differences in perceptions of the public relations officer's role. Basic attributes of a successful PR professional are outlined: good communication skills, an analytical…

  18. Préface

    NASA Astrophysics Data System (ADS)

    Mazière, D.

    2002-04-01

    Faisant suite aux deux précédents colloques "Matériaux pour les machines thermiques" et "Matériaux pour le nucléaire" , le colloque 2001 de l'INSTN intitulé "Matériaux pour les énergies propres" s'est focalisé sur les problèmes de matériaux encore à résoudre dans ce secteur industriel. Le colloque de métallurgie est traditionnellement organisé par des ense ignants du DEA Métallurgie et Matériaux et un comité scientifique choisi chaq ue année en liaison avec le thème traité. Les étudiants de ce DEA, qui est hab ilité entre Paris XI, Paris VI, l'Ecole des Mines de Paris, l'Ecole Centrale de Pari s et l'INSTN, sont invités à participer à ce colloque et aux débats scientifiques qui s'y déroulent. Des conférences invitées à caractère péda gogique permettent d'introduire les différents thèmes abordés qui sont ensuite développés dans des présentations plus novatrices. Cette manifestation a pour ambition de favoriser la rencontre de scientifiques d'horizons divers venant de milieux académiques ou industriels entre eux et avec les étudiants et thésards. Cette 44e édition, dont les comptes rendus sont publiés ici, a fait le point sur les problèmes de matériaux rencontrés lors de la production, du stockage et de la conversion des énergies dites propres en englobant lesprogrès constants des industriels de l'automobile. Ce colloque a réuni, du 26 au 28 juin 2001, 63 participants provenant d'universités ou grandes écoles (18), du CEA (17), du CNRS (10) et de l'industrie ou de centres de recherche associés. L'ensemble des problèmes de matériaux de ce secteur ont été examinés au cours des six sessions ci-dessous : dépollution des gaz d'échappement ; combustion catalytique en production thermique ; nouvelles batteries ; piles à combustibles ; production et stockage d'hydrogène ; production et stockage d'énergie solaire. Vingt huit communications dont vingt deux orales ont illustré les dével oppements en cours. Dix

  19. The binding of D-gluconohydroximo-1,5-lactone to glycogen phosphorylase. Kinetic, ultracentrifugation and crystallographic studies.

    PubMed Central

    Papageorgiou, A C; Oikonomakos, N G; Leonidas, D D; Bernet, B; Beer, D; Vasella, A

    1991-01-01

    Combined kinetic, ultracentrifugation and X-ray-crystallographic studies have characterized the effect of the beta-glucosidase inhibitor gluconohydroximo-1,5-lactone on the catalytic and structural properties of glycogen phosphorylase. In the direction of glycogen synthesis, gluconohydroximo-1,5-lactone was found to competitively inhibit both the b (Ki 0.92 mM) and the alpha form of the enzyme (Ki 0.76 mM) with respect to glucose 1-phosphate in synergism with caffeine. In the direction of glycogen breakdown, gluconohydroximo-1,5-lactone was found to inhibit phosphorylase b in a non-competitive mode with respect to phosphate, and no synergism with caffeine could be demonstrated. Ultracentrifugation and crystallization experiments demonstrated that gluconohydroximo-1,5-lactone was able to induce dissociation of tetrameric phosphorylase alpha and stabilization of the dimeric T-state conformation. A crystallographic binding study with 100 mM-gluconohydroximo-1,5-lactone at 0.24 nm (2.4 A) resolution showed a major peak at the catalytic site, and no significant conformational changes were observed. Analysis of the electron-density map indicated that the ligand adopts a chair conformation. The results are discussed with reference to the ability of the catalytic site of the enzyme to distinguish between two or more conformations of the glucopyranose ring. PMID:1900987

  20. Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

    PubMed Central

    Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

    2015-01-01

    X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

  1. Preliminary crystallographic characterization of an RNA helicase from Kunjin virus

    SciTech Connect

    Mastrangelo, Eloise; Bollati, Michela; Milani, Mario; Brisbarre, Nadège; Lamballerie, Xavier de; Coutard, Bruno; Canard, Bruno; Khromykh, Alexander; Bolognesi, Martino

    2006-09-01

    The C-terminal 440 amino acids of the NS3 protein from Kunjin virus (Flaviviridae) code for a helicase. The protein has been overexpressed and crystallized. Characterization of the isolated monoclinic crystal form and diffraction data (at 3.0 Å resolution) are presented, together with a preliminary molecular-replacement solution. Kunjin virus is a member of the Flavivirus genus and is an Australian variant of West Nile virus. The C-terminal domain of the Kunjin virus NS3 protein displays helicase activity. The protein is thought to separate daughter and template RNA strands, assisting the initiation of replication by unwinding RNA secondary structure in the 3′ nontranslated region. Expression, purification and preliminary crystallographic characterization of the NS3 helicase domain are reported. It is shown that Kunjin virus helicase may adopt a dimeric assembly in absence of nucleic acids, oligomerization being a means to provide the helicases with multiple nucleic acid-binding capability, facilitating translocation along the RNA strands. Kunjin virus NS3 helicase domain is an attractive model for studying the molecular mechanisms of flavivirus replication, while simultaneously providing a new basis for the rational development of anti-flaviviral compounds.

  2. Crystallographic Studies of Chemically Modified Nucleic Acids: A Backward Glance

    PubMed Central

    Egli, Martin; Pallan, Pradeep S.

    2010-01-01

    Chemically modified nucleic acids (CNAs) are widely explored as antisense oligonucleotide or small interfering RNA (siRNA) candidates for therapeutic applications. CNAs are also of interest in diagnostics, high-throughput genomics and target validation, nanotechnology and as model systems in investigations directed at a better understanding of the etiology of nucleic acid structure as well as the physical-chemical and pairing properties of DNA and RNA and for probing protein-nucleic acid interactions. In this article we review research conducted by our laboratory over the past two decades with a focus on crystal structure analyses of CNAs and artificial pairing systems. We highlight key insights into issues ranging from conformational distortions as a consequence of modification to the modulation of pairing strength and RNA affinity by stereoelectronic effects and hydration. Although crystal structures have only been determined for a subset of the large number of modifications that were synthesized and analyzed in the oligonucleotide context to date, they have yielded guiding principles for the design of new analogs with tailormade properties, including pairing specificity, nuclease resistance and cellular uptake. And, perhaps less obviously, crystallographic studies of CNAs and synthetic pairing systems have shed light on fundamental aspects of DNA and RNA structure and function that would not have been disclosed by investigations solely focused on the natural nucleic acids. PMID:20087997

  3. Nanocrystalline materials: recent advances in crystallographic characterization techniques

    PubMed Central

    Ringe, Emilie

    2014-01-01

    Most properties of nanocrystalline materials are shape-dependent, providing their exquisite tunability in optical, mechanical, electronic and catalytic properties. An example of the former is localized surface plasmon resonance (LSPR), the coherent oscillation of conduction electrons in metals that can be excited by the electric field of light; this resonance frequency is highly dependent on both the size and shape of a nanocrystal. An example of the latter is the marked difference in catalytic activity observed for different Pd nanoparticles. Such examples highlight the importance of particle shape in nanocrystalline materials and their practical applications. However, one may ask ‘how are nanoshapes created?’, ‘how does the shape relate to the atomic packing and crystallography of the material?’, ‘how can we control and characterize the external shape and crystal structure of such small nanocrystals?’. This feature article aims to give the reader an overview of important techniques, concepts and recent advances related to these questions. Nucleation, growth and how seed crystallography influences the final synthesis product are discussed, followed by shape prediction models based on seed crystallography and thermodynamic or kinetic parameters. The crystallographic implications of epitaxy and orientation in multilayered, core-shell nanoparticles are overviewed, and, finally, the development and implications of novel, spatially resolved analysis tools are discussed. PMID:25485133

  4. Towards automated crystallographic structure refinement with phenix.refine.

    PubMed

    Afonine, Pavel V; Grosse-Kunstleve, Ralf W; Echols, Nathaniel; Headd, Jeffrey J; Moriarty, Nigel W; Mustyakimov, Marat; Terwilliger, Thomas C; Urzhumtsev, Alexandre; Zwart, Peter H; Adams, Paul D

    2012-04-01

    phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods. PMID:22505256

  5. Towards automated crystallographic structure refinement with phenix.refine

    PubMed Central

    Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel; Headd, Jeffrey J.; Moriarty, Nigel W.; Mustyakimov, Marat; Terwilliger, Thomas C.; Urzhumtsev, Alexandre; Zwart, Peter H.; Adams, Paul D.

    2012-01-01

    phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods. PMID:22505256

  6. Crystallographic studies of the Anthrax lethal toxin. Annual report

    SciTech Connect

    Frederick, C.A.

    1996-07-01

    The lethal form of Anthrax results from the inhalation of anthrax spores. Death is primarily due to the effects of the lethal toxin (Protective Antigen (PA) + Lethal Factor) from the causative agent, Bacillus anthracis. All the Anthrax vaccines currently in use or under development contain or produce PA, the major antigenic component of anthrax toxin, and there is a clear need for an improved vaccine for human use. In the previous report we described the first atomic resolution structure of PA, revealing that the molecule is composed largely of beta-sheets organized into four domains. This information can be used in the design. of recombinant PA vaccines. In this report we describe additional features of the full-length PA molecule derived from further crystallographic refinement and careful examination of the structure. We compare two crystal forms of PA grown at different pH values and discuss the functional implications. A complete definition of the function of each domain must await the crystal structure of the PA63 heptamer. We have grown crystals of the heptamer under both detergent and detergent-free conditions, and made substantial progress towards the crystal structure. The mechanism of anthrax intoxication in the light of our results is reviewed.

  7. Crystallographic orientation variation of isothermal pearlite under high magnetic field

    SciTech Connect

    Meng, Lan Zhou, Xiaoling Chen, Jianhao

    2015-07-15

    Crystallographic orientation (CO) variation of magnetic-induced pearlite (MIP) during its microstructure evolution in 19.8 T was investigated by electron back-scatter diffraction (EBSD). It is closely related to the isothermal temperatures (ITs) and the applied magnetic time (MT) during the process of MIP formation. The <100> easy magnetization direction in MIP colonies is strengthened with the MT within the certain transformed fraction of MIP (f{sub MIP}) at the relatively lower IT (983 K) above the eutectoid temperature but below the magnetically shifted upward eutectoid temperature, while this special CO tends to be weakened at a relatively higher IT (995 K). For the same MT, the higher the IT, the relatively larger is the proportion in <100> orientation for MIP colonies at the early growth stage. These results have demonstrated that the change of <100> orientation of MIP is closely related to the growth rate of pearlite ferrite (PF), and strengthened mainly at early transformation stage. When f{sub MIP} reaches some value, the growth rate of MIP at other COs, such as <110>, even at the hard magnetization direction, turns to present speed-up. - Highlights: • HMF can induce pearlite with different fractions above the eutectoid temperature. • CO is closely related to isothermal temperatures and applied magnetic time. • <100> direction is related to the growth rate of PF, and strengthened at early stage. • When f{sub MIP} reaches some value, the growth rate at other COs turns to present speed-up.

  8. Integration of Nanotubes, Etch Tracks, and Nanoribbons in Crystallographic Alignment

    NASA Astrophysics Data System (ADS)

    Boland, Mathias J.; Hunley, D. Patrick; Sundrarajan, Abhishek; Nasseri, Mohsen; Strachan, Douglas R.

    2015-03-01

    Three nanomaterial components, carbon nanotubes (CNTs), few-layer graphene (FLG), and etch tracks exposing insulating SiO2 regions, are integrated to form crystallographically-aligned nanoscale systems. These integrated systems consist of CNTs grown across nanogap etch tracks and nanoribbons formed within the FLG films as a result of chemical vapor deposition (CVD) processing. Each nanoscale component is aligned along the underlying graphene lattice, resulting in their orientations being locked into precise values, with CNTs maintaining alignment even after crossing etch tracks. The growth of aligned CNTs across nanogap etch tracks and nanoribbons suggests that integrated formations can be achieved by growing CNTs directly over nanogap etch tracks and nanoribbons. This is supported by calculations of the vibrational energy of CNTs indicating that they should be capable of maintaining atomic registry with an underlying graphene lattice as they grow across a typical etch track, in agreement with our experimental results. Thus, this work is relevant to the integration of semiconducting, conducting, and insulating nano-materials all together into precise nano-electronic systems.

  9. Crystallographic structure of ubiquitin in complex with cadmium ions

    PubMed Central

    2009-01-01

    Background Ubiquitination plays a critical role in regulating many cellular processes, from DNA repair and gene transcription to cell cycle and apoptosis. It is catalyzed by a specific enzymatic cascade ultimately leading to the conjugation of ubiquitin to lysine residues of the target protein that can be the ubiquitin molecule itself and to the formation of poly-ubiquitin chains. Findings We present the crystal structure at 3.0 Å resolution of bovine ubiquitin crystallized in presence of cadmium ions. Two molecules of ubiquitin are present in the asymmetric unit. Interestingly this non-covalent dimeric arrangement brings Lys-6 and Lys-63 of each crystallographically-independent monomer in close contact with the C-terminal ends of the other monomer. Residues Leu-8, Ile-44 and Val-70 that form a hydrophobic patch at the surface of the Ub monomer are trapped at the dimer interface. Conclusions The structural basis for signalling by poly-Ub chains relies on a visualization of conformations of alternatively linked poly-Ub chains. This arrangement of ubiquitin could illustrate how linkages involving Lys-6 or Lys-63 of ubiquitin are produced in the cell. It also details how ubiquitin molecules can specifically chelate cadmium ions. PMID:20003470

  10. Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study.

    PubMed

    Sonani, Ravi Raghav; Sharma, Mahima; Gupta, Gagan Deep; Kumar, Vinay; Madamwar, Datta

    2015-08-01

    The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus-2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit-cell parameters a = 108.3, b = 108.4 Å, c = 116.6 Å, α = 78.94, β = 82.50, γ = 60.34°. The molecular-replacement solution confirmed the presence of 12 αβ monomers in the P1 cell. The Phormidium PE elutes as an (αβ)3 trimer of αβ monomers from a molecular-sieve column and exists as [(αβ)3]2 hexamers in the crystal lattice. Unlike red algal PE proteins, the hexamers of Phormidium PE do not form higher-order structures in the crystals. The existence of only one characteristic visual absorption band at 564 nm suggests the presence of phycoerythrobilin chromophores, and the absence of any other types of bilins, in the Phormidium PE assembly. PMID:26249689

  11. Crystallographic orientation inhomogeneity and crystal splitting in biogenic calcite

    PubMed Central

    Checa, Antonio G.; Bonarski, Jan T.; Willinger, Marc G.; Faryna, Marek; Berent, Katarzyna; Kania, Bogusz; González-Segura, Alicia; Pina, Carlos M.; Pospiech, Jan; Morawiec, Adam

    2013-01-01

    The calcitic prismatic units forming the outer shell of the bivalve Pinctada margaritifera have been analysed using scanning electron microscopy–electron back-scatter diffraction, transmission electron microscopy and atomic force microscopy. In the initial stages of growth, the individual prismatic units are single crystals. Their crystalline orientation is not consistent but rather changes gradually during growth. The gradients in crystallographic orientation occur mainly in a direction parallel to the long axis of the prism, i.e. perpendicular to the shell surface and do not show preferential tilting along any of the calcite lattice axes. At a certain growth stage, gradients begin to spread and diverge, implying that the prismatic units split into several crystalline domains. In this way, a branched crystal, in which the ends of the branches are independent crystalline domains, is formed. At the nanometre scale, the material is composed of slightly misoriented domains, which are separated by planes approximately perpendicular to the c-axis. Orientational gradients and splitting processes are described in biocrystals for the first time and are undoubtedly related to the high content of intracrystalline organic molecules, although the way in which these act to induce the observed crystalline patterns is a matter of future research. PMID:23804442

  12. Fe-spin reorientation in PrFeAsO: Evidences from resistivity and specific heat studies

    NASA Astrophysics Data System (ADS)

    Bhoi, D.; Mandal, P.; Choudhury, P.; Pandya, S.; Ganesan, V.

    2011-12-01

    We report the magnetic field dependence of resistivity (ρ) and specific heat (C) for the non-superconducting PrFeAsO compound. Our study shows a hitherto unobserved anomaly at TSR in the resistivity and specific heat data, which arises as a result of the interplay of antiferromagnetic (AFM) Pr and Fe sublattices. Below the AFM transition temperature (TNPr), Pr moment orders along the crystallographic c axis and its effect on the iron subsystem causes a reorientation of the ordered in-plane Fe moments in a direction out of the ab plane. Application of magnetic field introduces disorder in the AFM Pr sublattice, which, in turn, reduces the out-of-plane Pr-Fe exchange interaction responsible for Fe spin reorientation. Both in ρ(T) and d(C/T)/dT curves, the peak at TSR broadens with the increase of H due to the introduction of the disorder in the AFM Pr sublattice by magnetic field. In the ρ(T) curve, the peak shifts toward lower temperature with H and disappears above 6 T, while in the d(C/T)/dT curve, the peak remains visible up to 14 T. The broadening of the anomaly at TNPr in C(T) with increasing H further confirms that magnetic field induces disorder in the AFM Pr sublattice.

  13. Seedlayer and underlayer effects on the crystallographic orientation and magnetic recording performance of glass media

    NASA Astrophysics Data System (ADS)

    Zheng, Min; Choe, Geon; Johnson, Kenneth E.

    2002-05-01

    Seedlayer and underlayer effects on crystallographic orientation and recording performance were studied for CoCrPtB media sputtered on glass substrates. For this study, the seedlayers are XAl (X=Ni, Co, Ti, and Ru) and the underlayers are CrY (Y=V, Mo, W, and Ti). It was found that not only different seedlayers, but also different combinations of seedlayer and underlayer, led to different magnetic performance. NiAl and CoAl seedlayers orient the Co c axis to (10.0) and TiAl and RuAl seedlayers produce (11.0) Co orientation. For the NiAl and CoAl seedlayer, CrV and CrW underlayers develop less out-of-plane c-axis orientation and higher coercivity and coercive squareness while CrTi and CrMo underlayers work better for TiAl and RuAl seedlayers, respectively. Media with RuAl seedlayers have better parametric performance than media with NiAl and CoAl seedlayers. The detailed relationship between seedlayer and underlayer types and crystal orientation and recording performance is discussed.

  14. The first synthesis and X-ray crystallographic analysis of an oxygen-bridged planarized triphenylborane.

    PubMed

    Kitamoto, Yuichi; Suzuki, Takatsugu; Miyata, Yasuo; Kita, Hiroshi; Funaki, Kenji; Oi, Shuichi

    2016-06-01

    An oxygen-bridged planarized triphenylborane has been successfully synthesized. X-ray crystallographic analysis revealed that the molecule has a complete planarized structure and the shortest C-B bonds among the triarylboranes synthesized to date. PMID:27161278

  15. Crystallographic study of fatigue cracking in Ni{sub 3}Al(CrB) single crystal

    SciTech Connect

    Zhang, G.P.; Wang, Z.G.; Li, G.Y.; Wu, S.D.

    1997-03-01

    The effect of crystallographic orientation on the fatigue-crack initiation and propagation in Ni{sub 3}Al(CrB) single crystal was studied using a compact-tension specimen. Stage I crystallographic cracking and cleavage fracture were observed. Crystallographic cracking can occur on two or more {l_brace}111{r_brace} slip planes simultaneously. It was shown that the threshold stress intensity for crack initiation from the notch root exhibits a dependence on crystallographic orientation. In addition, an effect of orientation on microcracking behavior was also shown. The number of {l_brace}111{r_brace} planes intersecting with each other determines the different microscopic features on the cleavage fracture surface.

  16. Effects of crystallographic orientation on plastic deformation and SCC initiation of zirconium alloys

    NASA Astrophysics Data System (ADS)

    Kubo, T.; Wakashima, Y.; Amano, K.; Nagai, M.

    1985-05-01

    In order to investigate the effects of crystallographic orientation on deformation and crack initiation in iodine-induced SCC of zirconium alloys, uniaxial tensile tests of zirconium and Zircaloy-2 plates were conducted in an iodine atmosphere. The crystallographic orientation of individual grains was determined by an etch-pit technique prior to testing. After testing, the etch-pit technique showed that prismatic slip was predominant in the plastic deformation and that cleavage cracks extended along basal planes. The plastic deformation of individual grains was significantly influenced by their crystallographic orientations, which varied from one grain to another. Accordingly, inhomogeneous plastic deformation occurred between grains. The crack initiation took place preferentially at grain boundaries where differences of crystallographic orientations were large between adjacent grains. This indicated that crack initiations was caused by stress concentration due to strain incompatibility at those grain boundaries.

  17. Préface

    NASA Astrophysics Data System (ADS)

    Aspect, Alain

    2004-11-01

    COLOQ est une conférence regroupant, tous les deux ans, la communauté scientifique et industrielle nationale travaillant dans les domaines des lasers, de l'optique non-linéaire et de l'optique quantique. Elle s'est tenue pour sa huitième édition à Toulouse, du 3 au 5 septembre 2004, sur le campus de I'INSA. Comme il est de tradition tous les quatre ans, COLOQ était couplé avec Horizons de l'optique, avec en particulier une journée commune dont le programme avait été préparé en concertation par les deux comités scientifiques. Depuis sa création, COLOQ a pour but de favoriser les rencontres entre les chercheurs des différents laboratoires nationaux publics ou privés travaillant sur les lasers et l'optique quantique au sens large. C'est un moyen privilégié de resserrer les liens de cette communauté et d'y intégrer les jeunes chercheurs. Ces derniers y trouvent l'occasion de se connaître, de se faire connaître, de découvrir la communauté à laquelle ils appartiennent et d'élargir leurs connaissances des thèmes qui la structurent. La participation de 230 chercheurs et d'une vingtaine d'exposants de matériels spécialisés dans les lasers et l'optoélectronique témoigne de la vitalité de COLOQ et de son audience dans les laboratoires et chez les industriels de l'optique. Le programme de COLOQ 8 comportait d'une vingtaine de conférences générales données par des chercheurs de renom international, et des séances de communications par affiches, occasions privilégiées de rencontres et d'échanges. Les exposés ont porté sur des sujets particulièrement actifs au niveau national et international, avec un accent sur des thèmes importants pour la région toulousaine : contrôle cohérent, optique et nanosciences, optique et astronomie, sans oublier la traditionnelle rubrique phénomènes fondamentaux, éclectique pour ne pas dire hétéroclite, mais si représentative d'une des ambitions de COLOQ qui est d'offrir à ses participants une

  18. Influence of crystallographic texture in X70 pipeline steels on toughness anisotropy and delamination

    NASA Astrophysics Data System (ADS)

    Al-Jabr, Haytham M.

    The effects of microstructure and crystallographic texture in four commercially-produced API X70 pipeline steels and their relation to planar anisotropy of toughness and delamination were evaluated. The experimental steels were processed through either a hot strip mill, a Steckel mill, or a compact strip mill. Different processing routes were selected to obtain plates with potential variations in the microstructure and anisotropic characteristics. Tensile and Charpy impact testing were used to evaluate the mechanical properties in three orientations: longitudinal (L), transverse (T) and diagonal (D) with respect to the rolling direction to evaluate mechanical property anisotropy. The yield and tensile strengths were higher in the T orientation and toughness was lower in the D orientation for all plates. Delamination was observed in some of the ductile fracture surfaces of the impact samples. To further study the splitting behavior and effects on impact toughness, a modified impact test (MCVN) specimen with side grooves was designed to intensify induced stresses parallel to the notch root and thus facilitate evaluation of delamination. Scanning electron microscopy combined with electron backscattered diffraction (EBSD) were used to evaluate the grain size, microstructural constituents, and crystallographic texture to determine the factors leading to delamination and the anisotropy in toughness. The ferrite grain size is mainly responsible for the differences in DBTTs between the L and T orientations. The higher DBTT in the D orientation observed in pipeline steels is attributed to crystallographic texture. The higher DBTT in the D direction is due to the higher volume fraction of grains having their {100} planes parallel or close to the primary fracture plane for the D orientation. An equation based on a new "brittleness parameter," based on an assessment of grain orientations based on EBSD data, was developed to predict the changes in DBTTs with respect to sample

  19. Superconductivity of the Pr-substituted (Nd/sub 1-x/Pr/sub x/)Ba/sub 2/Cu/sub 3/O/sub 7-/delta// system

    SciTech Connect

    Ku, H.C.; Chen, C.C.; Hsu, S.W.

    1988-12-01

    Electrical, magnetic and crystallographic measurements have been carried out for the pseudoquaternary (Nd/sub 1-x/Pr/sub x/)Ba/sub 2/Cu/sub 3/O/sub 7-/delta// system. Orthorhombic phase persists from chi = 0.0 up to chi = 0.7 and transforms into the tetragonal structure only for chi /ge/ 0.8. Superconducting transition temperature T/sub c/ decreases linearly from 92 K for chi = 0.0 to below 10 K for chi = 0.3 and extrapolated to 0 K around chi = 0.35. Magnetic susceptibility indicates that the valence of the Pr ion is close to 4+. Pr/sup 4+/ is a very powerful oxidizing agent and may distort or move oxygen away from the Cu-O chain and/or the /CuO/sub 2/ planes and seriously suppress superconductivity.

  20. Préface

    NASA Astrophysics Data System (ADS)

    Ouerdane, Youcef; Laporte, Pierre

    2005-06-01

    L'objectif de la série de colloques UVX est de réunir, au rythme d'une fois tous les deux ans, les scientifiques et industriels travaillant dans le domaine du développement des sources de photon de grande énergie (UV, VUV, et X) et de leurs applications. En particulier cette manifestation est l'occasion de faire se rencontrer une communauté très pluridisciplinaire (physique, chimie, biologie, sciences de l'univers) liée à des domaines en forte évolution technologique (lasers et rayonnement synchrotron notamment). Le colloque UVX 2004 s'est tenu au Palais des Congrès de Saint-Étienne (42000) du 7 au 11 juin 2004. La période écoulée depuis l'édition précédente (Oléron 2002) a été particulièrement active dans tous les domaines concernés : grands projets de sources, méthodes de diagnostic au sens large. Une nouvelle fois on constate que le bref et l'ultra-bref ont une place privilégiée, qu'il s'agisse du travail sur les accélérateurs ou sur les lasers qui, bien sûr, dans la course aux temps courts remportent la palme avec la présence de spécialistes du domaine attoseconde. La communauté représentée a la chance d'être en prise directe avec de très grands projets en phase active de réalisation comme le Laser Megajoule (LMJ), la source SOLEIL, et un projet d'ampleur plus modeste mais remarquable dans son domaine : la source LASERIX d'Orsay/Palaiseau. On pourra citer aussi le projet Arc en Ciel qui, lui, est encore au stade de sa définition. - SOLEIL, source de nouvelle génération de rayonnement synchrotron (plateau de Saclay) est dans une phase active de réalisation : achèvement de l'infrastructure en 2005 et injection du 1o faisceau dans l'anneau de stockage prévu également en 2005. Cette source devrait être la meilleure au monde dans le domaine VUV/X mous, tout en restant très polyvalente (brillance, accordabilité, structure temporelle, polarisation) et complémentaire de l'ESRF. Au final on disposera de 21 lignes de lumi

  1. Préface

    NASA Astrophysics Data System (ADS)

    Cornet, Alain

    2004-11-01

    Le premier colloque Rayons X et Matière (Rx 95) s'est tenu à Strasbourg en 1995. Il était destiné à célébrer le centenaire de la découverte des rayons X par ROENTGEN et a alors réuni plus de cent trente chercheurs et industriels concernés par les rayons X et les matériaux. Parmi eux se trouvaient les Professeurs André GUINIER et Hans NEFF ainsi que Monsieur Michel BRUNEL qui hélas ne sont plus parmi nous à ce jour. La qualité et la convivialité des échanges entre les participants lors de cette première réunion ne pouvaient que nous inciter à la reconduire et nous avons pris rendez vous pour 1997, puis 1999, puis 2001 et enfin pour 2003, soient cinq colloques, un tous les deux ans pendant dix ans. Au cours des années, nous avons essayé d'adapter les thèmes abordés à l'évolution de la recherche et des techniques. Ces thèmes se sont naturellement ajoutés aux thèmes classiques comme la diffraction et la fluorescence. Les nanomatériaux, les microfaisceaux en sont des exemples. A de très rares exceptions les communications présentées étaient de très bon niveau et nous avons toujours eu beaucoup de plaisir à les publier. Ces colloques ont bien fonctionné en raison de la participation des industriels qui, dans leur grande majorité, nous ont accompagnés régulièrement. Ces colloques présentent l'avantage, par rapport à des colloques spécialisés, de couvrir (presque) tout le champ des applications des rayons X et seulement ce domaine. Toutefois il est clair que les données économiques évoluent et que la situation est chaque aimée plus difficile pour tout le monde, chercheurs et industriels. Temps et moyens sont comptés et maintenant chacun doit faire de plus en plus de choix, rentabilité oblige ! Le maintien du colloque Rayons X et Matière passera obligatoirement par une réflexion globale : redéfinition des objectifs, augmentation de l'ouverture européenne, recherche d'autres formes de participation associant mieux les

  2. Préface

    NASA Astrophysics Data System (ADS)

    Hamieh, Tayssir

    2005-05-01

    Né simultanément à Mulhouse et à Beyrouth en 1996 dans le cadre d'une collaboraiion franco-libanaise sur une initiative personnelle de Monsieur Tayssir HAMIEH. le Colloque Franco-Libanais sur la Science des Matériaux (CSM), qui s'inscrit dans le cadre des relations étroites entre la France et le Liban, est très vite devenu une occasion très importante de rencontre entre scientifiques de haut niveau, non seulement, du contour méditerranéen mais également des pays européens, américains et arabes. La quatrieme édition CSM4 est une véritable réussite grâce à la participation des chercheurs confirmés dans tous les domaines des sciences de matériaux et venant de plusieurs pays tels que la France, I'Algérie, Le Liban, la Syrie, le Maroc, la Tunisie, l'Italie, l'Espagne, le Portugal, le Royaume Uni, les États-Unis, la Russie, l'Allemagne, le Japon et I'Inde ; pour présenter plus de 350 communications orales et par affiche et couvrant presque toutes les disciplines des systèmes des matériaux. Le choix des diffèrents thèmes du colloque sur la science des matériaux a été dicté par l'importance capitale de cette discipline dans notre civilisation moderne. En fait, les matériaux utilisés pour la fabrication artisanale ou industrielle d'objets, de produits et de systèmes ainsi que pour la réalisation de constructions et d'équipements ont de tout temps défini le niveau de notre civilisation technique. La réalisation des objectifs communs de notre monde en plein développement, pour ne pas dire en pleine mutation, est en grande partie tributaire de la mise au point de nouveaux matériaux et de procédés de transformation et d'assemblages nouveaux, présentant des performances et des qualités améliorées. Le colloque a illustré et traduit, de manière remarquables, l'excellente collaboration entre chercheurs libanais et français. Le partenariat est exemplaire par la qualité des laboratoires impliqués et par le niveau scientifique des r

  3. Energetic, crystallographic and diffusion characteristics of hydrogen isotopes in iron

    NASA Astrophysics Data System (ADS)

    Sivak, A. B.; Sivak, P. A.; Romanov, V. A.; Chernov, V. M.

    2015-06-01

    Energetic, crystallographic and diffusion characteristics of various interstitial configurations of H atoms and their complexes with self-point defects (SIA - self-interstitial atom, V - vacancy) in bcc iron have been calculated by molecular statics and molecular dynamics using Fe-H interatomic interaction potential developed by Ramasubramaniam et al. (2009) and modified by the authors of the present work and Fe-Fe matrix potential M07 developed by Malerba et al. (2010). The most energetically favorable configuration of an interstitial H atom is tetrahedral configuration. The energy barrier for H atom migration is 0.04 eV. The highest binding energy of all the considered complexes "vacancy - H atom" and "SIA - H atom" is 0.54 and 0.15 eV, respectively. The binding energy of H atom with edge dislocations in slip systems <1 1 1>{1 1 0}, <1 1 1>{1 1 2}, <1 0 0>{1 0 0}, <1 0 0>{1 1 0} is 0.32, 0.30, 0.45, 0.54 eV, respectively. The binding energy of H atom in VHn complexes (n = 1 … 15) decreases from 0.54 to 0.35 eV with increasing of n from 1 to 6. At n > 6, it decreases to ∼0.1 eV. The temperature dependences of hydrogen isotopes (P, D, T) diffusivities have been calculated for the temperature range 70-1800 K. Arrhenius-type dependencies describe the calculated data at temperatures T < 100 K. At T > 250 K, the temperature dependencies of the diffusivities DP, DD, DT have a parabolic form. The diffusivities of H isotopes are within 10% at room temperature. The isotope effect becomes stronger at higher temperatures, e.g., ratios DP/DD and DP/DT at 1800 K equal 1.23 and 1.40, respectively.

  4. Variations in Reactivity on Different Crystallographic Orientations of Cerium Oxide

    SciTech Connect

    Mullins, David R; Albrecht, Peter M; Calaza, Florencia C

    2013-01-01

    Cerium oxide is a principal component in many heterogeneous catalytic processes. One of its key characteristics is the ability to provide or remove oxygen in chemical reactions. The different crystallographic faces of ceria present significantly different surface structures and compositions that may alter the catalytic reactivity. The structure and composition determine the number of coordination vacancies surrounding surface atoms, the availability of adsorption sites, the spacing between adsorption sites and the ability to remove O from the surface. To investigate the role of surface orientation on reactivity, CeO2 films were grown with two different orientations. CeO2(100) films were grown ex situ by pulsed laser deposition on Nb-doped SrTiO3(100). CeO2(111) films were grown in situ by thermal deposition of Ce metal onto Ru(0001) in an oxygen atmosphere. The chemical reactivity was characterized by the adsorption and decomposition of various molecules such as alcohols, aldehydes and organic acids. In general the CeO2(100) surface was found to be more active, i.e. molecules adsorbed more readily and reacted to form new products, especially on a fully oxidized substrate. However the CeO2(100) surface was less selective with a greater propensity to produce CO, CO2 and water as products. The differences in chemical reactivity are discussed in light of possible structural terminations of the two surfaces. Recently nanocubes and nano-octahedra have been synthesized that display CeO2(100) and CeO2(111) faces, respectively. These nanoparticles enable us to correlate reactions on high surface area model catalysts at atmospheric pressure with model single crystal films in a UHV environment.

  5. Magnetic and crystallographic structures in UTX intermetallic compounds

    SciTech Connect

    Robinson, R.A.; Lawson, A.C.; Sechovsky, V.; Havela, L.; Kergadallan, Y.; Nakotte, H.; de Boer, F.R.

    1993-08-01

    Uranium, along with other actinides and lanthanides, forms a large group of ternary intermetallic compounds of stoichiometry UTX (T = transition metal, X = p-electron metal). These compounds are formed in several structure types and the occurrence and stability of particular structures with respect to the transition metal content suggests reasonable systematics. The authors have also investigated the magnetic structures of selected UTX compounds and it is revealing to relate the crystallographic and magnetic structures, because of the relationship between the magnetic symmetry and that of the U-atom environment produced by the 5f-ligand hybridization, and the consequent anisotropic exchange. Those of ZrNiAl structure type are collinear, with moments along the hexagonal c-axis. In the orthorhombic NiSiTi structure type, the moments are confined to the b- c plane (perpendicular to the uranium chains) and the structures are often incommensurate. In the hexagonal CaIn{sub 2} (or GaGeLi) structure type, the magnetic structures form in an orthorhombic cell, and at least in the disordered centric group, again the moments lie perpendicular to the nearest-neighbor uranium spacing. This work presents a phenomenology of trends in UTX ternary compounds. It is shown that there is an apparent strong hybridization parallel to nearest neighbor U-U directions, with ferromagnetic coupling in the same directions. There may be a systematic relationship between the hybridization anisotropy and the magnetic anisotropy, in which the quantization axes are the same and the moments point along directions of relatively weak hybridization.

  6. Isolation and characterization of six pathogenesis-related (PR) proteins of Samsun NN tobacco.

    PubMed

    Kauffmann, S; Legrand, M; Fritig, B

    1990-03-01

    The purification to homogeneity of pathogenesis-related (PR) proteins R and S from Nicotiana tabacum cv. Samsun NN leaves has been achieved by using a combination of conventional and high-performance chromatographic supports. The same procedure allowed the purification and the characterization of four other proteins which displayed some properties characteristic of tobacco PR proteins and were shown to accumulate in tobacco leaves in response to virus infection. They can be, therefore, considered as new tobacco PR proteins which we designate as PR-s1, -s2, -r1 and -r2. The relative electrophoretic mobilities (Rf) under non-denaturing conditions were estimated to 0.30 for PR-r1 and -r2, 0.25 for Pr-R, 0.20 for PR-s1 and -s2 and 0.15 for PR-S. On SDS gels PR proteins R and S possessed the same apparent molecular weight (Mr 24,000) as did PR-proteins s1 and r1 (Mr 14,500) and PR-s2 and -r2 (Mr 13,000). However, proteins s1, s2, r1 and r2 had identical electrophoretic mobilities on SDS gels when the loading sample buffer contained no reducing agent. Polyclonal antisera were raised against PR proteins R and S and used in immunoblotting experiments. Proteins R and S were shown to be serologically closely related. No cross-reaction was detected with any of the four new tobacco PR proteins r1, r2, s1 and s2 or with the previously described PR proteins, i.e. PR-1a, -1b, -1c, -2, -N, -O, -P and -Q. PMID:2102821

  7. Préface

    NASA Astrophysics Data System (ADS)

    Jörgen Stevefelt, Henri Bachau Et

    2003-06-01

    UVX 2002, sixième édition du “Colloque sur les Sources Cohérentes et Incohérentes UV, VUV, et X : Applications et Développements Récents" s'est tenu du 11 au 14 juin 2002 au Centre CAES du CNRS “La Vieille, Perrotine", à Saint-Pierre d'Oléron. Le colloque a réunni une centaine de chercheurs et d'industriels et a permis de faire le point sur la production, la caractérisation et l'utilisation de rayonnement dans un domaine spectral s'étendant de l'ultraviolet aux rayons X. Les participants ont pu assister a trente conférences et une table ronde autour des problèmes locaux de pollution, une cinquantaine d'affiches ont été présentées au travers de deux sessions. Une douzaine d'industriels ont exposé leurs produits durant les séances d'affiches.Conformément aux éditions précédentes, les domaines couverts par le colloque UVX 2002 sont très variés et il est impossible de les résumer en quelques lignes. Parmi les activités en développement rapide on notera les lasers femtosecondes dont les applications se multiplient dans les laboratoires (propriétés des molécules, agrégats et solides), dans l'industrie (usinage, ablation...) et en médecine. L'absence de thermalisation ou de diffusion thermique ouvre aussi des perspectives pour la réalisation de films minces par ablation laser, un domaine où les lasers excimères sont traditionnellement utilisés, avec des applications importantes dans le secteur des télécommunications. Dans le domaine de l'extrème UV, des progrès significatifs ont été réalisés par plusieurs groupes dans la gamme de longueur d'onde de 5 à 20 nm, ouvrant ainsi la voie au développement industriel de la lithographie EUV. On note les progrès dans la réalisation des sources UV et X (laser X, génération d'harmoniques, laser a électrons libres) et la nécessité de développer des optiques adaptées. Une perspective intéressante, ouverte par la génération d'harmoniques, est la production d

  8. Crystallographic transformation of limestone during calcination under CO2.

    PubMed

    Valverde, Jose Manuel; Medina, Santiago

    2015-09-14

    The calcination reaction of limestone (CaCO3) to yield lime (CaO) is at the heart of many industrial applications as well as natural processes. In the recently emerged calcium-looping technology, CO2 capture is accomplished by the carbonation of CaO in a gas-solid reactor (carbonator). CaO is derived by the calcination of limestone in a calciner reactor under necessarily high CO2 partial pressure and high temperature. In situ X-ray diffraction (XRD) has been employed in this work to gain further insight into the crystallographic transformation that takes place during the calcination of limestone under CO2, at partial pressures (P) close to the equilibrium pressure (Peq) and at high temperature. Calcination under these conditions becomes extremely slow. The in situ XRD analysis presented here suggests the presence of an intermediate metastable CaO* phase stemming from the parent CaCO3 structure. According to the reaction mechanism proposed elsewhere, the exothermicity of the CaO* → CaO transformation and high values of P/Peq inhibit the nucleation of CaO at high temperatures. The wt% of CaO* remains at a relatively high level during slow calcination. Two diverse stages have been identified in the evolution of CaO crystallite size, L. Initially, L increases with CaCO3 conversion, following a logarithmic law. Slow calcination allows the crystallite size to grow up from a few nanometers at nucleation up to around 100 nm near the end of conversion. Otherwise, quick calcination at relatively lower CO2 concentrations limits CaO crystallite growth. Once calcination reaches an advanced state, the presence of CaO* drops to zero and the rate of increase of the CaO crystallite size is significantly hindered. Arguably, the first stage in CaO crystallite growth is driven by aggregation of the metastable CaO* nanocrystals, due to surface attractive forces, whereas the second one is consistent with sintering of the aggregated CaO crystals, and persists with time after full

  9. Surface structure, crystallographic and ice-nucleating properties of cellulose

    NASA Astrophysics Data System (ADS)

    Hiranuma, Naruki; Möhler, Ottmar; Kiselev, Alexei; Saathoff, Harald; Weidler, Peter; Shutthanandan, Shuttha; Kulkarni, Gourihar; Jantsch, Evelyn; Koop, Thomas

    2015-04-01

    Increasing evidence of the high diversity and efficient freezing ability of biological ice-nucleating particles is driving a reevaluation of their impact upon climate. Despite their potential importance, little is known about their atmospheric abundance and ice nucleation efficiency, especially non-proteinaceous ones, in comparison to non-biological materials (e.g., mineral dust). Recently, microcrystalline cellulose (MCC; non-proteinaceous plant structural polymer) has been identified as a potential biological ice-nucleating particle. However, it is still uncertain if the ice-nucleating activity is specific to the MCC structure or generally relevant to all cellulose materials, such that the results of MCC can be representatively scaled up to the total cellulose content in the atmosphere to address its role in clouds and the climate system. Here we use the helium ion microscopy (HIM) imaging and the X-ray diffraction (XRD) technique to characterize the nanoscale surface structure and crystalline properties of the two different types of cellulose (MCC and fibrous cellulose extracted from natural wood pulp) as model proxies for atmospheric cellulose particles and to assess their potential accessibility for water molecules. To complement these structural characterizations, we also present the results of immersion freezing experiments using the cold stage-based droplet freezing BINARY (Bielefeld Ice Nucleation ARaY) technique. The HIM results suggest that both cellulose types have a complex porous morphology with capillary spaces between the nanoscale fibrils over the microfiber surface. These surface structures may make cellulose accessible to water. The XRD results suggest that the structural properties of both cellulose materials are in agreement (i.e., P21 space group; a=7.96 Å, b=8.35 Å, c=10.28 Å) and comparable to the crystallographic properties of general monoclinic cellulose (i.e., Cellulose Iβ). The results obtained from the BINARY measurements suggest

  10. Préface

    NASA Astrophysics Data System (ADS)

    Moncorgé, R.

    2006-12-01

    Cette nouvelle édition du Colloque UVX avait pour objectifs de : - réunir les chercheurs et les industriels intéressés par les applications et les développements les plus récents obtenus sur les sources UV, VUV et X, cohérentes ou incohérentes, et les optiques et matériaux associés ; - dresser un bilan des sources de photons à haute énergie et de leurs applications courantes et futures ; - susciter de nouvelles collaborations ; - ouvrir de nouveaux champs disciplinaires. Elle a été organisée par le laboratoire CIRIL au VVF de Colleville-sur-Mer, dans le département du Calvados, du 6 au 9 juin 2006, la journée du 5 juin ayant été consacrée à une réunion de travail du GDR CNRS SAXO, ce GDR regroupant une majorité de scientifiques concernés par le Colloque UVX. La manifestation a réuni ainsi une centaine de participants dont une dizaine d'exposants industriels. Parmi ces participants, trente étaient invités à donner une conférence orale. Une sélection a été faite également parmi les meilleures communications soumises par affiches pour qu'elles soient présentées oralement. Une trentaine de ces communications ont été préparées sous la forme d'articles de 6 à 12 pages et font l'objet de cet ouvrage. De nombreux travaux récents ont été exposés tant au niveau des sources que des techniques de caractérisation et des applications, ceci dans des domaines très divers allant de la physique des lasers et de la mise en forme spatiale et temporelle des faisceaux au domaine de l'imagerie médicale et biologiques en passant par les techniques de fabrication des cristaux, fibres et films minces organiques et inorganiques. Plusieurs résultats marquants en sont ressortis. Dans le domaine des sources, la mise en forme spatiale du faisceau laser utilisé pour la production d'harmoniques d'ordre élevé dans les gaz, ceci à l'aide de lames de phase peu onéreuses et simples d'utilisation, semble être une bonne solution pour accroître les

  11. ESO PR Highlights in 2004

    NASA Astrophysics Data System (ADS)

    2005-01-01

    Last year proved again a wonderful one for astronomy in general and for ESO in particular. Certainly the most important astronomical event for a large public was the unique Transit of Venus : on June 8, 2004, Venus - the Earth's sister planet - passed in front of the Sun. This rare event - the last one occurred in 1882 - attracted the attention of millions of people all over the world. ESO in cooperation with several other institutes and with support from the European Commission organised through the whole year the Venus Transit 2004 (VT-2004) public education programme that successfully exposed the broad public to a number of fundamental issues at the crucial interface between society and basic science. The web site experienced a record 55 million webhits during a period of 8 hours around the transit. The programme also re-enacted the historical determination of the distance to the Sun (the "Astronomical Unit") by collecting 4550 timings of the four contacts made by more than 1500 participating group of observers and combining them in a calculation of the AU. This resulted in an astonishing accurate value of the Astronomical Unit. More details are available at the VT-2004 website, whose wealth of information will certainly make it a useful tool until the next transit in 2012! For ESO also, 2004 proved a very special year. Finland officially joined as eleventh member state and in December, the Chilean President, Ricardo Lagos, visited the Paranal Observatory. Last year was also the Fifth anniversary of the Very Large Telescope, ESO's flagship facility, as on April 1, 1999 the first 8.2-m VLT Unit Telescope, Antu (UT1), was "handed over" to the astronomers. On this occasion, ESO released several products, including a selection of the best astronomical images taken with the VLT, the VLT Top 20. But there is no doubt that the numerous high quality images published last year are all contenders to top the charts of best astronomical pictures. The year 2004 also saw many

  12. A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error.

    PubMed

    Read, Randy J; McCoy, Airlie J

    2016-03-01

    The crystallographic diffraction experiment measures Bragg intensities; crystallographic electron-density maps and other crystallographic calculations in phasing require structure-factor amplitudes. If data were measured with no errors, the structure-factor amplitudes would be trivially proportional to the square roots of the intensities. When the experimental errors are large, and especially when random errors yield negative net intensities, the conversion of intensities and their error estimates into amplitudes and associated error estimates becomes nontrivial. Although this problem has been addressed intermittently in the history of crystallographic phasing, current approaches to accounting for experimental errors in macromolecular crystallography have numerous significant defects. These have been addressed with the formulation of LLGI, a log-likelihood-gain function in terms of the Bragg intensities and their associated experimental error estimates. LLGI has the correct asymptotic behaviour for data with large experimental error, appropriately downweighting these reflections without introducing bias. LLGI abrogates the need for the conversion of intensity data to amplitudes, which is usually performed with the French and Wilson method [French & Wilson (1978), Acta Cryst. A35, 517-525], wherever likelihood target functions are required. It has general applicability for a wide variety of algorithms in macromolecular crystallography, including scaling, characterizing anisotropy and translational noncrystallographic symmetry, detecting outliers, experimental phasing, molecular replacement and refinement. Because it is impossible to reliably recover the original intensity data from amplitudes, it is suggested that crystallographers should always deposit the intensity data in the Protein Data Bank. PMID:26960124

  13. Phase diagram of the Pr-Mn-O system in composition-temperature-oxygen pressure coordinates

    NASA Astrophysics Data System (ADS)

    Vedmid', L. B.; Yankin, A. M.; Fedorova, O. M.; Kozin, V. M.

    2016-05-01

    The phase relations in the Pr-Mn-O system were studied by the static method at lowered oxygen pressure in combination with thermal analysis and high-temperature X-ray diffraction. The equilibrium oxygen pressure in dissociation of PrMn2O5 and PrMnO3 was measured, and the thermodynamic characteristics of formation of these compounds from elements were calculated. The P- T- x phase diagram of the Pr-Mn-O system was constructed in the "composition-oxygen pressure-temperature" coordinates.

  14. Directives préalables

    PubMed Central

    O’Sullivan, Rory; Mailo, Kevin; Angeles, Ricardo; Agarwal, Gina

    2015-01-01

    Résumé Objectif Établir la prévalence de patients dotés de directives préalables dans une pratique familiale et décrire les points de vue des patients quant au rôle du médecin de famille dans l’amorce de discussions à propos des directives préalables. Conception Un questionnaire auquel les patients ont répondu eux-mêmes. Contexte Une clinique d’enseignement en médecine familiale achalandée en milieu urbain, à Hamilton, en Ontario. Participants Un échantillon de commodité formé de patients adultes qui se sont présentés à la clinique durant une semaine de travail typique. Principaux paramètres à l’étude La prévalence des directives préalables dans une population de patients a été déterminée et les attentes à l’endroit du rôle de leur médecin de famille ont été sollicitées. Résultats Les répondants au sondage étaient au nombre de 800 (un taux de réponse de 72,5 %) et leurs groupes d’âges étaient bien répartis; 19,7 % d’entre eux avaient rédigé des directives préalables et 43,8 % avaient déjà discuté du sujet des directives préalables, mais seulement 4,3 % de ces discussions avaient eu lieu avec un médecin de famille. Dans 5,7 % des cas, un médecin de famille avait soulevé la question; 72,3 % des répondants croyaient que les patients devraient amorcer la discussion. Les patients qui considéraient les directives préalables d’une importance extrême étaient considérablement plus enclins à vouloir que leur médecin de famille commence la conversation (rapport de cotes de 3,98; p < ,05). Conclusion Les directives préalables n’étaient pas systématiquement abordées dans la pratique familiale. La plupart des patients préféraient amorcer la discussion des directives préalables. Toutefois, les patients qui considéraient le sujet d’une extrême importance voulaient que leur médecin de famille commence la discussion.

  15. High-temperature in situ crystallographic observation of reversible gas sorption in impermeable organic cages.

    PubMed

    Baek, Seung Bin; Moon, Dohyun; Graf, Robert; Cho, Woo Jong; Park, Sung Woo; Yoon, Tae-Ung; Cho, Seung Joo; Hwang, In-Chul; Bae, Youn-Sang; Spiess, Hans W; Lee, Hee Cheon; Kim, Kwang S

    2015-11-17

    Crystallographic observation of adsorbed gas molecules is a highly difficult task due to their rapid motion. Here, we report the in situ single-crystal and synchrotron powder X-ray observations of reversible CO2 sorption processes in an apparently nonporous organic crystal under varying pressures at high temperatures. The host material is formed by hydrogen bond network between 1,3,5-tris-(4-carboxyphenyl)benzene (H3BTB) and N,N-dimethylformamide (DMF) and by π-π stacking between the H3BTB moieties. The material can be viewed as a well-ordered array of cages, which are tight packed with each other so that the cages are inaccessible from outside. Thus, the host is practically nonporous. Despite the absence of permanent pathways connecting the empty cages, they are permeable to CO2 at high temperatures due to thermally activated molecular gating, and the weakly confined CO2 molecules in the cages allow direct detection by in situ single-crystal X-ray diffraction at 323 K. Variable-temperature in situ synchrotron powder X-ray diffraction studies also show that the CO2 sorption is reversible and driven by temperature increase. Solid-state magic angle spinning NMR defines the interactions of CO2 with the organic framework and dynamic motion of CO2 in cages. The reversible sorption is attributed to the dynamic motion of the DMF molecules combined with the axial motions/angular fluctuations of CO2 (a series of transient opening/closing of compartments enabling CO2 molecule passage), as revealed from NMR and simulations. This temperature-driven transient molecular gating can store gaseous molecules in ordered arrays toward unique collective properties and release them for ready use. PMID:26578758

  16. High-temperature in situ crystallographic observation of reversible gas sorption in impermeable organic cages

    PubMed Central

    Baek, Seung Bin; Moon, Dohyun; Graf, Robert; Cho, Woo Jong; Park, Sung Woo; Yoon, Tae-Ung; Cho, Seung Joo; Hwang, In-Chul; Bae, Youn-Sang; Spiess, Hans W.; Lee, Hee Cheon; Kim, Kwang S.

    2015-01-01

    Crystallographic observation of adsorbed gas molecules is a highly difficult task due to their rapid motion. Here, we report the in situ single-crystal and synchrotron powder X-ray observations of reversible CO2 sorption processes in an apparently nonporous organic crystal under varying pressures at high temperatures. The host material is formed by hydrogen bond network between 1,3,5-tris-(4-carboxyphenyl)benzene (H3BTB) and N,N-dimethylformamide (DMF) and by π–π stacking between the H3BTB moieties. The material can be viewed as a well-ordered array of cages, which are tight packed with each other so that the cages are inaccessible from outside. Thus, the host is practically nonporous. Despite the absence of permanent pathways connecting the empty cages, they are permeable to CO2 at high temperatures due to thermally activated molecular gating, and the weakly confined CO2 molecules in the cages allow direct detection by in situ single-crystal X-ray diffraction at 323 K. Variable-temperature in situ synchrotron powder X-ray diffraction studies also show that the CO2 sorption is reversible and driven by temperature increase. Solid-state magic angle spinning NMR defines the interactions of CO2 with the organic framework and dynamic motion of CO2 in cages. The reversible sorption is attributed to the dynamic motion of the DMF molecules combined with the axial motions/angular fluctuations of CO2 (a series of transient opening/closing of compartments enabling CO2 molecule passage), as revealed from NMR and simulations. This temperature-driven transient molecular gating can store gaseous molecules in ordered arrays toward unique collective properties and release them for ready use. PMID:26578758

  17. Experimental and Theoretical Investigation of Crystallographic Orientation Dependence of Nanoscratching of Single Crystalline Copper.

    PubMed

    Geng, Yanquan; Zhang, Junjie; Yan, Yongda; Yu, Bowen; Geng, Lin; Sun, Tao

    2015-01-01

    In the present work, we perform experiments and molecular dynamics simulations to elucidate the underlying deformation mechanisms of single crystalline copper under the load-controlled multi-passes nanoscratching using a triangular pyramidal probe. The correlation of microscopic deformation behavior of the material with macroscopically-observed machining results is revealed. Moreover, the influence of crystallographic orientation on the nanoscratching of single crystalline copper is examined. Our simulation results indicate that the plastic deformation of single crystalline Cu under the nanoscratching is exclusively governed by dislocation mechanisms. However, there is no glissile dislocation structure formed due to the probe oscillation under the load-controlled mode. Both experiments and MD simulations demonstrate that the machined surface morphologies in terms of groove depth and surface pile-up exhibit strong crystallographic orientation dependence, because of different geometries of activated slip planes cutting with free surfaces and strain hardening abilities associated with different crystallographic orientations. PMID:26147506

  18. Crystallographic texture engineering through novel melt strategies via electron beam melting: Inconel 718

    DOE PAGESBeta

    Dehoff, Ryan R.; Kirka, Michael M.; List, III, Frederick Alyious; Unocic, Kinga A.; Sames, William J.

    2014-01-01

    Preliminary research has demonstrated the ability to utilise novel scan strategies in the electron beam melting (EBM) process to establish control of crystallographic texture within Inconel 718 deposits. Conventional EBM scan strategies and process parameters yield coarse columnar grains aligned parallel to the build direction. Through varying process parameters such as beam power, beam velocity, beam focus and scan strategy, the behaviour of the electron beam can be manipulated from a line source to a point source. The net effect of these variations is that the resulting crystallographic texture is controlled in a manner to produce either epitaxial deposits ormore » fully equiaxed deposits. Furthermore, this research demonstrates the ability to change the crystallographic texture on the macroscale indicating that EBM technology can be used to create complex geometric components with both site-specific microstructures and material properties.« less

  19. Crystallographic texture engineering through novel melt strategies via electron beam melting: Inconel 718

    SciTech Connect

    Dehoff, Ryan R.; Kirka, Michael M.; List, III, Frederick Alyious; Unocic, Kinga A.; Sames, William J.

    2014-01-01

    Preliminary research has demonstrated the ability to utilise novel scan strategies in the electron beam melting (EBM) process to establish control of crystallographic texture within Inconel 718 deposits. Conventional EBM scan strategies and process parameters yield coarse columnar grains aligned parallel to the build direction. Through varying process parameters such as beam power, beam velocity, beam focus and scan strategy, the behaviour of the electron beam can be manipulated from a line source to a point source. The net effect of these variations is that the resulting crystallographic texture is controlled in a manner to produce either epitaxial deposits or fully equiaxed deposits. Furthermore, this research demonstrates the ability to change the crystallographic texture on the macroscale indicating that EBM technology can be used to create complex geometric components with both site-specific microstructures and material properties.

  20. Three sets of crystallographic sub-planar structures in quartz formed by tectonic deformation

    NASA Astrophysics Data System (ADS)

    Derez, Tine; Pennock, Gill; Drury, Martyn; Sintubin, Manuel

    2016-05-01

    In quartz, multiple sets of fine planar deformation microstructures that have specific crystallographic orientations parallel to planes with low Miller-Bravais indices are commonly considered as shock-induced planar deformation features (PDFs) diagnostic of shock metamorphism. Using polarized light microscopy, we demonstrate that up to three sets of tectonically induced sub-planar fine extinction bands (FEBs), sub-parallel to the basal, γ, ω, and π crystallographic planes, are common in vein quartz in low-grade tectonometamorphic settings. We conclude that the observation of multiple (2-3) sets of fine scale, closely spaced, crystallographically controlled, sub-planar microstructures is not sufficient to unambiguously distinguish PDFs from tectonic FEBs.

  1. Experimental and Theoretical Investigation of Crystallographic Orientation Dependence of Nanoscratching of Single Crystalline Copper

    PubMed Central

    Geng, Yanquan; Zhang, Junjie; Yan, Yongda; Yu, Bowen; Geng, Lin; Sun, Tao

    2015-01-01

    In the present work, we perform experiments and molecular dynamics simulations to elucidate the underlying deformation mechanisms of single crystalline copper under the load-controlled multi-passes nanoscratching using a triangular pyramidal probe. The correlation of microscopic deformation behavior of the material with macroscopically-observed machining results is revealed. Moreover, the influence of crystallographic orientation on the nanoscratching of single crystalline copper is examined. Our simulation results indicate that the plastic deformation of single crystalline Cu under the nanoscratching is exclusively governed by dislocation mechanisms. However, there is no glissile dislocation structure formed due to the probe oscillation under the load-controlled mode. Both experiments and MD simulations demonstrate that the machined surface morphologies in terms of groove depth and surface pile-up exhibit strong crystallographic orientation dependence, because of different geometries of activated slip planes cutting with free surfaces and strain hardening abilities associated with different crystallographic orientations. PMID:26147506

  2. Elasto-Plastic Behavior of High RRR Niobium: Effects of Crystallographic Texture, Microstructure and Hydrogen Concentration

    SciTech Connect

    G.R. Myneni; S.R. Agnew

    2002-11-01

    Conventional assessments of the mechanical properties of polycrystalline high RRR niobium via tensile testing have revealed unusually low apparent Young's moduli and yield strength in annealed samples. These observations motivated the current investigation of a variety of possible contributors: crystallographic texture, grain size, and impurity concentration. It is shown that the crystallographic textures of a single lot of niobium are essentially unchanged by post-recrystallization anneals at temperatures up to 800 C. Ultrasonic measurements reveal that the elastic response is not degraded by annealing. Rather, the material's extremely low yield point gives the impression of a low elastic modulus during tensile testing.

  3. Measurement of thermal diffusivity, elastic anisotropy and crystallographic orientation by interferometric photothermal microscopy

    NASA Astrophysics Data System (ADS)

    Jumel, Julien; Rochais, Denis

    2007-07-01

    This paper describes the use of interferometric photothermal microscopy for measuring the thermal diffusivity, crystallographic orientation and elastic anisotropy of a microscopic homogeneous volume of matter. This purely optical technique makes use of an intensity-modulated and focused laser beam to periodically heat the surface of the sample tested. An interferometer is used to detect the thermal expansion. After describing the experimental setup, we explain the inversion scheme allowing the determination of the local thermal diffusivity from the periodic sample surface displacement map, as well as the crystallographic orientation and elastic anisotropy in the case of cubic materials. These parameters are measured with a spatial resolution of a few cubic micrometres.

  4. The effect of silicon crystallographic orientation on the formation of silicon nanoclusters during anodic electrochemical etching

    SciTech Connect

    Timokhov, D. F. Timokhov, F. P.

    2009-01-15

    Possible ways for increasing the photoluminescence quantum yield of porous silicon layers have been investigated. The effect of the anodization parameters on the photoluminescence properties for porous silicon layers formed on silicon substrates with different crystallographic orientations was studied. The average diameters for silicon nanoclusters are calculated from the photoluminescence spectra of porous silicon. The influence of the substrate crystallographic orientation on the photoluminescence quantum yield of porous silicon is revealed. A model explaining the effect of the substrate orientation on the photoluminescence properties for the porous silicon layers formed by anode electrochemical etching is proposed.

  5. Effect of Pr Valence State on Interfacial Structure and Electrical Properties of Pr Oxide/PrON/Ge Gate Stack Structure

    NASA Astrophysics Data System (ADS)

    Kato, Kimihiko; Sakashita, Mitsuo; Takeuchi, Wakana; Kondo, Hiroki; Nakatsuka, Osamu; Zaima, Shigeaki

    2011-04-01

    In this study, we investigated the valence state and chemical bonding state of Pr in a Pr oxide/PrON/Ge structure. We clarified the relationship between the valence state of Pr and the Pr oxide/Ge interfacial reaction using Pr oxide/Ge and Pr oxide/PrON/Ge samples. We found the formation of three Pr oxide phases in Pr oxide films; hexagonal Pr2O3 (h-Pr2O3) (Pr3+), cubic Pr2O3 (c-Pr2O3) (Pr3+), and c-PrO2 (Pr4+). We also investigated the effect of a nitride interlayer on the interfacial reaction in Pr oxide/Ge gate stacks. In a sample with a nitride interlayer (Pr oxide/PrON/Ge), metallic Pr-Pr bonds are also formed in the c-Pr2O3 film. After annealing in H2 ambient, the diffusion of Ge into Pr oxide is not observed in this sample. Pr-Pr bonds probably prevent the interfacial reaction and Ge oxide formation, considering that the oxygen chemical potential of this film is lower than that of a GeO2/Ge system. On the other hand, the rapid thermal oxidation (RTO) treatment terminates the O vacancies and defects in c-Pr2O3. As a result, c-PrO2 with tetravalent Pr is formed in the Pr oxide/PrON/Ge sample with RTO. In this sample, the leakage current density is effectively decreased in comparison with the sample without RTO. Hydrogen termination works effectively in Pr oxide/PrON/Ge samples with and without RTO, and we can achieve an interface state density of as low as 4 ×1011 eV-1·cm-2.

  6. ESO PR Highlights in 2000

    NASA Astrophysics Data System (ADS)

    2001-01-01

    At the beginning of the new millennium, ESO and its staff are facing the future with confidence. The four 8.2-m Unit Telescopes of the Very Large Telescope (VLT) are in great shape and the VLT Interferometer (VLTI) will soon have "first fringes". The intercontinental ALMA project is progressing well and concepts for extremely large optical/infrared telescopes are being studied. They can also look back at a fruitful and rewarding past year. Perhaps the most important, single development has been the rapid transition of the Very Large Telescope (VLT). From being a "high-tech project under construction" it has now become a highly proficient, world-class astronomical observatory. This trend is clearly reflected in ESO's Press Releases , as more and more front-line scientific results emerge from rich data obtained at this very efficient facility. There were also exciting news from several of the instruments at La Silla. At the same time, the ESO community may soon grow, as steps towards membership are being taken by various European countries. Throughout 2000, a total of 54 PR communications were made, with a large number of Press Photos and Video Clips, cf. the 2000 PR Index. Some of the ESO PR highlights may be accessed directly via the clickable image on the present page. ESO PR Photo 01/01 is also available in a larger (non-clickable) version [ JPEG: 566 x 566 pix - 112k]. It may be reproduced, if credit is given to the European Southern Observatory.

  7. Crystallographic preferred orientation and deformation of deep Earth minerals

    NASA Astrophysics Data System (ADS)

    Kaercher, Pamela Michelle

    This thesis aims to provide further insight into crystallographic preferred orientation (CPO) and deformation mechanisms active at high pressure. Preferred orientation of iron-rich magnesiowustite (Mg,Fe)O, a major mantle mineral phase, stishovite (SiO2), the high pressure polymorph of quartz that is likely present in the lower crust and mantle, and in NaMgF3 + NaCl, an analog system to lower mantle minerals MgSiO3 + MgO, have been examined with synchrotron X-ray diffraction while at high pressure in either a diamond anvil cell or a multianvil press. Magnesiowustite, (Mg0.08Fe0.88)O, and wustite, Fe0.94O, were compressed up to 37 GPa at ambient temperature in diamond anvil cells (DAC) at the Advanced Light Source (ALS). X-ray diffraction patterns were taken in situ in radial geometry in order to study the evolution of CPO through the cubic-to-rhombohedral phase transition. Under uniaxial stress in the DAC, cubic texture developed (i.e. {100} c planes aligned perpendicular to the compression direction). Variant selection of preferred orientation was observed immediately following the transition to the rhombohedral phase. Upon decompression in the DAC, FeO reverted back to cubic symmetry and the cubic texture reappeared, demonstrating that the transition is reversible and has texture memory. The crystal structure of the high pressure SiO2 polymorph stishovite has been studied in detail, but little is known about texture development during deformation, which provides information for understanding subduction of quartz-bearing crustal rocks into the mantle. Radial DAC experiments were done at the ALS and the Advanced Photon Source (APS) while collecting X-ray diffraction patterns in radial geometry to examine in situ development of CPO. Starting pressure in the sample chamber was still in the quartz stability field, and compression of quartz produced a weak texture, likely due to Dauphine twinning. Following compression of quartz into the stishovite stability field

  8. Control of crystallographic orientation in diamond synthesis through laser resonant vibrational excitation of precursor molecules

    PubMed Central

    Xie, Zhi Qiang; Bai, Jaeil; Zhou, Yun Shen; Gao, Yi; Park, Jongbok; Guillemet, Thomas; Jiang, Lan; Zeng, Xiao Cheng; Lu, Yong Feng

    2014-01-01

    Crystallographic orientations determine the optical, electrical, mechanical, and thermal properties of crystals. Control of crystallographic orientations has been studied by changing the growth parameters, including temperature, pressure, proportion of precursors, and surface conditions. However, molecular dynamic mechanisms underlying these controls remain largely unknown. Here we achieved control of crystallographic orientations in diamond growth through a joint experimental and theoretical study of laser resonant vibrational excitation of precursor molecules (ethylene). Resonant vibrational excitation of the ethylene molecules using a wavelength-tunable CO2 laser steers the chemical reactions and promotes proportion of intermediate oxide species, which results in preferential growth of {100}-oriented diamond films and diamond single crystals in open air. Quantum molecular dynamic simulations and calculations of chemisorption energies of radicals detected from our mass-spectroscopy experiment provide an in-depth understanding of molecular reaction mechanisms in the steering of chemical reactions and control of crystallographic orientations. This finding opens up a new avenue for controlled chemical vapor deposition of crystals through resonant vibrational excitations to steer surface chemistry. PMID:24694918

  9. A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error

    PubMed Central

    Read, Randy J.; McCoy, Airlie J.

    2016-01-01

    The crystallographic diffraction experiment measures Bragg intensities; crystallo­graphic electron-density maps and other crystallographic calculations in phasing require structure-factor amplitudes. If data were measured with no errors, the structure-factor amplitudes would be trivially proportional to the square roots of the intensities. When the experimental errors are large, and especially when random errors yield negative net intensities, the conversion of intensities and their error estimates into amplitudes and associated error estimates becomes nontrivial. Although this problem has been addressed intermittently in the history of crystallographic phasing, current approaches to accounting for experimental errors in macromolecular crystallography have numerous significant defects. These have been addressed with the formulation of LLGI, a log-likelihood-gain function in terms of the Bragg intensities and their associated experimental error estimates. LLGI has the correct asymptotic behaviour for data with large experimental error, appropriately downweighting these reflections without introducing bias. LLGI abrogates the need for the conversion of intensity data to amplitudes, which is usually performed with the French and Wilson method [French & Wilson (1978 ▸), Acta Cryst. A35, 517–525], wherever likelihood target functions are required. It has general applicability for a wide variety of algorithms in macromolecular crystallography, including scaling, characterizing anisotropy and translational noncrystallographic symmetry, detecting outliers, experimental phasing, molecular replacement and refinement. Because it is impossible to reliably recover the original intensity data from amplitudes, it is suggested that crystallographers should always deposit the intensity data in the Protein Data Bank. PMID:26960124

  10. Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures

    SciTech Connect

    McLean, Larry R.; Zhang, Ying; Degnen, William; Peppard, Jane; Cabel, Dasha; Zou, Chao; Tsay, Joseph T.; Subramaniam, Arun; Vaz, Roy J.; Li, Yi

    2010-10-28

    Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were found to be structurally different from the corresponding compounds initially identified by virtual screening.

  11. Transverse wobbling in ^{135}pr.

    PubMed

    Matta, J T; Garg, U; Li, W; Frauendorf, S; Ayangeakaa, A D; Patel, D; Schlax, K W; Palit, R; Saha, S; Sethi, J; Trivedi, T; Ghugre, S S; Raut, R; Sinha, A K; Janssens, R V F; Zhu, S; Carpenter, M P; Lauritsen, T; Seweryniak, D; Chiara, C J; Kondev, F G; Hartley, D J; Petrache, C M; Mukhopadhyay, S; Lakshmi, D Vijaya; Raju, M Kumar; Madhusudhana Rao, P V; Tandel, S K; Ray, S; Dönau, F

    2015-02-27

    A pair of transverse wobbling bands is observed in the nucleus ^{135}Pr. The wobbling is characterized by ΔI=1, E2 transitions between the bands, and a decrease in the wobbling energy confirms its transverse nature. Additionally, a transition from transverse wobbling to a three-quasiparticle band comprised of strong magnetic dipole transitions is observed. These observations conform well to results from calculations with the tilted axis cranking model and the quasiparticle rotor model. PMID:25768759

  12. Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition.

    PubMed

    Xie, Kefang; Song, Shuh Chyung; Spitalnik, Steven L; Wedekind, Joseph E

    2005-10-01

    The NNA7 Fab antibody fragment recognizes the human N-type blood-group antigen comprised of the N-terminal glycopeptide of glycophorin A (GPA). A mutant form of this Fab fragment, NNA7-G91S, exhibits markedly reduced antigen binding. To provide insight into how these Fab fragments recognize this glycopeptide antigen, the crystal structures of NNA7 and NNA7-G91S were solved and refined to 1.83 and 1.97 A resolution, respectively. Both molecules are composed of the same heavy (H) chain Fd fragment, but each contains a slightly different light (L) chain owing to the G91S substitution. Specifically, the G91S mutation pushes the backbone of the neighboring H chain away from complementarity-determining region 3 (CDR3) of the L-chain variable region, allowing an additional glycerol cryoprotectant molecule to enter the antigen-combining site near the putative location of O-linked glycosylation. Each Fab fragment also possesses a well defined 2-(N-morpholino)ethanesulfonic acid (MES) molecule trapped in its antigen-combining site, as well as a crystallographic symmetry-related molecule comprising an amino-acid sequence that is virtually identical to the N-terminus of GPA. The MES molecule interacts with the H-chain CDR in a manner reminiscent of antibody-carbohydrate complexes. These results suggest a model for recognition of the glycopeptide antigen that accounts for the deleterious effect of the G91S substitution. PMID:16204891

  13. Development of crystallographic-orientation-dependent internal strains around a fatigue-crack tip during overloading and underloading

    SciTech Connect

    Lee, S.Y.; Huang, E.-W.; Wu, W.; Liaw, P.K.; Paradowska, A.M.

    2013-05-15

    In-situ neutron diffraction was employed to directly measure the crystallographic-orientation-dependent (i.e. hkl) internal strains as a function of distance from the crack tip on the pre-cracked Hastelloy C-2000 compact-tension specimen. Both in-plane (IP) and through-thickness (TT) strain evolutions for various grain orientations were examined during tensile overloading and compressive underloading cycles. After overloading, underloading and their combination loadings were applied and unloaded, the significantly different (hkl) residual strain profiles were obtained in the vicinity of the crack tip. The load responses of the (200) grain orientation in both the IP and TT directions were more significant than those of any other orientations. It is suggested that the different orientation-dependent strain distributions around the crack tip are caused by the combined effects of elastic and plastic anisotropy of each (hkl) reflection upon loading and the subsequent development of residual stresses generated near the crack tip during unloading as a result of the plastic deformation. - Highlights: ► (hkl) strains are examined in situ using neutron diffraction. ► Distinct strain responses are developed around the crack tip under loading. ► The strain response of the (200) grain orientation is more significant. ► Possible mechanisms for the orientation-dependent strain responses are provided.

  14. Upper-greenschist facies intragrain deformation of albite in mylonitic meta-pegmatite and the influence of crystallographic anisotropy on microstructure formation

    NASA Astrophysics Data System (ADS)

    Eberlei, Tobias; Habler, Gerlinde; Grasemann, Bernhard; Abart, Rainer

    2014-12-01

    We studied the deformation behaviour of albite from Permian meta-pegmatite in Cretaceous upper-greenschist facies shear zones from the Austroalpine Matsch Unit in the Eastern Alps (Italy). Sodium-feldspars from these rocks provide excellent natural examples for studying mechanisms of intragranular deformation under mid-crustal conditions in grains with different angular relations between their (010) planes and the kinematic frame. The studied rocks were deformed at c. 500 °C in localized shear zones with well characterized top-W shear kinematics supposedly during the Cretaceous upper-greenschist facies tectonometamorphic event. Microstructural and chemical data suggest that crystallographic anisotropies in albite exert a strong control on microstructure formation and that albite primarily deformed by a combination of brittle fracturing, dissolution-precipitation and incipient crystal plasticity as a function of the orientation of the crystallographic anisotropy relative to the supposed shortening direction. Dissolution along discontinuities forming stylolites perpendicular to the shortening direction is associated with the precipitation of fine-grained albite with some compositional variability (Ab96-98 and Ab89-91) in cracks. New albite precipitates form aggregates with straight segments of high angle grain boundaries, nearly 120° dihedral angles and only a poor or no orientation relation to the hosting clast. Intragranular kinking is related to continuous lattice rotation of up to 15° by a misorientation axis close to albite [100] and the formation of subgrain boundaries with maximum misorientations of 7°. Synthetic microshear zones supposedly nucleated on pre-existing cracks, and are associated with formation of subgrain boundaries in shortening quadrants and cracks together with precipitates of potassium feldspar in extensional quadrants adjacent to the microshear zone. New microstructural and textural data from mylonitic Permian meta-pegmatites document

  15. Oxygen vacancy ordering in strontium doped rare earth cobaltate perovskites Ln{sub 1-x}Sr {sub x}CoO{sub 3-{delta}} (Ln = La, Pr and Nd; x > 0.60)

    SciTech Connect

    James, M. . E-mail: mja@ansto.gov.au; Tedesco, T.; Cassidy, D.J.; Withers, R.L.

    2005-06-15

    A family of Sr-doped perovskite compounds Ln{sub 1-x}Sr {sub x}CoO{sub 3-{delta}} (Ln = La{sup 3+}, Pr{sup 3+} and Nd{sup 3+}; x > 0.60), were prepared by sol-gel chemistry and reaction at 1100 deg. C under 1 atm of oxygen. This structural family has been shown to be present only for rare earth ions larger than Sm{sup 3+} and an upper limit of Sr{sup 2+} solubility in these phases was found to exist between x = 0.90 and 0.95. X-ray diffraction shows oxygen-deficient, simple cubic (Pm-3m) perovskite crystal structures. The combination of electron and powder neutron diffraction reveals that oxygen vacancy ordering occurs, leading to a tetragonal (P4/mmm) superstructure and a doubling of the basic perovskite unit along the crystallographic c-axis. No additional Ln{sup 3+}/Sr{sup 2+} cation ordering was observed.

  16. Hydrothermal alteration of silicate minerals: effects of crystallographic orientation and fluid saturation state

    NASA Astrophysics Data System (ADS)

    Pollet-Villard, M.; Daval, D.; Saldi, G.; Knauss, K.; Wild, B.; Guyot, F. J.; Cabié, M.; Fritz, B.

    2014-12-01

    Prediction of reaction kinetics of fluid/rock interactions represents a critical issue for several geological and engineering concerns. In the specific context of geothermal energy, the relative intensities of primary mineral leaching and secondary phase formation significantly affect porosity and permeability of the reservoir, thereby influencing its hydraulic performance and the efficiency of a geothermal site. Moreover, it is noteworthy that in general, the circulation of aqueous fluids induces only modest modifications of their chemical composition, which slightly deviate from an equilibrium state. Therefore, fluid rock interactions take place at close-to-equilibrium conditions, where the rate-affinity relations are poorly known and intensively debated [1]. To unravel these points, in the context of the geothermal power station of Soultz-sous-Forêts (Alsace, France), our strategy consists in (1) investigating the dissolution of the main cleavages of K-spar, one of the prevalent primary minerals in the reservoir, in order to decipher the impact of crystallographic orientation and microstructural surface modifications on the dissolution kinetics and (2) proposing a relation between K-spar dissolution rate and the Gibbs free energy of reaction (∆G) over a wide range of ∆G conditions. Our experimental work relies on a coupled approach which combines classical experiments of K-spar dissolution monitored by aqueous chemical analyses (ICPAES) and innovative techniques of nm to μm-scale characterization of solid surface (FIB-TEM, AFM, VSI) [2]. Our ongoing experiments evidence that K-spar dissolution is an anisotropic process, with faces (-1-1 1) dissolving up to ten times faster than the slowest (001) faces. The complex evolution of surface topography with the occurrence of etch pits is at odds with the shrinking core model implemented in most of reactive-transport codes, representing a possible cause of an apparent modification of silicate dissolution rate over

  17. An NMR crystallographic approach to monitoring cation substitution in the aluminophosphate STA-2.

    PubMed

    Seymour, Valerie R; Eschenroeder, Eike C V; Wright, Paul A; Ashbrook, Sharon E

    2015-02-01

    The substitution of the divalent cations Mg(2+) and Zn(2+) into the aluminophosphate (AlPO) framework of STA-2 has been studied using an "NMR crystallographic" approach, combining multinuclear solid-state NMR spectroscopy, X-ray diffraction and first-principles calculations. Although the AlPO framework itself is inherently neutral, the positive charge of the organocation template in an as-made material is usually balanced either by the coordination to the framework of anions from the synthesis solution, such as OH(-) or F(-), and/or by the substitution of aliovalent cations. However, the exact position and distribution of the substituted cations can be difficult to determine, but can have a significant impact upon the catalytic properties a material exhibits once calcined. For as-made Mg substituted STA-2, the positive charge of the organocation template is balanced by the substitution of Mg(2+) for Al(3+) and, where required, by hydroxide anions coordinated to the framework [27] Al MAS NMR spectra show that Al is present in both tetrahedral and five-fold coordination, with the latter dependent on the amount of substituted cations, and confirms the bridging nature of the hydroxyl groups, while high-resolution MQMAS spectra are able to show that Mg appears to preferentially substitute on the Al1 site. This conclusion is also supported by first-principles calculations. The calculations also show that (31)P chemical shifts depend not only on the topologically-distinct site in the SAT framework, but also on the number of next-nearest-neighbour Mg species, and the exact nature of the coordinated hydroxyls (whether the P atom forms part of a six-membered ring, P(OAl)2OH, where OH bridges between two Al atoms). The calculations demonstrate a strong correlation between the (31)P isotropic chemical shift and the average 〈P-O-M〉 bond angle. In contrast, for Zn substituted STA-2, both X-ray diffraction and NMR spectroscopy show less preference for substitution onto Al1 or

  18. Crystallographic Texture and Orientation Variants in Al2O3-Y3Al5O12 Directionally Solidified Eutectic Crystals

    NASA Technical Reports Server (NTRS)

    Frazer, Colleen S.; Dickey, Elizabeth C.; Sayir, Ali; Farmer, Serene (Technical Monitor)

    2001-01-01

    Eutectic rods of Al2O3 and Y3Al5O12 were grown by a laser-heated float zone method, and their microstructure and crystallographic texture were studied by scanning electron microscopy, electron backscattered diffraction and x-ray diffraction. The composites were found to be highly textured with two twin-related crystallographic orientation relationships between the phases. Electron backscattered diffraction was employed to determine the spatial distribution of the orientational variants within the samples and to define the crystallographic orientation of various microstructural features.

  19. A crystallographic approach to structural transitions in icosahedral viruses.

    PubMed

    Indelicato, Giuliana; Cermelli, Paolo; Salthouse, David G; Racca, Simone; Zanzotto, Giovanni; Twarock, Reidun

    2012-04-01

    Viruses with icosahedral capsids, which form the largest class of all viruses and contain a number of important human pathogens, can be modelled via suitable icosahedrally invariant finite subsets of icosahedral 3D quasicrystals. We combine concepts from the theory of 3D quasicrystals, and from the theory of structural phase transformations in crystalline solids, to give a framework for the study of the structural transitions occurring in icosahedral viral capsids during maturation or infection. As 3D quasicrystals are in a one-to-one correspondence with suitable subsets of 6D icosahedral Bravais lattices, we study systematically the 6D-analogs of the classical Bain deformations in 3D, characterized by minimal symmetry loss at intermediate configurations, and use this information to infer putative viral-capsid transition paths in 3D via the cut-and-project method used for the construction of quasicrystals. We apply our approach to the Cowpea Chlorotic Mottle virus (CCMV) and show that the putative transition path between the experimentally observed initial and final CCMV structures is most likely to preserve one threefold axis. Our procedure suggests a general method for the investigation and prediction of symmetry constraints on the capsids of icosahedral viruses during structural transitions, and thus provides insights into the mechanisms underlying structural transitions of these pathogens. PMID:21611828

  20. Oxycodone/Naloxone PR: A Review in Severe Refractory Restless Legs Syndrome.

    PubMed

    Frampton, James E

    2015-06-01

    An oral, fixed-dose combination of prolonged-release (PR) oxycodone with PR naloxone (Targin(®), Targiniq(®), Targinact(®); hereafter referred to as oxycodone/naloxone PR) is approved in Europe for the second-line symptomatic treatment of patients with severe to very severe idiopathic restless legs syndrome (RLS), after failure of dopaminergic therapy. Coadministration of naloxone represents a targeted approach to counteracting opioid-induced bowel dysfunction without compromising therapeutic efficacy; because of its very low oral bioavailability, naloxone blocks the action of oxycodone at opioid receptors locally in the gut. The efficacy of oxycodone/naloxone PR in patients with severe RLS inadequately controlled by previous (mainly dopaminergic) treatment has been demonstrated in RELOXYN, a 12-week, randomized, double-blind study with a 40-week open-label extension. In this pivotal study, oxycodone/naloxone PR significantly improved RLS symptoms compared with placebo from week 2 onwards; a beneficial effect of oxycodone/naloxone PR was maintained through 1 year of treatment. Furthermore, improvements in RLS symptoms in oxycodone/naloxone PR recipients were accompanied by similarly sustained improvements in disease-specific quality of life and subjective sleep variables. Oxycodone/naloxone PR was generally well tolerated, with a treatment-related adverse event profile (e.g. gastrointestinal disorders, CNS disorders, fatigue and pruritus) that was consistent with that expected for opioid therapy. Notably, there were no confirmed cases of augmentation among oxycodone/naloxone PR recipients throughout the course of the study. Results from the well-designed RELOXYN trial have thus demonstrated the value of oxycodone/naloxone PR as a second-line therapy for severe refractory RLS; further investigation of this combination product as a first-line treatment for severe RLS is now warranted. PMID:26135898

  1. Crystallographic and magnetic structure of the perovskite-type compound BaFeO2.5: unrivaled complexity in oxygen vacancy ordering.

    PubMed

    Clemens, Oliver; Gröting, Melanie; Witte, Ralf; Perez-Mato, J Manuel; Loho, Christoph; Berry, Frank J; Kruk, Robert; Knight, Kevin S; Wright, Adrian J; Hahn, Horst; Slater, Peter R

    2014-06-16

    We report here on the characterization of the vacancy-ordered perovskite-type structure of BaFeO2.5 by means of combined Rietveld analysis of powder X-ray and neutron diffraction data. The compound crystallizes in the monoclinic space group P2(1)/c [a = 6.9753(1) Å, b = 11.7281(2) Å, c = 23.4507(4) Å, β = 98.813(1)°, and Z = 28] containing seven crystallographically different iron atoms. The coordination scheme is determined to be Ba7(FeO4/2)1(FeO3/2O1/1)3(FeO5/2)2(FeO6/2)1 = Ba7Fe([6])1Fe([5])2Fe([4])4O17.5 and is in agreement with the (57)Fe Mössbauer spectra and density functional theory based calculations. To our knowledge, the structure of BaFeO2.5 is the most complicated perovskite-type superstructure reported so far (largest primitive cell, number of ABX2.5 units per unit cell, and number of different crystallographic sites). The magnetic structure was determined from the powder neutron diffraction data and can be understood in terms of "G-type" antiferromagnetic ordering between connected iron-containing polyhedra, in agreement with field-sweep and zero-field-cooled/field-cooled measurements. PMID:24901981

  2. Expression, purification and preliminary crystallographic characterization of FlhF from Bacillus subtilis

    SciTech Connect

    Bange, Gert; Petzold, Georg; Wild, Klemens; Sinning, Irmgard

    2007-05-01

    Preliminary crystallographic data are reported for the third SRP GTPase FlhF from Bacillus subtilis. The Gram-positive bacterium Bacillus subtilis contains three proteins belonging to the signal recognition particle (SRP) type GTPase family. The well characterized signal sequence-binding protein SRP54 and the SRP receptor protein FtsY are universally conserved components of the SRP system of protein transport. The third member, FlhF, has been implicated in the placement and assembly of polar flagella. This article describes the overexpression and preliminary X-ray crystallographic analysis of an FlhF fragment that corresponds to the well characterized GTPase domains in SRP54 and FtsY. Three crystal forms are reported with either GDP or GMPPNP and diffract to a resolution of about 3 Å.

  3. Crystallographic dependence of CO activation on cobalt catalysts: HCP versus FCC.

    PubMed

    Liu, Jin-Xun; Su, Hai-Yan; Sun, Da-Peng; Zhang, Bing-Yan; Li, Wei-Xue

    2013-11-01

    Identifying the structure sensitivity of catalysts in reactions, such as Fischer-Tropsch synthesis from CO and H2 over cobalt catalysts, is an important yet challenging issue in heterogeneous catalysis. Based on a first-principles kinetic study, we find for the first time that CO activation on hexagonal close-packed (HCP) Co not only has much higher intrinsic activity than that of face centered-cubic (FCC) Co but also prefers a different reaction route, i.e., direct dissociation with HCP Co but H-assisted dissociation on the FCC Co. The origin is identified from the formation of various denser yet favorable active sites on HCP Co not available for FCC Co, due to their distinct crystallographic structure and morphology. The great dependence of the activity on the crystallographic structure and morphology of the catalysts revealed here may open a new avenue for better, stable catalysts with maximum mass-specific reactivity. PMID:24147726

  4. Growth and crystallographic feature-dependent characterization of spinel zinc ferrite thin films by RF sputtering

    PubMed Central

    2013-01-01

    ZnFe2O4 (ZFO) thin films exhibiting varying crystallographic features ((222)-epitaxially, (400)-epitaxially, and randomly oriented films) were grown on various substrates by radio-frequency magnetron sputtering. The type of substrate used profoundly affected the surface topography of the resulting ZFO films. The surface of the ZFO (222) epilayer was dense and exhibited small rectangular surface grains; however, the ZFO (400) epilayer exhibited small grooves. The surface of the randomly oriented ZFO thin film exhibited distinct three-dimensional island-like grains that demonstrated considerable surface roughness. Magnetization-temperature curves revealed that the ZFO thin films exhibited a spin-glass transition temperature of approximately 40 K. The crystallographic orientation of the ZFO thin films strongly affected magnetic anisotropy. The ZFO (222) epitaxy exhibited the strongest magnetic anisotropy, whereas the randomly oriented ZFO thin film exhibited no clear magnetic anisotropy. PMID:24354428

  5. Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase

    PubMed Central

    Jeudy, Sandra; Coutard, Bruno; Lebrun, Régine; Abergel, Chantal

    2005-01-01

    The complete sequence of the largest known double-stranded DNA virus, Acanthamoeba polyphaga mimivirus, has recently been determined [Raoult et al. (2004 ▶), Science, 306, 1344–1350] and revealed numerous genes not expected to be found in a virus. A comprehensive structural and functional study of these gene products was initiated [Abergel et al. (2005 ▶), Acta Cryst. F61, 212–215] both to better understand their role in the virus physiology and to obtain some clues to the origin of DNA viruses. Here, the preliminary crystallographic analysis of the viral nucleoside diphosphate kinase protein is reported. The crystal belongs to the cubic space group P213, with unit-cell parameter 99.425 Å. The self-rotation function confirms that there are two monomers per asymmetric unit related by a twofold non-crystallographic axis and that the unit cell thus contains four biological entities. PMID:16511098

  6. Novel Kac-Moody-type affine extensions of non-crystallographic Coxeter groups

    NASA Astrophysics Data System (ADS)

    Dechant, Pierre-Philippe; Bœhm, Céline; Twarock, Reidun

    2012-07-01

    Motivated by recent results in mathematical virology, we present novel asymmetric {Z}[\\tau ]-integer-valued affine extensions of the non-crystallographic Coxeter groups H2, H3 and H4 derived in a Kac-Moody-type formalism. In particular, we show that the affine reflection planes which extend the Coxeter group H3 generate (twist) translations along two-, three- and five-fold axes of icosahedral symmetry, and we classify these translations in terms of the Fibonacci recursion relation applied to different start values. We thus provide an explanation of previous results concerning affine extensions of icosahedral symmetry in a Coxeter group context, and extend this analysis to the case of the non-crystallographic Coxeter groups H2 and H4. These results will enable new applications of group theory in physics (quasicrystals), biology (viruses) and chemistry (fullerenes).

  7. Preferred crystallographic orientation in the ice I ← II transformation and the flow of ice II

    USGS Publications Warehouse

    Bennett, K.; Wenk, H.-R.; Durham, W.B.; Stern, L.A.; Kirby, S.H.

    1997-01-01

    The preferred crystallographic orientation developed during the ice I ← II transformation and during the plastic flow of ice II was measured in polycrystalline deuterium oxide (D2O) specimens using low-temperature neutron diffraction. Samples partially transformed from ice I to II under a non-hydrostatic stress developed a preferred crystallographic orientation in the ice II. Samples of pure ice II transformed from ice I under a hydrostatic stress and then when compressed axially, developed a strong preferred orientation of compression axes parallel to (1010). A match to the observed preferred orientation using the viscoplastic self-consistent theory was obtained only when (1010) [0001] was taken as the predominant slip system in ice II.

  8. Finding non-crystallographic symmetry in density maps of macromolecular structures.

    PubMed

    Terwilliger, Thomas C

    2013-09-01

    The internal symmetry of a macromolecule is both an important aspect of its function and a useful feature in obtaining a structure by X-ray crystallography and other techniques. A method is presented for finding internal symmetry and other non-crystallographic symmetry in a structure based on patterns of density in a density map for that structure. Regions in map that are similar are identified by cutting out a sphere of density from a region that has high local variation and using an FFT-based correlation search to find other regions that match. The relationships among correlated regions are then refined to maximize their correlations and are found to accurately represent non-crystallographic symmetry in the map. PMID:23881095

  9. Crystallographic Analysis of Nucleation at Hardness Indentations in High-Purity Aluminum

    NASA Astrophysics Data System (ADS)

    Xu, Chaoling; Zhang, Yubin; Lin, Fengxiang; Wu, Guilin; Liu, Qing; Juul Jensen, Dorte

    2016-08-01

    Nucleation at Vickers hardness indentations has been studied in high-purity aluminum cold-rolled 12 pct. Electron channeling contrast was used to measure the size of the indentations and to detect nuclei, while electron backscattering diffraction was used to determine crystallographic orientations. It is found that indentations are preferential nucleation sites. The crystallographic orientations of the deformed grains affect the hardness and the nucleation potentials at the indentations. Higher hardness gives increased nucleation probabilities. Orientation relationships between nuclei developed at different indentations within one original grain are analyzed and it is found that the orientation distribution of the nuclei is far from random. It is suggested that it relates to the orientations present near the indentation tips which in turn depend on the orientation of the selected grain in which they form. Finally, possible nucleation mechanisms are briefly discussed.

  10. The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN compiler

    NASA Technical Reports Server (NTRS)

    Stewart, J. M.; Kruger, G. J.; Ammon, H. L.; Dickinson, C.; Hall, S. R.

    1972-01-01

    A manual is presented for the use of a library of crystallographic programs. This library, called the X-ray system, is designed to carry out the calculations required to solve the structure of crystals by diffraction techniques. It has been implemented at the University of Maryland on the Univac 1108. It has, however, been developed and run on a variety of machines under various operating systems. It is considered to be an essentially machine independent library of applications programs. The report includes definition of crystallographic computing terms, program descriptions, with some text to show their application to specific crystal problems, detailed card input descriptions, mass storage file structure and some example run streams.

  11. Microstructure, crystallographic texture and mechanical properties of friction stir welded AA2017A

    SciTech Connect

    Ahmed, M.M.Z.; Wynne, B.P.; Rainforth, W.M.; Threadgill, P.L.

    2012-02-15

    In this study a thick section (20 mm) friction stir welded AA2017A-T451 has been characterized in terms of microstructure, crystallographic texture and mechanical properties. For microstructural analysis both optical and scanning electron microscopes have been used. A detailed crystallographic texture analysis has been carried out using the electron back scattering diffraction technique. Crystallographic texture has been examined in both shoulder and probe affected regions of the weld NG. An entirely weak texture is observed at the shoulder affected region which is mainly explained by the effect of the sequential multi pass deformation experienced by both tool probe and tool shoulder. The texture in the probe dominated region at the AS side of the weld is relatively weak but still assembles the simple shear texture of FCC metals with B/B{sup Macron} and C components existing across the whole map. However, the texture is stronger at the RS than at the AS of the weld, mainly dominated byB/B{sup Macron} components and with C component almost absent across the map. An alternating bands between (B) components and (B{sup Macron }) component are observed only at the AS side of the weld. - Highlights: Black-Right-Pointing-Pointer Detailed investigation of microstructure and crystallographic texture. Black-Right-Pointing-Pointer The grain size is varied from the top to the bottom of the NG. Black-Right-Pointing-Pointer An entirely weak texture is observed at the shoulder affected region. Black-Right-Pointing-Pointer The texture in the probe affected region is dominated by simple shear texture.

  12. Segregation anisotropy of Sn on different crystallographic orientation surfaces of coarse-grained Zircaloy-4

    NASA Astrophysics Data System (ADS)

    Xie, Shijing; Zhou, Bangxin; Chen, Chuanming; Wang, Boyang; Jiang, Dong

    2016-02-01

    X-ray photoelectron spectroscopy (XPS) technique was utilized to study the correlation between the tendency of Sn surface segregation and the crystallographic orientation of grain surface in coarse-grained (0.2-0.8 mm in diameter) Zircaloy-4 specimen. The results indicated that the intensity of Sn surface segregation was in an order of (0001) < (1 bar 2 1 bar 0) ≈ (01 1 bar 0) , and it was in agreement with the prediction from bond-breaking theory.

  13. Crystallographically oriented Zn nanocrystals formed in ZnO by Mn{sup +}-implantation

    SciTech Connect

    Li, Y. J.; Zhang, B.; Lu, W.; Wang, Y.; Zou, J.

    2008-09-29

    The nanostructural characteristics of ZnO implanted with Mn{sup +} to doses ranging from 1x10{sup 15} to 1x10{sup 17} cm{sup -2} are systematically studied for both as-implanted and postannealed cases. The detailed structural characterizations confirmed that the Mn{sup +} implantation and postannealing result in (1) the formation of crystallographically orientated Zn nanocrystals in the ZnO matrix and (2) Mn atoms occupy the Zn sites in ZnO.

  14. Validation of crystallographic models containing TLS or other descriptions of anisotropy

    PubMed Central

    Zucker, Frank; Champ, P. Christoph; Merritt, Ethan A.

    2010-01-01

    The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter-domain and other large-scale motions implied by the crystal structure. In either case it is desirable to validate that the crystallographic model, including the TLS description of anisotropy, conforms to our best understanding of protein structures and their modes of flexibility. A set of validation tests has been implemented that can be integrated into ongoing crystallographic refinement or run afterwards to evaluate a previously refined structure. In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. Automated validation checks have been added to the PARVATI and TLSMD web servers and incorporated into the CCP4i user interface. PMID:20693688

  15. Crystallographic preferred orientation of akimotoite and seismic anisotropy of Tonga slab.

    PubMed

    Shiraishi, Rei; Ohtani, Eiji; Kanagawa, Kyuichi; Shimojuku, Akira; Zhao, Dapeng

    2008-10-01

    The mineral akimotoite, ilmenite-structured MgSiO(3), exists at the bottom of the Earth's mantle transition zone and within the uppermost lower mantle, especially under low-temperature conditions. Akimotoite is thought to be a major constituent of the harzburgite layer of subducting slabs, and the most anisotropic mineral in the mantle transition zone. It has been predicted that if akimotoite crystals are preferentially oriented by plastic deformation, a cold subducted slab would be extremely anisotropic. However, there have been no studies of crystallographic preferred orientations and very few reports of plastic deformation experiments for MgSiO(3) ilmenite. Here we present plastic deformation experiments on polycrystalline akimotoite, which were conducted at confining pressures of 20-22 GPa and temperatures of 1,000-1,300 degrees C. We found a change in crystallographic preferred orientation pattern of akimotoite with temperature, where the c-axis maximum parallel to the compression direction develops at high temperature, whereas the c axes are preferentially oriented parallel to the shear direction or perpendicular to the compression direction at lower temperature. The previously reported difference in compressional-wave seismic anisotropy between the northern and southern segments of the Tonga slab at depths of the mantle transition zone can conceivably be attributed to the difference in the crystallographic preferred orientation pattern of akimotoite at varying temperature within the slab. PMID:18833278

  16. Model-building strategies for low-resolution X-ray crystallographic data

    SciTech Connect

    Karmali, Anjum M.; Blundell, Tom L.; Furnham, Nicholas

    2009-02-01

    Interpretation of low-resolution X-ray crystallographic data can prove to be a difficult task. The challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 Å is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.

  17. High-resolution neutron crystallographic studies of the hydration of the coenzyme cob(II)alamin

    SciTech Connect

    Jogl, Gerwald; Wang, Xiaoping; Mason, Sax A.; Kovalevsky, Andrey; Mustyakimov, Marat; Fisher, Zöe; Hoffman, Christina; Kratky, Christoph; Langan, Paul

    2011-06-01

    High-resolution crystallographic studies of the hydration of the coenzyme cob(II)alamin have provided hydrogen-bond parameters of unprecedented accuracy for a biomacromolecule. The hydration of the coenzyme cob(II)alamin has been studied using high-resolution monochromatic neutron crystallographic data collected at room temperature to a resolution of 0.92 Å on the original D19 diffractometer with a prototype 4° × 64° detector at the high-flux reactor neutron source run by the Institute Laue–Langevin. The resulting structure provides hydrogen-bonding parameters for the hydration of biomacromolecules to unprecedented accuracy. These experimental parameters will be used to define more accurate force fields for biomacromolecular structure refinement. The presence of a hydrophobic bowl motif surrounded by flexible side chains with terminal functional groups may be significant for the efficient scavenging of ligands. The feasibility of extending the resolution of this structure to ultrahigh resolution was investigated by collecting time-of-flight neutron crystallographic data during commissioning of the TOPAZ diffractometer with a prototype array of 14 modular 2° × 21° detectors at the Spallation Neutron Source run by Oak Ridge National Laboratory.

  18. Manipulating Crystallographic Texture of Sn Coatings by Optimization of Electrodeposition Process Conditions to Suppress Growth of Whiskers

    NASA Astrophysics Data System (ADS)

    Jagtap, Piyush; Kumar, Praveen

    2015-04-01

    The effects of two major electrodeposition process conditions, electrolyte bath temperature and current density, on the microstructure and crystallographic texture of pure tin coatings on brass and, ultimately, on the extent of whisker formation have been examined. The grain size of the deposited coatings increased with increasing electrolyte bath temperature and current density, which significantly affected the dominant texture: (211) or (420) was the dominant texture at low current densities whereas, depending on deposition temperature, (200) or (220) became the dominant texture at high current densities. After deposition, coatings were subjected to different environmental conditions, for example isothermal aging (room temperature, 50°C, or 150°C) for up to 90 days and thermal cycling between -25°C and 85°C for 100 cycles, and whisker growth was studied. The Sn coatings with low Miller index planes, for example (200) and (220), and with moderate aging temperature were more prone to whiskering than coating with high Miller index planes, for example (420), and high aging temperature. A processing route involving the optimum combination of current density and deposition temperature is proposed for suppressing whisker growth.

  19. Effect of Local Crystallographic Texture on the Fissure Formation During Charpy Impact Testing of Low-Carbon Steel

    NASA Astrophysics Data System (ADS)

    Ghosh, Abhijit; Patra, Sudipta; Chatterjee, Arya; Chakrabarti, Debalay

    2016-06-01

    The severity of the formation of fissures (also known as splitting or delamination) on the fracture surface of Charpy impact-tested samples of a low-carbon steel has been found to increase with the decrease in finish rolling temperature [1093 K to 923 K (820 °C to 650 °C)]. Combined scanning electron microscopy and electron back-scattered diffraction study revealed that crystallographic texture was the prime factor responsible for the fissure formation. Through-thickness texture band composed of cube [Normal Direction (ND)║<001>] and gamma [ND║<111>] orientations developed during the inter-critical rolling treatment. Strain incompatibility between these two texture bands causes fissure cracking on the main fracture plane. A new approach based on the angle between {001} planes of neighboring crystals has been employed in order to estimate the `effective grain size,' which is used to determine the cleavage fracture stress on different planes of a sample. The severity of fissure formation was found to be directly related to the difference in cleavage fracture stress between the `main fracture plane' and `fissure plane.' Clustering of ferrite grains having cube texture promoted the fissure crack propagation along the transverse `fissure plane,' by increasing the `effective grain size' and decreasing the cleavage fracture stress on that plane.

  20. Flexibility in the insulin receptor ectodomain enables docking of insulin in crystallographic conformation observed in a hormone-bound microreceptor.

    PubMed

    Vashisth, Harish

    2014-01-01

    Insulin binding to the insulin receptor (IR) is the first key step in initiating downstream signaling cascades for glucose homeostasis in higher organisms. The molecular details of insulin recognition by IR are not yet completely understood, but a picture of hormone/receptor interactions at one of the epitopes (Site 1) is beginning to emerge from recent structural evidence. However, insulin-bound structures of truncated IR suggest that crystallographic conformation of insulin cannot be accommodated in the full IR ectodomain due to steric overlap of insulin with the first two type III fibronectin domains (F1 and F2), which are contributed to the insulin binding-pocket by the second subunit in the IR homodimer. A conformational change in the F1-F2 pair has thus been suggested. In this work, we present an all-atom structural model of complex of insulin and the IR ectodomain, where no structural overlap of insulin with the receptor domains (F1 and F2) is observed. This structural model was arrived at by flexibly fitting parts of our earlier insulin/IR all-atom model into the simulated density maps of crystallized constructs combined with conformational sampling from apo-IR solution conformations. Importantly, our experimentally-consistent model helps rationalize yet unresolved Site. PMID:25309993

  1. Microstructure and Crystallographic Texture Evolution During the Friction-Stir Processing of a Precipitation-Hardenable Aluminum Alloy

    NASA Astrophysics Data System (ADS)

    Nadammal, Naresh; Kailas, Satish V.; Szpunar, Jerzy; Suwas, Satyam

    2015-05-01

    Friction-stir processing (FSP) has been proven as a successful method for the grain refinement of high-strength aluminum alloys. The most important attributes of this process are the fine-grain microstructure and characteristic texture, which impart suitable properties in the as-processed material. In the current work, FSP of the precipitation-hardenable aluminum alloy 2219 has been carried out and the consequent evolution of microstructure and texture has been studied. The as-processed materials were characterized using electron back-scattered diffraction, x-ray diffraction, and electron probe microanalysis. Onion-ring formation was observed in the nugget zone, which has been found to be related to the precipitation response and crystallographic texture of the alloy. Texture development in the alloy has been attributed to the combined effect of shear deformation and dynamic recrystallization. The texture was found heterogeneous even within the nugget zone. A microtexture analysis revealed the dominance of shear texture components, with C component at the top of nugget zone and the B and A2* components in the middle and bottom. The bulk texture measurement in the nugget zone revealed a dominant C component. The development of a weaker texture along with the presence of some large particles in the nugget zone indicates particle-stimulated nucleation as the dominant nucleation mechanism during FSP. Grain growth follows the Burke and Turnbull mechanism and geometrical coalescence.

  2. Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

    PubMed

    Mörschel, Philipp; Schmidt, Martin U

    2015-01-01

    A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies. PMID:25537386

  3. Similar quartz crystallographic textures in rocks of continental earth's crust (by neutron diffraction data): I. Quartz textures in monomineral rocks

    NASA Astrophysics Data System (ADS)

    Nikitin, A. N.; Ivankina, T. I.; Ullemeyer, K.; Vasin, R. N.

    2008-09-01

    Quartz crystallographic textures in different rocks have been investigated by neutron diffraction. Various types of crystallographic textures of quartz-bearing mineral associations in monomineral and multiphase rocks from a representative collection of samples have been revealed and classified. Experimental investigations have been performed on special neutron texture diffractometers designed at the Frank Laboratory of Neutron Physics and mounted in the seventh channel of the IBR-2 reactor at the Joint Institute for Nuclear Research (Dubna).

  4. Similar quartz crystallographic textures in rocks of continental earth's crust (by neutron diffraction data): I. Quartz textures in monomineral rocks

    SciTech Connect

    Nikitin, A. N. Ivankina, T. I.; Ullemeyer, K.; Vasin, R. N.

    2008-09-15

    Quartz crystallographic textures in different rocks have been investigated by neutron diffraction. Various types of crystallographic textures of quartz-bearing mineral associations in monomineral and multiphase rocks from a representative collection of samples have been revealed and classified. Experimental investigations have been performed on special neutron texture diffractometers designed at the Frank Laboratory of Neutron Physics and mounted in the seventh channel of the IBR-2 reactor at the Joint Institute for Nuclear Research (Dubna).

  5. The PR status of the originating cell of ER/PR-negative mouse mammary tumors.

    PubMed

    Dong, J; Zhao, W; Shi, A; Toneff, M; Lydon, J; So, D; Li, Y

    2016-08-01

    Progesterone receptor (PR) is usually co-localized with estrogen receptor (ER) in normal mammary cells. It is not known whether ER/PR-negative human breast cancer arises from an ER/PR-negative cell or from an ER/PR-positive cell that later lost ER/PR. Using intraductal injection of a lentivirus to deliver both an oncogene (ErbB2) and a floxed green fluorescent protein (GFP) in PR(Cre/+)mice, whose Cre gene is under the control of the PR promoter, we were able to trace the PR status of the infected cells as they progressed to cancer. We found that the resulting early lesions stained negative for PR in most of the cells and usually retained GFP. The resulting tumors lacked ER and PR, and 75% (15/20) of them retained the GFP signal in all tumor cells, suggesting PR was never expressed throughout the evolution of a majority of these tumors. In conclusion, our data demonstrate that ErbB2-initiated ER/PR-negative mammary tumors primarily originate from the subset of the mammary epithelium that is negative for PR and probably ER as well. These findings also provide an explanation for why antihormonal therapy fails to prevent ER-negative breast cancers. PMID:26640140

  6. Manipulating Ce Valence in RE2Fe14B Tetragonal Compounds by La-Ce Co-doping: Resultant Crystallographic and Magnetic Anomaly

    PubMed Central

    Jin, Jiaying; Zhang, Yujing; Bai, Guohua; Qian, Zeyu; Wu, Chen; Ma, Tianyu; Shen, Baogen; Yan, Mi

    2016-01-01

    Abundant and low-cost Ce has attracted considerable interest as a prospective alternative for those critically relied Nd/Pr/Dy/Tb in the 2:14:1-type permanent magnets. The (Nd, Ce)2Fe14B compound with inferior intrinsic magnetic properties to Nd2Fe14B, however, cannot provide an equivalent magnetic performance. Since Ce valence is sensitive to local steric environment, manipulating it towards the favorable trivalent state provides a way to enhance the magnetic properties. Here we report that such a desirable Ce valence can be induced by La-Ce co-doping into [(Pr, Nd)1−x(La, Ce)x]2.14Fe14B (0 ≤ x ≤ 0.5) compounds via strip casting. As verified by X-ray photoelectron spectroscopy results, Ce valence shifts towards the magnetically favorable Ce3+ state in the composition range of x > 0.3, owing to the co-doping of large radius La3+ into 2:14:1 phase lattice. As a result, both crystallographic and magnetic anomalies are observed in the same vicinity of x = 0.3, above which lattice parameters a and c, and saturation magnetization Ms increase simultaneously. Over the whole doping range, 2:14:1 tetragonal structure forms and keeps stable even at 1250 K. This finding may shed light on obtaining a favorable Ce valence via La-Ce co-doping, thus maintaining the intrinsic magnetic properties of 2:14:1-type permanent magnets. PMID:27457408

  7. Manipulating Ce Valence in RE2Fe14B Tetragonal Compounds by La-Ce Co-doping: Resultant Crystallographic and Magnetic Anomaly.

    PubMed

    Jin, Jiaying; Zhang, Yujing; Bai, Guohua; Qian, Zeyu; Wu, Chen; Ma, Tianyu; Shen, Baogen; Yan, Mi

    2016-01-01

    Abundant and low-cost Ce has attracted considerable interest as a prospective alternative for those critically relied Nd/Pr/Dy/Tb in the 2:14:1-type permanent magnets. The (Nd, Ce)2Fe14B compound with inferior intrinsic magnetic properties to Nd2Fe14B, however, cannot provide an equivalent magnetic performance. Since Ce valence is sensitive to local steric environment, manipulating it towards the favorable trivalent state provides a way to enhance the magnetic properties. Here we report that such a desirable Ce valence can be induced by La-Ce co-doping into [(Pr, Nd)1-x(La, Ce)x]2.14Fe14B (0 ≤ x ≤ 0.5) compounds via strip casting. As verified by X-ray photoelectron spectroscopy results, Ce valence shifts towards the magnetically favorable Ce(3+) state in the composition range of x > 0.3, owing to the co-doping of large radius La(3+) into 2:14:1 phase lattice. As a result, both crystallographic and magnetic anomalies are observed in the same vicinity of x = 0.3, above which lattice parameters a and c, and saturation magnetization Ms increase simultaneously. Over the whole doping range, 2:14:1 tetragonal structure forms and keeps stable even at 1250 K. This finding may shed light on obtaining a favorable Ce valence via La-Ce co-doping, thus maintaining the intrinsic magnetic properties of 2:14:1-type permanent magnets. PMID:27457408

  8. Manipulating Ce Valence in RE2Fe14B Tetragonal Compounds by La-Ce Co-doping: Resultant Crystallographic and Magnetic Anomaly

    NASA Astrophysics Data System (ADS)

    Jin, Jiaying; Zhang, Yujing; Bai, Guohua; Qian, Zeyu; Wu, Chen; Ma, Tianyu; Shen, Baogen; Yan, Mi

    2016-07-01

    Abundant and low-cost Ce has attracted considerable interest as a prospective alternative for those critically relied Nd/Pr/Dy/Tb in the 2:14:1-type permanent magnets. The (Nd, Ce)2Fe14B compound with inferior intrinsic magnetic properties to Nd2Fe14B, however, cannot provide an equivalent magnetic performance. Since Ce valence is sensitive to local steric environment, manipulating it towards the favorable trivalent state provides a way to enhance the magnetic properties. Here we report that such a desirable Ce valence can be induced by La-Ce co-doping into [(Pr, Nd)1‑x(La, Ce)x]2.14Fe14B (0 ≤ x ≤ 0.5) compounds via strip casting. As verified by X-ray photoelectron spectroscopy results, Ce valence shifts towards the magnetically favorable Ce3+ state in the composition range of x > 0.3, owing to the co-doping of large radius La3+ into 2:14:1 phase lattice. As a result, both crystallographic and magnetic anomalies are observed in the same vicinity of x = 0.3, above which lattice parameters a and c, and saturation magnetization Ms increase simultaneously. Over the whole doping range, 2:14:1 tetragonal structure forms and keeps stable even at 1250 K. This finding may shed light on obtaining a favorable Ce valence via La-Ce co-doping, thus maintaining the intrinsic magnetic properties of 2:14:1-type permanent magnets.

  9. Biological control of crystallographic architecture: hierarchy and co-alignment parameters.

    PubMed

    Maier, B J; Griesshaber, E; Alexa, P; Ziegler, A; Ubhi, H S; Schmahl, W W

    2014-09-01

    Mytilus edulis prismatic calcite and nacre layers exhibit a crystallographic structural hierarchy which differs substantially from the morphological hierarchy. This makes these biomaterials fundamentally different from classical crystalline materials. Morphological building units are defined by their surrounding organic matrix membranes, e.g. calcite fibers or nacre tablets. The crystallographic building units are defined by crystallographic co-orientation. Electron backscatter diffraction quantitatively shows how crystallographic co-orientation propagates across matrix membranes to form highly co-oriented low-mosaic composite-crystal grains, i.e. calcite fiber bundles with an internal mosaic spread of 0.5° full width at half maximum (FWHM) or nacre towergrains with an internal mosaic spread of 2° FWHM. These low-mosaic composite crystals form much larger composite-crystal supergrains, which exhibit a high mosaicity due to misorientations of their constituting calcite fiber bundles or nacre towergrains. For the aragonite layer these supergrains nucleate in one of three aragonite {110} twin orientations; as a consequence the nacre layer exhibits a twin-domain structure, i.e. the boundaries of adjacent supergrains exhibit a high probability for misorientations around the aragonite c-axis with an angle near 63.8°. Within the supergrains, the constituting towergrains exhibit a high probability for misorientations around the aragonite a-axis with a geometric mean misorientation angle of 10.6°. The calcite layer is composed of a single composite-crystal supergrain on at least the submillimeter length scale. Mutual misorientations of adjacent fiber bundles within the calcite supergrain are mainly around the calcite c-axis with a geometric mean misorientation angle of 9.4°. The c-axis is not parallel to the long axis of the fibers but rather to the (107) plane normal. The frequency distribution for the occurrence of misorientation angles within supergrains reflects

  10. ESO PR Highlights in 2003

    NASA Astrophysics Data System (ADS)

    2004-01-01

    Among the many astronomical highlights of 2003, the Transit of Mercury certainly attracted great attention as shown by the record number of hits the ESO web page received on that day. But this was a mere rehearsal of an even bigger event we will enjoy in 2004: the Venus Transit. ESO, in partnership with several institutions, is organising a major educational event in connection with it. During 2003, the ESO Educational Office was also involved in various other programmes. They included the web-based "Catch a Star!" and the "Physics and Life" projects, organised with EC sponsorship in connection with the 2003 European Science and Technology Week. The ALMA project, an European-North American collaboration to build an array of 64 12-m submillimetre antennas, moved forward with the signature of the agreement between ESO and the NSF and with the Ground-breaking at Chajnantor. Conceptual studies of a 100-m optical/infrared telescope (OWL) also proceeded well. Several new instruments were installed at ESO telescopes, e.g. HARPS . And the VLT Interferometer (VLTI) received a powerful Adaptive Optics System and made the first detection through infrared interferometry of an extragalactic object. A rapidly increasing number of new scientific results were obtained on the basis of data from ESO telescopes, some of which were highlighted in ESO Press Releases. A number of beautiful images were published. Many of these developments are described in ESO's Press Releases, most with Press Photos, cf. the 2003 PR Index. Some of last year's ESO PR highlights may be accessed directly via the clickable image above.

  11. Unveiling NO2π···Cdbnd C π-hole interactions: A combined computational and crystallographic study

    NASA Astrophysics Data System (ADS)

    Bauzá, Antonio; Frontera, Antonio

    2015-07-01

    A series of π-hole complexes involving the NO2 group and several isolated π systems have been evaluated at the BP86-D3/def2-TZVP level of theory. We have used ethene, ethyne and but-2-yne as electron donor moieties and nitrobenzene and 1,2,3,4,5-pentafluoro-6-nitrobenzene as electron acceptors. The SAPT and NBO analyses show that the dispersion term is the major contributor to the binding while π(Csbnd C) → π*(Csbnd N) donor-acceptor interactions also contribute to the overall stabilization. Finally several experimental examples were retrieved from the CSD highlighting the importance of this interaction.

  12. Conformation and tautomerism of methoxy-substituted 4-phenyl-4-thiazoline-2-thiones: a combined crystallographic and ab initio investigation.

    PubMed

    Balti, Monaem; Norberg, Bernadette; Efrit, Mohamed Lotfi; Lanners, Steve; Wouters, Johan

    2016-05-01

    4-Phenyl-4-thiazoline-2-thiol is an active pharmaceutical compound, one of whose activities is as a human indolenamine dioxygenase inhibitor. It has been shown recently that in both the solid state and the gas phase, the thiazolinethione tautomer should be preferred. As part of both research on this lead compound and a medicinal chemistry program, a series of substituted arylthiazolinethiones have been synthesized. The molecular conformations and tautomerism of 4-(2-methoxyphenyl)-4-thiazoline-2-thione and 4-(4-methoxyphenyl)-4-thiazoline-2-thione, both C10H9NOS2, are reported and compared with the geometry deduced from ab initio calculations [PBE/6-311G(d,p)]. Both the crystal structure analyses and the calculations establish the thione tautomer for the two substituted arylthiazolinethiones. In the crystal structure of the 2-methoxyphenyl regioisomer, the thiazolinethione unit was disordered over two conformations. Both isomers exhibit similar hydrogen-bond patterns [R2(2)(8) motif] and form dimers. The crystal packing is further reinforced by short S...S interactions in the 2-methoxyphenyl isomer. The conformations of the two regioisomers correspond to stable geometries calculated from an ab initio energy-relaxed scan. PMID:27146572

  13. Identifying the multiplicity of crystallographically equivalent variants generated by iterative phase transformations in Ti.

    PubMed

    Grammatikopoulos, Panagiotis; Pond, Robert Charles

    2016-02-01

    This work describes phase transformations in Ti from a purely crystallographic perspective. Iterative heating and cooling above and below 1155 K induce phase transitions between a low-temperature h.c.p. (hexagonal close packed) (6/m mm) and a high-temperature b.c.c. (body centred cubic) (m3m) structure. The crystallography of the two phases has been found to be related by the Burgers Orientation Relationship (Burgers OR). The transitions are accompanied by changes in texture, as an ever-increasing number of crystallographically equivalent variants occur with every cycle. Identifying their multiplicity is important to relate the textures before and after the transformation, in order to predict the resultant one and refine its microstructure. The four-dimensional Frank space was utilized to describe both h.c.p. and b.c.c. structures within the same orthogonal framework, and thus allow for their easy numerical manipulation through matrix algebra. Crystallographic group decomposition showed that the common symmetry maintained in both groups was that of group 2/m; therefore, the symmetry operations that generated the variants were of groups 3m and 23 for cubic and hexagonal generations, respectively. The number of all potential variants was determined for the first three variant generations, and degeneracy was indeed detected, reducing the number of variants from 72 to 57 and from 432 to 180 for the second and third generations, respectively. Degeneracy was attributed on some special alignments of symmetry operators, as a result of the Burgers OR connecting the relative orientation of the two structures. PMID:26830797

  14. Development of Dynamic Explicit Crystallographic Homogenization Finite Element Analysis Code to Assess Sheet Metal Formability

    NASA Astrophysics Data System (ADS)

    Nakamura, Yasunori; Tam, Nguyen Ngoc; Ohata, Tomiso; Morita, Kiminori; Nakamachi, Eiji

    2004-06-01

    The crystallographic texture evolution induced by plastic deformation in the sheet metal forming process has a great influence on its formability. In the present study, a dynamic explicit finite element (FE) analysis code is newly developed by introducing a crystallographic homogenization method to estimate the polycrystalline sheet metal formability, such as the extreme thinning and "earing." This code can predict the plastic deformation induced texture evolution at the micro scale and the plastic anisotropy at the macro scale, simultaneously. This multi-scale analysis can couple the microscopic crystal plasticity inhomogeneous deformation with the macroscopic continuum deformation. In this homogenization process, the stress at the macro scale is defined by the volume average of those of the corresponding microscopic crystal aggregations in satisfying the equation of motion and compatibility condition in the micro scale "unit cell," where the periodicity of deformation is satisfied. This homogenization algorithm is implemented in the conventional dynamic explicit finite element code by employing the updated Lagrangian formulation and the rate type elastic/viscoplastic constitutive equation. At first, it has been confirmed through a texture evolution analyses in cases of typical deformation modes that Taylor's "constant strain homogenization algorithm" yields extreme concentration toward the preferred crystal orientations compared with our homogenization one. Second, we study the plastic anisotropy effects on "earing" in the hemispherical cup deep drawing process of pure ferrite phase sheet metal. By the comparison of analytical results with those of Taylor's assumption, conclusions are drawn that the present newly developed dynamic explicit crystallographic homogenization FEM shows more reasonable prediction of plastic deformation induced texture evolution and plastic anisotropy at the macro scale.

  15. Superconducting behaviours in reduction-treated mixtures of fine Pr124 and Pr123 ceramics

    NASA Astrophysics Data System (ADS)

    Koyama, K.; Nakashima, R.; Magishi, K.; Saito, T.; Shima, T.; Hagiwara, M.

    2011-09-01

    Superconducting behaviours in reduction-treated mixtures of fine Pr124 and Pr123 ceramics synthesized using citrate pyrolysis precursor method are examined by electrical resistivity and magnetic measurements. With increasing the ratio of Pr123, the temperature dependence of ρ(T) changes to be semiconductor-like behaviour hugely, and there exist no broad maximum for as-sintered Pr124/Pr123 (1:1.5) and (1:2) samples contrary with the case of (1:1). By reduction treatment, the ρ(T) curve shows the maximum according to the increase of carrier concentration in the CuO double chain in Pr 124 grains. By subtracting the Pr3+ paramagnetic contribution from the temperature dependence of magnetization, the remnant magnetization shows weak diamagnetism below ~17 K, indicating small Meissner effect. The diamagnetic susceptibility is independent of magnetic field in the measured field range below 20 Oe.

  16. Use of Bayesian Inference in Crystallographic Structure Refinement via Full Diffraction Profile Analysis

    PubMed Central

    Fancher, Chris M.; Han, Zhen; Levin, Igor; Page, Katharine; Reich, Brian J.; Smith, Ralph C.; Wilson, Alyson G.; Jones, Jacob L.

    2016-01-01

    A Bayesian inference method for refining crystallographic structures is presented. The distribution of model parameters is stochastically sampled using Markov chain Monte Carlo. Posterior probability distributions are constructed for all model parameters to properly quantify uncertainty by appropriately modeling the heteroskedasticity and correlation of the error structure. The proposed method is demonstrated by analyzing a National Institute of Standards and Technology silicon standard reference material. The results obtained by Bayesian inference are compared with those determined by Rietveld refinement. Posterior probability distributions of model parameters provide both estimates and uncertainties. The new method better estimates the true uncertainties in the model as compared to the Rietveld method. PMID:27550221

  17. Regularities of crystallographic texture formation in cladding tubes from Zr-based alloys during their production

    NASA Astrophysics Data System (ADS)

    Isaenkova, M.; Perlovich, Yu; Fesenko, V.

    2016-04-01

    This paper summarizes researches of the authors, which are directed on the development of the methodological basis of X-ray studies in the materials science of zirconium and on the systematization of new experimental results obtained using developed methods. The paper describes regularities of the formation of the crystallographic texture and the substructure inhomogeneity of cladding tubes from zirconium alloys at various stages of their manufacturing, i.e. during hot and cold deformation, recrystallization, phase transformations and interactions of the above processes.

  18. Use of Bayesian Inference in Crystallographic Structure Refinement via Full Diffraction Profile Analysis.

    PubMed

    Fancher, Chris M; Han, Zhen; Levin, Igor; Page, Katharine; Reich, Brian J; Smith, Ralph C; Wilson, Alyson G; Jones, Jacob L

    2016-01-01

    A Bayesian inference method for refining crystallographic structures is presented. The distribution of model parameters is stochastically sampled using Markov chain Monte Carlo. Posterior probability distributions are constructed for all model parameters to properly quantify uncertainty by appropriately modeling the heteroskedasticity and correlation of the error structure. The proposed method is demonstrated by analyzing a National Institute of Standards and Technology silicon standard reference material. The results obtained by Bayesian inference are compared with those determined by Rietveld refinement. Posterior probability distributions of model parameters provide both estimates and uncertainties. The new method better estimates the true uncertainties in the model as compared to the Rietveld method. PMID:27550221

  19. Structure of Tl18Pb2Ti7S25 as a masterpiece of crystallographic symmetry

    NASA Astrophysics Data System (ADS)

    Borisov, S. V.; Magarill, S. A.; Pervukhina, N. V.

    2014-11-01

    A crystallographic analysis of the cubic structure of Tl18Pb2Ti7S25 has established the arrangement of all cations and anions according to the law of the 27-fold (with respect to volume) structure type of PbS(NaCl) with strictly fixed anionic vacancies. The nonintersecting axes of symmetry of four directions organizing the structure distribute cations differing in sizes, charges, and amounts over general and particular sites of the sp. gr. Pa3 to form a high-symmetry design in the simple atomic matrix.

  20. Crystallographic, luminescence and photoconductive characteristics of chemically tailored ZnO nanorods

    SciTech Connect

    Bayan, Sayan Chakraborty, Purushottam

    2014-04-24

    The optoelectronic properties of zinc oxide (ZnO) nanorods synthesized using two different chemical methods have been explored in the light of microstructural features. The presence/absence of band edge emission in the luminescence spectra of the nanorods is found to be governed by the crystallographic properties. Moreover, we observed a pronounced effect of variation in crystallite size on the UV photoconductivity of the nanorods. Understanding the influence of microstructural aspects on the optical and electronic properties of the nanostructures may help in the fabrication of prototype, miniaturized optoelectronic devices.

  1. Blocks and residual stresses in sapphire rods of different crystallographic orientations grown by the Stepanov method

    SciTech Connect

    Krymov, V. M. Nosov, Yu. G.; Bakholdin, S. I.; Maslov, V. N.; Shul’pina, I. L.

    2015-05-15

    The formation of blocks in shaped sapphire rods of two crystallographic orientations has been investigated. It is shown that, when growth occurs in the direction of the optical c axis, blocks are formed with a higher probability than in the case of growth in the a direction. A model of formation of blocks in rods of different orientations is proposed. The distribution of residual stresses over sapphire rod cross sections is measured by conoscopy. It is found that stresses increase from the middle of a rod to its periphery and reach 20 MPa.

  2. Chiral Properties in ^134Pr

    NASA Astrophysics Data System (ADS)

    Starosta, K.; Chiara, C. J.; Fossan, D. B.; Koike, T.; Beausang, C. W.; Hecht, A. A.; Boston, A. J.; Chantler, H. J.; Paul, E. S.; Scraggs, H. C.; Simons, A.; Wadsworth, R.; Clark, R. M.

    2001-04-01

    The πh_11/2νh_11/2 doublet bands in ^134Pr, which represent the best evidence to date for chiral symmetry breaking in odd-odd nuclei [1], were investigated with the GAMMASPHERE array using the ^116Cd(^23Na,5n) reaction at 115 MeV. From thin-target data, the nearly degenerate ΔI=1 side band was extended from a 9^+ bandhead up to a spin of 24^+ with E2 crossovers, a total of 15 units of spin, while the main yrast band was observed from an 8^+ bandhead to 24^+. Measured γ-ray intensities suggest a staggering of the B(M1)/B(E2) ratios in the main band with the ratio smaller for even-spin initial states; these compare well with those of other N=75 isotones. Relative transition rates for γ-rays linking the doublet bands have also been extracted. Analysis of backed-target data aimed at absolute transition rates is underway. The results will be compared to calculations with particle-hole triaxial-rotor and 3-D TAC models. [1mm] [1] C.M.Petrache, et al., Nucl.Phys.A597(1996)106; V.I.Dimitrov, et al., PRL 84(2000)5732; K. Starosta, et al., PRL 86(2001).

  3. Microscopic Picture of Atomic Dynamics in the Double Perovskite, PrBaCo2O6

    NASA Astrophysics Data System (ADS)

    Shoko, Elvis; Schwingenschlogl, Udo

    We have used a combination of lattice dynamics and ab initio molecular dynamics to study atomic dynamics in PrBaCo2O6, a prototype material for a large class of layered compounds of both fundamental and technological interest. We find clear signatures of the layered structure of this compound on the overall atomic dynamics. In particular, we find that O atom dynamics in the PrO layer is predominantly in-plane (ab-plane) in contrast to the predominantly out-of-plane dynamics in the CoO2 layer. This suggests that the oxide ionic conductivity is dominated by the O atoms in the PrO layer, a finding of interest in solid-oxide fuel cells. Additionally, our results reveal sharp low-energy vibrational modes below 20 meV for both Ba and Pr atoms leading to the intriguing possibility that this material may be engineered for thermoelectric applications.

  4. [Functions of prion protein PrPc].

    PubMed

    Cazaubon, Sylvie; Viegas, Pedro; Couraud, Pierre-Olivier

    2007-01-01

    It is now well established that both normal and pathological (or scrapie) isoforms of prion protein, PrPc and PrPsc respectively, are involved in the development and progression of various forms of neurodegenerative diseases, including scrapie in sheep, bovine spongiform encephalopathy (or "mad cow disease") and Creutzfeldt-Jakob disease in human, collectively known as prion diseases. The protein PrPc is highly expressed in the central nervous system in neurons and glial cells, and also present in non-brain cells, such as immune cells or epithelial and endothelial cells. Identification of the physiological functions of PrPc in these different cell types thus appears crucial for understanding the progression of prion diseases. Recent studies highlighted several major roles for PrPc that may be considered in two major domains : (1) cell survival (protection against oxidative stress and apoptosis) and (2) cell adhesion. In association with cell adhesion, distinct functions of PrPc were observed, depending on cell types : neuronal differentiation, epithelial and endothelial barrier integrity, transendothelial migration of monocytes, T cell activation. These observations suggest that PrPc functions may be particularly relevant to cellular stress, as well as inflammatory or infectious situations. PMID:17875293

  5. ER and PR signaling nodes during mammary gland development

    PubMed Central

    2012-01-01

    The ovarian hormones estrogen and progesterone orchestrate postnatal mammary gland development and are implicated in breast cancer. Most of our understanding of the molecular mechanisms of estrogen receptor (ER) and progesterone receptor (PR) signaling stems from in vitro studies with hormone receptor-positive cell lines. They have shown that ER and PR regulate gene transcription either by binding to DNA response elements directly or via other transcription factors and recruiting co-regulators. In addition they cross-talk with other signaling pathways through nongenomic mechanisms. Mouse genetics combined with tissue recombination techniques have provided insights about the action of these two hormones in vivo. It has emerged that hormones act on a subset of mammary epithelial cells and relegate biological functions to paracrine factors. With regards to hormonal signaling in breast carcinomas, global gene expression analyses have led to the identification of gene expression signatures that are characteristic of ERα-positive tumors that have stipulated functional studies of hitherto poorly understood transcription factors. Here, we highlight what has been learned about ER and PR signaling nodes in these different systems and attempt to lay out in which way the insights may converge. PMID:22809143

  6. Making red emitting phosphors with Pr 3+

    NASA Astrophysics Data System (ADS)

    Boutinaud, Philippe; Pinel, Eric; Oubaha, Mohamed; Mahiou, Rachid; Cavalli, Enrico; Bettinelli, Marco

    2006-01-01

    UV-excited red-emitting phosphors are obtained using Pr 3+ as the luminescent activator and host lattices containing closed-shell transition metal ions (especially titanates, vanadates and niobates). In these oxidant lattices, the quenching of the otherwise greenish-blue emitting 3P 0 level is induced by a low-lying Pr-to-metal intervalence charge transfer state (IVCT). A simple criterion based on the optical electronegativities of the d 0 lattice cations (M n+) and average Pr 3+ - M n+ distances is proposed to predict 3P 0 quenching in these lattices.

  7. The role of crystallographic texture in achieving low friction zinc oxide nanolaminate films

    NASA Astrophysics Data System (ADS)

    Mojekwu, Nneoma

    Metal oxide nanolaminate films are potential high temperature solid lubricants due to their ability to exhibit significant plasticity when grain size is reduced to the nanometer scale, and defective growth structure is achieved by condensation of oxygen vacancies to form intrinsic stacking faults. This is in contrast to conventional microcrystalline and single crystal oxides that exhibit brittle fracture during loading in a sliding contact. This study emphasizes the additional effect of growth orientation, in particular crystallographic texture, on determining the sliding friction behavior in nanocolumnar grain zinc oxide films grown by atomic layer deposition. It was determined that zinc oxide low (0002) versus higher (101¯3) surface energy crystallographic planes influenced the sliding friction coefficient. Texturing of the (0002) grains resulted in a decreased adhesive component of friction thereby lowering the sliding friction coefficient to ˜0.25, while the friction coefficient doubled to ˜0.5 with increasing contribution of surface (101¯3) grains. In addition, the variation of the x-ray grazing incident angle from 0.5° to 5° was studied to better understand the surface grain orientation as a function of ZnO layer thickness in one versus four bilayer nanolaminates where the under layer (seed layer) was load-bearing Zn(Ti,Zr)O3.

  8. Enhancing nanoscale SEM image segmentation and reconstruction with crystallographic orientation data and machine learning

    SciTech Connect

    Converse, Matthew I. Fullwood, David T.

    2013-09-15

    Current methods of image segmentation and reconstructions from scanning electron micrographs can be inadequate for resolving nanoscale gaps in composite materials (1–20 nm). Such information is critical to both accurate material characterizations and models of piezoresistive response. The current work proposes the use of crystallographic orientation data and machine learning for enhancing this process. It is first shown how a machine learning algorithm can be used to predict the connectivity of nanoscale grains in a Nickel nanostrand/epoxy composite. This results in 71.9% accuracy for a 2D algorithm and 62.4% accuracy in 3D. Finally, it is demonstrated how these algorithms can be used to predict the location of gaps between distinct nanostrands — gaps which would otherwise not be detected with the sole use of a scanning electron microscope. - Highlights: • A method is proposed for enhancing the segmentation/reconstruction of SEM images. • 3D crystallographic orientation data from a nickel nanocomposite is collected. • A machine learning algorithm is used to detect trends in adjacent grains. • This algorithm is then applied to predict likely regions of nanoscale gaps. • These gaps would otherwise be unresolved with the sole use of an SEM.

  9. Synthesis of crystallographically oriented olivine aggregates using colloidal processing in a strong magnetic field

    NASA Astrophysics Data System (ADS)

    Koizumi, Sanae; Suzuki, Tohru S.; Sakka, Yoshio; Yabe, Kosuke; Hiraga, Takehiko

    2016-07-01

    This study develops a fabrication technique to obtain Fe-free and Fe-bearing (Fe:Mg = 1:9) olivine aggregates not only with high density and fine grain size but with crystallographic preferred orientation (CPO). A magnetic field (≤12 T) is applied to synthetic, fine-grained (~120 nm), olivine particles dispersed in solvent. The alignment of certain crystallographic axes of the particles with respect to a magnetic direction is anticipated due to magnetic anisotropy of olivine. The dispersed particles are gradually consolidated on a porous alumina mold covered with a solid-liquid separation filter during drainage of the solvent. The resultant aligned consolidated aggregate is then isostatically pressed and vacuum sintered. We find that (1) preparation of fully reacted olivine particles, with less propensity to coalesce; (2) preparation of a suspension with highly dispersed particles; and (3) application of a certain strength of the magnetic field are essential to obtain well-sintered and well-aligned aggregates. High density (i.e., <1 vol% porosity) and fine grain size (~1 μm) Fe-free and Fe-bearing olivine aggregates were successfully synthesized with uniaxially aligned a- and c-axes, respectively. Attempts to uniaxially align the magnetization hard axis and to triaxially align Fe-bearing olivine by rotating the suspension in the magnetic field succeeded in obtaining weakly developed CPO aggregates.

  10. Erbium-ion implantation into various crystallographic cuts of Al2O3

    NASA Astrophysics Data System (ADS)

    Nekvindova, P.; Mackova, A.; Malinsky, P.; Cajzl, J.; Svecova, B.; Oswald, J.; Wilhelm, R. A.

    2015-12-01

    This paper reports on the importance of crystallographic cuts with a different orientation on the luminescent properties and structural changes of Al2O3 implanted with Er+ ions at 190 keV and with a fluence of 1.0 × 1016 cm-2. Post-implantation annealing at 1000 °C in oxygen atmosphere was also done. The chemical compositions and erbium concentration-depth profiles of implanted layers were studied by Rutherford Backscattering Spectrometry (RBS) and compared to SRIM simulations. The same value of the maximum erbium concentration (up to 2 at.%) was observed at a depth of about 40 nm for all crystallographic cuts. The structural properties of the prepared layers were characterised by RBS/channelling. The relative amount of disordered atoms of 70-80% was observed in the prepared implanted layers and discussed for various cuts. It has been found that erbium is positioned randomly in the Al2O3 crystalline matrix, and no preferential positions appeared even after the annealing procedure. Erbium luminescence properties were measured in the wavelength range of 1440-1650 nm for all samples. As-implanted Al2O3 samples had a significant luminescence band at 1530 nm. The best luminescence was repeatedly observed in the <0 0 0 1> cut of Al2O3. The annealing procedure significantly improved the luminescent properties.

  11. Influence of crystallographic orientation and anisotropy on Kapitza conductance via classical molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Duda, J. C.; Kimmer, C. J.; Soffa, W. A.; Zhou, X. W.; Jones, R. E.; Hopkins, P. E.

    2012-11-01

    We investigate the influence of crystallographic orientation and anisotropy on local phonon density of states, phonon transmissivity, and Kapitza conductance at interfaces between Lennard-Jones solids via classical molecular dynamics simulations. In agreement with prior works, we find that the Kapitza conductance at an interface between two face-centered cubic materials is independent of crystallographic orientation. On the other hand, at an interface between a face-centered cubic material and a tetragonal material, the Kapitza conductance is strongly dependent on the relative orientation of the tetragonal material, albeit this dependence is subject to the overlap in vibrational spectra of the cubic and tetragonal materials. Furthermore, we show that interactions between acoustic phonons in the cubic material and optical phonons in the tetragonal material can lead to the interface exhibiting greater "thermal anisotropy" as compared to that of the constituent materials. Finally, it is noted that the relative match or mismatch between the Debye temperatures of two materials comprising an interface does not serve an accurate gauge of the efficiency of interfacial thermal transport when those materials have different crystal structures.

  12. Differential Stability of the Crystallographic Interfaces of Mu- and Kappa-Opioid Receptors

    PubMed Central

    Johnston, Jennifer M.; Filizola, Marta

    2014-01-01

    The recent mu-opioid receptor (MOPr) and kappa-opioid receptor (KOPr) crystal structures have inspired hypotheses of physiologically relevant dimerization contacts, specifically: a closely packed interface involving transmembrane (TM) helices TM5 and TM6, and a less compact interface, involving TM1, TM2, and helix 8 (H8). While the former was only found in MOPr crystals, similar arrangements of the latter were identified for both KOPr and MOPr. The relevance of these interfaces outside of a crystal lattice is called into question by the possibility that they might be influenced by the specific crystallization conditions. In this study, we have employed umbrella sampling molecular dynamics simulations of coarse-grained representations of the interacting MOPr or KOPr crystallographic structures, in the absence of the T4 lysozyme, and in an explicit lipid-water environment, to determine the strength of receptor dimerization at the different crystallographic interfaces. We note that the shape of the interface plays a dominant role in the strength of the interaction, and the pattern of contacting residues defines the shape of the potential of mean force. This information can be used to guide experiments aimed at exploring the role of dimerization in opioid receptor function. PMID:24651466

  13. Identification of Material Properties of PZT Single Crystals through Crystallographic Homogenization Method

    NASA Astrophysics Data System (ADS)

    Uetsuji, Yasutomo; Tanaka, Satoshi; Tsuchiya, Kazuyoshi; Ueda, Sei; Nakamachi, Eiji

    Single crystals of lead zirconium titanate (PZT) are difficult to fabricate. Thus, not all material properties of PZT have been fully characterized. In this paper, the mechanical and electrical properties of a PZT single crystal, which can be assumed to be identical to those of a crystal grain in a polycrystal, have been computed from those of a polycrystalline PZT ceramic by the steepest decent method and multiscale finite element modeling based on crystallographic homogenization method. Crystallographic homogenization enables us to predict macroscopic properties of ceramics taking into account the inhomogeneous microstructure of an aggregate of crystal grains. The crystal morphology of the PZT ceramic was measured by the SEM·EBSD technique, and the result was used in the microscopic finite element model. Then, the mechanical and electrical properties of the crystal grain were derived by the steepest decent method so that its macroscopic properties would correspond to the measured properties of the PZT ceramic. The proposed computational method was applied to barium titanate (BT) and validated by comparison of the computed material properties with known properties of the BT single crystal. Finally, the computed material properties, such as the elastic compliance, and the dielectric and piezoelectric constants, were presented for the PZT single crystal.

  14. Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

    SciTech Connect

    Bennett, Joseph W.; Rabe, Karin M.

    2012-11-15

    In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb{sub 1/2}Mn{sub 1/2})O{sub 3} as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb{sub 2}O{sub 4}; and (3) ferroelectric semiconductors with formula M{sub 2}P{sub 2}(S,Se){sub 6}. A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties. - Graphical abstract: Integration of first-principles methods with crystallographic database mining, for the discovery and design of novel ferroelectric materials, could potentially lead to new classes of multifunctional materials. Highlights: Black-Right-Pointing-Pointer Integration of first-principles methods and database mining. Black-Right-Pointing-Pointer Minor structural families with desirable functional properties. Black-Right-Pointing-Pointer Survey of polar entries in the Inorganic Crystal Structural Database.

  15. Crystallographic study of grain refinement in low and medium carbon steels

    NASA Astrophysics Data System (ADS)

    Li, Ming; Li, Jianmin; Qiu, Dong; Zheng, Qing; Wang, Geoff; Zhang, Ming-Xing

    2016-05-01

    In order to clarify and articulate the long-standing problems associated with the role of various compounds in grain refinement of as-cast steels, a comprehensive crystallographic study on grain refiners in a number of low carbon steels has been conducted using the edge-to-edge matching (E2EM) model, which has been successfully applied to explain and predict effective grain refiners in light metals. Five commonly investigated compounds, namely NbO, CeS, TiN, Ce2O3 and TiC, in steels were examined. According to the extent of crystallographic matching, the predicted grain refining potency of these five grain refiners is ranked in the order of NbO > CeS > TiN > Ce2O3 > TiC, which is consistent with previously reported experimental results. Four different orientation relationships between δ-ferrite and these grain refiners were predicted. One of them has been verified by previously published experimental data. The similarity and the advantages of the E2EM model over conventional Bramfitt's model were also discussed.

  16. Distinguishing crystallographic misorientations of lanthanum zirconate epilayers on nickel substrates by electron backscatter diffraction.

    PubMed

    Ji, Yuan; Wang, Li; Zhang, Yinqi; Wei, Bin; Wang, Jianhong; Cheng, Yanling; Suo, Hongli

    2011-04-01

    Electron backscatter diffraction (EBSD) was used for distinguishing crystallographic orientations and local lattice misfits of a La(2)Zr(2)O(7) (LZO) buffer layer epitaxially grown on a cube textured Ni-5.%W (Ni-W) substrate for a YBCO superconductor film. Orientation data were obtained from the LZO epilayer using low energy primary electrons (5keV) and from the Ni-W substrate by increasing the voltage to 15keV. In-plane and out-of-plane orientations of the LZO epilayer were revealed with respect to its Ni-W substrate. A strong {100} 〈011〉 rotated-cube texture in the LZO epilayer was formed on the {100} 〈001〉 cube-textured Ni-W substrates. LZO and Ni in-plane crystallographic axes are related by an expected 45° rotation. The step-misorientations and the local misfit strains between the LZO epilayer and the substrate were also analyzed. PMID:21396525

  17. Crystallographic structure of Ni-Co coating on the affinity adsorption of histidine-tagged protein.

    PubMed

    Chang, Yaw-Jen; Chen, Sheng-Zheng; Ho, Ching-Yuan

    2015-04-01

    The principle of immobilized metal affinity chromatography (IMAC) has been recently implemented for protein microarrays for the study of protein abundance and function. Ni-Co film fabricated by electrodeposition is a novel microarray surface in an alloy type for immobilizing histidine-tagged proteins based on IMAC. In this paper, the effects of crystallographic structures and surface properties of Ni-Co coatings, with and without the annealing process, on the immobilization of histidine-tagged proteins were systematically investigated. The experimental results reveal that the stronger hcp texture, due to a higher Co content, results in better affinity adsorption for histidine-tagged biotin. Nevertheless, the allotropic phase transformation from hcp to fcc, due to the annealing process, leads to the decrease of affinity adsorption. The wettability property and the surface roughness of Ni-Co coating are, however, not important factors. Obviously, the crystallographic structure of Ni-Co coating is the dominant factor for the specific affinity adsorption of histidine-tagged protein. PMID:25731093

  18. The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results

    PubMed Central

    Rosenbaum, Gerd; Alkire, Randy W.; Evans, Gwyndaf; Rotella, Frank J.; Lazarski, Krzystof; Zhang, Rong-Guang; Ginell, Stephan L.; Duke, Norma; Naday, Istvan; Lazarz, Jack; Molitsky, Michael J.; Keefe, Lisa; Gonczy, John; Rock, Larry; Sanishvili, Ruslan; Walsh, Martin A.; Westbrook, Edwin; Joachimiak, Andrzej

    2008-01-01

    The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5–0.6 Å wavelength) with fluxes up to 8–18 × 1012 photons s−1 (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm × 1.0 mm (horizontal × vertical, unfocused) to 0.083 mm × 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a κ-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 × 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented. PMID:16371706

  19. High resolution neutron crystallographic studies of the hydration of coenzyme cob(II)alamin

    SciTech Connect

    Jogl, Gerwald; Wang, Xiaoping; Mason, Sax; Kovalevsky, Andrey; Mustyakimov, Marat; Fisher, Zoe; Hoffmann, Christina; Kratky, Christoph; Langan, Paul

    2011-01-01

    The hydration of coenzyme cob(II)alamin has been studied using high resolution monochromatic neutron crystallographic data collected at room temperature to a resolution of surrounded by flexible side chains with terminal functional groups may be significant for 0.92 on the original diffractometer D19 with a prototype 4o x 64o detector at the high-flux reactor neutron source run by the Institute Laue Langevin. The resulting structure provides H bonding parameters for the hydration of biomacromolecules to unprecedented accuracy. These experimental parameters will be used to define more accurate force-fields for biomacromolecular structure refinement. The presence of a hydrophobic bowl motif efficient scavenging of ligands. The feasibility of extending the resolution of this structure to ultra high resolution was investigated by collecting time-of-flight neutron crystallographic data on diffractometer TOPAZ with a prototype array of 14 modular 21o x 21o detectors at the Spallation Neutron Source run by Oak Ridge National Laboratory.

  20. Crystallographically controlled crystal-plastic deformation of zircon in shear zones

    NASA Astrophysics Data System (ADS)

    Kovaleva, Elizaveta; Klötzli, Urs

    2014-05-01

    Plastically-deformed zircons from various types of strained natural metamorphic rocks have been investigated in-situ by electron backscatter diffraction analysis (EBSD), allowing crystallographic orientation mapping at high spatial resolution. Plastic deformation often forms under the control of grain-internal heterogeneities. At the crystal structure scale deformation is controlled by the physical anisotropy of the lattice. Three most common slip systems in zircon are [100]{010}, [010]{001} and [001]{010} (Leroux et. al., 1999; Reddy et. al., 2007). They are genetically connected with the main zircon crystallographic directions: [001] (c-axis), [100] and [010] (a and b axes). Atomic models show weak planes normal to these directions that preferably evolve to glide planes in the deforming crystal. The visualization of seismic (elastic) properties of zircon with the MATLAB toolbox MTEX shows a similar pattern. The slowest S-wave velocities are observed in directions parallel to [100], [010] and [001] crystallographic directions. The highest Young's modulus values lie in the same directions. In natural zircon grains, the common slip systems are preferably activated when zircon is hosted by rheologically comparatively weaker phases or a fine-grained matrix. In these cases zircon behaves as a rigid clast. During progressive deformation high deviatoric stresses together with high strain rates concentrate at crystal tips, as shown by numerical modeling. Softer host phases allow more degrees of freedom for zircon to be deformed according to its crystallographic and internal properties. These conclusions are supported by the misorientation axes density distribution maps, derived with MTEX. Deformed zircon hosted by a relatively soft phase (mostly biotite) develops a crystallographic preferred orientation (CPO), which has not been documented for zircon before. At the same time deformation of zircon hosted by a rheologically stronger matrix causes the activation of less

  1. Photoheterotrophic growth of Agmenellum quadruplicatum PR-6

    SciTech Connect

    Lambert, D.H.; Stevens, S.E. Jr.

    1986-02-01

    The unicellular cyanobacterium Agmenellum quadruplicatum PR-6 grows in the presence of light on agar containing 10 ..mu..M 3-(3,4 dichlorophenyl)-1,1-dimethylurea and 1 to 30 mM glycerol. A derivative strain, PR-6G2, was tolerant of 100 mM glycerol. Photoheterotrophic growth conditions had little effect on transformation competence but did decrease the viability of single cells plated onto agar, particularly cells of the parent strain.

  2. Mechanically Shaped Two-Dimensional Covalent Organic Frameworks Reveal Crystallographic Alignment and Fast Li-Ion Conductivity.

    PubMed

    Vazquez-Molina, Demetrius A; Mohammad-Pour, Gavin S; Lee, Chain; Logan, Matthew W; Duan, Xiangfeng; Harper, James K; Uribe-Romo, Fernando J

    2016-08-10

    Covalent organic frameworks (COFs) usually crystallize as insoluble powders, and their processing for suitable devices is thought to be limited. We demonstrate that COFs can be mechanically pressed into shaped objects having anisotropic ordering with preferred orientation between hk0 and 00l crystallographic planes. Five COFs with different functionality and symmetry exhibited similar crystallographic behavior and remarkable stability, indicating the generality of this processing. Pellets prepared from bulk COF powders impregnated with LiClO4 displayed room temperature conductivity up to 0.26 mS cm(-1) and high electrochemical stability. This outcome portends use of COFs as solid-state electrolytes in batteries. PMID:27414065

  3. The use of combined cathodoluminescence and EBSD analysis: a case study investigating grain boundary migration mechanisms in quartz.

    PubMed

    Piazolo, S; Prior, D J; Holness, M D

    2005-02-01

    Grain boundary migration is an important mechanism of microstructural modification both in rocks and in metals. Combining detailed cathodoluminescence (CL) and electron backscatter diffraction (EBSD) analysis offers the opportunity to relate directly changes in crystallographic orientation to migrating boundaries. We observe the following features in naturally heated quartz grains from the thermal aureole of the Ballachulish Igneous Complex (Scotland, U.K.): (a) propagation of substructures and twin boundaries in swept areas both parallel and at an angle to the growth direction, (b) development of slightly different crystallographic orientations and new twin boundaries at both the growth interfaces and within the swept area and (c) a gradual change in crystallographic orientation in the direction of growth. All these features are compatible with a growth mechanism in which single atoms are attached and detached both at random and at preferential sites, i.e. crystallographically controlled sites or kinks in boundary ledges. Additionally, strain fields caused by defects and/or trace element incorporation may facilitate nucleation sites for new crystallographic orientations at distinct growth interfaces but also at continuously migrating boundaries. This study illustrates the usefulness of combined CL and EBSD in microprocess analysis. Further work in this direction may provide detailed insight into both the mechanism of static grain growth and the energies and mobilities of boundaries in terms of misorientation and grain boundary plane orientation. PMID:15683412

  4. Effect of crystallographic orientation on hillock formation in thermally cycled large grain tin films

    NASA Astrophysics Data System (ADS)

    Koppes, John Patrick

    Tin whiskers and hillocks grow spontaneously from the surfaces of polycrystalline Sn films at room temperature. Whiskers can grow long enough to cause short circuits in electronic devices. We hypothesized that the anisotropies of the crystal structure lead to locally high strain energies that are relieved by the growth of whiskers and hillocks. This research studies hillock formations on large grain Sn-alloy films relative to the crystallographic orientations of the adjacent grains. Large grain films were produced by solidifying 96.5wt% Sn - 3wt% Ag - 0.5wt% Cu solder alloy on a Cu substrate. These surface defects (hillocks) grew predominately at grain boundaries during thermal cycling. The formation of the surface defects between two grains created a pseudo-bi-crystal sample geometry, making it ideal for studying surface defects relative to the local crystallographic orientations and the grains' corresponding anisotropic properties. The crystallographic orientations of the grains were studied with Electron Backscatter Diffraction (EBSD) and Laue micro-diffraction at the Lawrence Berkeley National Laboratory Advanced Light Source. Local orientation studies of the surface defects and the surrounding grains indicated that the surface defects nucleated and grew with low dislocation densities. In addition, the linear surface defect densities along the grain boundaries were measured and observed to change as a function of orientation. The change in linear defect density with respect to orientation was due, in part, to the anisotropy of the coefficient of thermal expansion of β-Sn. In addition, it was important to account for elastic anisotropies. The elastic stresses, strains, and strain energy densities of the microstructures were determined with Object Oriented Finite element analysis. The simulations indicated that during thermal cycling the local stresses exceeded the yield strength. As a result, the highest linear defect densities did not occur at orientations

  5. The influence of LiH on the rehydrogenation behavior of halide free rare earth (RE) borohydrides (RE = Pr, Er).

    PubMed

    Heere, Michael; Payandeh GharibDoust, Seyed Hosein; Frommen, Christoph; Humphries, Terry D; Ley, Morten B; Sørby, Magnus H; Jensen, Torben R; Hauback, Bjørn C

    2016-09-21

    Rare earth (RE) metal borohydrides are receiving immense consideration as possible hydrogen storage materials and solid-state Li-ion conductors. In this study, halide free Er(BH4)3 and Pr(BH4)3 have been successfully synthesized for the first time by the combination of mechanochemical milling and/or wet chemistry. Rietveld refinement of Er(BH4)3 confirmed the formation of two different Er(BH4)3 polymorphs: α-Er(BH4)3 with space group Pa3[combining macron], a = 10.76796(5) Å, and β-Er(BH4)3 in Pm3[combining macron]m with a = 5.4664(1) Å. A variety of Pr(BH4)3 phases were found after extraction with diethyl ether: α-Pr(BH4)3 in Pa3[combining macron] with a = 11.2465(1) Å, β-Pr(BH4)3 in Pm3[combining macron]m with a = 5.716(2) Å and LiPr(BH4)3Cl in I4[combining macron]3m, a = 11.5468(3) Å. Almost phase pure α-Pr(BH4)3 in Pa3[combining macron] with a = 11.2473(2) Å was also synthesized. The thermal decomposition of Er(BH4)3 and Pr(BH4)3 proceeded without the formation of crystalline products. Rehydrogenation, as such, was not successful. However, addition of LiH promoted the rehydrogenation of RE hydride phases and LiBH4 from the decomposed RE(BH4)3 samples. PMID:27533740

  6. L-Arginine ethylester enhances in vitro amplification of PrP(Sc) in macaques with atypical L-type bovine spongiform encephalopathy and enables presymptomatic detection of PrP(Sc) in the bodily fluids.

    PubMed

    Murayama, Y; Ono, F; Shimozaki, N; Shibata, H

    2016-02-12

    Protease-resistant, misfolded isoforms (PrP(Sc)) of a normal cellular prion protein (PrP(C)) in the bodily fluids, including blood, urine, and saliva, are expected to be useful diagnostic markers of prion diseases, and nonhuman primate models are suited for performing valid diagnostic tests for human Creutzfeldt-Jakob disease (CJD). We developed an effective amplification method for PrP(Sc) derived from macaques infected with the atypical L-type bovine spongiform encephalopathy (L-BSE) prion by using mouse brain homogenate as a substrate in the presence of polyanions and L-arginine ethylester. This method was highly sensitive and detected PrP(Sc) in infected brain homogenate diluted up to 10(10) by sequential amplification. This method in combination with PrP(Sc) precipitation by sodium phosphotungstic acid is capable of amplifying very small amounts of PrP(Sc) contained in the cerebrospinal fluid (CSF), saliva, urine, and plasma of macaques that have been intracerebrally inoculated with the L-BSE prion. Furthermore, PrP(Sc) was detectable in the saliva or urine samples as well as CSF samples obtained at the preclinical phases of the disease. Thus, our novel method may be useful for furthering the understanding of bodily fluid leakage of PrP(Sc) in nonhuman primate models. PMID:26802462

  7. PrP Conformational Transitions Alter Species Preference of a PrP-specific Antibody*

    PubMed Central

    Zou, Wen-Quan; Langeveld, Jan; Xiao, Xiangzhu; Chen, Shugui; McGeer, Patrick L.; Yuan, Jue; Payne, Michael C.; Kang, Hae-Eun; McGeehan, John; Sy, Man-Sun; Greenspan, Neil S.; Kaplan, David; Wang, Gong-Xian; Parchi, Piero; Hoover, Edward; Kneale, Geoff; Telling, Glenn; Surewicz, Witold K.; Kong, Qingzhong; Guo, Jian-Ping

    2010-01-01

    The epitope of the 3F4 antibody most commonly used in human prion disease diagnosis is believed to consist of residues Met-Lys-His-Met (MKHM) corresponding to human PrP-(109–112). This assumption is based mainly on the observation that 3F4 reacts with human and hamster PrP but not with PrP from mouse, sheep, and cervids, in which Met at residue 112 is replaced by Val. Here we report that, by brain histoblotting, 3F4 did not react with PrP of uninfected transgenic mice expressing elk PrP; however, it did show distinct immunoreactivity in transgenic mice infected with chronic wasting disease. Compared with human PrP, the 3F4 reactivity with the recombinant elk PrP was 2 orders of magnitude weaker, as indicated by both Western blotting and surface plasmon resonance. To investigate the molecular basis of these species- and conformer-dependent preferences of 3F4, the epitope was probed by peptide membrane array and antigen competition experiments. Remarkably, the 3F4 antibody did not react with MKHM but reacted strongly with KTNMK (corresponding to human PrP-(106–110)), a sequence that is also present in cervids, sheep, and cattle. 3F4 also reacted with elk PrP peptides containing KTNMKHV. We concluded that the minimal sequence for the 3F4 epitope consists of residues KTNMK, and the species- and conformer-dependent preferences of 3F4 arise largely from the interactions between Met112 (human PrP) or Val115 (cervid PrP) and adjacent residues. PMID:20194495

  8. Power combiner

    DOEpatents

    Arnold, Mobius; Ives, Robert Lawrence

    2006-09-05

    A power combiner for the combining of symmetric and asymmetric traveling wave energy comprises a feed waveguide having an input port and a launching port, a reflector for reflecting launched wave energy, and a final waveguide for the collection and transport of launched wave energy. The power combiner has a launching port for symmetrical waves which comprises a cylindrical section coaxial to the feed waveguide, and a launching port for asymmetric waves which comprises a sawtooth rotated about a central axis.

  9. XAFS and crystallographic studies of Ni(II) porphyrins in single crystals and in solution

    SciTech Connect

    Renner, M.W.; Furenlid, L.R.; Barkigia, K.M.; Fajer, J.

    1996-09-01

    Abstract. Nickel porphyrins serve as models for the active sites of several biological processes. Crystallographic and EXAFS results for a Ni meso-tetrapropyl porphyrin (NiTPrP) yield different Ni-N distances in solution and in the solid state. The Ni-N distances determined by single crystal polarized XAS and X-ray diffraction agree well. Polarized XANES experiments further establish that the pre-edge feature observed in square planar Ni(II) complexes is a ls-4pz transition. The single crystal and solution EXAFS results demonstrate that conformational variations of the porphyrin macrocycle can readily be imposed by environmental and/or packing forces and can thereby modulate the chemical and physical properties of porphyrinic chromophores and prosthetic groups.

  10. Maximum a posteriori estimation of crystallographic phases in X-ray diffraction tomography

    PubMed Central

    Gürsoy, Doĝa; Biçer, Tekin; Almer, Jonathan D.; Kettimuthu, Raj; Stock, Stuart R.; De Carlo, Francesco

    2015-01-01

    A maximum a posteriori approach is proposed for X-ray diffraction tomography for reconstructing three-dimensional spatial distribution of crystallographic phases and orientations of polycrystalline materials. The approach maximizes the a posteriori density which includes a Poisson log-likelihood and an a priori term that reinforces expected solution properties such as smoothness or local continuity. The reconstruction method is validated with experimental data acquired from a section of the spinous process of a porcine vertebra collected at the 1-ID-C beamline of the Advanced Photon Source, at Argonne National Laboratory. The reconstruction results show significant improvement in the reduction of aliasing and streaking artefacts, and improved robustness to noise and undersampling compared to conventional analytical inversion approaches. The approach has the potential to reduce data acquisition times, and significantly improve beamtime efficiency. PMID:25939627