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Sample records for pr combined crystallographic

  1. Probing mesitylborane and mesitylborate ligation within the coordination sphere of Cp*Ru(P(i)Pr3)+: a combined synthetic, X-ray crystallographic, and computational study.

    PubMed

    Hesp, Kevin D; Kannemann, Felix O; Rankin, Matthew A; McDonald, Robert; Ferguson, Michael J; Stradiotto, Mark

    2011-03-21

    The reaction of Cp*Ru(P(i)Pr(3))Cl (1) with MesBH(2) (Mes = 2,4,6-trimethylphenyl) afforded the mesitylborate complex Cp*Ru(P(i)Pr(3))(BH(2)MesCl) (2, 66%). Exposure of 2 to the chloride abstracting agent LiB(C(6)F(5))(4)·2.5OEt(2) provided [Cp*Ru(P(i)Pr(3))(BH(2)Mes)](+)B(C(6)F(5))(4)(-) (3, 54%), which features an unusual η(2)-B-H monoborane ligand. The related borate complex Cp*Ru(P(i)Pr(3))(BH(3)Mes) (5, 65%) was prepared from 1 and LiH(3)BMes. Attempts to effect the insertion of unsaturated organic substrates into the B-H bonds of 3 were unsuccessful, and efforts to dehydrohalogenate 2 using KO(t)Bu instead afforded the mesitylborate complex Cp*(P(i)Pr(3))Ru(BH(2)MesOH) (6, 48%). Treatment of 1 with benzyl potassium generated an intermediate hydridoruthenium complex (7) resulting from dehydrogenation of a P(i)Pr fragment, which in turn was observed to react with MesBH(2) to afford the mesitylborate complex Cp*(P((i)Pr)(2)(CH(3)CCH(2)))Ru(BH(3)Mes) (8, 47%). Crystallographic characterization data are provided for 2, 3, 5, 6, and 8. A combined X-ray crystallographic and density functional theory (DFT) investigation of 3 and 5, using Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) analysis, revealed that 3 and 5 are best described as donor-acceptor complexes between a Cp*(P(i)Pr(3))Ru(+) fragment and a bis(η(2)-B-H) coordinating mesitylborane(borate) ligand. Significant σ-donation from the B-H bonds into the Ru(II) center exists as evidenced by the NBO populations, bond orders, and AIM delocalization indices. In the case of 3, the vacant p orbital on boron is stabilized by Ru→B π back-donation as well as by resonance with the mesityl group.

  2. 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.

  3. The Crystallographic Study of Pr Substituted Eu-123 High Tc Cuprate Superconductors

    NASA Astrophysics Data System (ADS)

    Huse, V. R.; Mote, V. D.; Hasan, K. I.; Dole, B. N.; Shah, S. S.

    2011-07-01

    We have investigated Eu1-xPrxBa2Cu3O7-δ high purity samples with compositions x = 0.0, 0.1, 0.2, 0.3, 0.4 and 0.5 by well known ceramic route. The XRD study of all samples is carried out. The XRD study of the samples prepared by ceramic route show EuPr-123 system has an orthorhombic pervoskite structure. The lattice parameters, oxygen content, volume of unit cell, orthorhombicity, X-ray density, bulk density and porosity were evaluated using XRD data. It is found that the lattice parameters, volume of unit cell and porosity increase while oxygen content orthorhombicity, X-ray density and bulk density decrease as doping percentage of Pr increases. We report such qualitative results of Pr substituted Eu-123 in this paper quantitatively.

  4. 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.

  5. Crystallographic parameters of magnetic Pr2Fe14-xCoxB-type alloys determined using anomalous x-ray diffraction with synchrotron radiation

    NASA Astrophysics Data System (ADS)

    Galego, E.; Serna, M. M.; Ramanathan, L. V.; Faria, R. N.

    2017-02-01

    Anomalous x-ray synchrotron diffraction was used to determine the crystallographic parameters of PrFeCoB-based magnetic alloys. The effect of cobalt concentration on the crystallographic parameters of the magnetically hard Pr2Fe14-xCoxB phase was studied. The results indicate that addition of cobalt has a marked effect on crystal structure. Variation of the c parameter decreased twice as much as the a parameter with increase in Co content. The positions of inequivalent atoms of the magnetically hard matrix phase ϕ in the Pr-based alloys were determined using Rietveld refinement. This permitted determination of the relative distance of each inequivalent atom from its nearest neighbors. Cobalt occupied the 16k2 site and Fe had a tendency to occupy the 8j2 sites located between the Kagomé layers.

  6. 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.

  7. 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. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

  8. Conformation-changing aggregation in hydroxyacetone: a combined low-temperature FTIR, jet, and crystallographic study.

    PubMed

    Sharma, Archna; Reva, Igor; Fausto, Rui; Hesse, Susanne; Xue, Zhifeng; Suhm, Martin A; Nayak, Susanta K; Sathishkumar, Ranganthan; Pal, Rumpa; Row, Tayur N Guru

    2011-12-21

    Aggregation in hydroxyacetone (HA) is studied using low-temperature FTIR, supersonic jet expansion, and X-ray crystallographic (in situ cryocrystallization) techniques. Along with quantum chemical methods (MP2 and DFT), the experiments unravel the conformational preferences of HA upon aggregation to dimers and oligomers. The O-H···O═C intramolecular hydrogen bond present in the gas-phase monomer partially opens upon aggregation in supersonic expansions, giving rise to intermolecular cooperatively enhanced O-H···O-H hydrogen bonds in competition with isolated O-H···O═C hydrogen bonds. On the other hand, low-temperature IR studies on the neat solid and X-ray crystallographic data reveal that HA undergoes profound conformational changes upon crystallization, with the HOCC dihedral angle changing from ~0° in the gas phase to ~180° in the crystalline phase, hence giving rise to a completely new conformation. These conclusions are supported by theoretical calculations performed on the geometry derived from the crystalline phase. © 2011 American Chemical Society

  9. Charge-assisted triel bonding interactions in solid state chemistry: A combined computational and crystallographic study

    NASA Astrophysics Data System (ADS)

    Bauzá, Antonio; García-Llinás, Xavier; Frontera, Antonio

    2016-12-01

    A combined energetic and geometric study of a series of triel bond complexes involving haloborane salts has been carried out at the M06-2X/def2-QZVPD level of theory. We have used 1-(dihaloboranyl)pyridin-1-ium compounds Py+BX2 (X = Cl, Br and I) as triel bond donors and Cl-, Br-, HCO2-, BF4- and ClO4- as electron donor moieties. In addition we have used Bader's theory of 'atoms in molecules' to further characterize the noncovalent interactions described herein. Finally, several examples were retrieved from the CSD (Cambridge Structural Database) in order to provide experimental support to the results presented in this work.

  10. Crystallographic Instrumentation

    NASA Astrophysics Data System (ADS)

    Aslanov, L. A.; Fetisov, G. V.; Howard, J. A. K.

    1998-07-01

    Innovations in crystallographic instrumentation and the rapid development of methods of diffraction measurement have led to a vast improvement in our ability to determine crystal and molecular structure. This up-to-date resource will allow the reader to harness the potential of X-ray diffraction instruments. Different sources of X-radiation used in crystallography are introduced, including synchrotron radiation, as well as a systematic review of detectors for X-rays and basic instruments for single crystal and powder diffractometry. The principles of the diffraction experiment are discussed and related to their practical application with a comparative description of different scan procedures. Diffraction data collection and processing are also reviewed and methods for error correction are described. This book will provide a useful guide for researchers and students starting in this area of science, as well as skilled crystallographers.

  11. Hydrogen-bond interactions of nicotine and acetylcholine salts: a combined crystallographic, spectroscopic, thermodynamic and theoretical study.

    PubMed

    Arnaud, Virginie; Berthelot, Michel; Evain, Michel; Graton, Jérôme; Le Questel, Jean-Yves

    2007-01-01

    The hydrogen-bond (HB) interactions of the monocharged active forms of nicotine and acetylcholine (ACh) have been compared theoretically by using density functional theory (DFT) calculations and experimentally on the basis of crystallographic observations and the measurement of equilibrium constants in solution. The 2,4,6-trinitrophenolate (picrate) counterion was used to determine the experimental HB basicity of the cations despite its potential multisite HB acceptor properties. The preferred HB interaction site of the ammonium picrate salts was determined from a survey of crystallographic data found in the Cambridge Structural Database (CSD) and is supported by theoretical calculations. Two distinct classes of ammonium groups were characterised depending on the absence (quaternary ammonium) or presence (tertiary, secondary and primary ammoniums) of an N(+)HO hydrogen bond linking the two ions. The crystal structure of nicotinium picrate was determined and compared with that of ACh. This analysis revealed the peculiar behaviour of the ammonium moiety of nicotinic acetylcholine receptor (nAChR) ligands towards the picrate anion. Dedicated methods have been developed to separate the individual contributions of the anion and cation accepting sites to the overall HB basicity of the ion pairs measured in solution. The HB basicities of the picrate anions associated with the two different ammonium classes were determined in dichloromethane solution by using several model ion pairs with non-basic ammonium cations. The experimental and theoretical studies performed on the nicotine and ACh cations consistently show the significant HB ability of the acceptor site of nAChR agonists in their charged form. Both the greater HB basicity of the pyridinic nitrogen over the carbonyl oxygen and the greater HB acidity of the N(+)H unit relative to N(+)CH could contribute to the higher affinity for nAChRs of nicotine-like ligands relative to ACh-like ligands.

  12. Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease.

    PubMed

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

    2010-09-24

    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 β-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.

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

    PubMed Central

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

    2010-01-01

    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 β-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. PMID:20685658

  14. 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.

  15. 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

  16. PrEP for key populations in combination HIV prevention in Nairobi: a mathematical modelling study.

    PubMed

    Cremin, Ide; McKinnon, Lyle; Kimani, Joshua; Cherutich, Peter; Gakii, Gloria; Muriuki, Festus; Kripke, Katharine; Hecht, Robert; Kiragu, Michael; Smith, Jennifer; Hinsley, Wes; Gelmon, Lawrence; Hallett, Timothy B

    2017-05-01

    -$51 560), respectively. PrEP could be a useful contribution to combination prevention, especially for under-served key populations in Nairobi. An ongoing demonstration project will provide important information regarding practical aspects of implementing PrEP for key populations in this setting. The Bill & Melinda Gates Foundation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. 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.

  18. Site preferences in hetero-metallic [Fe9-xNix] clusters: a combined crystallographic, spectroscopic and theoretical analysis.

    PubMed

    Georgopoulou, Anastasia N; Al-Ameed, Karrar; Boudalis, Athanassios K; Anagnostopoulos, Dimitrios F; Psycharis, Vassilis; McGrady, John E; Sanakis, Yiannis; Raptopoulou, Catherine P

    2017-09-18

    The reaction of mixtures of Fe(O2CMe)2·2H2O and Ni(O2CMe)2·4H2O of various compositions with di-2-pyridyl ketone (py2CO, dpk) in MeCN under an inert atmosphere afforded a family of hetero-metallic enneanuclear clusters with general formula [Fe9-xNix(μ4-OH)2(O2CMe)8(py2CO2)4] (2, x = 1.00; 3: x = 6.02; 4, x = 7.46; 5, x = 7.81). Clusters 2-5 are isomorphous to the homo-metallic [Fe9] cluster (1) previously reported by some of us, and also isostructural to the known homo-metallic [Ni9] cluster. All four clusters contain a central M(II) ion in an unusual 8-coordinate site and eight peripheral M(II) ions in distorted octahedral environments. The distribution of Fe(II) and Ni(II) ions over these two distinct coordination sites in 2-5 can be established through a combination of X-ray fluorescence and Mössbauer spectroscopies, which show that Fe(II) preferentially occupies the unique 8-coordinate metal site while Ni(II) accumulates in the octahedral holes. Density functional theory indicates that the distribution of ions across the two sites arises not from any intrinsic preference of the Fe(II) ions for the 8-coordinate sites, but rather because of the large ligand field stabilization energy available to Ni(II) in octahedral coordination.

  19. 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.

  20. 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.

  1. Towards a fair consideration of PrEP as part of combination HIV prevention in Latin America

    PubMed Central

    Ravasi, Giovanni; Grinsztejn, Beatriz; Baruch, Ricardo; Guanira, Juan Vicente; Luque, Ricardo; Cáceres, Carlos F; Ghidinelli, Massimo

    2016-01-01

    Introduction Despite progress in scaling up antiretroviral treatment, HIV prevention strategies have not been successful in significantly curbing HIV incidence in Latin America. HIV prevention interventions need to be expanded to target the most affected key populations with a combination approach, including new high impact technologies. Oral pre-exposure prophylaxis (PrEP) is recommended as additional prevention choice for individuals at higher risk of infection and could become a cost-effective prevention tool. We discuss the barriers and solutions for a fair consideration of PrEP as part of combination HIV prevention strategies in Latin America. Discussion Although demonstration projects are ongoing or being planned in a number of countries, to date no Latin American country has implemented a public PrEP programme. The knowledge of policymakers about PrEP implementation needs to be strengthened, and programmatic guidance and cost estimate tools need to be developed to support adequate planning. Despite high levels of awareness among health providers, especially if engaged in HIV or key population care, willingness to prescribe PrEP is still low due to the lack of national policies and guidelines. Key populations, especially men who have sex with men, transgender women and sex workers, have been engaged in demonstration projects, and qualitative research shows high awareness and willingness to use PrEP, especially if accessible in the public sector for free or at affordable price. Concerns of safety, adherence, effectiveness and risk compensation need to be addressed through targeted social communication strategies to improve PrEP knowledge and stimulate demand. Alliance among policymakers, civil society and representatives from key populations, healthcare providers and researchers will be critical for the design and successful implementation of PrEP demonstration projects of locally adapted delivery models. The use of mechanisms of joint negotiation and

  2. Towards a fair consideration of PrEP as part of combination HIV prevention in Latin America.

    PubMed

    Ravasi, Giovanni; Grinsztejn, Beatriz; Baruch, Ricardo; Guanira, Juan Vicente; Luque, Ricardo; Cáceres, Carlos F; Ghidinelli, Massimo

    2016-01-01

    Despite progress in scaling up antiretroviral treatment, HIV prevention strategies have not been successful in significantly curbing HIV incidence in Latin America. HIV prevention interventions need to be expanded to target the most affected key populations with a combination approach, including new high impact technologies. Oral pre-exposure prophylaxis (PrEP) is recommended as additional prevention choice for individuals at higher risk of infection and could become a cost-effective prevention tool. We discuss the barriers and solutions for a fair consideration of PrEP as part of combination HIV prevention strategies in Latin America. Although demonstration projects are ongoing or being planned in a number of countries, to date no Latin American country has implemented a public PrEP programme. The knowledge of policymakers about PrEP implementation needs to be strengthened, and programmatic guidance and cost estimate tools need to be developed to support adequate planning. Despite high levels of awareness among health providers, especially if engaged in HIV or key population care, willingness to prescribe PrEP is still low due to the lack of national policies and guidelines. Key populations, especially men who have sex with men, transgender women and sex workers, have been engaged in demonstration projects, and qualitative research shows high awareness and willingness to use PrEP, especially if accessible in the public sector for free or at affordable price. Concerns of safety, adherence, effectiveness and risk compensation need to be addressed through targeted social communication strategies to improve PrEP knowledge and stimulate demand. Alliance among policymakers, civil society and representatives from key populations, healthcare providers and researchers will be critical for the design and successful implementation of PrEP demonstration projects of locally adapted delivery models. The use of mechanisms of joint negotiation and procurement of antiretrovirals

  3. Crystallographic and physical properties of new orthorhombic Cu-1212 R(Ba 2-xR‧ x)Cu 3O 7+y system (R, R‧La, Pr, Nd; 0.65

    NASA Astrophysics Data System (ADS)

    Lin, B. N.; Lin, Y. H.; Luo, H. M.; Lee, T. J.; Ho, J. C.; Ku, H. C.

    Structural, magnetic, calorimetric and transport results are reported for the new orthorhombic Cu-1212 R(Ba 2-xR‧ x)Cu 3O 7+y cuprates (R, R‧La, Pr, Nd; 0.65 < x < 1). Powder X-ray Rietveld refinement analysis for oxygenated R 1.7Ba 1.3Cu 3O 7+y (RLa, Pr, Nd; y ∼ 0.3) indicates that the new orthorhombic O(II)-phase with space group Cmmm and lattice parameters a 0 < b o ∼ 0.55 nm, c ∼ 1.16 nm is very similar to the Bi-2212 structure except that (BiO) 2 bi-layer is replaced by a single CuO 1+y plane. For the oxygenated Pr(Ba 2-xR x)Cu 3O 7+y O(II)-phase cuprates (RLa, Pr; y > 0.2), anomalous Pr ordering temperature T N(Pr) decreases sharply from 18 K for O(I)-phase PrBa 2Cu 3O 7 (space group Pmmm, a o < b o ∼ 0.39 nm and c ∼ 1.17 nm), to 5.5 K for Pr(Ba 1.3Pr 0.7)Cu 3O 7.25 and 6 K for Pr(Ba 1.3La 0.7)Cu 3O 7.29. The dramatically decreasing T N(Pr) is closely related with longer PrO bond length in the O(II)-phase which effectively decreases Pr 4f-O 2p π orbital hybridization. No superconductivity was observed for these new insulating cuprates.

  4. 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…

  5. 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…

  6. PR-104 a bioreductive pre-prodrug combined with gemcitabine or docetaxel in a phase Ib study of patients with advanced solid tumours

    PubMed Central

    2012-01-01

    Background The purpose of this phase Ib clinical trial was to determine the maximum tolerated dose (MTD) of PR-104 a bioreductive pre-prodrug given in combination with gemcitabine or docetaxel in patients with advanced solid tumours. Methods PR-104 was administered as a one-hour intravenous infusion combined with docetaxel 60 to 75 mg/m2 on day one given with or without granulocyte colony stimulating factor (G-CSF) on day two or administrated with gemcitabine 800 mg/m2 on days one and eight, of a 21-day treatment cycle. Patients were assigned to one of ten PR-104 dose-levels ranging from 140 to 1100 mg/m2 and to one of four combination groups. Pharmacokinetic studies were scheduled for cycle one day one and 18F fluoromisonidazole (FMISO) positron emission tomography hypoxia imaging at baseline and after two treatment cycles. Results Forty two patients (23 females and 19 males) were enrolled with ages ranging from 27 to 85 years and a wide range of advanced solid tumours. The MTD of PR-104 was 140 mg/m2 when combined with gemcitabine, 200 mg/m2 when combined with docetaxel 60 mg/m2, 770 mg/m2 when combined with docetaxel 60 mg/m2 plus G-CSF and ≥770 mg/m2 when combined with docetaxel 75 mg/m2 plus G-CSF. Dose-limiting toxicity (DLT) across all four combination settings included thrombocytopenia, neutropenic fever and fatigue. Other common grade three or four toxicities included neutropenia, anaemia and leukopenia. Four patients had partial tumour response. Eleven of 17 patients undergoing FMISO scans showed tumour hypoxia at baseline. Plasma pharmacokinetics of PR-104, its metabolites (alcohol PR-104A, glucuronide PR-104G, hydroxylamine PR-104H, amine PR-104M and semi-mustard PR-104S1), docetaxel and gemcitabine were similar to that of their single agents. Conclusions Combination of PR-104 with docetaxel or gemcitabine caused dose-limiting and severe myelotoxicity, but prophylactic G-CSF allowed PR-104 dose escalation with docetaxel. Dose-limiting thrombocytopenia

  7. Combined microspectrophotometric and crystallographic examination of chemically-reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus

    PubMed Central

    Liu, Bin; Chen, Ying; Doukov, Tzanko; Soltis, S. Michael; Stout, C. David; Fee, James A.

    2009-01-01

    Three paths are described to obtain crystals of reduced (II-E4Q/I-K258R) cytochrome ba3, and the structures of these are reported at ∼2.8 to 3.0 Å resolution. Microspectrophotometry of single crystals of Thermus ba3 oxidase at 100 K was used to show that crystals of the oxidized enzyme are reduced in an intense X-ray (beam line 7-1 at the Stanford Synchrotron Radiation Laboratory, U.S.A) being nearly complete in one minute. The previously reported structures of ba3 (PDB codes 1EHK and 1XME), having a crystallographically detectable water between the CuB and Fea3 metals of the dinuclear center, actually represent the X-ray radiation-reduced enzyme. Dithionite reduced crystals or crystals formed from dithionite reduced enzyme revealed the absence of the above mentioned water and an increase in the CuB - Fea3 distance of ∼0.3 A. The new structures are discussed in terms of enzyme function. An unexpected optical absorption envelope at ∼590 nm is also reported. This spectral feature is tentatively thought to arise from a 5-coordinate, low-spin, ferrous heme-a3 that is trapped in the frozen crystals. PMID:19140675

  8. 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.

  9. Improved low-resolution crystallographic refinement with Phenix and Rosetta.

    PubMed

    DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J; Terwilliger, Thomas C; Adams, Paul D; Baker, David

    2013-11-01

    Refinement of macromolecular structures against low-resolution crystallographic data is limited by the ability of current methods to converge on a structure with realistic geometry. We developed a low-resolution crystallographic refinement method that combines the Rosetta sampling methodology and energy function with reciprocal-space X-ray refinement in Phenix. On a set of difficult low-resolution cases, the method yielded improved model geometry and lower free R factors than alternate refinement methods.

  10. Phaser crystallographic software.

    PubMed

    McCoy, Airlie J; Grosse-Kunstleve, Ralf W; Adams, Paul D; Winn, Martyn D; Storoni, Laurent C; Read, Randy J

    2007-08-01

    Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F(+) and F(-), give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences DeltaF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

  11. Phaser crystallographic software

    PubMed Central

    McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Winn, Martyn D.; Storoni, Laurent C.; Read, Randy J.

    2007-01-01

    Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F + and F −, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community. PMID:19461840

  12. CIF (Crystallographic Information File): A Standard for Crystallographic Data Interchange

    PubMed Central

    Brown, I. D.

    1996-01-01

    The Crystallographic Information File (CIF) uses the self-defining STAR file structure. This requires the creation of a dictionary of data names and definitions. A basic dictionary of terms needed to describe the crystal structures of small molecules was approved in 1991 and is currently used for the submission of papers to Acta Crystallographica C. A number of extensions to this dictionary are in preparation. By storing the dictionary itself as a STAR file, the definitions and relationships in the CIF dictionary become computer interpretable. This offers many possibilities for the automatic handling of crystallographic information. PMID:27805170

  13. Crystallographic Groups, Groupoids, and Orbifolds

    SciTech Connect

    Johnson, C.K.

    2000-09-11

    In this note, We first discuss the relationship among crystallographic lattice groups, space groups, and point groups by using a short exact sequence, then in footnotes indicate the classification of those groups. We then introduce screw and glide groupoids as an extension of point groups in a new exact sequence, and list the one-translational-dimension screw and glide groupoids, which require torus and truncated cylinder projection representations in addition to the spherical projection used for point groups. We then briefly discuss the two and three translational dimension groupoids associated with the remaining point groups. Examples of space groups and their groupoid based nomenclature, which is mainly the extended Hermana-Mauguin international crystallographic nomenclature system plus a specific type of coset decomposition, are then given. Next the crystallographic orbifolds are defined and some application problems associated with orbifolds discussed. Finally, the derivation of might be called orbifoldoids is suggested as future research.

  14. PrEP as a feature in the optimal landscape of combination HIV prevention in sub-Saharan Africa

    PubMed Central

    McGillen, Jessica B; Anderson, Sarah-Jane; Hallett, Timothy B

    2016-01-01

    Introduction The new WHO guidelines recommend offering pre-exposure prophylaxis (PrEP) to people who are at substantial risk of HIV infection. However, where PrEP should be prioritised, and for which population groups, remains an open question. The HIV landscape in sub-Saharan Africa features limited prevention resources, multiple options for achieving cost saving, and epidemic heterogeneity. This paper examines what role PrEP should play in optimal prevention in this complex and dynamic landscape. Methods We use a model that was previously developed to capture subnational HIV transmission in sub-Saharan Africa. With this model, we can consider how prevention funds could be distributed across and within countries throughout sub-Saharan Africa to enable optimal HIV prevention (that is, avert the greatest number of infections for the lowest cost). Here, we focus on PrEP to elucidate where, and to whom, it would optimally be offered in portfolios of interventions (alongside voluntary medical male circumcision, treatment as prevention, and behaviour change communication). Over a range of continental expenditure levels, we use our model to explore prevention patterns that incorporate PrEP, exclude PrEP, or implement PrEP according to a fixed incidence threshold. Results At low-to-moderate levels of total prevention expenditure, we find that the optimal intervention portfolios would include PrEP in only a few regions and primarily for female sex workers (FSW). Prioritisation of PrEP would expand with increasing total expenditure, such that the optimal prevention portfolios would offer PrEP in more subnational regions and increasingly for men who have sex with men (MSM) and the lower incidence general population. The marginal benefit of including PrEP among the available interventions increases with overall expenditure by up to 14% (relative to excluding PrEP). The minimum baseline incidence for the optimal offer of PrEP declines for all population groups as expenditure

  15. An aluminophosphate molecular sieve with 36 crystallographically distinct tetrahedral sites.

    PubMed

    Lee, Jun Kyu; Turrina, Alessandro; Zhu, Liangkui; Seo, Seungwan; Zhang, Daliang; Cox, Paul A; Wright, Paul A; Qiu, Shilun; Hong, Suk Bong

    2014-07-14

    The structure of the new medium-pore aluminophosphate molecular sieve PST-6 is determined by the combined use of rotation electron diffraction tomography, synchrotron X-ray powder diffraction, and computer modeling. PST-6 was prepared by calcination of another new aluminophosphate material with an unknown structure synthesized using diethylamine as a structure-directing agent, which is thought to contain bridging hydroxy groups. PST-6 has 36 crystallographically distinct tetrahedral sites in the asymmetric unit and is thus crystallographically the most complex zeolitic structure ever solved. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. 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.

  17. 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

  18. Counter machines and crystallographic structures.

    PubMed

    Jonoska, N; Krajcevski, M; McColm, G

    2016-03-01

    One way to depict a crystallographic structure is by a periodic (di)graph, i.e., a graph whose group of automorphisms has a translational subgroup of finite index acting freely on the structure. We establish a relationship between periodic graphs representing crystallographic structures and an infinite hierarchy of intersection languages ℒ d , d = 0, 1, 2, …, within the intersection classes of deterministic context-free languages. We introduce a class of counter machines that accept these languages, where the machines with d counters recognize the class ℒ d An intersection of d languages in ℒ1 defines ℒ d . We prove that there is a one-to-one correspondence between sets of walks starting and ending in the same unit of a d-dimensional periodic (di)graph and the class of languages in ℒ d . The proof uses the following result: given a digraph Δ and a group G, there is a unique digraph Γ such that G ≤ Aut Γ, G acts freely on the structure, and Γ/G ≅ Δ.

  19. Counter machines and crystallographic structures

    PubMed Central

    Krajcevski, M.; McColm, G.

    2016-01-01

    One way to depict a crystallographic structure is by a periodic (di)graph, i.e., a graph whose group of automorphisms has a translational subgroup of finite index acting freely on the structure. We establish a relationship between periodic graphs representing crystallographic structures and an infinite hierarchy of intersection languages 𝒟𝒞ℒd, d = 0, 1, 2, …, within the intersection classes of deterministic context-free languages. We introduce a class of counter machines that accept these languages, where the machines with d counters recognize the class 𝒟𝒞ℒd An intersection of d languages in 𝒟𝒞ℒ1 defines 𝒟𝒞ℒd. We prove that there is a one-to-one correspondence between sets of walks starting and ending in the same unit of a d-dimensional periodic (di)graph and the class of languages in 𝒟𝒞ℒd. The proof uses the following result: given a digraph Δ and a group G, there is a unique digraph Γ such that G ≤ Aut Γ, G acts freely on the structure, and Γ/G ≅ Δ. PMID:27616944

  20. Peptidomimetic Src/pretubulin inhibitor KX-01 alone and in combination with paclitaxel suppresses growth, metastasis in human ER/PR/HER2-negative tumor xenografts

    PubMed Central

    Anbalagan, Muralidharan; Ali, Alaa; Jones, Ryan K; Marsden, Carolyn G; Sheng, Mei; Carrier, Latonya; Bu, Yahao; Hangauer, David; Rowan, Brian G

    2012-01-01

    Src kinase is elevated in breast tumors that are ER/PR negative and do not overexpress HER2 but clinical trials with Src inhibitors have demonstrated little activity. The present study evaluated preclinical efficacy of a novel peptidomimetic compound, KX-01 (KX2-391), that exhibits dual action as a Src and pretubulin inhibitor. KX-01 was evaluated as a single agent and in combination with paclitaxel in MDA-MB-231, MDA-MB-157, and MDA-MB-468 human ER/PR/HER2-negative breast cancer cells. Treatments were evaluated by growth/apoptosis, isobologram analysis, migration/invasion assays, tumor xenograft volume, metastasis, and measurement of Src, FAK, microtubules, Ki67, and microvessel density. KX-01 inhibited cell growth in vitro and in combination with paclitaxel resulted in synergistic growth inhibition. KX-01 resulted in a dose dependent inhibition of MDA-MB-231 and MDA-MB-157 tumor xenografts (1 and 5 mg/kg, BID). KX-01 inhibited activity of Src and downstream mediator FAK in tumors that was coincident with reduced proliferation and angiogenesis, and increased apoptosis. KX01 also resulted in microtubule disruption in tumors. Combination of KX-01 with paclitaxel resulted in significant regression of MDA-MB-231 tumors and reduced metastasis to mouse lung and liver. KX-01 is a potently active Src/pretubulin inhibitor that inhibits breast tumor growth and metastasis. As ER/PR/HER2-negative patients are candidates for paclitaxel therapy, combination with KX-01 may potentiate antitumor efficacy in management of this aggressive breast cancer subtype. PMID:22784709

  1. 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

  2. Recovery of crystallographic texture in remineralized dental enamel.

    PubMed

    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

  3. From direct-space discrepancy functions to crystallographic least squares.

    PubMed

    Giacovazzo, Carmelo

    2015-01-01

    Crystallographic least squares are a fundamental tool for crystal structure analysis. In this paper their properties are derived from functions estimating the degree of similarity between two electron-density maps. The new approach leads also to modifications of the standard least-squares procedures, potentially able to improve their efficiency. The role of the scaling factor between observed and model amplitudes is analysed: the concept of unlocated model is discussed and its scattering contribution is combined with that arising from the located model. Also, the possible use of an ancillary parameter, to be associated with the classical weight related to the variance of the observed amplitudes, is studied. The crystallographic discrepancy factors, basic tools often combined with least-squares procedures in phasing approaches, are analysed. The mathematical approach here described includes, as a special case, the so-called vector refinement, used when accurate estimates of the target phases are available.

  4. 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.

  5. Internet Based Open Access Crystallographic Databases

    NASA Astrophysics Data System (ADS)

    Upreti, Girish; Seipel, Bjoern; Harvey, Morgan; Garrick, Will; Moeck, Peter

    2006-05-01

    Two freely accessible crystallographic databases are discussed: the Crystallographic Open Database (COD, http://crystallography.net) which contains over 37,000 crystal structures, and the Nano-Crystallography Database (NCD, http://nanocrystallography.research.pdx.edu) which we recently started to support image-based nanocrystallography and (nano) materials science education. Both databases collect crystallographic relevant information in a standardized format; the Crystallographic Information File (CIF). CIF is the standard file format adopted by the International Union of Crystallography (http://iucr.org) for the archiving and distribution of crystallographic information. A subset of the COD, the Predicted Crystallographic Online Database, allows for 3D structural displays of structural polyhedra and wireframes of approximately 2,600 entries. Since electron microscopist are interested in simple, yet technologically important materials, the crystallographic information for those materials will be included in our database. At our NCD site, entries in the COD and the NCD can be visualized in three dimensions (3D) along with (2D) lattice fringe fingerprints plots. The latter supports the identification of unknown nanocrystal phases from high-resolution transmission electron microscopy (HRTEM) images. Morphological crystal information from the database ``Bestimmungstabellen f"ur Kristalle/ ???????????? ??????????,'' (A.K. Boldyrew and W.W. Doliwo-Dobrowolsky, Zentrales Wissenschaftlichers Institute der Geologie und Sch"urfung, Leningrad/ Moscow, 1937/1939) will also be included in the NCD to support image-based nanocrystallography in 3D.

  6. 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.

  7. 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

  8. 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

  9. Efficacy and safety profile of prolonged release oxycodone in combination with naloxone (OXN PR) in Parkinson's disease patients with chronic pain.

    PubMed

    Madeo, Graziella; Schirinzi, Tommaso; Natoli, Silvia; Pierantozzi, Mariangela; Stefani, Alessandro; Dauri, Mario; Pisani, Antonio

    2015-09-01

    Pain is a relevant and often underestimated non-motor symptom affecting the quality of life of patients with Parkinson's disease (PD). Although some pain symptoms can be effectively treated by dopaminergic medication, a correct diagnosis of the different types and distribution of pain in PD is challenging, and accordingly, its treatment remains troublesome. We evaluated the efficacy and the safety of a prolonged release oral formulation of oxycodone hydrochloride combined with naloxone hydrochloride dehydrate, in a fixed ratio of 2:1 (OXN PR). A total of 16 PD patients with history of pain with a minimum intensity of four on numerical rating scale (NRS) received low-dose OXN PR (5/2.5 mg twice daily) and were observed for a period of 8 weeks. The primary efficacy measure was the pain severity measured with NRS and Brief Pain Inventory (BPI). Secondary efficacy measured the safety profile by recording the occurrence of side effects, clinical global impression of change (CGI-C), Parkinson's disease sleep scale 2 (PDSS-2), Bowel function index (BFI). Data were collected and analyzed using descriptive statistics. Patients who completed the study (14 out of 16) reported a significant pain relief as observed by the reduction of NRS and BPI scores. No adjustment of dopaminergic therapy was required. No significant changes were observed in bowel function and constipation symptoms as measured by the BFI during the 8-week period. Similarly, no changes were observed in PDSS-2 score, whereas an improvement was recorded by CGI-C compared to baseline. Low-dose oral OXN PR was efficacious for the management of pain symptoms of patients with PD. More importantly, patients did not experience significant side effects, such as constipation or sedation. Our study provides evidence that opioids can be used to treat pain symptoms in PD patients.

  10. Defining the Crystallographic Fingerprint of Extraterrestrial Treasures

    NASA Astrophysics Data System (ADS)

    Forman, L. V.; Bland, P. A.; Timms, N. E.; Daly, L.; Benedix, G. K.; Trimby, P. W.

    2016-08-01

    An approach to determine the crystallographic fingerprint of chondritic matrix grains, which is complimentary to the geochemical signature commonly identified to constrain some aspects of the petrogenesis of a sample.

  11. CRYSTMET -- The NRCC Metals Crystallographic Data File

    SciTech Connect

    Wood, G.H.; Rodgers, J.R.; Gough, S.R.; Villars, P.

    1996-05-01

    CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60,000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool.

  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

    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.

  13. Gallium composition dependence of crystallographic and thermoelectric properties in polycrystalline type-I Ba{sub 8}Ga{sub x}Si{sub 46-x} (nominal x=14-18) clathrates prepared by combining arc melting and spark plasma sintering methods

    SciTech Connect

    Anno, Hiroaki; Yamada, Hiroki; Nakabayashi, Takahiro; Hokazono, Masahiro; Shirataki, Ritsuko

    2012-09-15

    The gallium composition dependence of crystallographic and thermoelectric properties in polycrystalline n-type Ba{sub 8}Ga{sub x}Si{sub 46-x} (nominal x=14-18) compounds with the type-I clathrate structure is presented. Samples were prepared by combining arc melting and spark plasma sintering methods. Powder x-ray diffraction, Rietveld analysis, scanning electron microscopy, and energy-dispersive x-ray spectroscopy show that the solubility limit of gallium in the type-I clathrate phase is close to x=15, which is slightly higher than that for a single crystal. The carrier concentration at room temperature decreases from 2 Multiplication-Sign 10{sup 21} cm{sup -3} to 4 Multiplication-Sign 10{sup 20} cm{sup -3} as the Ga content x increases. The Seebeck coefficient, the electrical conductivity, and the thermal conductivity vary systematically with the carrier concentration when the Ga content x varies. The effective mass (2.0m{sub 0}), the carrier mobility (10 cm{sup 2} V{sup -1} s{sup -1}), and the lattice thermal conductivity (1.1 W m{sup -1} K{sup -1}) are determined for the Ga content x=14.51. The dimensionless thermoelectric figure of merit ZT is about 0.55 at 900 K for the Ga content x=14.51. The calculation of ZT using the experimentally determined material parameters predicts ZT=0.8 (900 K) at the optimum carrier concentration of about 2 Multiplication-Sign 10{sup 20} cm{sup -3}. - Graphical abstract: The gallium composition dependence of crystallographic and thermoelectric properties is presented on polycrystalline n-type Ba{sub 8}Ga{sub x}Si{sub 46-x} with the type-I clathrate structure prepared by combining arc melting and spark plasma sintering methods. The thermoelectric figure of merit ZT reaches 0.55 at 900 K due to the increase in the Ga content (close to x=15), and a calculation predicts further improvement of ZT at the optimized carrier concentration. Highlights: Black-Right-Pointing-Pointer Crystallographic properties of Ba{sub 8}Ga{sub x}Si{sub 46

  14. Asymmetrical quartz crystallographic fabrics formed during constrictional deformation

    NASA Astrophysics Data System (ADS)

    Sullivan, W. A.; Beane, R. J.

    2010-10-01

    Numerical simulations predict unique quartz crystallographic fabric patterns for plane strain, flattening, and constriction. Multiple studies support the predictions for plane strain and flattening. To test predictions for constriction, this paper analyzes five examples of quartz crystallographic fabrics from a 1-km-wide domain of L tectonites in the Pigeon Point high-strain zone, Klamath Mountains, California, U.S.A. These samples were deformed under greenschist- to amphibolite-facies conditions. Quartz c-axis fabrics are similar to the predicted double-girdle fabrics except that amphibolite-facies samples exhibit c-axis maxima and are distinctly asymmetrical about the elongation lineations. Activation of different slip systems combined with small deviations from pure constriction account for the c-axis maxima, and noncoaxial flow accounts for the fabric asymmetry. The simple-shear component is randomly oriented in geographic coordinates throughout the domain of L tectonites. These data confirm that numerical simulations predict the quartz c-axis fabric geometry developed during constriction for some deformation conditions, and they confirm the quartz a-axis patterns predicted for constriction for the first time. These data also demonstrate that the relationship between quartz crystallographic fabrics and strain geometry is not straightforward, and they indicate that a-axis fabrics may be more useful indicators of strain geometry variations.

  15. Novel preclinical models of topical PrEP pharmacodynamics provide rationale for combination of drugs with complementary properties.

    PubMed

    Mesquita, Pedro M M; Srinivasan, Priya; Johnson, Todd J; Rastogi, Rachna; Evans-Strickfaden, Tammy; Kay, Michael S; Buckheit, Karen W; Buckheit, Robert W; Smith, James M; Kiser, Patrick F; Herold, Betsy C

    2013-10-24

    The limited success of recent HIV topical pre-exposure prophylaxis clinical trials highlights the need for more predictive models of drug efficacy that better simulate what may happen during sexual exposure. To address this gap, we developed complementary in vitro models to evaluate the ability of drugs to retain anti-HIV activity if cells were washed with seminal plasma (simulating what may happen following exposure to ejaculate), and to protect drug-naive T cells (representing newly recruited immune cells) co-cultured with explants that had been pretreated with drug. We focused on tenofovir disoproxil fumarate (TDF), the non-nucleoside reverse transcriptase inhibitors dapivirine (DPV) and IQP-0528, and the entry inhibitors maraviroc (MVC) and the D-peptide chol-PIE-12 trimer (PIE12). Studies were extended to macaques and the ability of cervical biopsies obtained from animals treated with an intravaginal ring formulation of IQP-0528 to protect ex vivo co-cultured T cells was determined. The antiviral activity of cervicovaginal lavage samples against a primary Clade C isolate was also measured and correlated with drug levels. Cells exposed to TDF were equally protected from HIV whether or not the drug-treated cells were washed with medium or seminal plasma prior to challenge. In contrast, several-fold higher concentrations of NNRTIs and entry inhibitors were needed to attain similar levels of HIV inhibition following a wash with seminal plasma. Conversely, the NNRTIs and PIE12, but not TDF or MVC, were effectively transferred from ex vivo treated explants and protected co-cultured T cells. Biopsies obtained from IQP-0528 ring-treated macaques also protected co-cultured T cells with viral inhibition ranging from 42-72%. Antiviral activity correlated with the concentration of drug recovered. Combinations of TDF with IQP-0528 protected in both in vitro models. Together, these models suggest that intracellularly retained drugs such as TDF may protect resident immune

  16. Novel preclinical models of topical PrEP pharmacodynamics provide rationale for combination of drugs with complementary properties

    PubMed Central

    2013-01-01

    Background The limited success of recent HIV topical pre-exposure prophylaxis clinical trials highlights the need for more predictive models of drug efficacy that better simulate what may happen during sexual exposure. To address this gap, we developed complementary in vitro models to evaluate the ability of drugs to retain anti-HIV activity if cells were washed with seminal plasma (simulating what may happen following exposure to ejaculate), and to protect drug-naive T cells (representing newly recruited immune cells) co-cultured with explants that had been pretreated with drug. We focused on tenofovir disoproxil fumarate (TDF), the non-nucleoside reverse transcriptase inhibitors dapivirine (DPV) and IQP-0528, and the entry inhibitors maraviroc (MVC) and the D-peptide chol-PIE-12 trimer (PIE12). Studies were extended to macaques and the ability of cervical biopsies obtained from animals treated with an intravaginal ring formulation of IQP-0528 to protect ex vivo co-cultured T cells was determined. The antiviral activity of cervicovaginal lavage samples against a primary Clade C isolate was also measured and correlated with drug levels. Results Cells exposed to TDF were equally protected from HIV whether or not the drug-treated cells were washed with medium or seminal plasma prior to challenge. In contrast, several-fold higher concentrations of NNRTIs and entry inhibitors were needed to attain similar levels of HIV inhibition following a wash with seminal plasma. Conversely, the NNRTIs and PIE12, but not TDF or MVC, were effectively transferred from ex vivo treated explants and protected co-cultured T cells. Biopsies obtained from IQP-0528 ring-treated macaques also protected co-cultured T cells with viral inhibition ranging from 42-72%. Antiviral activity correlated with the concentration of drug recovered. Combinations of TDF with IQP-0528 protected in both in vitro models. Conclusions Together, these models suggest that intracellularly retained drugs such as TDF

  17. Estimating 13.8-GHz Path-Integrated Attenuation from 10.7-GHz Brightness Temperatures for the TRMM Combined PR-TMI Precipitation Algorithm.

    NASA Astrophysics Data System (ADS)

    Smith, Eric A.; Turk, F. Joseph; Farrar, Michael R.; Mugnai, Alberto; Xiang, Xuwu

    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 TB measurements obtained from the TRMM microwave imager. Because the PR measures at an attenuating frequency, an independent estimate of PIA is used to constrain the solution to the radar equation, which incorporates effects of attenuation propagation along a radar beam. 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. The derived relationship expressing 13.8-GHz PIAs as a function of 10.7-GHz TB's is based on statistical fitting of many thousands of radiative transfer (RTE) calculations in which the relevant physical and radiative parameters affecting transmission, absorption, and scattering in a raining column and

  18. 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.

  19. Confessions of an icosahedral virus crystallographer.

    PubMed

    Johnson, John E

    2013-02-01

    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.

  20. 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

  1. Metrics for comparison of crystallographic maps

    PubMed Central

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

    2014-01-01

    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. PMID:25286844

  2. Uncertainty in retained austenite measurements applied to individual crystallographic orientations

    NASA Astrophysics Data System (ADS)

    Creuziger, A.; Gnäupel-Herold, T.

    2015-04-01

    A technique to measure the phase volume fraction of an individual orientation and the uncertainty in the measurement is demonstrated in this paper. The technique of complete pole figure averaging using neutron diffraction was used to assess the phase fraction of retained austenite in transformation induced plasticity (TRIP) steels and quantify the uncertainty in the phase fraction. In parallel, an ensemble of orientation distribution functions was calculated to assess crystallographic volume fractions of particular orientations and the uncertainty of these volume fractions using Monte Carlo techniques. These methods were combined to measure the retained austenite phase volume fraction of an individual orientation.

  3. 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…

  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

    DOE PAGES

    Sliwiak, Joanna; Dauter, Zbigniew; Kowiel, Marcin; ...

    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

  5. 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

    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 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.

  6. 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

  7. The effectiveness of nano chemotherapeutic particles combined with mifepristone depends on the PR isoform ratio in preclinical models of breast cancer

    PubMed Central

    Rojas, Paola; Lamb, Caroline; Colombo, Lucas; May, María; Molinolo, Alfredo; Lanari, Claudia

    2014-01-01

    There is clinical and experimental evidence suggesting that antiprogestins might be used for the treatment of selected breast cancer patients. Our aim was to evaluate the effect of albumin-bound paclitaxel (Nab-paclitaxel) and pegylated doxorubicin liposomes (PEG-LD) in combination with mifepristone (MFP) in experimental breast cancer models expressing different ratios of progesterone receptor (PR) isoforms A and B. We used two antiprogestin-responsive (PRA>PRB) and two resistant (PRA

  8. 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.

  9. The globalization of crystallographic knowledge.

    PubMed

    Murray-Rust, P

    1998-11-01

    The rapid growth of the World Wide Web provides major new opportunities for distributed databases, especially in macromolecular science. A new generation of technology, based on structured documents (SD), is being developed which will integrate documents and data in a seamless manner. This offers experimentalists the chance to publish and archive high-quality data from any discipline. Data and documents from different disciplines can be combined and searched using technology such as eXtensible Markup Language (XML) and its associated support for hypermedia (XLL), metadata (RDF) and stylesheets (XSL). Opportunities in crystallography and related disciplines are described.

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

    SciTech Connect

    Ringrose, Sharon

    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.

  11. Conventional and Eccentric Uses of Crystallographic Databases in Practical Materials Identification Problems

    PubMed Central

    Kaduk, James A.

    1996-01-01

    The crystallographic databases are powerful and cost-effective tools for solving materials identification problems, both individually and in combination. Examples of the conventional and unconventional use of the databases in solving practical problems involving organic, coordination, and inorganic compounds are provided. The creation and use of fully-relational versions of the Powder Diffraction File and NIST Crystal Data are described. PMID:27805165

  12. Metrics for comparison of crystallographic maps

    DOE PAGES

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; ...

    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

  13. A preliminary neutron crystallographic study of thaumatin.

    PubMed

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

    2008-05-01

    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 A 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.

  14. A preliminary neutron crystallographic study of thaumatin

    PubMed Central

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

    2008-01-01

    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. PMID:18453706

  15. Quantum crystallographic charge density of urea

    DOE PAGES

    Wall, Michael E.

    2016-06-08

    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

  16. Quantum crystallographic charge density of urea

    SciTech Connect

    Wall, Michael E.

    2016-06-08

    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. 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.

  17. 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.

  18. 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.

  19. Crystallographic texture determinations from inverse susceptibility measurements

    NASA Astrophysics Data System (ADS)

    Lewis, L. H.; Welch, D. O.

    1997-04-01

    Determination of the quantitative relationship between crystallographic texture and magnetic properties in advanced permanent magnets may be hampered by complex microstructures, which complicate methods that rely on diffraction, or by interparticulate interactions, which adversely affect methods based on magnetic remanence measurements. To this end, new techniques in the determination of texture of bulk permanent magnets are being explored to overcome these inherent experimental difficulties. The analysis of inverse paramagnetic susceptibility measurements constitutes a new method to investigate crystallographic texture. Such measurements also provide Curie temperature data, which are sensitive to chemical changes that may have occurred in the magnetic phase during processing. The mathematical formalism underlying the analysis of inverse susceptibility measurements is outlined, and is used to evaluate magnetic measurements taken from a series of Nd2Fe14B magnets that have been processed by different means, and thus contain different degrees of texture. While this method does provide qualitative information concerning the relative crystallographic alignment of magnet samples, it needs calibration to obtain an explicit value for a texture order parameter.

  20. Crystallographic preferred orientations and deformation mechanisms in mantle shear zones

    NASA Astrophysics Data System (ADS)

    Drury, Martyn; Pennock, Gill; Palasse, Laurie; Ave Lallemant, Hans; Vissers, Reinoud

    2013-04-01

    In this contribution we will review our research on deformation mechanisms and olivine crystallographic preferred orientation (CPO) development in naturally deformed peridotites from mantle shear zones. In naturally deformed exhumed upper mantle rocks a strong olivine crystallographic preferred orientation (CPO) is generally developed in coarse grained rocks. Fine grained peridotites (grain size less than 15 microns) tend to have random to weak olivine CPO and this weak CPO is usually interpreted in terms of dominant grain size sensitive deformation mechanisms. Recently examples have been found of modest CPO development in pyroxene rich olivine rocks with ultra-fine grain size and microstructures consistent with dominant grain boundary sliding and diffusion creep. Several mechanisms can explain CPO development and preservation during grain size sensitive creep, indicating that the magnitude of seismic anisotropy in mantle shear zones may not be simply related to deformation mechanisms. The studies on mantle rocks indicate that grain size sensitive creep is often important in exhumed mantle shear zones, although, in many cases deformation involves a combination of dislocation creep and grain size sensitive mechanisms. We will discuss the significance of observations made on exhumed mantle rocks to shear zones in the lithosphere and asthenosphere.

  1. 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.

  2. Crystallographic orientations of olivine inclusions in diamonds

    NASA Astrophysics Data System (ADS)

    Milani, S.; Nestola, F.; Angel, R. J.; Nimis, P.; Harris, J. W.

    2016-11-01

    In this work we report for the first time the crystallographic orientations of olivine inclusions trapped in diamonds from the Kaapvaal craton (South Africa) determined by single-crystal X-ray diffraction, and analyze them together with all available data in the literature. The overall data set indicates no preferred orientation of the olivine inclusions with respect to their diamond hosts. However, diamonds containing multiple olivine inclusions sometimes show clusters of olivines with the same orientation in the same diamond host. We conclude that such clusters can only be interpreted as the remnants of single olivine crystals pre-dating the growth of the host diamonds.

  3. Crystallographic Studies of the Anthrax Lethal Toxin.

    DTIC Science & Technology

    1997-01-01

    Singh, K. R. Klimpel, C. P. Quinn, Y. K. Chaudhary, J. Biol. Chem. 266, 15493-97 (1991). The carboxyl- terminal end of protective antigen is required for...AD CONTRACT NUMBER DAMD17-94-C-4047 TITLE: Crystallographic Studies of the Anthrax Lethal Toxin PRINCIPAL INVESTIGATOR: Christin A. Frederick, Ph.D...FUNDING NUMBERS Anthrax Lethal Toxin DAMDI7-94-C-4047 6. AUTHOR(S) Christin A. Frederick, Ph.D. 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8

  4. 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.

  5. Low Resolution Refinement of Atomic Models Against Crystallographic Data.

    PubMed

    Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

    2017-01-01

    This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, Pro

  6. 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…

  7. 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

  8. Crystallographic education in the 21st century.

    PubMed

    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

    2015-12-01

    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.

  9. Correlating Atom Probe Crystallographic Measurements with Transmission Kikuchi Diffraction Data.

    PubMed

    Breen, Andrew J; Babinsky, Katharina; Day, Alec C; Eder, K; Oakman, Connor J; Trimby, Patrick W; Primig, Sophie; Cairney, Julie M; Ringer, Simon P

    2017-03-14

    Correlative microscopy approaches offer synergistic solutions to many research problems. One such combination, that has been studied in limited detail, is the use of atom probe tomography (APT) and transmission Kikuchi diffraction (TKD) on the same tip specimen. By combining these two powerful microscopy techniques, the microstructure of important engineering alloys can be studied in greater detail. For the first time, the accuracy of crystallographic measurements made using APT will be independently verified using TKD. Experimental data from two atom probe tips, one a nanocrystalline Al-0.5Ag alloy specimen collected on a straight flight-path atom probe and the other a high purity Mo specimen collected on a reflectron-fitted instrument, will be compared. We find that the average minimum misorientation angle, calculated from calibrated atom probe reconstructions with two different pole combinations, deviate 0.7° and 1.4°, respectively, from the TKD results. The type of atom probe and experimental conditions appear to have some impact on this accuracy and the reconstruction and measurement procedures are likely to contribute further to degradation in angular resolution. The challenges and implications of this correlative approach will also be discussed.

  10. 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

  11. 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

  12. High-power direct green laser oscillation of 598 mW in Pr(3+)-doped waterproof fluoroaluminate glass fiber excited by two-polarization-combined GaN laser diodes.

    PubMed

    Nakanishi, Jun; Horiuchi, Yuya; Yamada, Tsuyoshi; Ishii, Osamu; Yamazaki, Masaaki; Yoshida, Minoru; Fujimoto, Yasushi

    2011-05-15

    We demonstrated a high-power and highly efficient Pr-doped waterproof fluoride glass fiber laser at 522.2 nm excited by two-polarization-combined GaN laser diodes and achieved a subwatt output power of 598 mW and slope efficiency of 43.0%. This system will enable us to make a vivid laser display, a photocoagulation laser for eye surgery, a color confocal scanning laser microscope, and an effective laser for material processing. Direct visible ultrashort pulse generation is also expected.

  13. Improved Crystallographic Structures using Extensive Combinatorial Refinement

    PubMed Central

    Nwachukwu, Jerome C.; Southern, Mark R.; Kiefer, James R.; Afonine, Pavel V.; Adams, Paul D.; Terwilliger, Thomas C.; Nettles, Kendall W.

    2013-01-01

    Summary Identifying errors and alternate conformers, and modeling multiple main-chain conformers in poorly ordered regions are overarching problems in crystallographic structure determination that have limited automation efforts and structure quality. Here, we show that implementation of a full factorial designed set of standard refinement approaches, which we call ExCoR (Extensive Combinatorial Refinement), significantly improves structural models compared to the traditional linear tree approach, in which individual algorithms are tested linearly, and only incorporated if the model improves. ExCoR markedly improved maps and models, and reveals building errors and alternate conformations that were masked by traditional refinement approaches. Surprisingly, an individual algorithm that renders a model worse in isolation could still be necessary to produce the best overall model, suggesting that model distortion allows escape from local minima of optimization target function, here shown to be a hallmark limitation of the traditional approach. ExCoR thus provides a simple approach to improving structure determination. PMID:24076406

  14. 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

  15. Current Concepts for PrEP Adherence

    PubMed Central

    Haberer, Jessica E.

    2016-01-01

    Purpose of review This review describes 1) the current understanding of adherence to oral PrEP, 2) methods for adherence measurement, 3) approaches to supporting PrEP adherence, and 4) guidance for defining PrEP adherence goals within the larger context of HIV prevention. Recent findings PrEP adherence has generally been higher in recent trials, open-label extensions, and demonstration projects compared to the initial clinical trials; potential explanations include known PrEP efficacy and different motivations to take PrEP. Recent studies have explored adherence monitoring through electronic pill containers, short message service (SMS), and drug concentrations in hair and dried blood spots. The few PrEP adherence interventions developed to date include combinations of enhanced counseling, feedback of objective adherence measurement, and SMS. Conceptualization of PrEP adherence is evolving. The goal is not 100% adherence indefinitely, as it was in clinical trials. PrEP adherence should be defined with respect to HIV exposure, which varies over time by sexual behavior and use of other prevention strategies. Summary PrEP adherence beyond clinical trials has generally been high enough to achieve reliable HIV prevention. Future efforts to measure and support PrEP adherence should focus on the context of risk for HIV acquisition, accounting for dynamic behaviors and choices among HIV prevention options. PMID:26633638

  16. 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.

  17. 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.

  18. Crystallographic Description for Nanoparticle Asemblies - Application to Cadmium Selenide Clusters

    DTIC Science & Technology

    2001-01-01

    Application to Cadmium Selenide Clusters DISTRIBUTION: Approved for public release, distribution unlimited This paper is part of the following report...Proc. Vol. 635 © 2001 Materials Research Society Crystallographic Description for Nanoparticle Asemblies - Application to Cadmium Selenide Clusters. A

  19. 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.

  20. Correlation between Crystallographic Orientation and Surface Faceting in UO2

    SciTech Connect

    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.

  1. Crystallographic interpretation of Galois symmetries for magnetic pentagonal ring

    NASA Astrophysics Data System (ADS)

    Milewski, J.; Lulek, T.; Łabuz, M.

    2017-03-01

    Galois symmetry of exact Bethe Ansatz eigenstates for the magnetic pentagonal ring within the XXX model are investigated by a comparison with crystallographic constructions of space groups. It follows that the arithmetic symmetry of Bethe parameters for the interior of the Brillouin zone admits crystallographic interpretation, in terms of the periodic square Z2 ×Z2 , that is the two-dimensional crystal lattice with Born-Karman period two in both directions.

  2. CRYSTMET-The NRCC Metals Crystallographic Data File.

    PubMed

    Wood, Gordon H; Rodgers, John R; Gough, S Roger; Villars, Pierre

    1996-01-01

    CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60 000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool.

  3. Crystallographic texture analysis of archaeological metals: interpretation of manufacturing techniques

    NASA Astrophysics Data System (ADS)

    Artioli, G.

    2007-12-01

    Neutron probes and high energy X-rays are sources of primary importance for the non-invasive characterization of materials related to cultural heritage. Their employment in the characterization of archaeological metal objects, combined with the recent instrumental and computational developments in the field of crystallographic texture analysis (CTA) from diffraction data proves to be a powerful tool for the interpretation of ancient metal working techniques. Diffraction based CTA, when performed using penetrating probes and adequate detector coverage of reciprocal space, for example using large detector arrays and/or ToF mode, allows simultaneous identification and quantification of crystalline phases, besides the microstructural and textural characterization of the object, and it can be effectively used as a totally non-invasive tool for metallographic analysis. Furthermore, the chemical composition of the object may also be obtained by the simultaneous detection of prompt gamma rays induced by neutron activation, or by the fluorescence signal from high energy X-rays, in order to obtain a large amount of complementary information in a single experiment. The specific application of neutron CTA to the characterization of the manufacturing processes of prehistoric copper axes is discussed in detail.

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

    DOE PAGES

    Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; ...

    2016-08-31

    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–AFITTrefinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentiallymore » 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–AFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIX–AFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented,PHENIX–AFITTrefinements result in more chemically accurate models for small-molecule ligands.« less

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

    PubMed Central

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

    2016-01-01

    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

  6. 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.

  7. CRYSTMET—The NRCC Metals Crystallographic Data File

    PubMed Central

    Wood, Gordon H.; Rodgers, John R.; Gough, S. Roger; Villars, Pierre

    1996-01-01

    CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60 000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool. PMID:27805157

  8. 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.

  9. 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

  10. Interplay of structural chemistry and magnetism in perovskites; A study of CaLn2Ni2WO9; Ln=La, Pr, Nd

    NASA Astrophysics Data System (ADS)

    Chin, Chun-Mann; Paria Sena, Robert; Hunter, Emily C.; Hadermann, Joke; Battle, Peter D.

    2017-07-01

    Polycrystalline samples of CaLn2Ni2WO9 (Ln=La, Pr, Nd) have been synthesized and characterised by a combination of X-ray and neutron diffraction, electron microscopy and magnetometry. Each composition adopts a perovskite-like structure with a 5.50, b 5.56, c 7.78 Å, β 90.1° in space group P21/n. Of the two crystallographically distinct six-coordinate sites, one is occupied entirely (Ln=Pr) or predominantly (Ln=La, Nd) by Ni2+ and the other by Ni2+ and W6+ in a ratio of approximately 1:2. None of the compounds shows long-range magnetic order at 5 K. The magnetometry data show that the magnetic moments of the Ni2+ cations form a spin glass below 30 K in each case. The Pr3+ moments in CaPr2Ni2WO9 also freeze but the Nd3+ moments in CaNd2Ni2WO9 do not. This behaviour is contrasted with that observed in other (A,A')B2B'O9 perovskites.

  11. Diagnostic Accuracy of a Combined Analysis of Cerebrospinal Fluid t-PrP, t-tau, p-tau, and Aβ42 in the Differential Diagnosis of Creutzfeldt-Jakob Disease from Alzheimer’s Disease with Emphasis on Atypical Disease Variants

    PubMed Central

    Abu Rumeileh, Samir; Lattanzio, Francesca; Stanzani Maserati, Michelangelo; Rizzi, Romana; Capellari, Sabina; Parchi, Piero

    2016-01-01

    According to recent studies, the determination of cerebrospinal fluid (CSF) total tau (t-tau)/phosphorylated tau (p-tau) ratio and total prion protein (t-PrP) levels significantly improves the accuracy of the diagnosis of Alzheimer’s disease (AD) in atypical cases with clinical or laboratory features mimicking Creutzfeldt-Jakob disease (CJD). However, this has neither been validated nor tested in series including atypical CJD variants. Furthermore, the added diagnostic value of amyloid-β (Aβ)42 remains unclear. To address these issues, we measured t-PrP, 14-3-3, t-tau, p-tau, and Aβ42 CSF levels in 45 typical and 44 atypical/rapidly progressive AD patients, 54 typical and 54 atypical CJD patients, and 33 controls. CJD patients showed significantly lower CSF t-PrP levels than controls and AD patients. Furthermore, atypical CJD was associated with lower t-PrP levels in comparison to typical CJD. T-tau, 14-3-3, or t-PrP alone yielded, respectively, 80.6, 63.0, and 73.0% sensitivity and 75.3, 92.1, and 75% specificity in distinguishing AD from CJD. On receiver operating characteristic (ROC) curve analyses of biomarker combinations, the (t-tau×Aβ42)/(p-tau×t-PrP) ratio achieved the best accuracy, with 98.1% sensitivity and 97.7% specificity overall, and 96.2% sensitivity and 95.5% specificity for the “atypical” disease groups. Our results show that the combined analysis of CSF t-PrP, t-tau, p-tau, and Aβ42 is clinically useful in the differential diagnosis between CJD and AD. Furthermore, the finding of reduced CSF t-PrP levels in CJD patients suggest that, likewise Aβ42 in AD, CSF t-PrP levels reflect the extent of PrPc conversion into abnormal PrP (PrPSc) and the burden of PrPSc deposition in CJD. PMID:27886009

  12. 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

  13. Crystallographic orientation and concentric layers in spicules of calcareous sponges.

    PubMed

    Rossi, André Linhares; Ribeiro, Bárbara; Lemos, Moara; Werckmann, Jacques; Borojevic, Radovan; Fromont, Jane; Klautau, Michelle; Farina, Marcos

    2016-11-01

    In this work, the crystallography of calcareous sponges (Porifera) spicules and the organization pattern of the concentric layers present in their inner structure were investigated in 10 species of the subclass Calcaronea and three species of the subclass Calcinea. Polished spicules had specific concentric patterns that varied depending on the plane in which the spicules were sectioned. A 3D model of the concentric layers was created to interpret these patterns and the biomineralization process of the triactine spicules. The morphology of the spicules was compared with the crystallographic orientation of the calcite crystals by analyzing the Kikuchi diffraction patterns using a scanning electron microscope. Triactine spicules from the subclass Calcinea had actines (rays) elongated in the 〈210〉 direction, which is perpendicular to the c-axis. The scale spicules of the hypercalcified species Murrayona phanolepis presented the c-axis perpendicular to the plane of the scale, which is in accordance with the crystallography of all other Calcinea. The triactine spicules of the calcaronean species had approximately the same crystallographic orientation with the unpaired actine elongated in the ∼[211] direction. Only one Calcaronea species, whose triactine was regular, had a different orientation. Three different crystallographic orientations were found in diactines. Spicules with different morphologies, dimensions and positions in the sponge body had similar crystallographic directions suggesting that the crystallographic orientation of spicules in calcareous sponges is conserved through evolution.

  14. 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.

  15. Shape and crystallographic orientation of nanodiamonds for quantum sensing.

    PubMed

    Ong, S Y; Chipaux, M; Nagl, A; Schirhagl, R

    2017-01-23

    Nanodiamonds with dimensions down to a few tens of nanometers containing nitrogen-vacancy (NV) color centers have revealed their potential as powerful and versatile quantum sensors with a unique combination of spatial resolution and sensitivity. The NV centers allow transducing physical properties, such as strain, temperature, and electric or magnetic field, to an optical transition that can be detected in the single photon range. For example, this makes it possible to sense a single electron spin or a few nuclear spins by detecting their magnetic resonance. The location and orientation of these defects with respect to the diamond surface play a crucial role in interpreting the data and predicting their sensitivities. Despite its relevance, the geometry of these nanodiamonds has never been thoroughly investigated. Without accurate data, spherical models have been applied to interpret or predict results in the past. With the use of High Resolution Transmission Electron Microscopy (HR-TEM), Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM), we investigated nanodiamonds with an average hydrodynamic diameter of 25 nm (the most common type for quantum sensing) and found a flake-like geometry, with 23.2 nm and 4.5 nm being the average lateral and vertical dimensions. We have also found evidence for a preferred crystallographic orientation of the main facet in the (110) direction. Furthermore, we discuss the consequences of this difference in geometry on diamond-based applications. Shape not only influences the creation efficiency of nitrogen-vacancy centers and their quantum coherence properties (and thus sensing performance), but also the optical properties of the nanodiamonds, their interaction with living cells, and their surface chemistry.

  16. Effect of methyl jasmonate in combination with carbohydrates on gene expression of PR proteins, stilbene and anthocyanin accumulation in grapevine cell cultures.

    PubMed

    Belhadj, Assia; Telef, Nadège; Saigne, Cassandrine; Cluzet, Stéphanie; Barrieu, François; Hamdi, Saïd; Mérillon, Jean-Michel

    2008-04-01

    Grapevine (Vitis vinifera L.) is subject to a number of diseases which affect yield and wine quality. After veraison, berries become strongly susceptible to pathogens due to different physiological changes including the accumulation of glucose and fructose, on the one hand, and to the decrease of anti-microbial compounds called stilbenes, on the other. To obtain berry protection, pesticides are excessively used leading to important cost to the grower and to undesirable environmental impact of the residues, especially in grape, soil and water. As a consequence, alternative strategies have to be developed. Exogenously applied biotic elicitors induce defense responses. We studied the effects of methyl jasmonate in combination with sucrose on defense-related gene expression, stilbene and anthocyanin production in grapevine cell suspensions. The methyl jasmonate/sucrose treatment was effective in stimulating phenylalanine ammonia lyase, chalcone synthase, stilbene synthase, UDP-glucose: flavonoid-O-glucosyltransferase, proteinase inhibitor and chitinase gene expression, and triggered accumulation of both piceids and anthocyanins in cells, and trans-resveratrol and piceids in the extracellular medium. Methyl jasmonate treatment might be an efficient natural strategy to protect grapevine berries in vineyard.

  17. Die-upset hybrid Pr-Fe-B nanocomposite magnets

    NASA Astrophysics Data System (ADS)

    Gabay, A. M.; Zhang, Y.; Hadjipanayis, G. C.

    2004-07-01

    Anisotropic nanocomposite R-Fe-B/Fe magnets (R =Pr, Tb) were synthesized by hot pressing and subsequent die upsetting blends of R-rich and R-lean melt-spun ribbons. The magnets have a layered structure, in which alternating layers of the two starting alloys lay perpendicularly to the pressing direction. A crystallographic alignment of the R2Fe14B grains is observed in the R-rich layers, whose microstructure is identical to that of the conventional die-upset magnets. The R-lean layers consisting of exchange-coupled R2Fe14B and α-Fe grains retain the random crystallographic orientation. The obtained bulk R-lean magnets show better properties than magnets of the same overall composition prepared from a single alloy.

  18. 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.

  19. 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. (c) 2009 Wiley-Liss, Inc.

  20. 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

  1. 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)

  2. 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)

  3. Crystallographic Mapping of Guided Nanowires by Second Harmonic Generation Polarimetry

    PubMed Central

    2017-01-01

    The growth of horizontal nanowires (NWs) guided by epitaxial and graphoepitaxial relations with the substrate is becoming increasingly attractive owing to the possibility of controlling their position, direction, and crystallographic orientation. In guided NWs, as opposed to the extensively characterized vertically grown NWs, there is an increasing need for understanding the relation between structure and properties, specifically the role of the epitaxial relation with the substrate. Furthermore, the uniformity of crystallographic orientation along guided NWs and over the substrate has yet to be checked. Here we perform highly sensitive second harmonic generation (SHG) polarimetry of polar and nonpolar guided ZnO NWs grown on R-plane and M-plane sapphire. We optically map large areas on the substrate in a nondestructive way and find that the crystallographic orientations of the guided NWs are highly selective and specific for each growth direction with respect to the substrate lattice. In addition, we perform SHG polarimetry along individual NWs and find that the crystallographic orientation is preserved along the NW in both polar and nonpolar NWs. While polar NWs show highly uniform SHG along their axis, nonpolar NWs show a significant change in the local nonlinear susceptibility along a few micrometers, reflected in a reduction of 40% in the ratio of the SHG along different crystal axes. We suggest that these differences may be related to strain accumulation along the nonpolar wires. We find SHG polarimetry to be a powerful tool to study both selectivity and uniformity of crystallographic orientations of guided NWs with different epitaxial relations. PMID:28094977

  4. Crystallographic Mapping of Guided Nanowires by Second Harmonic Generation Polarimetry.

    PubMed

    Neeman, Lior; Ben-Zvi, Regev; Rechav, Katya; Popovitz-Biro, Ronit; Oron, Dan; Joselevich, Ernesto

    2017-02-08

    The growth of horizontal nanowires (NWs) guided by epitaxial and graphoepitaxial relations with the substrate is becoming increasingly attractive owing to the possibility of controlling their position, direction, and crystallographic orientation. In guided NWs, as opposed to the extensively characterized vertically grown NWs, there is an increasing need for understanding the relation between structure and properties, specifically the role of the epitaxial relation with the substrate. Furthermore, the uniformity of crystallographic orientation along guided NWs and over the substrate has yet to be checked. Here we perform highly sensitive second harmonic generation (SHG) polarimetry of polar and nonpolar guided ZnO NWs grown on R-plane and M-plane sapphire. We optically map large areas on the substrate in a nondestructive way and find that the crystallographic orientations of the guided NWs are highly selective and specific for each growth direction with respect to the substrate lattice. In addition, we perform SHG polarimetry along individual NWs and find that the crystallographic orientation is preserved along the NW in both polar and nonpolar NWs. While polar NWs show highly uniform SHG along their axis, nonpolar NWs show a significant change in the local nonlinear susceptibility along a few micrometers, reflected in a reduction of 40% in the ratio of the SHG along different crystal axes. We suggest that these differences may be related to strain accumulation along the nonpolar wires. We find SHG polarimetry to be a powerful tool to study both selectivity and uniformity of crystallographic orientations of guided NWs with different epitaxial relations.

  5. Magnetic properties of PrX 2 compounds (X = Pt, Rh, Ru, Ir) studied by hyperfine specific heat, magnetization and neutron-diffraction measurements

    NASA Astrophysics Data System (ADS)

    Greidanus, F. J. A. M.; de Jongh, L. J.; Huiskamp, W. J.; Fischer, P.; Furrer, A.; Buschow, K. H. J.

    1983-04-01

    Magnetic ordering phenomena in rare-earth intermetallic compounds can be unravelled most advantageously in the case of simple crystallographic structure and when a combination of microscopic techniques is applied. Here we shall present the temperature and magnetic field dependence of the magnetic moment of the cubic PrX 2 compounds (X = Pt, Rh, Ru, Ir), as inferred from hyperfine specific-heat, magnetization and neutron-diffraction measurements. The results are compared with a mean-field calculation, taking crystalline electric field and bilinear (dipolar) exchange interactions into account. Adopting experimental values of the Lea, Leask and Wolf parameters x and W from inelastic neutron scattering results, we find satisfactory agreement between our magnetic data and the mean-field theory. An observed discrepancy of about 15% between the calculated and measured saturation values of the spontaneous magnetization can be explained by the presence of quadrupolar interactions.

  6. ``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

  7. Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

    NASA Astrophysics Data System (ADS)

    Rosenfeld, Robin J.; Goodsell, David S.; Musah, Rabi A.; Morris, Garrett M.; Goodin, David B.; Olson, Arthur J.

    2003-08-01

    The W191G cavity of cytochrome c peroxidase is useful as a model system for introducing small molecule oxidation in an artificially created cavity. A set of small, cyclic, organic cations was previously shown to bind in the buried, solvent-filled pocket created by the W191G mutation. We docked these ligands and a set of non-binders in the W191G cavity using AutoDock 3.0. For the ligands, we compared docking predictions with experimentally determined binding energies and X-ray crystal structure complexes. For the ligands, predicted binding energies differed from measured values by ± 0.8 kcal/mol. For most ligands, the docking simulation clearly predicted a single binding mode that matched the crystallographic binding mode within 1.0 Å RMSD. For 2 ligands, where the docking procedure yielded an ambiguous result, solutions matching the crystallographic result could be obtained by including an additional crystallographically observed water molecule in the protein model. For the remaining 2 ligands, docking indicated multiple binding modes, consistent with the original electron density, suggesting disordered binding of these ligands. Visual inspection of the atomic affinity grid maps used in docking calculations revealed two patches of high affinity for hydrogen bond donating groups. Multiple solutions are predicted as these two sites compete for polar hydrogens in the ligand during the docking simulation. Ligands could be distinguished, to some extent, from non-binders using a combination of two trends: predicted binding energy and level of clustering. In summary, AutoDock 3.0 appears to be useful in predicting key structural and energetic features of ligand binding in the W191G cavity.

  8. 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.

  9. 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

  10. {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.

  11. Tunable and laser-reconfigurable 2D heterocrystals obtained by epitaxial stacking of crystallographically incommensurate Bi2Se3 and MoS2 atomic layers

    PubMed Central

    Vargas, Anthony; Liu, Fangze; Lane, Christopher; Rubin, Daniel; Bilgin, Ismail; Hennighausen, Zachariah; DeCapua, Matthew; Bansil, Arun; Kar, Swastik

    2017-01-01

    Vertical stacking is widely viewed as a promising approach for designing advanced functionalities using two-dimensional (2D) materials. Combining crystallographically commensurate materials in these 2D stacks has been shown to result in rich new electronic structure, magnetotransport, and optical properties. In this context, vertical stacks of crystallographically incommensurate 2D materials with well-defined crystallographic order are a counterintuitive concept and, hence, fundamentally intriguing. We show that crystallographically dissimilar and incommensurate atomically thin MoS2 and Bi2Se3 layers can form rotationally aligned stacks with long-range crystallographic order. Our first-principles theoretical modeling predicts heterocrystal electronic band structures, which are quite distinct from those of the parent crystals, characterized with an indirect bandgap. Experiments reveal striking optical changes when Bi2Se3 is stacked layer by layer on monolayer MoS2, including 100% photoluminescence (PL) suppression, tunable transmittance edge (1.1→0.75 eV), suppressed Raman, and wide-band evolution of spectral transmittance. Disrupting the interface using a focused laser results in a marked the reversal of PL, Raman, and transmittance, demonstrating for the first time that in situ manipulation of interfaces can enable “reconfigurable” 2D materials. We demonstrate submicrometer resolution, “laser-drawing” and “bit-writing,” and novel laser-induced broadband light emission in these heterocrystal sheets. PMID:28740860

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

    DOE PAGES

    Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; ...

    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

  13. Crystallographic Transitions in Perovskite Crystals Observed with Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Castillo-Andaeta, F.; Mura-Mardones, J.; Cabrera, G. B.; Cabrera, A. L.; Altamirano-Busschots, L. A.

    2001-03-01

    We have studied the interaction of carbon dioxide with the surface of ferroelectric oxides such as barium titanate and potassium niobate. The surface chemistry of KNbO3 towards CO2 changes when the oxide particles become smaller than 100 microns. We have used Micro-Raman spectroscopy to determine if the structure of the grains change depending on their size and temperature. We have been able of observing crystallographic transition in small grains of the Perovskite with Raman spectroscopy. Small grains of 50 microns BaTiO3 undergo a transition at 133 degree C and small grains of 50 microns KNbO3 undergo a transition around 224 and 408 degrees C. A correlation between CO2 desorption and crystallographic changes can be observed. References: [1] A. L. Cabrera, F. Vargas and R. Zarate J. Phys. Chem. Sol. 55 (1994) 1303. [2] A. L. Cabrera, F. Vargas and J. J. Albers, Surf. Sci. 336 (1995) 280.

  14. 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.

  15. 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.

  16. 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.

  17. Crystallographic Relationships of Silicate-hosted Magnetite Inclusions Determined with Electron Backscatter Pattern Indexing (EBSP)

    NASA Astrophysics Data System (ADS)

    Feinberg, J. M.; Wenk, H.; Renne, P. R.; Scott, G. R.

    2002-12-01

    Crystallographically controlled laths of magnetite exsolved in silicates such as clinopyroxene and plagioclase are common features in gabbros and mafic granulite facies rocks. As the inclusions cool below the Curie temperature of magnetite (580°C) they record a component of the direction and intensity of the Earth's ambient magnetic field. The extreme anisotropy of the inclusions' aspect ratio allows them to retain an unusually stable magnetization, as exemplified by their single-domain behavior. In order to transform these magnetite inclusions into a useful paleomagnetic tool it is necessary to clearly describe the epitaxial relationship between the magnetite and its host silicate phases. In the past the crystallographic orientation of magnetite inclusions and their host silicates were determined using single-crystal X-ray diffraction or diffraction patterns obtained with a transmission electron microscope. Although both of these techniques are ultimately successful, they are time consuming and cumbersome. The Electron Backscatter Diffraction Pattern (EBSP) technique is an alternative approach that uses diffraction patterns of Kikuchi bands generated in a scanning electron microscope. The geometric relationships between intersecting Kikuchi bands can be used to determine the orientation of a crystal. Generally the EBSP technique is used to determine preferred orientation patterns in aggregates. However, in this application we use it to investigate local crystallographic relationships. First, inclusions in a thin section are visualized on a backscattered electron image and verified chemically with an EDX signal. Then EBSPs are produced for both the host silicate and the magnetite inclusions and the orientation relationship is ascertained. The EBSP technique's straightforward sample preparation and rapid measurement time, combined with the broad accessibility of scanning electron microscopes allow scientists to more efficiently determine crystallographic

  18. 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.

  19. 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.

  20. Crystallographic influences on pressure solution in a Quartzose Sandstone

    SciTech Connect

    Hicks, B.D.; Houseknecht, D.W.; Applin, K.R.

    1985-02-01

    The solubility of quartz differs with crystallographic direction. A universal stage was used to measure the orientations of the optic axes and contact planes of 160 pairs of quartz grains in the Bromide Formation (Simpson Group) of Oklahoma. These quartz grains exhibit long, sutured, and concave-convex contacts. Results indicate that the geometry of a pressolved contact is independent of the crystallographic orientation of opposing grains. However, given a concave-convex contact, the optic axis of the concave grain tends to lie at a higher angle to the contact plane than the optic axis of the convex grain. The authors conclude that the extent and type of pressure-solution contacts in quartzose sandstones are not significantly influenced by crystallographic orientation. Other factors, such as grain size and clay content, are probably more important in controlling the pressure-solution features. Geometric etch pits, which form at the point of emergence of crystal defects, were produced by hydrothermally etching quartz crystals, quartz sand, and quartzose sandstones. The abundance, nature, and distribution pattern of crystal defects inherited from source rocks might be more important factors in affecting pressure solution of quartz grains than differences in quartz solubilities arising solely from variations in Si-O bond strengths. The extent of etch-pit formation on quartz cement may also serve as a qualitative indicator of the dissolved silica saturation in pore fluids.

  1. 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.

  2. 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.

  3. Mode decomposition based on crystallographic symmetry in the band-unfolding method

    NASA Astrophysics Data System (ADS)

    Ikeda, Yuji; Carreras, Abel; Seko, Atsuto; Togo, Atsushi; Tanaka, Isao

    2017-01-01

    The band-unfolding method is widely used to calculate the effective band structures of a disordered system from its supercell model. The unfolded band structures show the crystallographic symmetry of the underlying structure, where the difference of chemical components and the local atomic relaxation are ignored. However, it has still been difficult to decompose the unfolded band structures into the modes based on the crystallographic symmetry of the underlying structure, and therefore detailed analyses of the unfolded band structures have been restricted. In this study, a procedure to decompose the unfolded band structures according to the small representations (SRs) of the little groups is developed. The decomposition is performed using the projection operators for SRs derived from the group representation theory. The current method is employed to investigate the phonon band structure of disordered face-centered-cubic Cu0.75Au0.25 , which has large variations of atomic masses and force constants among the atomic sites due to the chemical disorder. In the unfolded phonon band structure, several peculiar behaviors such as discontinuous and split branches are found in the decomposed modes corresponding to specific SRs. They are found to occur because different combinations of the chemical elements contribute to different regions of frequency.

  4. Schools Need the PR's.

    ERIC Educational Resources Information Center

    Palmer, George C.

    1980-01-01

    PR is an acronym standing for philosophic revitalization, planned reactions, proper rhetoric, and personal responsibility. A look at these PRs can challenge school personnel's thinking toward meeting the goals of the district. (Author/MLF)

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Substructures of the (252) ferrous martensite and their crystallographic significance

    SciTech Connect

    Wang Shidao |; Hei Zukun

    1999-04-23

    Many ferrous martensites have been found to possess a macroscopically invariant habit plane close to (252){sub f} and to exhibit complex and variable substructures that cannot be not only satisfactorily explained but also fully characterized so far. The present work attempts to examine the mechanism of occurrence of the complex substructures and their correlation to other crystallographic properties, esp. to the shape strain, on the basis of a new theory. The theory describes the atomic movements in the lattice change represented with the Bain distortion in the past.

  10. PR-PR: cross-platform laboratory automation system.

    PubMed

    Linshiz, Gregory; Stawski, Nina; Goyal, Garima; Bi, Changhao; Poust, Sean; Sharma, Monica; Mutalik, Vivek; Keasling, Jay D; Hillson, Nathan J

    2014-08-15

    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.

  11. 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.

  12. 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

  13. Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin.

    PubMed

    Murakami, Midori; Kouyama, Tsutomu

    2015-01-01

    Upon absorption of light, the retinal chromophore in rhodopsin isomerizes from the 11-cis to the trans configuration, initiating a photoreaction cycle. The primary photoreaction state, bathorhodopsin (BATHO), relaxes thermally through lumirhodopsin (LUMI) into a photoactive state, metarhodopsin (META), which stimulates the conjugated G-protein. Previous crystallographic studies of squid and bovine rhodopsins have shown that the structural change in the primary photoreaction of squid rhodopsin is considerably different from that observed in bovine rhodopsin. It would be expected that there is a fundamental difference in the subsequent thermal relaxation process between vertebrate and invertebrate rhodopsins. In this work, we performed crystallographic analyses of the LUMI state of squid rhodopsin using the P62 crystal. When the crystal was illuminated at 100 K with blue light, a half fraction of the protein was converted into BATHO. This reaction state relaxed into LUMI when the illuminated crystal was warmed in the dark to 170 K. It was found that, whereas trans retinal is largely twisted in BATHO, it takes on a more planar configuration in LUMI. This relaxation of retinal is accompanied by reorientation of the Schiff base NH bond, the hydrogen-bonding partner of which is switched to Asn185 in LUMI. Unlike bovine rhodopsin, the BATHO-to-LUMI transition in squid rhodopsin was accompanied by no significant change in the position/orientation of the beta-ionone ring of retinal.

  14. Incorporating crystallographic orientation in the development of resonant ultrasound spectroscopy

    NASA Astrophysics Data System (ADS)

    Adebisi, R. A.; Sathish, S.; Shade, P. A.

    2017-02-01

    Resonant ultrasound spectroscopy (RUS) measures the mechanical resonance of solids and uses the resonance frequencies to extract a complete set of elastic constants of the solid material. One of the advantages of the RUS method is its applicability to small single crystals. In the past two decades, the RUS technique has gained more acceptance as a nondestructive method to measure elastic properties. The inherent assumptions in the conventional RUS algorithm include free boundary condition on the specimen faces and the faces of the specimens are normal/parallel to the principal crystallographic axes. This assumption is fulfilled through a time consuming procedure that typically involves multiple iterations of sample cutting and inspection using an x-ray Laue method. Such an intensive method is not suitable for many samples in engineering applications. To estimate the elastic constants of such samples, a modified RUS algorithm has been developed to incorporate the sample crystallographic orientation expressed in terms of Euler angles. This modified RUS algorithm has been applied to estimate the elastic constants of cubic and hexagonal crystal structure samples with known orientation. The obtained values are comparable to literature values. With the incorporation of crystal orientation into the RUS algorithm, the elastic constants of samples with random crystal orientation were obtained.

  15. 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.

  16. Crystallographic Orientation Effect on Electromigration in Ni-Sn Microbump

    NASA Astrophysics Data System (ADS)

    Huang, Yi-Ting; Chen, Chih-Hao; Chakroborty, Subhendu; Wu, Albert T.

    2017-09-01

    This article addresses the reliability challenges regarding electromigration in developing three-dimensional integrated circuits (3D-ICs). The line-type sandwich structure of Ni/Sn3.5Ag(15 μm)/Ni was used to simulate microbumps to examine the reliability of electromigration in 3D-IC technology. The solder strip of Ni/Sn3.5Ag(15 μm)/Ni was stressed with a current density of 1.0 × 104 A/cm2 at 150°C. The current stressing enhanced the reaction between the solder and Ni to form Ni3Sn4, which occupied the entire joint and transformed into a Ni/Ni3Sn4/Ni structure when the solder was completely consumed. Electron backscatter diffraction was used to analyze the crystallographic characteristics of Sn and Ni3Sn4 as related to the electromigration effect. The results indicated that the crystallographic orientation of Sn plays a significant role in the Ni/Sn3.5Ag/Ni, whereas the orientation of Ni3Sn4 is the dominant factor of diffusion behavior in the Ni/Ni3Sn4/Ni.

  17. Crystallographic Orientation Control in PZT Thin Films for Microelectromechanical Applications

    NASA Astrophysics Data System (ADS)

    Maack, Bryan; Gibbons, Brady; Mason, Ashley

    2011-10-01

    Pb(Zr1-xTix)O3 (PZT) is widely used in ferroelectric and piezoelectric applications both in bulk and thin film form. As the piezoelectric response is strongly anisotropic, it is highly desirable to control the crystallographic orientation in order to maximize the displacement (for actuation) or charge generated (for sensing). Control of crystallographic texture in PZT thin films has been shown to be dependent on a variety of processing conditions including deposition method, substrate choice, chemical doping, etc. This work is focused on systematically exploring how processing conditions and substrate choice affect orientation in chemical solution derived PZT films. It was found that sputtered Pt/TiOx/SiO2/Si substrates provided a significantly improved template over evaporated Pt/Ti/SiO2/Si substrates. Additionally, alternative adhesion layers to Ti and TiOx resulted in improved chemical homogeneity within the PZT itself, which should lead to enhanced piezoelectric properties. Ongoing work to demonstrate improved piezoelectric properties will be presented.

  18. Crystallographic Orientation Effect on Electromigration in Ni-Sn Microbump

    NASA Astrophysics Data System (ADS)

    Huang, Yi-Ting; Chen, Chih-Hao; Chakroborty, Subhendu; Wu, Albert T.

    2017-07-01

    This article addresses the reliability challenges regarding electromigration in developing three-dimensional integrated circuits (3D-ICs). The line-type sandwich structure of Ni/Sn3.5Ag(15 μm)/Ni was used to simulate microbumps to examine the reliability of electromigration in 3D-IC technology. The solder strip of Ni/Sn3.5Ag(15 μm)/Ni was stressed with a current density of 1.0 × 104 A/cm2 at 150°C. The current stressing enhanced the reaction between the solder and Ni to form Ni3Sn4, which occupied the entire joint and transformed into a Ni/Ni3Sn4/Ni structure when the solder was completely consumed. Electron backscatter diffraction was used to analyze the crystallographic characteristics of Sn and Ni3Sn4 as related to the electromigration effect. The results indicated that the crystallographic orientation of Sn plays a significant role in the Ni/Sn3.5Ag/Ni, whereas the orientation of Ni3Sn4 is the dominant factor of diffusion behavior in the Ni/Ni3Sn4/Ni.

  19. 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.

  20. Diffusion-equation method for crystallographic figure of merits.

    PubMed

    Markvardsen, Anders J; David, William I F

    2010-09-01

    Global optimization methods play a significant role in crystallography, particularly in structure solution from powder diffraction data. This paper presents the mathematical foundations for a diffusion-equation-based optimization method. The diffusion equation is best known for describing how heat propagates in matter. However, it has also attracted considerable attention as the basis for global optimization of a multimodal function [Piela et al. (1989). J. Phys. Chem. 93, 3339-3346]. The method relies heavily on available analytical solutions for the diffusion equation. Here it is shown that such solutions can be obtained for two important crystallographic figure-of-merit (FOM) functions that fully account for space-group symmetry and allow the diffusion-equation solution to vary depending on whether atomic coordinates are fixed or not. The resulting expression is computationally efficient, taking the same order of floating-point operations to evaluate as the starting FOM function measured in terms of the number of atoms in the asymmetric unit. This opens the possibility of implementing diffusion-equation methods for crystallographic global optimization algorithms such as structure determination from powder diffraction data.

  1. Crystallographic alignment of high-density gallium nitride nanowire arrays.

    PubMed

    Kuykendall, Tevye; Pauzauskie, Peter J; Zhang, Yanfeng; Goldberger, Joshua; Sirbuly, Donald; Denlinger, Jonathan; Yang, Peidong

    2004-08-01

    Single-crystalline, one-dimensional semiconductor nanostructures are considered to be one of the critical building blocks for nanoscale optoelectronics. Elucidation of the vapour-liquid-solid growth mechanism has already enabled precise control over nanowire position and size, yet to date, no reports have demonstrated the ability to choose from different crystallographic growth directions of a nanowire array. Control over the nanowire growth direction is extremely desirable, in that anisotropic parameters such as thermal and electrical conductivity, index of refraction, piezoelectric polarization, and bandgap may be used to tune the physical properties of nanowires made from a given material. Here we demonstrate the use of metal-organic chemical vapour deposition (MOCVD) and appropriate substrate selection to control the crystallographic growth directions of high-density arrays of gallium nitride nanowires with distinct geometric and physical properties. Epitaxial growth of wurtzite gallium nitride on (100) gamma-LiAlO(2) and (111) MgO single-crystal substrates resulted in the selective growth of nanowires in the orthogonal [1\\[Evec]0] and [001] directions, exhibiting triangular and hexagonal cross-sections and drastically different optical emission. The MOCVD process is entirely compatible with the current GaN thin-film technology, which would lead to easy scale-up and device integration.

  2. X-ray diffraction and extended X-ray absorption fine structure study of epitaxial mixed ternary bixbyite Pr{sub x}Y{sub 2-x}O{sub 3} (x = 0-2) films on Si (111)

    SciTech Connect

    Niu, G.; Zoellner, M. H.; Zaumseil, P.; Pouliopoulos, A.; Boscherini, F.

    2013-01-28

    Ternary single crystalline bixbyite Pr{sub x}Y{sub 2-x}O{sub 3} films over the full stoichiometry range (x = 0-2) have been epitaxially grown on Si (111) with tailored electronic and crystallographic structure. In this work, we present a detailed study of their local atomic environment by extended X-ray absorption fine structure at both Y K and Pr L{sub III} edges, in combination with complementary high resolution x-ray diffraction measurements. The local structure exhibits systematic variations as a function of the film composition. The cation coordination in the second and third coordination shells changes with composition and is equal to the average concentration, implying that the Pr{sub x}Y{sub 2-x}O{sub 3} films are indeed fully mixed and have a local bixbyite structure with random atomic-scale ordering. A clear deviation from the virtual crystal approximation for the cation-oxygen bond lengths is detected. This demonstrates that the observed Vegard's law for the lattice variation as a function of composition is based microscopically on a more complex scheme related to local structural distortions which accommodate the different cation-oxygen bond lengths.

  3. 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

  4. Crystallographic shear mechanisms in Rh one-dimensional oxides

    NASA Astrophysics Data System (ADS)

    Hernando, María; Boulahya, Khalid; Parras, Marina; González-Calbet, José M.

    2005-02-01

    Electron diffraction and high resolution electron microscopy have been used to characterize two new one-dimensional superstructures in the A sbnd Rh sbnd O system (A = Ca, Sr) related to the 2H-ABO 3-type. They are formed by the intergrowth of n A 3A'BO 6 blocks, showing the Sr 4RhO 6-type, with A 12A' 2B 8O 30 blocks, constituted by two A 3O 9 and two A 3A'O 6 layers alternating in the stacking sequence 1:1, leading to the A 27A' 7B 13O 60 ( n=5) and A 30A' 8B 14O 66 ( n=6) compositions. A crystallographic shear mechanism is proposed to describe the structural relationship between Sr 4RhO 6 (A 3A'BO 6-type) and the new superstructures.

  5. 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

  6. Rapid visualization of hydrogen positions in protein neutron crystallographic structures.

    PubMed

    Munshi, Parthapratim; Chung, Shang-Lin; Blakeley, Matthew P; Weiss, Kevin L; Myles, Dean A A; Meilleur, Flora

    2012-01-01

    Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25004962

  8. Crystallographic analysis of a series of inorganic compounds

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    The method of crystallographic analysis relies on the mechanical-wave concept that treats the crystalline state as the result of ordering of atomic positions by families of parallel equidistant planes. Using this method, a large set of fluoride, oxide and sulfide structures was analyzed. The pseudo-translational ordering of various atomic groups (including the presence of cation and anion sublattices) in the structures of various classes of inorganic compounds was established. The crucial role of local ordering of heavy cations (coherent assembly) in the structures comprising large cluster fragments (Keggin polyanions, polyoxoniobates, etc.) is discussed. The role of symmetry and the regular distribution of heavy atoms in the formation of stable crystal structures, which is to be taken into account in the targeted design, is considered. The universality of configurations of atomic positions in the structures of various classes of inorganic compounds resulting from the ordering mechanism organized by mechanical (elastic) forces is demonstrated. The bibliography includes 158 references.

  9. Crystallographic and spectroscopic study on a known orally active progestin.

    PubMed

    Ferraboschi, Patrizia; Ciuffreda, Pierangela; Ciceri, Samuele; Grisenti, Paride; Castellano, Carlo; Meneghetti, Fiorella

    2015-12-01

    6,17α-Dimethyl-4,6-pregnadiene-3,20-dione (medrogestone, 2) is for a long time known steroid endowed with progestational activity. In order to study its crystallographic and NMR spectroscopic properties with the aim to fill the literature gap, we prepared medrogestone following a traditional procedure. A careful NMR study allowed the complete assignment of the (1)H and (13)C NMR signals not only of medrogestone but also of its synthetic intermediates. The structural and stereochemical characterizations of medrogestone together with its precursor 17α-methyl-3-ethoxy-pregna-3,5-dien-20-one were described by means of X-ray analysis, allowing a deepened conformational investigation.

  10. Crystallographic preferred orientation (CPO) of gypsum measured by electron backscatter diffraction (EBSD).

    PubMed

    Hildyard, R C; Prior, D J; Mariani, E; Faulkner, D R

    2009-12-01

    An investigation by electron backscatter diffraction on gypsum shows that this technique can be used to study the microstructures and crystallographic preferred orientation of gypsum. Presented here are the methods, verification tests and data obtained from a naturally deformed sample of gypsum-rich rock. The electron backscatter diffraction data show the sample has a strong crystallographic preferred orientation.

  11. Ocean acidification reduces the crystallographic control in juvenile mussel shells.

    PubMed

    Fitzer, Susan C; Cusack, Maggie; Phoenix, Vernon R; Kamenos, Nicholas A

    2014-10-01

    Global climate change threatens the oceans as anthropogenic carbon dioxide causes ocean acidification and reduced carbonate saturation. Future projections indicate under saturation of aragonite, and potentially calcite, in the oceans by 2100. Calcifying organisms are those most at risk from such ocean acidification, as carbonate is vital in the biomineralisation of their calcium carbonate protective shells. This study highlights the importance of multi-generational studies to investigate how marine organisms can potentially adapt to future projected global climate change. Mytilus edulis is an economically important marine calcifier vulnerable to decreasing carbonate saturation as their shells comprise two calcium carbonate polymorphs: aragonite and calcite. M. edulis specimens were cultured under current and projected pCO2 (380, 550, 750 and 1000μatm), following 6months of experimental culture, adults produced second generation juvenile mussels. Juvenile mussel shells were examined for structural and crystallographic orientation of aragonite and calcite. At 1000μatm pCO2, juvenile mussels spawned and grown under this high pCO2 do not produce aragonite which is more vulnerable to carbonate under-saturation than calcite. Calcite and aragonite were produced at 380, 550 and 750μatm pCO2. Electron back scatter diffraction analyses reveal less constraint in crystallographic orientation with increased pCO2. Shell formation is maintained, although the nacre crystals appear corroded and crystals are not so closely layered together. The differences in ultrastructure and crystallography in shells formed by juveniles spawned from adults in high pCO2 conditions may prove instrumental in their ability to survive ocean acidification. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Oriented crystallographic textures of olivine in quenched silicate melt spherules

    NASA Astrophysics Data System (ADS)

    Isobe, H.

    2015-12-01

    Olivine is one of the most common minerals in the planetary materials including solid Earth and chondritic meteorites. Olivine crystals show characteristic textures in chondrules and micrometeorites (MMs) depending on heating and cooling histories, especially in extraordinary quick cooling rates. We have constructed a fine particle free fall apparatus in a high temperature furnace and carried out crystallization experiments of fine particles with quick heating and quenching (Isobe and Gondo, 2013). The falling particles in the furnace can reach 1400 degrees C within 2 seconds, keep above 1400 degrees C more than 1 second, and are quenched within 1 second. Run products from olivine particles show various textures depending on proportions of three kinds of starting materials in the particles. Fayalite particles melt completely and form barred olivine-like spherules with low pyramid structures on the surface. Dendritic olivine crystals with regulated crystallographic orientation are developed in melted particles. Surface texture of melted particles may be affected by the dendritic olivine crystals grown in the spherules. Oriented dendrites of magnetite also occur between olivine crystals. The texture of oriented dendrite of olivine with tiny magnetite is quite similar to natural cosmic spherules (CSs). In the completely melted spherules, barred olivine-like structures can be seen. Due to extraordinary high cooling rate up to 2×10^6 degrees C/hour and degrees of supercooling, olivine bars show chained structure of H-shaped or hourglass shaped units which are distinctive characteristics for quick growth of olivine in quenching. In spite of quite short period of crystal growth processes, chained olivine aligns parallel bars in the almost entire spherule. Nucleation of barred olivine crystals may be initiated at surface of spherules. Starting points of olivine growth can be seen as peaks on surface of the spherules. The crystallographic textures of olivine develop

  13. Preliminary crystallographic analysis of the bacteriophage P22 portal protein.

    PubMed

    Cingolani, Gino; Moore, Sean D; Prevelige, Peter E; Johnson, John E

    2002-07-01

    Portal proteins are components of large oligomeric dsDNA pumps connecting the icosahedral capsid of tailed bacteriophages to the tail. Prior to the tail attachment, dsDNA is actively pumped through a central cavity formed by the subunits. We have studied the portal protein of bacteriophage P22, which is the largest connector characterized among the tailed bacteriophages. The molecular weight of the monomer is 82.7 kDa, and it spontaneously assembles into an oligomeric structure of approximately 1.0 MDa. Here we present a preliminary biochemical and crystallographic characterization of this large macromolecular complex. The main difficulties related to the crystallization of P22 portal protein lay in the intrinsic dynamic nature of the portal oligomer. Recombinant connectors assembled from portal monomers expressed in Escherichia coli form rings of different stoichiometry in solution, which cannot be separated on the basis of their size. To overcome this intrinsic heterogeneity we devised a biochemical purification that separates different ring populations on the basis of their charge. Small ordered crystals were grown from drops containing a high concentration of the kosmotropic agent tert-butanol and used for data collection. A preliminary crystallographic analysis to 7.0-A resolution revealed that the P22 portal protein crystallized in space group I4 with unit cell dimensions a=b=409.4A, c=260.4A. This unit cell contains a total of eight connectors. Analysis of the noncrystallographic symmetry by the self-rotation function unambiguously confirmed that bacteriophage P22 portal protein is a dodecamer with a periodicity of 30 degrees. The cryo-EM reconstruction of the dodecahedral bacteriophage T3 portal protein will be used as a model to initiate phase extension and structure determination.

  14. 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

  15. In vitro neutralization of prions with PrPSc-specific antibodies

    PubMed Central

    Taschuk, Ryan; Van der Merwe, Jacques; Marciniuk, Kristen; Potter, Andrew; Cashman, Neil; Griebel, Philip; Napper, Scott

    2015-01-01

    Abstract Prion diseases reflect the misfolding of a self-protein (PrPC) into an infectious, pathological isomer (PrPSc). By targeting epitopes uniquely exposed by misfolding, our group developed PrPSc-specific vaccines to 3 disease specific epitopes (DSEs). Here, antibodies induced by individual DSE vaccines are evaluated for their capacity to neutralize prions in vitro. For both purified antibodies and immunoreactive sera, the PrPSc-specific antibodies were equally effective in neutralizing prions. Further, there was no significant increase in neutralizing activity when multiple DSEs were targeted within an assay. At a low antibody concentration, the PrPSc-specific antibodies matched the neutralization achieved by an antibody that may act via both PrPC and PrPSc. At higher doses, however, this pan-specific antibody was more effective, potentially due to a combined deactivation of PrPSc and depletion of PrPC. PMID:26284508

  16. In vitro neutralization of prions with PrP(Sc)-specific antibodies.

    PubMed

    Taschuk, Ryan; Van der Merwe, Jacques; Marciniuk, Kristen; Potter, Andrew; Cashman, Neil; Griebel, Philip; Napper, Scott

    2015-01-01

    Prion diseases reflect the misfolding of a self-protein (PrP(C)) into an infectious, pathological isomer (PrP(Sc)). By targeting epitopes uniquely exposed by misfolding, our group developed PrP(Sc)-specific vaccines to 3 disease specific epitopes (DSEs). Here, antibodies induced by individual DSE vaccines are evaluated for their capacity to neutralize prions in vitro. For both purified antibodies and immunoreactive sera, the PrP(Sc)-specific antibodies were equally effective in neutralizing prions. Further, there was no significant increase in neutralizing activity when multiple DSEs were targeted within an assay. At a low antibody concentration, the PrP(Sc)-specific antibodies matched the neutralization achieved by an antibody that may act via both PrP(C) and PrP(Sc). At higher doses, however, this pan-specific antibody was more effective, potentially due to a combined deactivation of PrP(Sc) and depletion of PrP(C).

  17. Forsteritic olivine: effect of crystallographic direction on dissolution kinetics

    NASA Astrophysics Data System (ADS)

    Awad, Aida; Koster van Groos, A. F.; Guggenheim, Stephen

    2000-05-01

    Directional dissolution along the three crystallographic axes of gem-quality olivine (Fo 91), San Carlos, Arizona was studied at pH 1 and pH 2 at 23, 50, 70, and 90°C and 1 atm. The rate constant of dissolution for olivine at pH 1 and 70°C down the a-, b-, and c-axis (based on space group Pbnm) is 2.7 × 10 -4, 5.6 × 10 -3, and 8.1 × 10 -4 mm/h, respectively. At pH 2 and 70°C the dissolution rates are 1.3 × 10 -4, 2.1 × 10 -3, and 4.3 × 10 -4 mm/h, respectively. At 50°C and 90°C, these rates are ˜0.2 and 5 times the rates at 70°C. The much higher dissolution rate in the direction of the b-axis is attributed to preferential protonation of the oxygen atoms around the M(1) site, which would result in a higher dissolution rate of the SiO 2-M(1) network. The activation energy of dissolution E adis in the direction down the a-, b-, and c-axis is 114.5 ± 23 kJ/mol, 69.9 ± 8 kJ/mol, and 72.9 ± 15 kJ/mol, respectively. Because of differences in the directional E adis, dissolution in the direction down the a-axis will become dominant at temperatures above ˜140°C. The bulk E adis, based on the dissolution rate along the crystallographic axes, is 71.5 ± 12 kJ/mol at the temperature range of the study. Because of the larger E adis perpendicular to the a-axis, bulk E adis must increase with temperature. The results indicate that the weathering rate of olivine is more temperature dependent than was considered previously.

  18. 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

  19. Determination of parameters of a system of charge carriers in Y1-2 x Ca x Pr x Ba2Cu3O y within a combined analysis of temperature dependences of thermoelectric power and Nernst-Ettingshausen coefficients

    NASA Astrophysics Data System (ADS)

    Gasumyants, V. E.; Martynova, O. A.; Dubrovin, R. M.

    2015-12-01

    The temperature dependences of thermoelectric power S and transverse Nernst-Ettingshausen effect Q in high-temperature superconductors of the Y1-2 x Ca x Pr x Ba2Cu3O y system with different concentrations of dopants have been investigated experimentally. It has been shown that all the specific features revealed in the behavior of the two kinetic coefficients under investigation can be described using the narrowband model with a single concept of the structure of an energy spectrum and a common set of model parameters that characterize the structure of the spectrum and properties of a system of charge carriers. Based on the quantitative analysis of the dependences S( T) and Q( T), the values of these parameters for samples of the studied composition have been determined and the character of their changes with an increase in the impurity content has been analyzed. It has been demonstrated that, for the explanation of the obtained results, it is necessary to take into account the interaction of calcium and praseodymium ions upon their simultaneous introduction into the lattice. It has been found that the mobility of charge carriers has extremely low values and almost does not depend on the level of doping, which is associated with the character of changes in the structure of the energy spectrum of Y1-2 x Ca x Pr x Ba2Cu3O y upon doping. It has been concluded that the structure of the energy spectrum of high-temperature superconductors in the yttrium system is characterized by an asymmetry of the dispersion curve.

  20. 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

  1. Nanocrystalline materials: recent advances in crystallographic characterization techniques.

    PubMed

    Ringe, Emilie

    2014-11-01

    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.

  2. Cassia grandis Linn. f. seed galactomannan: structural and crystallographical studies.

    PubMed

    Joshi, Harsha; Kapoor, Virendra P

    2003-09-01

    Cassia grandis is a small or medium sized tree, found in abundance throughout India. The seeds contain about 50% endosperm gum and possess the characteristics of becoming a potential source of seed gum. The purified polysaccharide has been characterized as a pure galactomannan having a mannose-galactose ratio of 3.15; molecular weight (Mw) 80,200; polydispersity (Mw/Mn), 1.35 and intrinsic viscosity [eta], 848 mL/g. Methylation, periodate oxidation, Smith degradation and 13C NMR studies confirm that the polysaccharide has the basic structure of legume galactomannans consisting of a beta-(1-->4)-linked main mannan backbone to which galactose units are attached at O-6. The orthorhombic lattice constants of the hydrated gum are as follows: a=9.00, b=24.81, c=10.30 A. The crystallographic data establish that the probable space group symmetry of the unit cell is P2(1)2(1)2. The results are in contradiction to earlier reports (Indian J. Chem. 16B (1978) 966; J. Indian Chem. Soc. 55 (1978) 1216) in which a non-galactomannan polysaccharide structure has been assigned having a main chain of (1-->4)-linked galactose and mannose units in the molar ratio 6:3, where 50% of the galactose units branched with two galactose and one mannose through 1-->3 linkage.

  3. 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.

  4. Crystallographic Orientation of Cuttlebone Shield Determined by Electron Backscatter Diffraction

    NASA Astrophysics Data System (ADS)

    Cusack, Maggie; Chung, Peter

    2014-01-01

    In common with many cephalopod mollusks, cuttlefish produce an internal biomineral buoyancy device. This cuttlebone is analogous to a surf board in shape and structure, providing rigidity and a means of controlling buoyancy. The cuttlebone is composed of calcium carbonate in the form of aragonite and comprises an upper dorsal shield and a lower lamellar matrix. The lamellar matrix comprises layers of chambers with highly corrugated walls. The dorsal shield comprises bundles of aragonite needles stacked on top of each other. Electron backscatter diffraction analyses of the dorsal shield reveal that the c-axis of aragonite is parallel with the long axis of the needles in the bundles such that any spread in crystallographic orientation is consistent with the spread in orientation of the fibers as they radiate to form the overall structure of the dorsal shield. This arrangement of c-axis coincident with the long axis of the biomineral structure is similar to the arrangement in corals and in contrast to the situation in the molluskan aragonite nacre of brachiopod calcite where the c-axis is perpendicular to the aragonite tablet or calcite fiber, respectively.

  5. 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

  6. Crystallization and preliminary crystallographic analysis of recombinant human galectin-1

    PubMed Central

    Scott, Stacy A.; Scott, Ken; Blanchard, Helen

    2007-01-01

    Galectin-1 is considered to be a regulator protein as it is ubiquitously expressed throughout the adult body and is responsible for a broad range of cellular regulatory functions. Interest in galectin-1 from a drug-design perspective is founded on evidence of its overexpression by many cancers and its immunomodulatory properties. The development of galectin-1-specific inhibitors is a rational approach to the fight against cancer because although galectin-1 induces a plethora of effects, null mice appear normal. X-ray crystallographic structure determination will aid the structure-based design of galectin-1 inhibitors. Here, the crystallization and preliminary diffraction analysis of human galectin-1 crystals generated under six different conditions is reported. X-ray diffraction data enabled the assignment of unit-cell parameters for crystals grown under two conditions, one belongs to a tetragonal crystal system and the other was determined as monoclinic P21, representing two new crystal forms of human galectin-1. PMID:18007053

  7. Mantle dynamics inferred from the crystallographic preferred orientation of bridgmanite

    NASA Astrophysics Data System (ADS)

    Tsujino, Noriyoshi; Nishihara, Yu; Yamazaki, Daisuke; Seto, Yusuke; Higo, Yuji; Takahashi, Eiichi

    2016-11-01

    Seismic shear wave anisotropy is observed in Earth’s uppermost lower mantle around several subducted slabs. The anisotropy caused by the deformation-induced crystallographic preferred orientation (CPO) of bridgmanite (perovskite-structured (Mg,Fe)SiO3) is the most plausible explanation for these seismic observations. However, the rheological properties of bridgmanite are largely unknown. Uniaxial deformation experiments have been carried out to determine the deformation texture of bridgmanite, but the dominant slip system (the slip direction and plane) has not been determined. Here we report the CPO pattern and dominant slip system of bridgmanite under conditions that correspond to the uppermost lower mantle (25 gigapascals and 1,873 kelvin) obtained through simple shear deformation experiments using the Kawai-type deformation-DIA apparatus. The fabrics obtained are characterized by [100] perpendicular to the shear plane and [001] parallel to the shear direction, implying that the dominant slip system of bridgmanite is [001](100). The observed seismic shear- wave anisotropies near several subducted slabs (Tonga-Kermadec, Kurile, Peru and Java) can be explained in terms of the CPO of bridgmanite as induced by mantle flow parallel to the direction of subduction.

  8. 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

  9. 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.

  10. 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.

  11. Crystallization and preliminary crystallographic analysis of recombinant human galectin-1

    SciTech Connect

    Scott, Stacy A.; Scott, Ken; Blanchard, Helen

    2007-11-01

    Human galectin-1 has been cloned, expressed in E. coli, purified and crystallized in the presence of both lactose (ligand) and β-mercaptoethanol under six different conditions. The X-ray diffraction data obtained have enabled the assignment of unit-cell parameters for two novel crystal forms of human galectin-1. Galectin-1 is considered to be a regulator protein as it is ubiquitously expressed throughout the adult body and is responsible for a broad range of cellular regulatory functions. Interest in galectin-1 from a drug-design perspective is founded on evidence of its overexpression by many cancers and its immunomodulatory properties. The development of galectin-1-specific inhibitors is a rational approach to the fight against cancer because although galectin-1 induces a plethora of effects, null mice appear normal. X-ray crystallographic structure determination will aid the structure-based design of galectin-1 inhibitors. Here, the crystallization and preliminary diffraction analysis of human galectin-1 crystals generated under six different conditions is reported. X-ray diffraction data enabled the assignment of unit-cell parameters for crystals grown under two conditions, one belongs to a tetragonal crystal system and the other was determined as monoclinic P2{sub 1}, representing two new crystal forms of human galectin-1.

  12. 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.

  13. Magnetic and XMCD studies of Pr1-xSrxMnO3 manganite films

    NASA Astrophysics Data System (ADS)

    Samoshkina, Yu. E.; Edelman, I. S.; Stepanova, E. A.; Neznakhin, D. S.; Ollefs, K.; Andreev, N. V.; Chichkov, V. I.

    2017-04-01

    Magnetic properties of the Pr0.8Sr0.2MnO3 and Pr0.6Sr0.4MnO3 polycrystalline films have been studied using temperature and magnetic field dependences of the static magnetization and X-ray magnetic circular dichroism (XMCD) spectroscopy. For the both compositions, the difference between the temperature dependences of magnetization obtained in the zero fields cooling (ZFC) and field cooling (FC) modes has been revealed. The ZFC curves demonstrate a pronounced maximum at temperature Tm. It is shown that the Tm value dependence on the magnetic field follows the Almeida-Thouless line typical for the classic spin glass, what allows us to assume the possible spin-glass behavior of the films. Effect of the disorder in a direction of the crystallites easy-axis on the difference between FC and ZFC curves has been discussed also. Magnetic field dependences of the sample magnetization are presented by the hysteresis loops with the shape changing upon temperature variation. This behavior has been attributed to the effect of crystallographic anisotropy and Pr ions. The spectra and magnetic field dependences of XMCD at the Pr L2- and Mn K-edges have been studied at 90 K. The magnetic field dependences of the XMCD at the Pr L2-edge had shown Van Vleck paramagnetism from Pr3+ ions.

  14. 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

  15. Anti-oxidant behavior of functionalized chalcone-a combined quantum chemical and crystallographic structural investigation

    NASA Astrophysics Data System (ADS)

    Mathew, Bijo; Adeniyi, Adebayo A.; Joy, Monu; Mathew, Githa Elizabeth; Singh-Pillay, Ashona; Sudarsanakumar, C.; Soliman, Mahmoud E. S.; Suresh, Jerad

    2017-10-01

    Compound (2E)-3-(methoxyphenyl)-1-(4-methylphenyl) prop-2-en-1-one (Ch) was synthesized by the Claisen-Schmidt condensation reaction between para-methylacetophenone and para-methoxybenzaldehyde under basic condition. The structure of the molecule was elucidated using X-ray diffraction. Compound (Ch) demonstrated higher antioxidant activities in the DPPH test and H2O2 assay (IC50 = 12.23 ± 0.53 and 15.62 ± 0.98) than with the standard ascorbic acid (IC50 = 17.32 ± 0.44 and 19.07 ± 0.35). An evaluation of the atomic and molecular properties of ascorbic acid and Ch were computed based on their antioxidant activities. The molecular properties give insight into possible reasons for the enhanced antioxidant properties of Ch compared to ascorbic acid. The atomic properties provide further insight into chemical changes of the atoms of the compounds. Such changes include electronic shifting of the compounds electrophilic and/or nucleophilic states which highlight chemical moieties which characterize the antioxidant activity but do not directly relate to a variation in their antioxidant activities. The results obtained reflect oxygen atoms having significant nucleophilic interactions of each of the compounds. This was characterized by higher Fukui indices, isotropic and anisotropic hyperfine and orbital coupling stability energy.

  16. Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.

    PubMed

    Dullweber, F; Stubbs, M T; Musil, D; Stürzebecher, J; Klebe, G

    2001-10-26

    The binding of a series of low molecular weight ligands towards trypsin and thrombin has been studied by isothermal titration calorimetry and protein crystallography. In a series of congeneric ligands, surprising changes of protonation states occur and are overlaid on the binding process. They result from induced pK(a) shifts depending on the local environment experienced by the ligand and protein functional groups in the complex (induced dielectric fit). They involve additional heat effects that must be corrected before any conclusion on the binding enthalpy (DeltaH) and entropy (DeltaS) can be drawn. After correction, trends in both contributions can be interpreted in structural terms with respect to the hydrogen bond inventory or residual ligand motions. For all inhibitors studied, a strong negative heat capacity change (DeltaC(p)) is detected, thus binding becomes more exothermic and entropically less favourable with increasing temperature. Due to a mutual compensation, Gibbs free energy remains virtually unchanged. The strong negative DeltaC(p) value cannot solely be explained by the removal of hydrophobic surface portions of the protein or ligand from water exposure. Additional contributions must be considered, presumably arising from modulations of the local water structure, changes in vibrational modes or other ordering parameters. For thrombin, smaller negative DeltaC(p) values are observed for ligand binding in the presence of sodium ions compared to the other alkali ions, probably due to stabilising effects on the protein or changes in the bound water structure. Copyright 2001 Academic Press.

  17. 3D Strain Geometry and Crystallographic Fabric in Experimental HT Deformation of Solnhofen Limestone

    NASA Astrophysics Data System (ADS)

    Llana-Funez, S.; Rutter, E. H.

    2003-12-01

    Under conditions where calcite deforms plastically, high temperature deformation tests on Solnhofen limestone have been run using different strain configurations: axi-symmetric shortening and extension, and direct shear. The aim of the work is to relate strain geometry and the development of crystallographic fabrics in different strain paths. We produced constrictional, flattening, and nearly plane strain deformations. In addition to this, we were also able to obtain strain geometries where the vorticity axis in a non-coaxial deformation was either perpendicular to the extension direction (as in simple and sub-simple shear) or parallel to it. In order to keep constant as many parameters as possible, all experiments used the same starting material and the same experimental conditions of temperature 600 \\deg C, confining pressure 200 MPa and comparable strain rates 10-4s-1. At these conditions, and taking into account the special features of Solnhofen limestone (i.e. fine grain size and the presence of impurities preventing grain growth), the predominant deformation mechanism was intracrystalline plasticity. We used pole figures of different calcite lattice elements, measured by electron back-scattered diffraction techniques (EBSD), to characterize the asymmetry of the crystallographic patterns and particularly c-axis pole figures to identify the presence of different fabric components. Further analysis of inverse pole figures in particular experimental directions allowed us to characterize the extension and compression directions of the strain ellipsoid as they geometrically determine the operation of slip systems. Two main aspects can be highlighted from our experimental results. First, it proved particularly useful to combine inverse pole figures with pole figures to characterize not only the shape of the strain ellipsoid in predominantly plastic deformation but also the sense of shear. Second, there is an extraordinary sensitivity of crystal-plastic deformation

  18. CRYSTALLOGRAPHICALLY ANISOTROPIC SHAPE OF FORSTERITE: NEW PROBE FOR EVALUATING DUST FORMATION HISTORY FROM INFRARED SPECTROSCOPY

    SciTech Connect

    Takigawa, Aki; Tachibana, Shogo

    2012-05-10

    Crystalline dust has been observed by infrared spectroscopy around dust-enshrouded asymptotic giant branch stars, in protoplanetary disks, and from some comets. Crystalline materials often have a specific shape related to a specific crystallographic orientation (crystallographically anisotropic shape), which reflects the anisotropic nature of crystals, and their infrared spectral features depend on crystallographically anisotropic shapes. The crystallographically anisotropic shape is thus a potentially powerful probe to evaluate circumstellar dust-forming conditions quantitatively. In order to assess the possibility to determine the crystallographically anisotropic shape from infrared spectra, we calculated mass absorption coefficients for ellipsoidal forsterite particles, the most abundant circumstellar crystalline silicate, elongated and flattened along the crystallographic a-, b-, and c-axes with various aspect ratios in the wavelength range of 9-70 {mu}m. It was found that differences in infrared features caused by various crystallographicaly anisotropic shapes are distinguishable from each other irrespective of the effects of temperature, size, chemical composition, and grain edges of forsterite in the range of 9-12 {mu}m and 15-20 {mu}m. We thus concluded that the crystallographically anisotropic shape of forsterite can be deduced from peak features in infrared spectra. We also showed that the crystallographically anisotropic shapes formed by evaporation and condensation of forsterite can be distinguished from each other and the temperature condition for evaporation can be evaluated from the peak features. We applied the present results to the infrared spectrum of a protoplanetary disk HD100546 and found that a certain fraction ({approx}25%) of forsterite dust may have experienced high-temperature evaporation (>1600 K).

  19. All-atom contact model for understanding protein dynamics from crystallographic B-factors.

    PubMed

    Li, Da-Wei; Brüschweiler, Rafael

    2009-04-22

    An all-atom local contact model is described that can be used to predict protein motions underlying isotropic crystallographic B-factors. It uses a mean-field approximation to represent the motion of an atom in a harmonic potential generated by the surrounding atoms resting at their equilibrium positions. Based on a 400-ns molecular dynamics simulation of ubiquitin in explicit water, it is found that each surrounding atom stiffens the spring constant by a term that on average scales exponentially with the interatomic distance. This model combines features of the local density model by Halle and the local contact model by Zhang and Brüschweiler. When applied to a nonredundant set of 98 ultra-high resolution protein structures, an average correlation coefficient of 0.75 is obtained for all atoms. The systematic inclusion of crystal contact contributions and fraying effects is found to enhance the performance substantially. Because the computational cost of the local contact model scales linearly with the number of protein atoms, it is applicable to proteins of any size for the prediction of B-factors of both backbone and side-chain atoms. The model performs as well as or better than several other models tested, such as rigid-body motional models, the local density model, and various forms of the elastic network model. It is concluded that at the currently achievable level of accuracy, collective intramolecular motions are not essential for the interpretation of B-factors.

  20. Ordered arrays of vertically aligned [110] silicon nanowires by suppressing the crystallographically preferred <100> etching directions.

    PubMed

    Huang, Zhipeng; Shimizu, Tomohiro; Senz, Stephan; Zhang, Zhang; Zhang, Xuanxiong; Lee, Woo; Geyer, Nadine; Gösele, Ulrich

    2009-07-01

    The metal-assisted etching direction of Si(110) substrates was found to be dependent upon the morphology of the deposited metal catalyst. The etching direction of a Si(110) substrate was found to be one of the two crystallographically preferred 100 directions in the case of isolated metal particles or a small area metal mesh with nanoholes. In contrast, the etching proceeded in the vertical [110] direction, when the lateral size of the catalytic metal mesh was sufficiently large. Therefore, the direction of etching and the resulting nanostructures obtained by metal-assisted etching can be easily controlled by an appropriate choice of the morphology of the deposited metal catalyst. On the basis of this finding, a generic method was developed for the fabrication of wafer-scale vertically aligned arrays of epitaxial [110] Si nanowires on a Si(110) substrate. The method utilized a thin metal film with an extended array of pores as an etching catalyst based on an ultrathin porous anodic alumina mask, while a prepatterning of the substrate prior to the metal depostion is not necessary. The diameter of Si nanowires can be easily controlled by a combination of the pore diameter of the porous alumina film and varying the thickness of the deposited metal film.

  1. Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.

    PubMed

    Du, Hongying; Brender, Jeffrey R; Zhang, Jian; Zhang, Yang

    2015-01-01

    Structure based virtual screening has largely been limited to protein targets for which either an experimental structure is available or a strongly homologous template exists so that a high-resolution model can be constructed. The performance of state of the art protein structure predictions in virtual screening in systems where only weakly homologous templates are available is largely untested. Using the challenging DUD database of structural decoys, we show here that even using templates with only weak sequence homology (<30% sequence identity) structural models can be constructed by I-TASSER which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied. For 65% of the targets, the I-TASSER models, which are constructed essentially in the apo conformations, reached 70% of the virtual screening performance of using the holo-crystal structures. A correlation was observed between the success of I-TASSER in modeling the global fold and local structures in the binding pockets of the proteins versus the relative success in virtual screening. The virtual screening performance can be further improved by the recognition of chemical features of the ligand compounds. These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies, especially for the proteins lacking crystallographic structures.

  2. A complement to the modern crystallographer's toolbox: caged gadolinium complexes with versatile binding modes.

    PubMed

    Stelter, Meike; Molina, Rafael; Jeudy, Sandra; Kahn, Richard; Abergel, Chantal; Hermoso, Juan A

    2014-06-01

    A set of seven caged gadolinium complexes were used as vectors for introducing the chelated Gd(3+) ion into protein crystals in order to provide strong anomalous scattering for de novo phasing. The complexes contained multidentate ligand molecules with different functional groups to provide a panel of possible interactions with the protein. An exhaustive crystallographic analysis showed them to be nondisruptive to the diffraction quality of the prepared derivative crystals, and as many as 50% of the derivatives allowed the determination of accurate phases, leading to high-quality experimental electron-density maps. At least two successful derivatives were identified for all tested proteins. Structure refinement showed that the complexes bind to the protein surface or solvent-accessible cavities, involving hydrogen bonds, electrostatic and CH-π interactions, explaining their versatile binding modes. Their high phasing power, complementary binding modes and ease of use make them highly suitable as a heavy-atom screen for high-throughput de novo structure determination, in combination with the SAD method. They can also provide a reliable tool for the development of new methods such as serial femtosecond crystallography.

  3. Challenges in quantitative crystallographic characterization of 3D thin films by ACOM-TEM.

    PubMed

    Kobler, A; Kübel, C

    2017-02-01

    Automated crystal orientation mapping for transmission electron microscopy (ACOM-TEM) has become an easy to use method for the investigation of crystalline materials and complements other TEM methods by adding local crystallographic information over large areas. It fills the gap between high resolution electron microscopy and electron back scatter diffraction in terms of spatial resolution. Recent investigations showed that spot diffraction ACOM-TEM is a quantitative method with respect to sample parameters like grain size, twin density, orientation density and others. It can even be used in combination with in-situ tensile or thermal testing. However, there are limitations of the current method. In this paper we discuss some of the challenges and discuss solutions, e.g. we present an ambiguity filter that reduces the number of pixels with a '180° ambiguity problem'. For that an ACOM-TEM tilt series of nanocrystalline Pd thin films with overlapping crystallites was acquired and analyzed. Copyright © 2017. Published by Elsevier B.V.

  4. Variation in the dispersion of axisymmetric waves in infinite circular rods with crystallographic wire texture

    SciTech Connect

    Mason, T.A. )

    1999-09-01

    This paper presents the solution to the frequency equation for a number of polycrystalline, textured circular rods having transverse isotropy. The effective, second-order elastic stiffness tensors were estimated using the recursive general Hill arithmetic mean (GHAM). The velocity dispersion curves for a number of combinations of materials and crystallographic fiber or wire textures were calculated and the variation due to texture displayed. At large wavelengths, the velocity dispersion of fiber textured materials exhibits a lowest-order axisymmetric mode which varies only with the directional Poisson[close quote]s ratios in a manner similar to that of isotropic aggregates. In this wavelength regime, the waves propagate nondispersively at the wave speed, C[sub 0], as dictated by the directional Young[close quote]s modulus. At wavelengths smaller than the rod radius, the dispersion curves were more influenced by the full anisotropy of the wire textures. At these wavelengths, the dispersion curves for the anisotropic materials deviated significantly from those of the isotropic materials and one another with the higher axisymmetric vibration modes exhibiting extreme differences. This deviation is a function of the single crystal anisotropy and nature of the wire textures. < --[AN] -->

  5. Crystallographic control on the substructure of nacre tablets.

    PubMed

    Checa, Antonio G; Mutvei, Harry; Osuna-Mascaró, Antonio J; Bonarski, Jan T; Faryna, Marek; Berent, Katarzyna; Pina, Carlos M; Rousseau, Marthe; Macías-Sánchez, Elena

    2013-09-01

    Nacre tablets of mollusks develop two kinds of features when either the calcium carbonate or the organic portions are removed: (1) parallel lineations (vermiculations) formed by elongated carbonate rods, and (2) hourglass patterns, which appear in high relief when etched or in low relief if bleached. In untreated tablets, SEM and AFM data show that vermiculations correspond to aligned and fused aragonite nanogloblules, which are partly surrounded by thin organic pellicles. EBSD mapping of the surfaces of tablets indicates that the vermiculations are invariably parallel to the crystallographic a-axis of aragonite and that the triangles are aligned with the b-axis and correspond to the advance of the {010} faces during the growth of the tablet. According to our interpretation, the vermiculations appear because organic molecules during growth are expelled from the a-axis, where the Ca-CO3 bonds are the shortest. In this way, the subunits forming nacre merge uninterruptedly, forming chains parallel to the a-axis, whereas the organic molecules are expelled to the sides of these chains. Hourglass patterns would be produced by preferential adsorption of organic molecules along the {010}, as compared to the {100} faces. A model is presented for the nanostructure of nacre tablets. SEM and EBSD data also show the existence within the tablets of nanocrystalline units, which are twinned on {110} with the rest of the tablet. Our study shows that the growth dynamics of nacre tablets (and bioaragonite in general) results from the interaction at two different and mutually related levels: tablets and nanogranules. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Calculation of Crystallographic Texture of BCC Steels During Cold Rolling

    NASA Astrophysics Data System (ADS)

    Das, Arpan

    2017-05-01

    BCC alloys commonly tend to develop strong fibre textures and often represent as isointensity diagrams in φ 1 sections or by fibre diagrams. Alpha fibre in bcc steels is generally characterised by <110> crystallographic axis parallel to the rolling direction. The objective of present research is to correlate carbon content, carbide dispersion, rolling reduction, Euler angles (ϕ) (when φ 1 = 0° and φ 2 = 45° along alpha fibre) and the resulting alpha fibre texture orientation intensity. In the present research, Bayesian neural computation has been employed to correlate these and compare with the existing feed-forward neural network model comprehensively. Excellent match to the measured texture data within the bounding box of texture training data set has been already predicted through the feed-forward neural network model by other researchers. Feed-forward neural network prediction outside the bounds of training texture data showed deviations from the expected values. Currently, Bayesian computation has been similarly applied to confirm that the predictions are reasonable in the context of basic metallurgical principles, and matched better outside the bounds of training texture data set than the reported feed-forward neural network. Bayesian computation puts error bars on predicted values and allows significance of each individual parameters to be estimated. Additionally, it is also possible by Bayesian computation to estimate the isolated influence of particular variable such as carbon concentration, which exactly cannot in practice be varied independently. This shows the ability of the Bayesian neural network to examine the new phenomenon in situations where the data cannot be accessed through experiments.

  7. 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.

  8. Chemical and crystallographic events in the caries process.

    PubMed

    LeGeros, R Z

    1990-02-01

    The chemical and crystallographic events associated with the caries process can be described based on the results from the following studies: (a) effects of carbonate, magnesium, fluoride, and strontium on the physico-chemical properties--lattice parameters, crystallinity (crystal size and strain); dissolution properties of synthetic apatites; (b) factors influencing the in vitro formation and transformation of DCPD, OCP, AP (Ca-deficient apatites), FAP, beta-TCMP (Mg-substituted), and CaF2; and (c) studies on properties (crystallinity, composition, chemical, and thermal stabilities) of enamel, dentin, and bone. The dissolution of CO3-rich/Mg-rich/F-poor dental apatite crystals and re-precipitation of CO3-poor/Mg-poor/F-rich apatite in the presence of F- ions in solution contribute to a more acid-resistant surface layer of the caries lesion. Fluoride promotes the formation of less Ca-deficient and more stable apatite crystals. The presence of Ca, P, and F in solution inhibits dissolution of apatite more than does the presence of F alone. Low levels of F in solution promote the formation of (F, OH)-apatite, even under very acid conditions; an increase in F levels causes the formation of CaF2 at the expense of DCPD or apatite, especially in acid conditions. F in apatite and/or in solution suppresses extensive dissolution of dental apatite and enhances the formation of (F, OH)-apatite crystals which are more resistant against acid-dissolution than are F-free apatite crystals.

  9. 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

  10. 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

  11. 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

  12. Anomalous magnetism of Pr in PrCoAsO

    SciTech Connect

    Tiwari, Brajesh; Awana, V. P. S.; Pal, Anand

    2014-01-15

    Detailed magnetization and magneto-transport measurements studies are carried out to unearth the anomalous magnetism of Pr in PrCoAsO compound. The studied PrCoAsO sample is single phase and crystallized in the tetragonal structure with space group P4/nmm in analogy of ZrCuSiAs type compounds. Detailed magnetization measurements showed that Co moments in PrCoAsO exhibit weakly itinerant ferromagnetic Co spins ordering at below 80 K with a small magnetic moments of ∼ 0.12 μ{sub B}/f.u. High temperatures Curie-Weiss fit, resulted in effective paramagnetic moment μ{sub eff} (exp) of 5.91 μ{sub B}/f.u., which can be theoretically assigned to 3d Co (3.88 μ{sub B}) and 4f Pr (3.58 μ{sub B}). Further, a positive Curie-Weiss temperature (Θ) of 136 K is seen, indicating predominant ferromagnetic interactions in PrCoAsO. Detailed transport measurements showed that PrCoAsO exhibit metallic behavior and negative magneto-resistance below ferro-magnetically (FM) ordered state. Surprisingly, the situation of PrCoAsO is similar to non magnetic La containing LaCoAsO and strikingly different than that as reported for magnetic Nd, Sm and Gd i.e., (Nd/Sm/Gd)CoAsO. The magnetic behavior of PrCoAsO being closed to LaCoAsO and strikingly different to that of (Nd/Sm/Gd)CoAsO is unusual.

  13. 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

  14. Préface

    NASA Astrophysics Data System (ADS)

    Schober, Helmut; Fischer, Henry; Leclercq-Hugeux, Françoise

    2003-09-01

    L'École Thématique “Structure et Dynamique des Systèmes Désordonnés” [1] s'inscrit dans le cadre des écoles organisées sous l'impulsion de la Société Française de la Neutronique (SFN). Elle s'est deroulée en mai 2002 sur la Presqu'île de Giens (Var) en première partie des 11émes Journées de la Diffusion Neutronique. L'Édition de ces cours constitue ainsi le cinquième ouvrage introduisant les techniques neutroniques et leurs apports à differentes thématiques [2]. Le désordre est un facteur déterminant pour pratiquement toutes les propriétés des matériaux. Il est inhérent dans les matériaux amorphes ou liquides, mais il détermine également les propriétés mécaniques et électroniques d'autres composés d'importance technologique comme les matériaux métalliques, dont l'aspect “désordonné” est moins évident. Le désordre enfin joue un rôle essentiel dans tout ce que touche à la vie. En fait, il est difficile d'imaginer des systèmes, à part quelques exceptions rares comme l'hélium ou le silicium de haute pureté, où il n'y ait pas de désordre. En dehors de cet aspect pratique, la description scientifique du désordre atomique pose toujours des problèmes fondamentaux faute de concepts pertinents. Une des tâches importantes du scientifique ou de l'ingenieur est de préciser quel genre de désordre existe à une échelle d'espace et de temps donnée. Un materiau peut très bien être homogène à l'échelle atomique et présenter des défauts ou des hétrogéneité visibles à l'œil et inversement. De même, un système désordonné à un instant donné, peut apparaître ordonné si on moyenne dans le temps. Les techniques de diffusion des neutrons sont idéales pour aborder ces questions. Les neutrons sondent directement les noyaux et ont à la fois des longueurs d'ondes proches des distances inter atomiques et des énergies avoisinant celles des excitations élémentaires de la matière condensée. Ils permettent ainsi

  15. 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

  16. 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

  17. Préface

    NASA Astrophysics Data System (ADS)

    Rozelot, J.-P.; Bijaoui, A.

    2002-03-01

    Ce livre reprend pour l'essentiel des cours qui ont été dispensées lors de deux Écoles thématiques réalisées avec le concours du CNRS. La première fait partie du cycle des Écoles d'Astrophysique Solaire d'Oléron (F), dont le succès est grandissant dans la communauté concernée. La seconde s'est tenue spécifiquement à La Grande Motte près de Montpellier (F). L'objectif de ces Écoles, qui se sont tenues à une année d'intervalle, était de donner aux chercheurs concernés, qu'ils soient du secteur des Sciences de l'Univers ou de celui des Sciences pour l'Ingénieur, une formation aux nouvelles méthodes d'analyses de données, afin de leur faire bien comprendre l'intérêt de ces nouveaux outils pour la résolution de leurs problèmes scientifiques. En effet, les chercheurs disposent d'une quantité de plus en plus grande d'informations obtenues grâce aux très nombreux observatoires spatiaux et au sol. Pour l'analyse de ces données, des logiciels complexes ont été mis au point et distribués dans les laboratoires. Grâce au réseau, chacun peut extraire d'une banque de données les signaux ou les images observées, les réduire avec des programmes disposant d'une documentation élaborée et obtenir des résultats scientifiques pertinents. Mais les chercheurs sont souvent limités dans leurs connaissances pour aborder les problèmes d'analyse des données, et ils sont perplexes devant le choix de l'algorithme a utiliser. L'analyse des données est une discipline vaste, ayant justement pour tâche de permettre l'extraction des informations pertinentes des observations. La formation à ces méthodes contemporaines, formation qui a été proposée et est relatée dans ce livre, permet à chacun de mieux concevoir sa stratégie d'analyse pour pouvoir ainsi choisir les programmes de manière judicieuse. Cet ouvrage, novateur, se veut d'offrir de nouvelles idées et d'ouvrir de nouvelles voies. Il est divisé en trois grandes parties qui permettent au

  18. 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

  19. 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

  20. Partitioning of aluminum atoms in crystallographically non-equivalent tetrahedral sites of the zeolite offretite by 29Si MAS NMR

    NASA Astrophysics Data System (ADS)

    Chen, T. H.; Wang, K. X.; Luo, W. L.; Yuan, Z. Y.; Wang, J. Z.; Ding, D. T.; Li, H. X.; Hu, C.

    1996-04-01

    For the zeolite offretite, a formula is proposed which includes the framework Si/Al ratio ( R), the partitioning ratio of Al over two crystallographically non-equivalent tetrahedral sites ( r) and intensities of the observed peaks in the 29Si MAS NMR spectrum. By this formula, the framework Si/Al ratio of offretite can be estimated from the 29Si MAS NMR spectrum. Combined with chemical analysis of the Si/Al ratio, Al partitioning in two kinds of T sites can also be deduced. It is concluded that the T B sites are favored by Al atoms in parent offretites and Al atoms at T B sites can more easily be substituted isomorphously by Si when treated with (NH 4) 2SiF 6. The formula proposed here is based only on experiments and may be used to testify some statistical models of Al distributions in offretites.

  1. 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.

  2. Cost utility of telaprevir-PR (peginterferon-ribavirin) versus boceprevir-PR and versus PR alone in chronic hepatitis C in The Netherlands.

    PubMed

    Vellopoulou, Aikaterini; van Agthoven, Michel; van der Kolk, Annemarie; de Knegt, Robert J; Berdeaux, Gilles; Cure, Sandrine; Bianic, Florence; Lamotte, Mark

    2014-12-01

    The hepatitis C virus may lead to cirrhosis, liver cancer, liver transplant, and increased mortality. With standard treatment peginterferon-alpha and ribavirin (PR), sustained viral response (SVR) was less than 50 %. SVR rates improve greatly when PR is combined with telaprevir or boceprevir. The aim of this study was to assess the cost utility of telaprevir-peginterferon-ribavirin (TPR) versus PR and boceprevir-peginterferon-ribavirin (BPR) in treatment-naïve (TN) and treatment-experienced (TE) adults with chronic hepatitis C in the Netherlands. A Markov model with a lifelong time horizon and annual cycles was developed. Clinical data stemmed from phase III trials (TPR vs PR, BPR vs PR). A mixed treatment comparison (MTC) was developed to compare TPR and BPR indirectly. Unit costs and utilities based on EQ-5D were established in a Dutch cross-sectional study. Cost per quality-adjusted life-years (QALYs) was calculated according to the societal perspective. Treating TN patients with TPR generates 1.12 additional QALYs with €333 additional cost compared with PR, resulting in an incremental cost-utility ratio of €299/QALY. In TE patients, TPR dominates PR with cost savings (-€7,819) and 1.63 additional QALYs. TPR dominates BPR yielding additional QALYs (0.26 in TN; 0.71 in TE) and cost savings (-€7,296, -€18,144, respectively). TPR seems a cost-effective alternative to PR in TN patients and dominant in TE patients. TPR was a dominant, more effective and less costly alternative to BPR in both patient types. The cost effectiveness of both TPR and BPR is well below generally accepted willingness-to-pay thresholds and may be considered cost effective.

  3. 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

  4. Synthesis and characterization of TpiPrMoO(S2PR2) (R = Pri, Ph, OEt, OPri, (-)-mentholate) and {HB(OMe)(Pripz)2}MoO(S2PPri2), including isomers of known 1,2-borotropically-shifted complexes.

    PubMed

    Young, Charles G; Malarek, Michael S; Evans, David J; Doonan, Christian J; Ng, Victor Wee Lin; White, Jonathan M

    2009-03-02

    Green/blue TpiPrMoO(S2PR2) (TpiPr = hydrotris(3-isopropylpyrazolyl)borate; R = Pri, Ph, OEt, OPri, (-)-mentholate) complexes were synthesized and characterized by elemental analysis, mass spectrometry, IR and NMR spectroscopy, and X-ray crystallography. The diamagnetic, six-coordinate, oxo-Mo(IV) complexes possess distorted octahedral geometries defined by terminal oxo, bidentate dithio acid, and tridentate TpiPr ligands. The R = Pri and Ph derivatives are isomers of previously reported 1,2-borotropically shifted complexes, TpiPr*MoO(S2PR2) (TpiPr* = hydrobis(3-isopropylpyrazolyl)(5-isopropylpyrazolyl)borate; ref: Inorg. Chem. 1996, 35, 5368). Conversion of TpiPrMoO(S2PPh2) into TpiPr*MoO(S2PPh2) at elevated temperatures (>80 degrees C) showed that the borotropically shifted isomer was thermodynamically more stable than the unshifted species. Reaction with methanol converts TpiPrMoO(S2PPri2) into {HB(OMe)(Pripz)2}MoO(S2PPri2) (Pripz = 3-isopropylpyrazolyl), which was characterized by spectroscopic and crystallographic methods.

  5. Crystallographic Preferred Orientation of Amphibole Experimentally Deformed in Simple Shear

    NASA Astrophysics Data System (ADS)

    Ko, B.; Jung, H.

    2013-12-01

    Seismic anisotropy of the intermediate to lower crust can be attributed to the crystallographic preferred orientation (CPO) of deformed amphibole because of its high anisotropy and abundance in the deep crust. However, the lack of in-depth studies on simple-shear experiments of amphibole has obstructed the view of the CPO of amphibole to explain the intricate flow patterns in the crust. Therefore, we conducted simple-shear deformation experiments of amphibolite at the pressure of 1 GPa and at the temperatures of 500 - 700°C. Starting material is a fine-grained natural amphibolite which consists of hornblende (70 %), anorthite (30 %), and minor ilmenite and titanite (~2 %). Sample was deformed to large shear strain with a strain rate of 10-5 to 10-4 s-1 by using a modified griggs apparatus installed at Seoul National University (SNU). Microstructure of the deformed amphibolite was observed by scanning electron microscope, and the CPO of hornblende was analyzed by electron backscatter diffraction (EBSD) technique with Channel 5 software. Deformed amphibolites showed strong grain-size reduction by fracturing with strain localization, suggesting that the dominant deformation mechanism was cataclastic flow accompanied by mechanical rotation of grains. We found three types of CPOs of hornblende: type-I, type-II, and type-III. All fabric types showed (100) plane aligning nearly parallel to the shear plane. Type-I fabric represented that [001] axes are aligned subparallel to the shear direction. Type-II fabric represented that (010) poles are aligned subparallel to the shear direction. Type-III fabric represented that (010) poles and [001] axes form a girdle nearly parallel to the shear plane. Type-I fabric was produced at low temperatures (500 - 550°C), but type-II and type-III fabrics were developed at higher temperatures (600 - 700°C) in a dry and wet condition, respectively. Seismic velocities and anisotropies corresponding to each CPO type were calculated. The P

  6. Magnetic anisotropy induced by crystallographic orientation and morphological alignment in directionally-solidified eutectic Mn-Sb alloy

    NASA Astrophysics Data System (ADS)

    Lou, Chang-Sheng; Liu, Tie; Dong, Meng; Wu, Chun; Shao, Jian-Guo; Wang, Qiang

    2017-02-01

    The influences of the crystallographic orientation and morphological alignment upon the magnetic anisotropic behavior of polycrystalline materials were investigated. Microstructures obtained in eutectic Mn-Sb alloys via directional solidification simultaneously displayed crystallographic orientation and morphological alignment. Both the crystallographic orientation and the morphological alignment were able to induce magnetic anisotropy in the alloys, wherein the influence of the crystallographic orientation and the morphological alignment upon the magnetic anisotropic behavior of the alloys strongly depended upon their directions and exhibited either mutual promotion or competition. These findings may provide useful guidance for the fabrication design of functional magnetic materials.

  7. Préface

    NASA Astrophysics Data System (ADS)

    Paulus, Werner; Meinnel, Jean

    2003-02-01

    de vue européen, si les sources de l'ILL et d'ISIS peuvent encore être considérées comme des leaders au point de vue mondial, il est évidemment souhaitable que la nouvelle source neutronique à spallation (European Spallation Source : ESS) soit rapidement réalisée. Aujourd'hui ce projet est bien avancé, cette source devrait dépasser le flux des sources actuelles par près de deux ordres de grandeur et ainsi de maintenir au meilleur niveau les compétences Européennes. Il est évident qu'une utilisation efficace et intelligente des sources existantes, mais aussi de celles de la nouvelle génération, implique une certaine infrastructure nationale tant au niveau de la conception, de la réalisation que du fonctionnement des différents spectromètres. Ceci implique un très fort engagement des universités dans les différents projets de recherche. Le devoir des universités qui en résulte est donc d'intégrer l'utilisation des “grands instruments" dans leur programme d'enseignement. Dans ce sens, nous souhaitons que ce cours, entièrement rédigé en français, contribue à la fois à aider les chercheurs “non spécialistes” à accéder plus facilement au domaine neutronique, mais aussi à servir de base aux enseignants pour l'organisation et la préparation de leurs cours.Nous tenons à remercier tous les collègues qui ont accepté de rédiger de façon détaillée les cours qu'ils avaient présentés oralement dans la grande salle du VVF de Trégastel, ainsi que toutes les personnes qui ont contribué à la réussite du séjour ou à la réalisation de ce fascicule. Nous gardons un excellent souvenir de l'atmosphère de l'École qui a eu lieu à Trégastel, en plein centre de la côte de granite rose en Bretagne, en mai 2001 et était jumelée avec les Journées de la diffusion neutronique, elles aussi organisées sous l'égide de la SFN.Nous souhaitons que la lecture de cet ouvrage soit utile à un maximum de chercheurs.

  8. 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

  9. 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.

  10. 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.

  11. Influence of Defects and Crystallographic Orientation on Mechanical Behavior of Nanocrystalline Aluminium

    NASA Astrophysics Data System (ADS)

    Cai, Jun; Deng, Qiong; An, Min-Rong; Song, Hai-Yang; Su, Meng-Jia

    2016-10-01

    Simulation of molecular dynamics using Embedded Atom Method (EAM) potentials is performed to investigate the mechanical properties of single crystal Al along various crystallographic orientations under tensile loading. The specimens are provided with one or two embedded circular voids to analyze the damage evolution by void growth and coalescence. The simulation result shows that the Young's modulus, yielding stress and ultimate stress decrease with the emergence of the voids. Besides, the simulations show that the single-crystal Al in different crystallographic orientations behaves differently in elongation deformations. The single-crystal Al with <100> crystallographic orientations has greater ductility than other orientated specimens. The incipient plastic deformation and the stress-strain curves are presented and discussed for further understanding of the mechanical properties of single-crystal Al. Supported by the National Science Foundation of China under Grant No. 11572259

  12. Crystallographic Features of The Martensitic Transformation in PbTiO3 Compound

    NASA Astrophysics Data System (ADS)

    Navruz, N.

    2010-01-01

    Martensitic transformations are displacive in nature and occur in the solid state in a wide variety of metallic and non metallic materials. Although the occurrence of martensitic transformations in inorganic and ceramic compounds has been well recognized for many years, it is only in the last decade that they have achieved prominence. An important group of materials in which martensitic transformations play a significant role in determining microstructure and thus properties are the perovskite-type oxides such as PbTiO3. In this study, emphasis is given to the crystallography of the paraelectric cubic to ferroelectric tetragonal phase transformation in PbTiO3 compound. A detailed crystallographic analysis is performed in Lead Titanate (PbTiO3) and the crystallographic parameters are calculated. The predictions of the crystallographic analysis are compared with the experimental results available.

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

    DOE PAGES

    Dehoff, Ryan R.; Kirka, Michael M.; List, III, Frederick Alyious; ...

    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

  14. Advanced yield strength of interconnector ribbon for photovoltaic module using crystallographic texture control

    NASA Astrophysics Data System (ADS)

    Kang, Byungjun; Park, Nochang; Tark, Sung Ju; Oh, Won Wook; Park, Sungeun; Kim, Young Do; Lee, Hae-Seok; Kim, Donghwan

    2014-03-01

    This paper reports a study on reducing the yield strength of Cu ribbon wire used for Si solar cell interconnections in solar panels. Low yield strength Cu core should be used as the interconnector ribbon to minimize the fracture of Si solar cells during the tabbing process. We lowered the yield strength of Cu ribbon by controlling the crystallographic texture without increasing the annealing time and temperature. The crystallographic texture was controlled by lubrication in a cold rolling process. The crystallographic texture was observed by scanning electron microscopy with electron back scattered diffraction. A tensile test was performed for the comparison of the mechanical properties of Cu with and without lubrication. The average yield strength was 91.2 MPa with lubrication whereas the yield strength was 99.6 MPa without lubrication. The lower value of the lubricated samples seemed to be caused by the higher cube texture intensity than that of the samples without lubrication.

  15. Crystallographic Texture Evolution of a Zinc Sheet Subjected to Different Strain Paths

    NASA Astrophysics Data System (ADS)

    Schlosser, Fernando; Schwindt, Claudio; Fuster, Valeria; Tommasi, Andrea; Signorelli, Javier Walter

    2017-06-01

    The use of zinc sheets has largely increased in the last years, fundamentally because of new tendencies in architecture and, at the same time, due to its excellent properties, as corrosion resistance under aggressive climatic conditions, malleability, recyclability, and surface finishing aspect. In the present work, the X-ray diffraction technique is used to characterize the crystallographic texture evolution of a strongly anisotropic Zn20 zinc sheet (Zn-Cu-Ti) subjected to uniaxial tension, plane strain, and equibiaxial tension, for specimens cut at 0, 45, and 90 deg with respect to the rolling direction. The crystallographic texture evolution is evaluated by means of pole figures, orientation distribution function, and Kearns factors. For all tested strain paths, deformation produces a decrease in the intensity of the crystallographic textures, due to a dispersion of the orientations of the different axes around the initial maxima.

  16. 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

  17. 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.

  18. 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

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

    SciTech Connect

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

    2016-08-31

    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.PHENIXAFITTrefinement 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.PHENIXAFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIXAFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented,PHENIXAFITTrefinements result in more chemically accurate models for small-molecule ligands.

  20. PrEP implementation research in Africa: what is new?

    PubMed

    Cowan, Frances M; Delany-Moretlwe, Sinead; Sanders, Eduard J; Mugo, Nelly R; Guedou, Fernand A; Alary, Michel; Behanzin, Luc; Mugurungi, Owen; Bekker, Linda-Gail

    2016-01-01

    Of the two million new HIV infections in adults in 2014, 70% occurred in sub-Saharan Africa. Several African countries have already approved guidelines for pre-exposure prophylaxis (PrEP) for individuals at substantial risk of HIV as part of combination HIV prevention but key questions remain about how to identify and deliver PrEP to those at greatest need. Throughout the continent, individuals in sero-discordant relationships, and members of key populations (sex workers, men who have sex with men (MSM), transgender women and injection drug users) are likely to benefit from the availability of PrEP. In addition, adolescent girls and young women (AGYW) are at substantial risk in some parts of the continent. It has been estimated that at least three million individuals in Africa are likely to be eligible for PrEP according to WHO's criteria. Tens of demonstration projects are planned or underway across the continent among a range of countries, populations and delivery settings. In each of the target populations, there are overarching issues related to (i) creating demand for PrEP, (ii) addressing supply-side issues and (iii) providing appropriate and tailored adherence support. Critical for creating demand for PrEP is the normalization of HIV prevention. Community-level interventions which engage opinion leaders as well as empowerment interventions for those at highest risk will be key. Critical to supply of PrEP is that services are accessible for all, including for stigmatized populations. Establishing accessible integrated services provides the opportunity to address other public health priorities including the unmet need for HIV testing, contraception and sexually transmitted infections treatment. National policies need to include minimum standards for training and quality assurance for PrEP implementation and to address supply chain issues. Adherence support needs to recognize that social and structural factors are likely to have an important influence

  1. PrEP implementation research in Africa: what is new?

    PubMed Central

    Cowan, Frances M; Delany-Moretlwe, Sinead; Sanders, Eduard J; Mugo, Nelly R; Guedou, Fernand A; Alary, Michel; Behanzin, Luc; Mugurungi, Owen; Bekker, Linda-Gail

    2016-01-01

    Introduction Of the two million new HIV infections in adults in 2014, 70% occurred in sub-Saharan Africa. Several African countries have already approved guidelines for pre-exposure prophylaxis (PrEP) for individuals at substantial risk of HIV as part of combination HIV prevention but key questions remain about how to identify and deliver PrEP to those at greatest need. Throughout the continent, individuals in sero-discordant relationships, and members of key populations (sex workers, men who have sex with men (MSM), transgender women and injection drug users) are likely to benefit from the availability of PrEP. In addition, adolescent girls and young women (AGYW) are at substantial risk in some parts of the continent. It has been estimated that at least three million individuals in Africa are likely to be eligible for PrEP according to WHO's criteria. Tens of demonstration projects are planned or underway across the continent among a range of countries, populations and delivery settings. Discussion In each of the target populations, there are overarching issues related to (i) creating demand for PrEP, (ii) addressing supply-side issues and (iii) providing appropriate and tailored adherence support. Critical for creating demand for PrEP is the normalization of HIV prevention. Community-level interventions which engage opinion leaders as well as empowerment interventions for those at highest risk will be key. Critical to supply of PrEP is that services are accessible for all, including for stigmatized populations. Establishing accessible integrated services provides the opportunity to address other public health priorities including the unmet need for HIV testing, contraception and sexually transmitted infections treatment. National policies need to include minimum standards for training and quality assurance for PrEP implementation and to address supply chain issues. Adherence support needs to recognize that social and structural factors are likely to have an

  2. The N-Terminal, Polybasic Region of PrPC Dictates the Efficiency of Prion Propagation by Binding to PrPSc

    PubMed Central

    Turnbaugh, Jessie A.; Unterberger, Ursula; Saá, Paula; Massignan, Tania; Fluharty, Brian R.; Bowman, Frederick P.; Miller, Michael B.; Supattapone, Surachai; Biasini, Emiliano; Harris, David A.

    2012-01-01

    Prion propagation involves a templating reaction in which the infectious form of the prion protein (PrP Sc) binds to the cellular form (PrP C), generating additional molecules of PrP Sc. While several regions of the PrP C molecule have been suggested to play a role in PrP Sc formation based on in vitro studies, the contribution of these regions in vivo is unclear. Here, we report that mice expressing PrP deleted for a short, polybasic region at the N terminus (residues 23–31) display a dramatically reduced susceptibility to prion infection and accumulate greatly reduced levels of PrP Sc. These results, in combination with biochemical data, demonstrate that residues 23–31 represent a critical site on PrP C that binds to PrP Sc and is essential for efficient prion propagation. It may be possible to specifically target this region for treatment of prion diseases as well as other neurodegenerative disorders due to β-sheet-rich oligomers that bind to PrP C. PMID:22745483

  3. 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

  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. The Ultrasonic Measurement of Crystallographic Orientation for Imaging Anisotropic Components with 2d Arrays

    NASA Astrophysics Data System (ADS)

    Lane, C. J. L.; Dunhill, A. K.; Drinkwater, B. W.; Wilcox, P. D.

    2011-06-01

    Single crystal components are used widely in the gas-turbine industry. However, these components are elastically anisotropic which causes difficulties when performing NDE inspections with ultrasound. Recently an ultrasonic algorithm for a 2D array has been corrected to perform the reliable volumetric inspection of single crystals. For the algorithm to be implemented the crystallographic orientation of the components must be known. This paper, therefore, develops and reviews crystallographic orientation methods using 2D ultrasonic arrays. The methods under examination are based on the anisotropic propagation of surface and bulk waves and an image-based orientation method is also considered.

  6. Crystallographic point groups of five-dimensional space. 1. Their elements and their subgroups.

    PubMed

    Veysseyre, R; Veysseyre, H

    2002-09-01

    The purpose of this work is to introduce a method with a view to obtaining the crystallographic point groups of five-dimensional space, i.e. the subgroups of the holohedries of these space crystal families. This paper is specifically devoted to numerical analysis, whereas the following ones deal with some applications to crystallography. These results have been obtained through a collaboration between two teams: H. Veysseyre (Institut Supérieur des Matériaux) for the numerical analysis, R. Veysseyre, D. Weigel and Th. Phan (Ecole Centrale Paris) for the crystallographic part.

  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. Unraveling the neuroprotective mechanisms of PrPC in excitotoxicity

    PubMed Central

    Llorens, Franc; del Río, José Antonio

    2012-01-01

    Knowledge of the natural roles of cellular prion protein (PrPC) is essential to an understanding of the molecular basis of prion pathologies. This GPI-anchored protein has been described in synaptic contacts, and loss of its synaptic function in complex systems may contribute to the synaptic loss and neuronal degeneration observed in prionopathy. In addition, Prnp knockout mice show enhanced susceptibility to several excitotoxic insults, GABAA receptor-mediated fast inhibition was weakened, LTP was modified and cellular stress increased. Although little is known about how PrPC exerts its function at the synapse or the downstream events leading to PrPC-mediated neuroprotection against excitotoxic insults, PrPC has recently been reported to interact with two glutamate receptor subunits (NR2D and GluR6/7). In both cases the presence of PrPC blocks the neurotoxicity induced by NMDA and Kainate respectively. Furthermore, signals for seizure and neuronal cell death in response to Kainate in Prnp knockout mouse are associated with JNK3 activity, through enhancing the interaction of GluR6 with PSD-95. In combination with previous data, these results shed light on the molecular mechanisms behind the role of PrPC in excitotoxicity. Future experimental approaches are suggested and discussed. PMID:22437735

  9. Conversion of raft associated prion protein to the protease-resistant state requires insertion of PrP-res (PrP(Sc)) into contiguous membranes.

    PubMed

    Baron, Gerald S; Wehrly, Kathy; Dorward, David W; Chesebro, Bruce; Caughey, Byron

    2002-03-01

    Prion protein (PrP) is usually attached to membranes by a glycosylphosphatidylinositol-anchor that associates with detergent-resistant membranes (DRMs), or rafts. To model the molecular processes that might occur during the initial infection of cells with exogenous transmissible spongiform encephalopathy (TSE) agents, we examined the effect of membrane association on the conversion of the normal protease-sensitive PrP isoform (PrP-sen) to the protease-resistant isoform (PrP-res). A cell-free conversion reaction approximating physiological conditions was used, which contained purified DRMs as a source of PrP-sen and brain microsomes from scrapie-infected mice as a source of PrP-res. Interestingly, DRM-associated PrP-sen was not converted to PrP-res until the PrP-sen was either released from DRMs by treatment with phosphatidylinositol-specific phospholipase C (PI-PLC), or the combined membrane fractions were treated with the membrane-fusing agent polyethylene glycol (PEG). PEG-assisted conversion was optimal at pH 6--7, and acid pre-treating the DRMs was not sufficient to permit conversion without PI-PLC or PEG, arguing against late endosomes/lysosomes as primary compartments for PrP conversion. These observations raise the possibility that generation of new PrP-res during TSE infection requires (i) removal of PrP-sen from target cells; (ii) an exchange of membranes between cells; or (iii) insertion of incoming PrP-res into the raft domains of recipient cells.

  10. 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.

  11. 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

  12. 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.

  13. Crystallographic structural organization of human rhinovirus serotype 16, 14, 3, 2 and 1A

    NASA Astrophysics Data System (ADS)

    Janner, A.

    2006-07-01

    The capsid of the icosahedral virion is encapsulated between two polyhedra scaled according to the golden mean, each being composed of an icosahedron and a dodecahedron. Structural units of the coat proteins are enclosed into forms whose projections along the icosahedral symmetry axes obey the crystallographic law of rational indices.

  14. Crystallization and preliminary X-ray crystallographic studies of human cyclophilin J

    SciTech Connect

    Hu, Hao; Huang, Chao-Qun; Liu, He-Li; Han, Yi; Yu, Long; Bi, Ru-Chang

    2005-02-01

    Human cyclophilin J is a member of the cyclophilin family and recent studies have indicated that it plays a role in the formation of liver cancers as a regulation factor or messenger. The preparation, crystallization and preliminary X-ray crystallographic studies of human cyclophilin J are reported.

  15. Contribution to crystallographic slip assessment by means of topographic measurements achieved with atomic force microscopy

    SciTech Connect

    Kahloun, C.; Badji, R.; Bacroix, B.; Bouabdallah, M.

    2010-09-15

    In this paper, atomic force microscopy (AFM) is used to quantitatively characterize the plastic glide occurring during tensile deformation of a duplex 2205 stainless steel sample. We demonstrate that an appropriate treatment of the topographic image issued from AFM measurements allows precise and quantitative information about the characteristics of plastic deformation and especially the amount of crystallographic slip.

  16. 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

  17. Evaluating Your School PR Investment.

    ERIC Educational Resources Information Center

    Bagin, Rich

    Educational public relations (PR) is a planned and systematic management function designed to help improve the programs and services of an educational organization. The standards and techniques discussed in this guide are based on the nearly 50 years of experience of the National School Public Relations Association (NSPRA). The guidebook offers…

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Mineralogical, crystallographic and redox features of the earliest stages of fluid alteration in CM chondrites

    NASA Astrophysics Data System (ADS)

    Pignatelli, Isabella; Marrocchi, Yves; Mugnaioli, Enrico; Bourdelle, Franck; Gounelle, Matthieu

    2017-07-01

    The CM chondrites represent the largest group of hydrated meteorites and span a wide range of conditions, from less altered (i.e., CM2) down to heavily altered (i.e., CM1). The Paris chondrite is considered the least altered CM and thus enables the earliest stages of aqueous alteration processes to be deciphered. Here, we report results from a nanoscale study of tochilinite/cronstedtite intergrowths (TCIs) in Paris-TCIs being the emblematic secondary mineral assemblages of CM chondrites, formed from the alteration of Fe-Ni metal beads (type-I TCIs) and anhydrous silicates (type-II TCIs). We combined high-resolution transmission electron microscopy, scanning transmission X-ray microscopy and electron diffraction tomography to characterize the crystal structure, crystal chemistry and redox state of TCIs. The data obtained are useful to reconstruct the alteration conditions of Paris and to compare them with those of other meteorites. Our results show that tochilinite in Paris is characterized by a high hydroxide layer content (n = 2.1-2.2) regardless of the silicate precursors. When examined alongside other CMs, it appears that the hydroxide layer and iron contents of tochilinites correlate with the degree of alteration experienced by the chondrites. The Fe3+/ΣFe ratios of TCIs are high: 8-15% in tochilinite, 33-60% in cronstedtite and 70-80% in hydroxides. These observations suggest that alteration of CM chondrites took place under oxidizing conditions that could have been induced by significant H2 release during serpentinization. Similar results were recently reported in CR chondrites (Le Guillou et al., 2015), suggesting that the process(es) controlling the redox state of the secondary mineral assemblages were quite similar in the CM and CR parent bodies despite the different alteration conditions. According to our mineralogical and crystallographic survey, the formation of TCIs in Paris occurred at temperatures lower than 100 °C, under neutral, slightly alkaline

  4. Progesterone receptor (PR) variants exist in breast cancer cells characterised as PR negative.

    PubMed

    Cork, David M W; Lennard, Thomas W J; Tyson-Capper, Alison J

    2012-12-01

    Progesterone receptor (PR) expression is measured in breast cancer by immunohistochemistry using N-terminally targeted antibodies and serves as a biomarker for endocrine therapeutic decisions. Extensive PR alternative splicing has been reported which may generate truncated PR variant proteins which are not detected by current breast cancer screening or may alter the function of proteins detected in screening. However, the existence of such truncated PR variants remains controversial. We have characterised PR protein expression in breast cancer cell lines using commercial PR antibodies targeting different epitopes. Truncated PR proteins are detected in reportedly PR negative MDA-MB-231 cells using a C-terminally targeted antibody. Antibody specificity was confirmed by immunoblotting following siRNA knockdown of PR expression. We have further demonstrated that alternatively spliced PR mRNA is present in MDA-MB-231 cells and in reportedly PR-negative breast tumour tissue which could encode the truncated PR proteins detected by the C-terminal antibody. The potential function of PR variant proteins present in MDA-MB-231 cells was also assessed, indicating the ability of these PR variants to bind progesterone, interact with a nuclear PR co-factor and bind DNA. These findings suggest that alternative splicing may generate functional truncated PR variant proteins which are not detected by breast cancer screening using N-terminally targeted antibodies leading to misclassification as PR negative.

  5. Transverse Wobbling in 135Pr

    NASA Astrophysics Data System (ADS)

    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.

    2015-02-01

    A pair of transverse wobbling bands is observed in the nucleus 135Pr . The wobbling is characterized by Δ I =1 , E 2 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.

  6. Promoter hypermethylation of progesterone receptor isoform B (PR-B) in endometriosis.

    PubMed

    Wu, Yan; Strawn, Estil; Basir, Zainab; Halverson, Gloria; Guo, Sun-Wei

    2006-01-01

    The physiological effects of progesterone (P) are mediated by two isoforms of progesterone receptors (PRs): PR-A and PR-B. Progestins have long been used in the treatment of endometriosis but unfortunately the relief of pain is relatively short-term. In addition, about nine percent of women with endometriosis simply do not respond to progestin therapy due to unknown reasons. In fact, a general tendency for relative progesterone resistance within eutopic and ectopic endometrium of women with endometriosis and also the downregulation of PR-B, but not PR-A, in endometriosis have been noted. Since promoter hypermethylation is well-documented to be associated with transcriptional silencing, we sought to determine the methylation status of the PR-A and PR-B promoter regions in the epithelial component of endometriotic implants using a combination of laser capture microdissection (LCM), methylation specific PCR, and bisulfite sequencing. We found that the promoter region of PR-B, but not PR-A, is hypermethylated in endometriosis as compared with controls. In addition, the PR-B expression was significantly reduced in the ectopic endometrium. Our finding suggests that progesterone resistance in endometriosis in general and the down regulation of PR-B, but not PR-A, in particular, are a result of promoter hypermethylation of PR-B, but not PR-A. This, in conjunction with our reported aberrant methylation of HOXA10 in the eutopic endometrium of women with endometriosis, strongly suggests that endometriosis is an epigenetic disease. This perspective should potentially open up new avenues for the delineation of pathogenesis of endometriosis, and might also lead to novel ways to treat the disease through reversing aberrant methylation via pharmacological means.

  7. 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.

  8. Influence of different kinds of rolling on the crystallographic texture and magnetic induction of a NOG 3 wt% Si steel

    NASA Astrophysics Data System (ADS)

    Silva, J. M.; Baêta Júnior, E. S.; Moraes, N. R. D. C.; Botelho, R. A.; Felix, R. A. C.; Brandao, L.

    2017-01-01

    The purpose of this work was to study the influence of different kinds of rolling on the magnetic properties of NOG steel, an electric steel widely used in electrical motors. These properties are highly correlated with the crystallographic texture of the material, which can be changed by rolling. Three kinds of rolling were examined: conventional rolling, cross-rolling and asymmetrical rolling. The crystallographic texture was determined by X-ray diffraction and the magnetic properties were calculated from a theoretical model that related the magnetic induction to crystallographic texture through the anisotropy energy. The results show that cross-rolling yields higher values of magnetic induction than the other processes.

  9. Differences in Cumulative Exposure and Adherence to Tenofovir in the VOICE, iPrEx OLE, and PrEP Demo Studies as Determined via Hair Concentrations.

    PubMed

    Koss, Catherine A; Bacchetti, Peter; Hillier, Sharon L; Livant, Edward; Horng, Howard; Mgodi, Nyaradzo; Mirembe, Brenda G; Gomez Feliciano, Kailazarid; Horn, Stephanie; Liu, Albert Y; Glidden, David V; Grant, Robert M; Benet, Leslie Z; Louie, Alexander; van der Straten, Ariane; Chirenje, Z Mike; Marrazzo, Jeanne M; Gandhi, Monica

    2017-03-02

    Pre-exposure prophylaxis (PrEP) with oral tenofovir disoproxil fumarate (TDF)/emtricitabine (FTC) prevented HIV acquisition among men and women in several trials and is broadly recommended. In the VOICE and FEM-PrEP trials, however, TDF/FTC-based PrEP did not prevent HIV acquisition among women in eastern and southern Africa. Tenofovir was detected in plasma, reflecting exposure and adherence in recent days, in fewer than one-third of participants. Drug concentrations in hair, which represent cumulative exposure and adherence over weeks to months, have never previously been examined among women on PrEP. We compared tenofovir hair concentrations among women assigned to oral TDF/FTC in the VOICE trial to those among men and transgender women enrolled in 2 open-label PrEP studies, the iPrEx open-label extension (OLE) study and the U.S. PrEP Demonstration Project (PrEP Demo). Tenofovir hair concentrations were detectable in 55% of person-visits in VOICE, 75% of person-visits in iPrEx OLE (p = .006), and 98% of person-visits in PrEP Demo (p < .001). Median tenofovir hair concentrations corresponded to an estimated 0.2, 2.9, and 6.0 TDF/FTC doses taken per week in the three studies, respectively. In VOICE, combining tenofovir concentration data from plasma and hair suggested inconsistent, low-level product use. Incorporation of both short- and long-term adherence measures may allow for an improved understanding of patterns of drug-taking among women during global PrEP roll-out.

  10. 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

    2013-11-06

    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.

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

    PubMed

    Liang, Yuan-Chang; Hsia, Hao-Yuan

    2013-12-19

    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.

  12. 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.

  13. Application of electron backscatter diffraction for crystallographic characterization of tin whiskers.

    PubMed

    Michael, Joseph R; McKenzie, Bonnie B; Susan, Donald F

    2012-08-01

    Understanding the growth of whiskers or high aspect ratio features on substrates can be aided when the crystallography of the feature is known. This study has evaluated three methods that utilize electron backscatter diffraction (EBSD) for the determination of the crystallographic growth direction of an individual whisker. EBSD has traditionally been a technique applied to planar, polished samples, and thus the use of EBSD for out-of-surface features is somewhat more difficult and requires additional steps. One of the methods requires the whiskers to be removed from the substrate resulting in the loss of valuable physical growth relationships between the whisker and the substrate. The other two techniques do not suffer this disadvantage and provide the physical growth information as well as the crystallographic growth directions. The final choice of method depends on the information required. The accuracy and the advantages and disadvantages of each method are discussed.

  14. 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.

  15. Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7

    SciTech Connect

    Quesada, Odayme; Gurda, Brittney; Govindasamy, Lakshmanan; McKenna, Robert; Kohlbrenner, Erik; Aslanidi, George; Zolotukhin, Sergei; Muzyczka, Nicholas; Agbandje-McKenna, Mavis

    2007-12-01

    Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids have been produced which diffract X-rays to ∼3.0 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to ∼3.0 Å resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 Å in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R{sub merge} of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of a capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.

  16. Crystallographic Characterization on Polycrystalline Ni-Mn-Ga Alloys with Strong Preferred Orientation

    PubMed Central

    Li, Zongbin; Yang, Bo; Zou, Naifu; Zhang, Yudong; Esling, Claude; Gan, Weimin; Zhao, Xiang; Zuo, Liang

    2017-01-01

    Heusler type Ni-Mn-Ga ferromagnetic shape memory alloys can demonstrate excellent magnetic shape memory effect in single crystals. However, such effect in polycrystalline alloys is greatly weakened due to the random distribution of crystallographic orientation. Microstructure optimization and texture control are of great significance and challenge to improve the functional behaviors of polycrystalline alloys. In this paper, we summarize our recent progress on the microstructure control in polycrystalline Ni-Mn-Ga alloys in the form of bulk alloys, melt-spun ribbons and thin films, based on the detailed crystallographic characterizations through neutron diffraction, X-ray diffraction and electron backscatter diffraction. The presented results are expected to offer some guidelines for the microstructure modification and functional performance control of ferromagnetic shape memory alloys. PMID:28772826

  17. 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).

  18. Crystallographic anisotropy of the resistivity size effect in single crystal tungsten nanowires.

    PubMed

    Choi, Dooho; Moneck, Matthew; Liu, Xuan; Oh, Soong Ju; Kagan, Cherie R; Coffey, Kevin R; Barmak, Katayun

    2013-01-01

    This work demonstrates an anisotropic increase in resistivity with decreasing width in single crystal tungsten (W) nanowires having a height of 21 nm. Nanowire-widths were in the range of 15-451 nm, with the anisotropy observed for widths below 50 nm. The longitudinal directions of the nanowires coincided with the <100>, <110> and <111> orientations of the body centered cubic phase of W. The resistivity increase was observed to be minimized for the <111>-oriented single crystal nanowires, exhibiting a factor of two lower increase in resistivity at a width of ~15 nm, relative to the thin film resistivity (i.e., an infinitely wide wire). The observed anisotropy is attributed to crystallographic anisotropy of the Fermi velocity and the resultant anisotropy of the electron mean free path in W, and underscores the critical role of crystallographic orientation in nanoscale metallic conduction.

  19. INTRINSIC FINE-SCALE STRUCTURE IN COMPLEX MATERIALS: BEYOND GLOBAL CRYSTALLOGRAPHIC ANALYSIS

    SciTech Connect

    A. MIGLIORI; ET AL

    2000-12-01

    Many important classes of materials owe their interesting properties to structures and patterns produced by local atomic deviations from ideal crystallographic positions. The pattern scale may vary from a few atomic spacings to many microns. In a macroscopic sample these deviations may still average to an ideal lattice while retaining the intrinsic fine-scale structures, or a phase transition may create a pattern of variants of a new crystallographic structure. We have carried out experiments on the formation of fine-scale structures in a range of materials, particularly those produced by phase transitions. We have used Resonant Ultrasound Spectroscopy for elastic properties and dissipation, neutron pair-distribution function, and electronic transport measurements to characterize samples. We have carried out extensive dynamical modeling based on Ginzberg-Landau formalisms to simulate the development and appearance of the structures. Our results highlight the importance of long-range strain fields and the intrinsic unstable equilibrium features of the materials studied.

  20. Mineralogical, crystallographic and morphological characteristics of natural kaolins from the Ivory Coast (West Africa)

    NASA Astrophysics Data System (ADS)

    Sei, J.; Morato, F.; Kra, G.; Staunton, S.; Quiquampoix, H.; Jumas, J. C.; Olivier-Fourcade, J.

    2006-10-01

    Thirteen clay samples from four deposits in the Ivory Coast (West Africa) were studied using X-ray diffraction, thermogravimetric analysis and chemical analysis. Mineralogical, crystallographic and morphological characteristics of these samples are given. Kaolinite is the principal mineral but other minerals are present in small quantities: illite, quartz, anatase and iron oxides (oxides and oxyhydroxides). The crystallographic, morphological and surface characteristics are influenced by the presence of these impurities. In particular, the presence of iron oxides was associated with reduced structural ordering and thermal stability of kaolinite and increased specific surface area. These clays could be used in the ceramics industry to make tiles and bricks, and also in agronomy as supports for chemical fertilizers or for environmental protection by immobilising potentially toxic waste products.

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

    PubMed

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

    2009-02-01

    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 A 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.

  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 anisotropy of the resistivity size effect in single crystal tungsten nanowires

    PubMed Central

    Choi, Dooho; Moneck, Matthew; Liu, Xuan; Oh, Soong Ju; Kagan, Cherie R.; Coffey, Kevin R.; Barmak, Katayun

    2013-01-01

    This work demonstrates an anisotropic increase in resistivity with decreasing width in single crystal tungsten (W) nanowires having a height of 21 nm. Nanowire-widths were in the range of 15–451 nm, with the anisotropy observed for widths below 50 nm. The longitudinal directions of the nanowires coincided with the <100>, <110> and <111> orientations of the body centered cubic phase of W. The resistivity increase was observed to be minimized for the <111>-oriented single crystal nanowires, exhibiting a factor of two lower increase in resistivity at a width of ~15 nm, relative to the thin film resistivity (i.e., an infinitely wide wire). The observed anisotropy is attributed to crystallographic anisotropy of the Fermi velocity and the resultant anisotropy of the electron mean free path in W, and underscores the critical role of crystallographic orientation in nanoscale metallic conduction. PMID:24005230

  4. 3D mapping of crystallographic phase distribution using energy-selective neutron tomography.

    PubMed

    Woracek, Robin; Penumadu, Dayakar; Kardjilov, Nikolay; Hilger, Andre; Boin, Mirko; Banhart, John; Manke, Ingo

    2014-06-25

    Nondestructive 3D mapping of crystallographic phases is introduced providing distribution of phase fractions within the bulk (centimeter range) of samples with micrometer-scale resolution. The novel neutron tomography based technique overcomes critical limitations of existing techniques and offers a wide range of potential applications. It is demonstrated for steel samples exhibiting phase transformation after being subjected to tensile and torsional deformation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. 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.

  6. Crystallization and preliminary crystallographic analysis of acetophenone reductase from Geotrichum candidum NBRC 4597

    PubMed Central

    Sugiyama, Yosuke; Senda, Miki; Senda, Toshiya; Matsuda, Tomoko

    2015-01-01

    Acetophenone reductase (APRD) from Geotrichum candidium NBRC 4597 was crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as a precipitant. The crystal belonged to space group P6522, with unit-cell parameters a = b = 104.5, c = 273.7 Å, and diffracted to 2.6 Å resolution. Phasing using the single-wavelength anomalous diffraction method was successful. Model building and crystallographic refinement are in progress. PMID:25760708

  7. Keep it together: restraints in crystallographic refinement of macromolecule–ligand complexes

    PubMed Central

    Steiner, Roberto A.; Tucker, Julie A.

    2017-01-01

    A short introduction is provided to the concept of restraints in macromolecular crystallographic refinement. A typical ligand restraint-generation process is then described, covering types of input, the methodology and the mechanics behind the software in general terms, how this has evolved over recent years and what to look for in the output. Finally, the currently available restraint-generation software is compared, concluding with some thoughts for the future. PMID:28177305

  8. Keep it together: restraints in crystallographic refinement of macromolecule-ligand complexes.

    PubMed

    Steiner, Roberto A; Tucker, Julie A

    2017-02-01

    A short introduction is provided to the concept of restraints in macromolecular crystallographic refinement. A typical ligand restraint-generation process is then described, covering types of input, the methodology and the mechanics behind the software in general terms, how this has evolved over recent years and what to look for in the output. Finally, the currently available restraint-generation software is compared, concluding with some thoughts for the future.

  9. Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

    PubMed Central

    Xue, Yi; Skrynnikov, Nikolai R

    2014-01-01

    Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

  10. Crystallization and preliminary crystallographic analysis of San Miguel sea lion virus: an animal calicivirus.

    PubMed

    Chen, Rong; Neill, John D; Prasad, B V Venkataram

    2003-02-01

    The Caliciviridae is a family of nonenveloped, icosahedral, positive-sense single-stranded RNA viruses. This family of viruses consists of both animal and human pathogens. Adapting human caliciviruses to cell culture has not been successful, whereas some animal caliciviruses, including San Miguel sea lion virus, have been successfully propagated in vitro. Here we report the crystallization of San Miguel sea lion virus serotype 4 (SMSV4) and the preliminary X-ray crystallographic analysis of the crystals. SMSV4 have been crystallized using the hanging-drop method. These crystals diffracted to approximately 3A resolution using a synchrotron radiation source. A single crystal under cryo-conditions yielded a complete set of diffraction data. Data processing of the diffraction patterns showed that SMSV crystals belong to I23 space group with cell dimensions a=b=c=457 A. The crystallographic asymmetric unit includes five icosahedral asymmetric units, each consisting of three capsid protein subunits. In the space group I23, given the icosahedral symmetry and the size of the virus particle, the location of the particle is constrained to be at the point where the crystallographic 2- and 3-fold axes intersect. The orientation of the virus particle in the unit cell was ascertained by self-rotation function calculations.

  11. 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

  12. 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.

  13. IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein-Protein Interfaces.

    PubMed

    Da Silva, Franck; Desaphy, Jérémy; Bret, Guillaume; Rognan, Didier

    2015-09-28

    Protein-protein interactions are becoming a major focus of academic and pharmaceutical research to identify low molecular weight compounds able to modulate oligomeric signaling complexes. As the number of protein complexes of known three-dimensional structure is constantly increasing, there is a need to discard biologically irrelevant interfaces and prioritize those of high value for potential druggability assessment. A Random Forest model has been trained on a set of 300 protein-protein interfaces using 45 molecular interaction descriptors as input. It is able to predict the nature of external test interfaces (crystallographic vs biological) with accuracy at least equal to that of the best state-of-the-art methods. However, our method presents unique advantages in the early prioritization of potentially ligandable protein-protein interfaces: (i) it is equally robust in predicting either crystallographic or biological contacts and (ii) it can be applied to a wide array of oligomeric complexes ranging from small-sized biological interfaces to large crystallographic contacts.

  14. 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.

  15. Novel nerve-agent antidote design based on crystallographic and mass spectrometric analyses of tabun-conjugated acetylcholinesterase in complex with antidotes.

    PubMed

    Ekström, F J; Astot, C; Pang, Y-P

    2007-09-01

    Organophosphorus compound-based nerve agents inhibit the essential enzyme acetylcholinesterase (AChE) causing acute toxicity and death. Clinical treatment of nerve-agent poisoning is to use oxime-based antidotes to reactivate the inhibited AChE. However, the nerve agent tabun is resistant to oximes. To design improved oximes, crystal structures of a tabun-conjugated AChE in complex with different oximes are needed to guide the structural modifications of known antidotes. However, this type of structure is extremely challenging to obtain because both deamidation of the tabun conjugate and reactivation of AChE occur during crystallographic experiments. Here we report, for the first time, the crystal structures of Ortho-7 and HLö-7 in complex with AChE that is conjugated to an intact tabun. These structures were determined by our new strategy of combining crystallographic and mass spectrometric analyses of AChE crystals. The results explain the relative reactivation potencies of the two oximes and offer insights into improving known medical antidotes.

  16. 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.

  17. Strain control of Urbach energy in Cr-doped PrFeO3

    NASA Astrophysics Data System (ADS)

    Kumar, Anil; Warshi, M. Kamal; Mishra, Vikash; Saxena, Shailendra K.; Kumar, Rajesh; Sagdeo, Pankaj R.

    2017-09-01

    Polycrystalline samples of PrFe1- x CrxO3 having average particle size of 90 nm have been prepared by wet chemical route. The structural phase purity of the prepared samples is confirmed by powder X-ray diffraction followed by Rietveld refinements. It is observed that with Cr doping, the Urbach energy ( E u) increases. The E u is measure of the various disorders present in the sample, such as chemical and structural. To understand the contribution to the E u due to chemical and structural disorders, we have probed the chemical and structural disorders in the samples by elemental mappings and through X-ray diffraction experiments, respectively. Elemental mapping confirms chemical homogeneity of prepared samples. It is observed that with Cr doping the crystallographic strain increases and Urbach energy shows the similar scaling.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Development of olivine crystallographic preferred orientation in response to strain-induced fabric geometry

    NASA Astrophysics Data System (ADS)

    Chatzaras, Vasileios; Kruckenberg, Seth C.; Cohen, Shaina M.; Medaris, L. Gordon, Jr.; Withers, Anthony C.; Bagley, Brian

    2016-04-01

    The effect of finite strain ellipsoid geometry on crystallographic preferred orientation (CPO) is well known for crustal minerals (e.g., quartz, calcite, biotite, and hornblende). In the upper mantle, however, it remains poorly constrained how strain and fabric may affect olivine CPO. We present data from a suite of 40 spinel peridotite xenoliths from Marie Byrd Land (west Antarctica), which support an interpretation that fabric geometry rather than deformation conditions control the development of olivine CPO. We use X-ray computed tomography (XRCT) to quantitatively determine spinel fabric (orientation and geometry). Olivine CPOs, determined by Electron Backscattered Diffraction (EBSD), are plotted with respect to the XRCT-derived spinel foliation and lineation; this approach allows for the accurate, and unbiased, identification of CPO symmetries and types in mantle xenoliths. The combined XRCT and EBSD data show that the xenoliths are characterized by a range of fabric geometries (from oblate to prolate) and olivine CPO patterns; we recognize the A-type, axial-[010], axial-[100], and B-type patterns. The mantle xenoliths equilibrated at temperatures 779-1198 oC, as determined by 2-Px geothermometry. Using a geotherm consistent with the stability of spinel in all xenoliths, the range of equilibration temperatures occurs at depths between 39 and 72 km. Olivine recrystallized grain size piezometry reveals differential stresses ranging 2-60 MPa. Analysis of low-angle misorientation axes show a wide range in the distribution of rotation axes, with dominant {0kl}[100] slip. We use Fourier Transform Infrared (FTIR) spectroscopy to estimate the water content in the xenolith with the B-type CPO pattern. FTIR analysis shows that the equilibrium H concentration in olivine is low (4-13 ppm H2O). Combining these data, we observe that olivine CPO symmetry is controlled neither by the deformation conditions (stress, temperature, pressure, water content) for the range of

  3. 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

    2016-07-26

    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.

  4. 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

  5. The influence on intrinsic light emission of calcium tungstate and molybdate powders by multivalence Pr codoping

    NASA Astrophysics Data System (ADS)

    Zhu, Fang; Xiao, Zhisong; Yan, Lu; Zhang, Feng; Huang, Anping

    2010-12-01

    For trivalent praseodymium (Pr3+) and quadrivalent praseodymium (Pr4+) codoped CaMO4 (M = W, Mo) powders, the luminescence propriety of matrix is obviously influenced by carrier concentration. The light emission intensity of CaWO4 matrix decreases exponentially with increasing of Pr concentration because oxygen-deficient (WO3\\cdot VO^{bullet bullet}) obtains an electron supplied by Pr3+ (5 d). However, the light emission intensity of CaMoO4 is enhanced by Pr codoping because the quasi-free electrons increase the probability of radiative combination. The difference of photoluminescence properties in the two materials are attributed to the bonding character of M and O in the CaMO4 structure.

  6. Structure and magnetism of epitaxial PrVO3 films.

    PubMed

    Copie, O; Rotella, H; Boullay, P; Morales, M; Pautrat, A; Janolin, P-E; Infante, I C; Pravathana, D; Lüders, U; Prellier, W

    2013-12-11

    The interplay between charge, spin, orbital and lattice degrees of freedom in transition metal oxides has motivated extensive research aiming to understand the coupling phenomena in these multifunctional materials. Among them, rare earth vanadates are Mott insulators characterized by spin and orbital orderings strongly influenced by lattice distortions. Using epitaxial strain as a means to tailor the unit cell deformation, we report here on the first thin films of PrVO3 grown on (001)-oriented SrTiO3 substrate by pulsed laser deposition. An extensive structural characterization of the PrVO3 films, combining x-ray diffraction and high-resolution transmission electron microscopy studies, reveals the presence of oriented domains and a unit cell deformation tailored by the growth conditions. We have also investigated the physical properties of the PrVO3 films. We show that, while PrVO3 exhibits an insulating character, magnetic measurements indicate low-temperature hard-ferromagnetic behavior below 80 K. We discuss these properties in view of the thin-film structure.

  7. The pyrochlore-type molybdate Pr1.37Ca0.63Mo2O7

    PubMed Central

    Gall, P.; Gougeon, P.

    2008-01-01

    Praseodymium calcium dimolybdenum hepta­oxide, Pr1.37Ca0.63Mo2O7, crystallizes in the cubic pyrochlore-type structure. In the crystal structure, MoO6 octa­hedra are linked together by common corners, forming a three-dimensional [Mo2O6] network. The Pr and Ca atoms and the remaining O atoms are located in the voids of the [Mo2O6] network. The Pr and Ca atoms are distributed statistically over the same 16c crystallographic position with site-occupancy factors of 0.684 (3) and 0.316 (3), respectively. They are surrounded by eight O atoms forming a ditrigonal scalenohedron. All atoms lie on special positions. The (Pr, Ca) and Mo atoms are, respectively in the 16c and 16d positions with m symmetry, and the O atoms in the 48f or 8a positions with mm or 3m site symmetry, respectively. PMID:21202443

  8. 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.

  9. 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.

  10. Crystallographic dependence of photocatalytic activity of WO3 thin films prepared by molecular beam epitaxy.

    PubMed

    Li, Guoqiang; Varga, Tamas; Yan, Pengfei; Wang, Zhiguo; Wang, Chongmin; Chambers, Scott A; Du, Yingge

    2015-06-21

    We investigated the impact of crystallographic orientation on the photocatalytic activity of single crystalline WO3 thin films prepared by molecular beam epitaxy on the photodegradation of rhodamine B (RhB). A clear effect is observed, with (111) being the most reactive surface, followed by (110) and (001). Photoreactivity is directly correlated with the surface free energy determined by density functional theory calculations. The RhB photodegradation mechanism is found to involve hydroxyl radicals in solution formed from photo-generated holes and differs from previous studies performed on nanoparticles and composites.

  11. 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

  12. A crystallographic model for the tensile and fatigue response for Rene N4 at 982 C

    NASA Technical Reports Server (NTRS)

    Sheh, M. Y.; Stouffer, D. C.

    1990-01-01

    An anisotropic constitutive model based on crystallographic slip theory was formulated for nickel-base single-crystal superalloys. The current equations include both drag stress and back stress state variables to model the local inelastic flow. Specially designed experiments have been conducted to evaluate the existence of back stress in single crystals. The results showed that the back stress effect of reverse inelastic flow on the unloading stress is orientation-dependent, and a back stress state variable in the inelastic flow equation is necessary for predicting inelastic behavior. Model correlations and predictions of experimental data are presented for the single crystal superalloy Rene N4 at 982 C.

  13. Phonon softening and crystallographic orientation of strained graphene studied by Raman spectroscopy

    PubMed Central

    Huang, Mingyuan; Yan, Hugen; Chen, Changyao; Song, Daohua; Heinz, Tony F.; Hone, James

    2009-01-01

    We present a systematic study of the Raman spectra of optical phonons in graphene monolayers under tunable uniaxial tensile stress. Both the G and 2D bands exhibit significant red shifts. The G band splits into 2 distinct subbands (G+, G−) because of the strain-induced symmetry breaking. Raman scattering from the G+ and G− bands shows a distinctive polarization dependence that reflects the angle between the axis of the stress and the underlying graphene crystal axes. Polarized Raman spectroscopy therefore constitutes a purely optical method for the determination of the crystallographic orientation of graphene. PMID:19380746

  14. 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

    2016-08-23

    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.

  15. 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.

  16. 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.

  17. PrP Antibody Binding-Induced Epitope Modulation Evokes Immunocooperativity

    PubMed Central

    Chang, Binggong; Miller, Michael W.; Bulgin, Marie S.; Sorenson-Melson, Sharon; Balachandran, Aru; Chiu, Allen; Rubenstein, Richard

    2008-01-01

    We have characterized the antibody-antigen binding events of the prion protein (PrP) utilizing three new PrP-specific monoclonal antibodies (Mabs). The degree of immunoreactivity was dependent on the denaturation treatment with the combination of heat and SDS resulting in the highest levels of epitope accessibility and antibody binding. Interestingly however, this harsh denaturation treatment was not sufficient to completely and irreversibly abolish protein conformation. The Mabs differed in their PrP epitopes with Mab 08-1/11F12 binding in the region of PrP93–122, Mab 08-1/8E9 reacting to PrP155–200 and Mab 08-1/5D6 directed to an undefined conformational epitope. Using normal and infected brains from hamsters, sheep and deer, we demonstrate that the binding of PrP to one Mab triggers PrP epitope unmasking, which enhances the binding of a second Mab. This phenomenon, termed positive immunocooperativity, is specific regarding epitope and the sequence of binding events. Positive immunocooperativity will likely increase immunoassay sensitivity since assay conditions for PrPSc detection does not require protease digestion. PMID:18977037

  18. PrP antibody binding-induced epitope modulation evokes immunocooperativity.

    PubMed

    Chang, Binggong; Miller, Michael W; Bulgin, Marie S; Sorenson-Melson, Sharon; Balachandran, Aru; Chiu, Allen; Rubenstein, Richard

    2008-12-15

    We have characterized the antibody-antigen binding events of the prion protein (PrP) utilizing three new PrP-specific monoclonal antibodies (Mabs). The degree of immunoreactivity was dependent on the denaturation treatment with the combination of heat and SDS resulting in the highest levels of epitope accessibility and antibody binding. Interestingly however, this harsh denaturation treatment was not sufficient to completely and irreversibly abolish protein conformation. The Mabs differed in their PrP epitopes with Mab 08-1/11F12 binding in the region of PrP(93-122), Mab 08-1/8E9 reacting to PrP(155-200) and Mab 08-1/5D6 directed to an undefined conformational epitope. Using normal and infected brains from hamsters, sheep and deer, we demonstrate that the binding of PrP to one Mab triggers PrP epitope unmasking, which enhances the binding of a second Mab. This phenomenon, termed positive immunocooperativity, is specific regarding epitope and the sequence of binding events. Positive immunocooperativity will likely increase immunoassay sensitivity since assay conditions for PrP(Sc) detection does not require protease digestion.

  19. Role of Pr segregation in acceptor-state formation at ZnO grain boundaries.

    PubMed

    Sato, Yukio; Buban, James P; Mizoguchi, Teruyasu; Shibata, Naoya; Yodogawa, Masatada; Yamamoto, Takahisa; Ikuhara, Yuichi

    2006-09-08

    The role of Pr doping on double Schottky barrier formations at ZnO single grain boundaries was investigated by the combination of current-voltage measurements, atomic-resolution Z-contrast scanning transmission electron microscopy, and first-principles calculations. Although Pr segregated to the specific atomic site along the boundaries, it was found not to be the direct cause of nonlinear current-voltage properties. Instead, under appropriate annealing conditions, Pr enhances formations of acceptor-type native defects that are essential for the creation of double Schottky barriers in ZnO.

  20. Preliminary X-ray crystallographic analysis of α-carbonic anhydrase from Thiomicrospira crunogena XCL-2.

    PubMed

    Díaz Torres, Natalia; González, Guillermo; Biswas, Shyamasri; Scott, Kathleen M; McKenna, Robert

    2012-09-01

    Thiomicrospira crunogena XCL-2 is a novel sulfur-oxidizing chemolithoautotroph that plays a significant role in the sustainability of deep-sea hydrothermal vent communities. This recently discovered gammaproteobacterium encodes and expresses four carbonic anhydrases (CAs) from three evolutionarily and structurally distinct CA families: an α-CA, two β-CAs and a γ-CA. In order to characterize and elucidate the physiological roles of these CAs, X-ray crystallographic structural studies have been initiated on the α-CA. The α-CA crystallized in space group C2. The crystals diffracted to a maximum resolution of 2.6 Å, with unit-cell parameters a = 127.1, b = 102.2, c = 105.0 Å, β = 127.3°, and a calculated Matthews coefficient of 2.04 Å(3) Da(-1) with four identical protein molecules in the crystallographic asymmetric unit. A preliminary solution was determined by molecular replacement with the PHENIX AutoMR wizard, which had an initial TFZ score of 17.9. Refinement of the structure is currently in progress.

  1. Magnetic transition temperatures follow crystallographic symmetry in Samarium under high-pressures and low-temperatures

    SciTech Connect

    Vohra, Yogesh K.; Tsoi, Georgiy M.; Johnson, Craig R.

    2016-12-21

    Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating different magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm → dhcp → fcc/dist.fcc → hP3 structure sequence at high-pressures and low-temperatures.

  2. Magnetic transition temperatures follow crystallographic symmetry in Samarium under high-pressures and low-temperatures

    DOE PAGES

    Vohra, Yogesh K.; Tsoi, Georgiy M.; Johnson, Craig R.

    2016-12-21

    Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating differentmore » magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm → dhcp → fcc/dist.fcc → hP3 structure sequence at high-pressures and low-temperatures.« less

  3. 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.

  4. Magnetic transition temperatures follow crystallographic symmetry in samarium under high-pressures and low-temperatures

    NASA Astrophysics Data System (ADS)

    Johnson, Craig R.; Tsoi, Georgiy M.; Vohra, Yogesh K.

    2017-02-01

    Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating different magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm  →  dhcp  →  fcc/dist.fcc  →  hP3 structure sequence at high-pressures and low-temperatures.

  5. Crystallographic Studies of the Ribosomal A-Site Molecular Switches by Using Model RNA Oligomers.

    PubMed

    Kondo, Jiro

    2016-01-01

    An RNA molecular switch in the aminoacyl-tRNA decoding site (A site) of the ribosome plays a key role in the decoding process of the protein biosynthesis. The switch discriminates a single cognate-tRNA from near-cognate tRNAs by changing its conformation from "off" to "on" states and recognizing the first two base pairs of codon-anticodon mini-helix to check whether these base pairs are of the canonical Watson-Crick type or not. Aminoglycoside antibiotics specifically target the "on" state of the bacterial A-site molecular switch and disturb the fidelity of the decoding process, resulting to cell death. If it occurs in human who was given aminoglycosides, it can lead to undesirable side effects. In order to understand the molecular bases of the decoding and the antibacterial and toxic side effects of aminoglycosides, it is necessary to determine the three-dimensional structures of the A-site molecular switches both in the presence and absence of aminoglycosides. This chapter focuses on methods in crystallographic studies of the A-site switches by using model RNA oligomers. The methods can be utilized in crystallographic studies of any DNA/RNA oligomers.

  6. Crystallographic superstructure in R2PdSi3 compounds (R=heavy rare earth)

    NASA Astrophysics Data System (ADS)

    Tang, Fei; Frontzek, Matthias; Dshemuchadse, Julia; Leisegang, Tilmann; Zschornak, Matthias; Mietrach, Robert; Hoffmann, Jens-Uwe; Löser, Wolfgang; Gemming, Sibylle; Meyer, Dirk C.; Loewenhaupt, Michael

    2011-09-01

    The R2PdSi3 intermetallic compounds have been reported to crystallize in a hexagonal AlB2-derived structure, with the rare earth atoms on the Al sites and Pd and Si atoms randomly distributed on the B sites. However, the intricate magnetic properties observed in the series of compounds have always suggested complications to the assumed structure. To clarify the situation, x-ray and neutron diffraction measurements were performed on the heavy rare earth compounds with R=Gd, Tb, Dy, Ho, Er, Tm, which revealed the existence of a crystallographic superstructure. The superstructure features a doubled unit cell in the hexagonal basal plane and an octuplication along the perpendicular c direction with respect to the primitive cell. No structural transition was observed between 300 and 1.5 K. Extended x-ray absorption fine structure (EXAFS) analysis as well as density functional theory (DFT) calculations were utilized to investigate the local environments of the respective atoms. In this paper the various experimental results will be presented and it will be shown that the superstructure is mainly due to the Pd-Si order on the B sites. A structure model will be proposed to fully describe the superstructure of Pd-Si order in R2PdSi3. The connection between the crystallographic superstructure and the magnetic properties will be discussed in the framework of the presented model.

  7. Real-time detection and resolution of atom bumping in crystallographic models.

    PubMed

    Liu, Yu

    2017-09-01

    A basic principle in crystal structure determination is that there should be proper distances between adjacent atoms. Therefore, detection of atom bumping is of fundamental significance in structure determination, especially in the direct-space method where crystallographic models are just randomly generated. Presented in this article is an algorithm that detects atom bonding in a unit cell based on the sweep and prune algorithm of axis-aligned bounding boxes and running in the O(n log n) time bound, where n is the total number of atoms in the unit cell. This algorithm only needs the positions of individual atoms in the unit cell and does not require any prior knowledge of existing bonds, and is thus suitable for modelling of inorganic crystals where the bonding relations are often unknown a priori. With this algorithm, computation routines requiring bonding information, e.g. anti-bumping and computation of coordination numbers and valences, can be performed efficiently. As an example application, an evaluation function for atom bumping is proposed, which can be used for real-time elimination of crystallographic models with unreasonably short bonds during the procedure of global optimization in the direct-space method.

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

  9. Molecular dynamics analysis of HIV-1 matrix protein: clarifying differences between crystallographic and solution structures.

    PubMed

    Verli, Hugo; Calazans, Alexandre; Brindeiro, Rodrigo; Tanuri, Amilcar; Guimarães, Jorge A

    2007-07-01

    One of the main structural features of the mature HIV-1 virion is the matrix protein (p17). This partially globular protein presents four helixes centrally organized and a fifth one, H5, projecting away from the packed bundle of helixes. Comparison between solution and crystallographic data of p17 indicates a 6 A displacement of a short 3(10) helix and a partial unfolding of H5 in solution related to crystal. While the behavior of the 3(10) helix has been previously addressed to virion assembly, the relevance and origin of H5 partial unfolding is possibly related to the contacts between p17 and other viral elements, such as p24. In this context, we present a 40 ns conformational sampling of monomeric p17 using molecular dynamics simulations. The performed simulations presented a progressive conversion of the p17 crystallographic structure to the NMR conformation, suggesting that the biological form of this protein may have its C-terminal portion partially unfolded.

  10. Reaction temperature variations on the crystallographic state of spinel cobalt aluminate.

    PubMed

    Taguchi, Minori; Nakane, Takayuki; Hashi, Kenjiro; Ohki, Shinobu; Shimizu, Tadashi; Sakka, Yoshio; Matsushita, Akiyuki; Abe, Hiroya; Funazukuri, Toshitaka; Naka, Takashi

    2013-05-21

    In this study, we report a rapid and simple technique for obtaining cobalt aluminate having a spinel structure. The products were prepared from a hydroxide precursor synthesized by coprecipitation of cobalt (Co(2+)) and aluminum (Al(3+)) nitrates with an alkaline solution. The chosen precursor enabled low temperature fabrication of cobalt aluminate with a spinel structure by sintering it for 2 hours at low temperatures (>400 °C). Crystallographic and thermal analyses suggest that the low-temperature-sintered products contain Co(3+) ions stabilized by chemisorbed water and/or hydroxide groups, which was not observed for products sintered at temperatures higher than 1000 °C. The color of the products turned from clear blue (Thenard's blue) to dark green when sintering temperatures were below 1000 °C. Magnetic quantities, Curie constants, and Weiss temperatures show a strong dependence on the sintering temperature. These findings suggest that there are mixed valent states, i.e. Co(2+) and Co(3+), and unique cation distributions at the different crystallographic sites in the spinel structure, especially in the products sintered at lower temperatures.

  11. Determination of precise crystallographic directions for mask alignment in wet bulk micromachining for MEMS

    NASA Astrophysics Data System (ADS)

    Singh, Sajal Sagar; Pal, Prem; Pandey, Ashok Kumar; Xing, Yan; Sato, Kazuo

    2016-12-01

    In wet bulk micromachining, the etching characteristics are orientation dependent. As a result, prolonged etching of mask openings of any geometric shape on both Si{100} and Si{110} wafers results in a structure defined by the slowest etching planes. In order to fabricate microstructures with high dimensional accuracy, it is vital to align the mask edges along the crystal directions comprising of these slowest etching planes. Thus, precise alignment of mask edges is important in micro/nano fabrication. As a result, the determination of accurate crystal directions is of utmost importance and is in fact the first step to ensure dimensionally accurate microstructures for improved performance. In this review article, we have presented a comprehensive analysis of different techniques to precisely determine the crystallographic directions. We have covered various techniques proposed in the span of more than two decades to determine the crystallographic directions on both Si{100} and Si{110} wafers. Apart from a detailed discussion of each technique along with their design and implementation, we have provided a critical analysis of the associated constraints, benefits and shortcomings. We have also summed up the critical aspects of each technique and presented in a tabular format for easy reference for readers. This review article comprises of an exhaustive discussion and is a handy reference for researchers who are new in the field of wet anisotropic etching or who want to get abreast with the techniques of determination of crystal directions.

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

    SciTech Connect

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

    2005-06-01

    A. polyphaga mimivirus, the largest known double-stranded DNA virus, is the first virus to exhibit a nucleoside diphosphate kinase gene. The expression and crystallization of the viral NDK are reported. 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 P2{sub 1}3, 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.

  13. 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.

  14. The fourth crystallographic closest packing unveiled in the gold nanocluster crystal

    NASA Astrophysics Data System (ADS)

    Gan, Zibao; Chen, Jishi; Wang, Juan; Wang, Chengming; Li, Man-Bo; Yao, Chuanhao; Zhuang, Shengli; Xu, An; Li, Lingling; Wu, Zhikun

    2017-03-01

    Metal nanoclusters have recently attracted extensive interest not only for fundamental scientific research, but also for practical applications. For fundamental scientific research, it is of major importance to explore the internal structure and crystallographic arrangement. Herein, we synthesize a gold nanocluster whose composition is determined to be Au60S6(SCH2Ph)36 by using electrospray ionization mass spectrometry and single crystal X-ray crystallography (SCXC). SCXC also reveals that Au60S6(SCH2Ph)36 consists of a fcc-like Au20 kernel protected by a pair of giant Au20S3(SCH2Ph)18 staple motifs, which contain 6 tetrahedral-coordinate μ4-S atoms not previously reported in the Au-S interface. Importantly, the fourth crystallographic closest-packed pattern, termed 6H left-handed helical (6HLH) arrangement, which results in the distinct loss of solid photoluminescence of amorphous Au60S6(SCH2Ph)36, is found in the crystals of Au60S6(SCH2Ph)36. The solvent-polarity-dependent solution photoluminescence is also demonstrated. Overall, this work provides important insights about the structure, Au-S bonding and solid photoluminescence of gold nanoclusters.

  15. Geometrical and crystallographic constraints determine the self-organization of shell microstructures in Unionidae (Bivalvia: Mollusca).

    PubMed Central

    Checa, A. G.; Rodríguez-Navarro, A.

    2001-01-01

    Unionid shells are characterized by an outer aragonitic prismatic layer and an inner nacreous layer. The prisms of the outer shell layer are composed of single-crystal fibres radiating from spheruliths. During prism development, fibres progressively recline to the growth front. There is competition between prisms, leading to the selection of bigger, evenly sized prisms. A new model explains this competition process between prisms, using fibres as elementary units of competition. Scanning electron microscopy and X-ray texture analysis show that, during prism growth, fibres become progressively orientated with their three crystallographic axes aligned, which results from geometric constraints and space limitations. Interestingly transition to the nacreous layer does not occur until a high degree of orientation of fibres is attained. There is no selection of crystal orientation in the nacreous layer and, as a result, the preferential orientation of crystals deteriorates. Deterioration of crystal orientation is most probably due to accumulation of errors as the epitaxial growth is suppressed by thick or continuous organic coats on some nacre crystals. In conclusion, the microstructural arrangement of the unionid shell is, to a large extent, self-organized with the main constraints being crystallographic and geometrical laws. PMID:11321067

  16. 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.

  17. Crystallographic and electronic properties of AlCrN films that absorb visible light

    NASA Astrophysics Data System (ADS)

    Tatemizo, N.; Imada, S.; Miura, Y.; Nishio, K.; Isshiki, T.

    2017-05-01

    We investigate the crystallographic and electronic properties of wurtzite Cr-doped AlN (AlCrN) films (Cr ≤12.0%) that absorb visible light. We confirmed that the films consist of wurtzite columnar single crystals that are densely packed, c-axis oriented, and exhibit a random rotation along the a-axis in plane by using transmission electron microscopy. The oxidation state of Cr was found to be 3+ using Cr K-edge X-ray absorption near edge structure, which implies that Cr can be a substitute for Al3+ in AlN. The first nearest neighbor distances estimated using Cr K-edge extended X-ray absorption fine structure (EXAFS) were found to be nearly isotropic for incident light with electric fields that are parallel and perpendicular to the plane. The results of ab initio lattice relaxation calculations for the model of wurtzite Al1-xCrxN supercell where Cr replaces Al support the EXAFS results. The calculations for the model showed that additional energy bands are formed in the band gap of AlN, in which the Fermi energy (EF) is present. As expected from the calculation results, the electrical conductivity increases with increase in the Cr concentration, implying that the density of states at EF increases monotonically. From these results, we can conclude that AlCrN films are an intermediate band material with respect to their crystallographic and electric properties.

  18. Purpose and Features of Web-Based Open-Access Crystallographic Databases

    NASA Astrophysics Data System (ADS)

    Sondergeld, Peter; Moeck, Peter; Dusek, Boris; Hanke, Hynek

    2008-05-01

    Roughly 5,000 new crystal structures are added to the (approximately 104,000 entry) Inorganic Crystal Structure Database each year (see http://icsdweb.fiz-karlsruhe.de/index.php for an approximately 4,000 entry demonstration version). Other commercial crystallographic databases specialize in organics, metals and alloys, and ``non-organics'' including minerals. This presentation gives an overview over these databases and evaluates the potential of open-access databases such as the (approximately 68,000 entry) Crystallography Open Database (http://crystallography.net/) and Portland State University's (PSU's) Wiki Crystallography Database, Crystal Morphology Database, and Nano-Crystallography Database (http://nanocrystallography.research.pdx.edu/CIF-searchable). Key features of open-access crystallographic databases are: a universal data exchange format, unrestricted internet access to the actual data (including downloads), search capabilities, and crystal structure identification functionalities. Interactive three-dimensional structure or morphology visualizations are also available at PSU's site. Most recently, we implemented at PSU community-based, Wikipedia-inspired data upload and database content management provisions. A selection of all of these features will be demonstrated (online) during the presentation.

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

    PubMed

    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

    2006-01-01

    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 A wavelength) with fluxes up to 8-18 x 10(12) 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 x 1.0 mm (horizontal x vertical, unfocused) to 0.083 mm x 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 kappa-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 x 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.

  20. 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

  1. Searching for stereoisomerism in crystallographic databases: algorithm, analysis and chiral curiosities.

    PubMed

    Grothe, E; Meekes, H; de Gelder, R

    2017-06-01

    The automated identification of chiral centres in molecular residues is a non-trivial task. Current tools that allow the user to analyze crystallographic data entries do not identify chiral centres in some of the more complex ring structures, or lack the possibility to determine and compare the chirality of multiple structures. This article presents an approach to identify asymmetric C atoms, which is based on the atomic walk count algorithm presented by Rücker & Rücker [(1993), J. Chem. Inf. Comput. Sci. 33, 683-695]. The algorithm, which we implemented in a computer program named ChiChi, is able to compare isomeric residues based on the chiral centres that were identified. This allows for discrimination between enantiomers, diastereomers and constitutional isomers that are present in crystallographic databases. ChiChi was used to process 254 354 organic entries from the Cambridge Structural Database (CSD). A thorough analysis of stereoisomerism in the CSD is presented accompanied by a collection of chiral curiosities that illustrate the strength and versatility of this approach.

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

    PubMed

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

    2011-06-01

    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.

  3. Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP.

    PubMed

    Bayden, Alexander S; Moustakas, Demetri T; Joseph-McCarthy, Diane; Lamb, Michelle L

    2015-08-24

    The SZMAP method computes binding free energies and the corresponding thermodynamic components for water molecules in the binding site of a protein structure [ SZMAP, 1.0.0 ; OpenEye Scientific Software Inc. : Santa Fe, NM, USA , 2011 ]. In this work, the ability of SZMAP to predict water structure and thermodynamic stability is examined for the X-ray crystal structures of a series of protein-ligand complexes. SZMAP results correlate with higher-level replica exchange thermodynamic integration double decoupling calculations of the absolute free energy of bound waters in the test set complexes. In addition, SZMAP calculations show good agreement with experimental data in terms of water conservation (across multiple crystal structures) and B-factors over a subset of the test set. In particular, the SZMAP neutral entropy difference term calculated at crystallographic water positions within each of the complex structures correlates well with whether that crystallographic water is conserved or displaceable. Furthermore, the calculated entropy of the water probe relative to the continuum shows a significant degree of correlation with the B-factors associated with the oxygen atoms of the water molecules. Taken together, these results indicate that SZMAP is capable of quantitatively predicting water positions and their energetics and is potentially a useful tool for determining which waters to attempt to displace, maintain, or build in through water-mediated interactions when evolving a lead series during a drug discovery program.

  4. Protein Crystallization in Agarose Gel with High Strength: Developing an Automated System for Protein Crystallographic Processes

    NASA Astrophysics Data System (ADS)

    Sugiyama, Shigeru; Tanabe, Kana; Hirose, Mika; Kitatani, Tomoya; Hasenaka, Hitoshi; Takahashi, Yoshinori; Adachi, Hiroaki; Takano, Kazufumi; Murakami, Satoshi; Mori, Yusuke; Inoue, Tsuyoshi; Matsumura, Hiroyoshi

    2009-07-01

    Agarose gel media reduce convection and prevent crystal sedimentation, resulting in the production of high-quality protein crystals. However, crystallographers have only tested agarose gel at concentrations between 0.0 and 0.6% (w/v), where it exhibits low gel strength. The effect of agarose gel on protein structures remains to be elucidated, because only a few structural studies have been performed using gel-grown protein crystals. Here, we crystallize thaumatin and elastase using a variety of crystallization methods in 2.0% (w/v) agarose gels, which are completely gellified and have sufficiently high-strength. This new crystallization approach using semi-solid agarose gels is compatible with several conventional crystallization techniques. A comparison of structures crystallized in non-gelled solution and those crystallized in 2.0% (w/v) agarose gels indicates that the crystal structures were not affected by the high-concentration agarose gels. This technique offers the practical advantages of efficient protection by the semi-solid gel media surrounding the protein crystals, allowing them to be handled and transported without affecting any later crystallographic analysis, and thereby providing an automated system for crystal capturing and mounting.

  5. 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

    2016-11-01

    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.

  6. 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.

  7. 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

  8. 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.

  9. Pre-exposure Prophylaxis (PrEP) for HIV Infection: How Antiretroviral Pharmacology helps to Monitor and Improve Adherence

    PubMed Central

    Blumenthal, Jill; Haubrich, Richard

    2014-01-01

    Pre-exposure prophylaxis (PrEP) with antiretroviral drugs is a novel biomedical intervention that can prevent HIV transmission among high-risk populations. As findings from multiple PrEP studies have suggested that adherence is vital to achieve the full prevention benefits of PrEP, it is important to understand the clinical pharmacology and pharmacokinetic (PK) properties of PrEP antiretrovirals, the association of PK and PrEP efficacy and the potential for drug concentration measurement to be used as a tool to monitor PrEP adherence. In this review, we examine studies related to PrEP adherence with attention to the clinical pharmacology and pharmacokinetics of current and novel PrEP agents. Studies of animal models, pharmacokinetics and clinical trials related to PrEP and adherence were reviewed. In summary, when combined as part of a comprehensive prevention strategy that includes use of condoms and risk reduction counseling, PrEP has tremendous promise as a adjunctive biomedical HIV prevention intervention, providing that adherence is maintained. PMID:23800167

  10. Generation of crystallographic packing candidates with fixed helical symmetry and axial advance: Application to PI-2 polyimide

    SciTech Connect

    Waller, J.M.; Eby, R.K.

    1995-12-31

    A normal coordinate approach was used to generate crystallographic packing candidates of a multitorsional polyimide synthesized from 3,3`,4,4`-benzophenonetetracarboxylic acid (BTDA) and 2,2-dimethyl-1,3-(4-aminophenoxy) propane (DMDA) (PI-2). Candidates were obtained under conditions of fixed axial advance of 24.6 {Angstrom} per monomer, and imposed 2/1 helical or 1/0 translational symmetry, consistent with the observed WAXD meridional layer line spacing. The ability of combinatorially generated torsional states to adopt the desired geometry was examined. Necessary corrections to the conformational parameter equations have been made. The procedure described allowed crystallographic conformations satisfying explicit geometric and MM3 intramolecular energy criteria to be generated for a linear multitorsional polyimide prior to the application of crystallographic screening or refinement procedures. 20 refs., 7 figs., 1 tab.

  11. 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.

  12. Combined Science at Leeds University

    ERIC Educational Resources Information Center

    Williams, W. F.

    1971-01-01

    Briefly reviews the broad-based first degree programs in British Universities and considers the general problems of such programs. Explains the general approach used at the University of Leeds, including seven combined degree programs with physics as one principle subject. Employment prospects for graduates are considered good. (PR)

  13. 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

  14. Expression, purification and preliminary crystallographic analysis of sucrose phosphate synthase (SPS) from Halothermothrix orenii

    SciTech Connect

    Huynh, Frederick; Tan, Tien-Chye; Swaminathan, Kunchithapadam; Patel, Bharat K. C.

    2005-01-01

    The first crystallographic study of a sucrose phosphate synthase from H. orenii, an organism that is both thermophilic and halophilic, is reported. The protein crystal diffracts X-rays to 3.01 Å. This is the first report of the crystallization of a sucrose phosphate synthase (SPS; EC 2.4.1.14). It also constitutes the first study of a sucrose phosphate synthase from a non-photosynthetic thermohalophilic anaerobic bacterium, Halothermothrix orenii. The purified recombinant spsA protein has been crystallized in the monoclinic space group C2, with unit-cell parameters a = 154.2, b = 47.9, c = 72.3 Å, β = 103.16°, using the hanging-drop vapour-diffusion method. The crystal diffracts X-rays to a resolution limit of 3.01 Å. Heavy-metal and halide-soaking trials are currently in progress to solve the structure.

  15. Bi-crystallographic lattice structure directs grain boundary motion under shear stress

    NASA Astrophysics Data System (ADS)

    Wan, Liang; Han, Weizhong; Chen, Kai

    2015-08-01

    Shear stress driven grain boundary (GB) migration was found to be a ubiquitous phenomenon in small grained polycrystalline materials. Here we show that the GB displacement shift complete (DSC) dislocation mechanism for GB shear coupled migration is still functioning even if the geometry orientation of the GBs deviates a few degrees from the appropriate coincidence site lattice (CSL) GBs. It means that any large angle GB can have a considerable chance to be such a “CSL-related GB” for which the shear coupled GB migration motion can happen by the GB DSC dislocation mechanism. We conclude that the CSL-DSC bi-crystallographic lattice structure in GB is the main reason that GB can migrate under shear stress.

  16. Preparation, crystallization and preliminary crystallographic analysis of old yellow enzyme from Trypanosoma cruzi

    SciTech Connect

    Sugiyama, Shigeru; Tokuoka, Keiji; Uchiyama, Nahoko; Okamoto, Naoki; Okano, Yousuke; Matsumura, Hiroyoshi; Inaka, Koji; Urade, Yoshihiro; Inoue, Tsuyoshi

    2007-10-01

    Old yellow enzyme from Trypanosoma cruzi, has been crystallized using the hanging-drop vapour-diffusion method. Old yellow enzyme (OYE) is an NADPH oxidoreductase that contains a flavin mononucleotide as a prosthetic group. The OYE from Trypanosoma cruzi, which produces prostaglandin F{sub 2α}, a potent mediator of various physiological and pathological processes, from prostaglandin H2. The protein was recombinantly expressed and purified from Escherichia coli and was crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 56.3, b = 78.8, c = 78.8 Å, β = 93.4° and two molecules per asymmetric unit. The crystals were suitable for X-ray crystallographic studies and diffracted to 1.70 Å resolution. A Patterson search method is in progress using the structure of OYE from Pseudomonas putida as a starting model.

  17. Crystallization and preliminary X-ray crystallographic analysis of rabbit l-gulonate 3-dehydrogenase

    SciTech Connect

    Asada, Yukuhiko; Kuroishi, Chizu; Ukita, Yoko; Sumii, Rie; Endo, Satoshi; Matsunaga, Toshiyuki; Hara, Akira; Kunishima, Naoki

    2008-03-01

    The preliminary X-ray crystallographic study of rabbit l-gulonate 3-dehydrogenase is described. Rabbit l-gulonate 3-dehydrogenase was crystallized using the oil-microbatch method at 295 K. X-ray diffraction data were collected to 1.70 Å resolution from a crystal at 100 K using synchrotron radiation. The crystal belongs to the C-centred monoclinic space group C2, with unit-cell parameters a = 71.81, b = 69.08, c = 65.64 Å, β = 102.7°. Assuming the presence of a monomeric protomer in the asymmetric unit gives a V{sub M} value of 2.21 Å{sup 3} Da{sup −1} and a solvent content of 44.4%. A cocrystal with NADH, which was isomorphous to the apo form, was also prepared and diffraction data were collected to 1.85 Å resolution using Cu Kα radiation at 100 K.

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

    NASA Astrophysics Data System (ADS)

    Bennett, Joseph W.; Rabe, Karin M.

    2012-11-01

    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(Sb1/2Mn1/2)O3 as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb2O4; and (3) ferroelectric semiconductors with formula M2P2(S,Se)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.

  19. Crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis chorismate mutase

    SciTech Connect

    Qamra, Rohini; Prakash, Prachee; Aruna, Bandi; Hasnain, Seyed E.; Mande, Shekhar C.

    2005-05-01

    Chorismate mutase from M. tuberculosis has been crystallized. Preliminary X-ray crystallographic studies reveal the occurrence of a dimeric molecule in the crystal asymmetric unit. Chorismate mutase catalyzes the first committed step in the biosynthesis of the aromatic amino acids phenylalanine and tyrosine in bacteria, fungi and higher plants. The recent re-annotation of the Mycobacterium tuberculosis genome has revealed the presence of a duplicate set of genes coding for chorismate mutase. The mycobacterial gene Rv1885c bears <20% sequence homology to other bacterial chorismate mutases, thus serving as a potential target for the development of inhibitors specific to the pathogen. The M. tuberculosis chorismate mutase was crystallized in space group C2 and the crystals diffracted to a resolution of 2.2 Å. Matthews coefficient and self-rotation function calculations revealed the presence of two monomers in the asymmetric unit.

  20. Water-assisted highly enhanced crystallographic etching of graphene by iron catalysts

    NASA Astrophysics Data System (ADS)

    Xue, Lei-Jiang; Yu, Fang; Zhou, Hai-Qing; Sun, Lian-Feng

    2015-03-01

    We report the assisted role of water vapor in crystallographic cutting of graphene via iron catalysts in reduced atmosphere. Without water, graphene can be tailored with smooth trenches composed of straight lines with angles of 60° or 120° between two adjacent trenches. After the addition of water, new chacteristics are found: such as almost no iron particles can be detected along the trenches; each trench becomes longer and lots of graphene nanoribbons can be generated. The underlying mechanism is proposed and discussed, which is attributed to stimulating and lengthening of the catalytic activity of iron particles by water vapor. Project supported by the National Natural Science Foundation of China (Grant No. 10774032) and the Instrument Developing Project of the Chinese Academy of Sciences (Grant No. Y2010031).

  1. Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

    SciTech Connect

    Mitchell, M.; Nam, H; Carter, A; McCall, A; Rence, C; Bennett, A; Gurda, B; McKenna, R; Porter, M; et. al.

    2009-01-01

    Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetric unit capsid have been determined by molecular-replacement methods and structure determination is in progress.

  2. 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.

  3. Platinum Group Thiophenoxyimine Complexes: Syntheses,Crystallographic and Computational Studies of Structural Properties

    SciTech Connect

    Krinsky, Jamin L.; Arnold, John; Bergman, Robert G.

    2006-10-03

    Monomeric thiosalicylaldiminate complexes of rhodium(I) and iridium(I) were prepared by ligand transfer from the homoleptic zinc(II) species. In the presence of strongly donating ligands, the iridium complexes undergo insertion of the metal into the imine carbon-hydrogen bond. Thiophenoxyketimines were prepared by non-templated reaction of o-mercaptoacetophenone with anilines, and were complexed with rhodium(I), iridium(I), nickel(II) and platinum(II). X-ray crystallographic studies showed that while the thiosalicylaldiminate complexes display planar ligand conformations, those of the thiophenoxyketiminates are strongly distorted. Results of a computational study were consistent with a steric-strain interpretation of the difference in preferred ligand geometries.

  4. Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: I, theoretical foundations.

    PubMed

    Pezzotti, Giuseppe; Zhu, Wenliang; Boffelli, Marco; Adachi, Tetsuya; Ichioka, Hiroaki; Yamamoto, Toshiro; Marunaka, Yoshinori; Kanamura, Narisato

    2015-05-01

    The Raman spectroscopic method has quantitatively been applied to the analysis of local crystallographic orientation in both single-crystal hydroxyapatite and human teeth. Raman selection rules for all the vibrational modes of the hexagonal structure were expanded into explicit functions of Euler angles in space and six Raman tensor elements (RTE). A theoretical treatment has also been put forward according to the orientation distribution function (ODF) formalism, which allows one to resolve the statistical orientation patterns of the nm-sized hydroxyapatite crystallite comprised in the Raman microprobe. Close-form solutions could be obtained for the Euler angles and their statistical distributions resolved with respect to the direction of the average texture axis. Polarized Raman spectra from single-crystalline hydroxyapatite and textured polycrystalline (teeth enamel) samples were compared, and a validation of the proposed Raman method could be obtained through confirming the agreement between RTE values obtained from different samples.

  5. Twists on the Torus Equivariant under the 2-Dimensional Crystallographic Point Groups

    NASA Astrophysics Data System (ADS)

    Gomi, Kiyonori

    2017-03-01

    A twist is a datum playing a role of a local system for topological K-theory. In equivariant setting, twists are classified into four types according to how they are realized geometrically. This paper lists the possible types of twists for the torus with the actions of the point groups of all the 2-dimensional space groups (crystallographic groups), or equivalently, the torus with the actions of all the possible finite subgroups in its mapping class group. This is carried out by computing Borel's equivariant cohomology and the Leray-Serre spectral sequence. As a byproduct, the equivariant cohomology up to degree three is determined in all cases. The equivariant cohomology with certain local coefficients is also considered in relation to the twists of the Freed-Moore K-theory.

  6. Crystallographic and magnetic structure of UCu{sub 1.5}Sn{sub 2}

    SciTech Connect

    Purwanto, A.; Robinson, R.A.; Nakotte, H.; Swainson, I.; Torikachvili, M.

    1995-09-01

    We report on the crystallographic and magnetic structures of the antiferromagnet UCu{sub 1.5}Sn{sub 2}, as determined by x-ray and neutron powder diffraction. It forms in the tetragonal CaBe{sub 2}Ge{sub 2} structure type, with space group P/4nmm, and we find no site disorder between two different Sn 2c sites, in contrast with a previous report. UCu{sub 1.5}Sn{sub 2} orders antiferromagnetically with a Neel temperature of about 110 K. This is unusually high amongst uranium intermetallics. The uranium moments align along the c-axis in a collinear arrangement but alternating along the c-axis. The low-temperature uranium moment is 1.95{mu}{sub B}.

  7. Synthesis, structure-activity relationship and crystallographic studies of 3-substituted indolin-2-one RET inhibitors.

    PubMed

    Mologni, Luca; Rostagno, Roberta; Brussolo, Stefania; Knowles, Phillip P; Kjaer, Svend; Murray-Rust, Judith; Rosso, Enrico; Zambon, Alfonso; Scapozza, Leonardo; McDonald, Neil Q; Lucchini, Vittorio; Gambacorti-Passerini, Carlo

    2010-02-15

    The synthesis, structure-activity relationships (SAR) and structural data of a series of indolin-2-one inhibitors of RET tyrosine kinase are described. These compounds were designed to explore the available space around the indolinone scaffold within RET active site. Several substitutions at different positions were tested and biochemical data were used to draw a molecular model of steric and electrostatic interactions, which can be applied to design more potent and selective RET inhibitors. The crystal structures of RET kinase domain in complex with three inhibitors were solved. All three compounds bound in the ATP pocket and formed two hydrogen bonds with the kinase hinge region. Crystallographic analysis confirmed predictions from molecular modelling and helped refine SAR results. These data provide important information for the development of indolinone inhibitors for the treatment of RET-driven cancers. Copyright 2010 Elsevier Ltd. All rights reserved.

  8. Quantification of thin film crystallographic orientation using X-ray diffraction with an area detector.

    PubMed

    Baker, Jessy L; Jimison, Leslie H; Mannsfeld, Stefan; Volkman, Steven; Yin, Shong; Subramanian, Vivek; Salleo, Alberto; Alivisatos, A Paul; Toney, Michael F

    2010-06-01

    As thin films become increasingly popular (for solar cells, LEDs, microelectronics, batteries), quantitative morphological and crystallographic information is needed to predict and optimize the film's electrical, optical, and mechanical properties. This quantification can be obtained quickly and easily with X-ray diffraction using an area detector in two sample geometries. In this paper, we describe a methodology for constructing complete pole figures for thin films with fiber texture (isotropic in-plane orientation). We demonstrate this technique on semicrystalline polymer films, self-assembled nanoparticle semiconductor films, and randomly packed metallic nanoparticle films. This method can be immediately implemented to help understand the relationship between film processing and microstructure, enabling the development of better and less expensive electronic and optoelectronic devices.

  9. Crystallographic features and growth of creep cavities in a Ni-18Cr-18Fe alloy

    SciTech Connect

    Wei, R.P.; Liu, H.; Gao, M.

    1997-12-19

    The crystallographic nature and growth of creep cavities in a Ni-18Cr-18Fe alloy were examined as part of the study of behavior of nickel base superalloys at high temperatures. Creep experiments were carried out at 973 K and 52 MPa, and grain boundary cavitation damage was examined in polished sections, as well as by scanning electron microfractography of surfaces exposed after hydrogen charging. Well developed cavities, whose development tended to favor one side of the grain boundary, were observed and identified with vacancy condensation on {l_brace}111{r_brace} planes. The preference is attributed to cavity nucleation in the grain in which the carbide-matrix interface is incoherent and vacancy condensation is energetically favored. A model for cavity growth patterned after crystal growth is suggested and discussed.

  10. Expression, purification, crystallization and preliminary crystallographic analysis of human Rad GTPase

    SciTech Connect

    Yanuar, Arry; Sakurai, Shigeru; Kitano, Ken; Hakoshima, Toshio

    2005-11-01

    Human Rad has been crystallized. A diffraction data set was collected to a resolution of 1.8 Å. Human Rad is a new member of the Ras GTPase superfamily and is overexpressed in human skeletal muscle of individuals with type II diabetes. The GTPase core domain was overexpressed in Escherichia coli and purified for crystallization. Crystals were obtained at 293 K by vapour diffusion using a crystallization robot. The crystals were found to belong to space group P2{sub 1}, with unit-cell parameters a = 52.2, b = 58.6, c = 53.4 Å, β = 97.9°, and contained two Rad molecules in the crystallographic asymmetric unit. A diffraction data set was collected to a resolution of 1.8 Å using synchrotron radiation at SPring-8.

  11. A new systematic framework for crystallographic analysis of atom probe data.

    PubMed

    Araullo-Peters, Vicente J; Breen, Andrew; Ceguerra, Anna V; Gault, Baptiste; Ringer, Simon P; Cairney, Julie M

    2015-07-01

    In this article, after a brief introduction to the principles behind atom probe crystallography, we introduce methods for unambiguously determining the presence of crystal planes within atom probe datasets, as well as their characteristics: location; orientation and interplanar spacing. These methods, which we refer to as plane orientation extraction (POE) and local crystallography mapping (LCM) make use of real-space data and allow for systematic analyses. We present here application of POE and LCM to datasets of pure Al, industrial aluminium alloys and doped-silicon. Data was collected both in DC voltage mode and laser-assisted mode (in the latter of which extracting crystallographic information is known to be more difficult due to distortions). The nature of the atomic planes in both datasets was extracted and analysed.

  12. Purification, identification and preliminary crystallographic studies of Pru du amandin, an allergenic protein from Prunus dulcis

    SciTech Connect

    Gaur, Vineet; Sethi, Dhruv K.; Salunke, Dinakar M.

    2008-01-01

    The purification, identification, crystallization and preliminary crystallographic studies of an allergy-related protein, Pru du amandin, from P. dulcis nuts are reported. Food allergies appear to be one of the foremost causes of hypersensitivity reactions. Nut allergies account for most food allergies and are often permanent. The 360 kDa hexameric protein Pru du amandin, a known allergen, was purified from almonds (Prunus dulcis) by ammonium sulfate fractionation and ion-exchange chromatography. The protein was identified by a BLAST homology search against the nonredundant sequence database. Pru du amandin belongs to the 11S legumin family of seed storage proteins characterized by the presence of a cupin motif. Crystals were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 150.7, c = 164.9 Å.

  13. Direct observation of the crystallographic relationship between interlamellar membranes and aragonite tablets in bivalve nacre.

    PubMed

    Xu, Jun; Zhang, Gangsheng

    2016-12-23

    Nacre is one of the most attractive models for understanding the fundamental principles of biomineralization and for designing bio-inspired materials due to its simple structure but with unusual mechanical properties. It is made up of lamellae of aragonite tablets bonded together by the organic interlamellar membranes (ILMs), of which the latter occupy less than 5wt% of nacre. For a long time, previous authors failed to directly observe the crystallographic relationship between the ILM and aragonite tablet in bivalve shells. Here, using high resolution transmission electron microscope (HRTEM), we investigate the interfacial structure of the domed tablets that coexist with the flat ones in green mussels. We directly observed that the ILMs are oriented with the underlying tablets and connected with the latter via a superlattice region. The finding advances our current knowledge of nacre biomineralization and may help to design novel nacre-like materials.

  14. Transport Properties of Crystallographically Aligned Heterostructures of Graphene and Hexagonal Boron Nitride

    NASA Astrophysics Data System (ADS)

    Wang, Peng; Cheng, Bin; Miao, Tengfei; Martynov, Oleg; Bockrath, Marc

    2014-03-01

    Graphene and hexagonal boron nitride (hBN) heterostructures have been heavily studied due to graphene's high electronic mobility in this system. Hexagonal BN also shows possibilities to alter graphene's electronic properties. Recently several research groups have demonstrated accurate placement of graphene on hBN with crystallographic alignment. Due to the resulting superlattice formed in the graphene/hBN heterostructures, an energy gap, secondary Dirac Points, and Hofstadter quantization in a magnetic field have been observed. However, many aspects of the electronic properties of graphene/hBN heterostructures remain unexplored. Using aligned layer transfer we are able to produce graphene/hBN heterostructures with 1 degree alignment accuracy, and measure the transport properties of the resulting systems. We will discuss our latest transport data, which contribute towards a greater understanding the electron motion in the graphene/hBN interface.

  15. Metal impurities in crystallographic voids of beta-rhombohedral boron lattice: Binding energies and electron levels

    NASA Astrophysics Data System (ADS)

    Chkhartishvili, Levan; Murusidze, Ivane; Darchiashvili, Maguli; Tsagareishvili, Otar; Gabunia, Domenti

    2012-11-01

    Applying quasi-classical approach, the binding energies and electron levels of metal impurities (Li, Mg, Al, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zr, Nb, Hf, Ta, and Re) introduced into crystallographic voids of types A, D and E in the beta-rhombohedral boron lattice are calculated. Binding energies are estimated as ˜1 eV-60 eV per bond. The most of the obtained metal-boron bond lengths are very close to the mean radii of voids in the undoped crystal. Relatively light impurities (from Li to Cu) are found to form donor electron states directly inside the conduction band, i.e., they cause metallization of the material being introduced at sufficiently high concentrations. Heavy impurities (from Zr to Re) form shallow or deep donor levels inside the band gap or even valence band depending on dopants and voids of accommodation.

  16. EBSD study on crystallographic texture and microstructure development of cold-rolled FePd alloy

    SciTech Connect

    Lin, Hung-Pin; Ng, Tin-San; Kuo, Jui-Chao; Chen, Yen-Chun; Chen, Chun-Liang; Ding, Shi-Xuan

    2014-07-01

    The crystallographic texture and microstructure of FePd alloy after cold-rolling deformation were investigated using electron backscatter diffraction. The major orientations of twin copper and copper after 50% thickness reduction were observed in face-centered cubic-disordered FePd alloy, whereas the main orientation was obtained from brass type after 90% cold rolling. Increase in cold rolling resulted in the change of preferred orientation from copper to brass. Decrease in orientation intensity of copper also increased that of Goss and brass. - Highlights: • The evolution of texture and microstructure in FePd alloy was investigated after cold rolling using EBSD. • Increasing in reduction leads to the change of texture from Copper-type to Brass-type. • The reduction of Copper orientation results in increasing in Goss and Brass orientations.

  17. Crystallographic, Ferroelectric and Electronic Properties of the Sr2ZrTiO6 Double Perovskite

    NASA Astrophysics Data System (ADS)

    Landínez Téllez, D. A.; Carrero Bermúdez, L. A.; Deluque Toro, C. E.; Cardona, R.; Roa-Rojas, J.

    2013-08-01

    In this paper, we report structural analysis, ferroelectric behavior and electronic structure of Sr2ZrTiO6 double perovskite. Samples were produced by the solid state reaction recipe. Crystallographic analysis was performed by Rietveld refinement of experimental X-ray diffraction patterns. Results show that this material crystallizes in a tetragonal perovskite structure which corresponds to the space group I4/m. The curve of polarization as a function of applied voltage evidences a ferroelectric character with saturation polarization on the application of voltages up to 1800 V. Calculations of density of states and band structure for this manganite-like material were carried out by means of the density functional theory implemented into the Wien2k code. Results of total and partial density of states reveal the insulator character of this material with an energy gap of 2.66 eV.

  18. Chemical and Crystallographic Characterization of the Tip Apex in Scanning Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Hofmann, Thomas; Pielmeier, Florian; Giessibl, Franz J.

    2014-02-01

    The apex atom of a W scanning probe tip reveals a nonspherical charge distribution as probed by a CO molecule bonded to a Cu(111) surface [Welker et al., Science 336, 444 (2012).]. Three high-symmetry images were observed and related to three low-index crystallographic directions of the W bcc crystal. Open questions remained, such as the detectability of a contamination of W tips by sample material (here Cu), and the applicability of the method to distinguish other atomic species. In this work, we investigate bulk Cu and Fe tips. In both cases, we can associate our data with the fcc (Cu) and bcc (Fe) crystal structures using a simple electrostatic model that is based on the partial filling of d orbitals.

  19. Intrinsic Compressibility of Sperm Whale Myoglobin Determined from High-Pressure Crystallographic Structures

    NASA Astrophysics Data System (ADS)

    Clark, Jeremy

    2005-04-01

    Myoglobin, considered a paradigm for biocomplexity, may serve as a model system for studying the role of cavities and volume fluctuations in proteins. Volume fluctuations are directly probed by pressure via the compressibility. While the physico-chemical basis for pressure effects is well established, effects in structurally complex systems have yet to be fully explored. Biocomplexity can lead to significant effects at moderate, kilo-atmosphere pressures, and is the reason detailed structural information under pressure is needed to understand pressure effects in proteins and other biological systems. Structural determination of proteins at kilo-atmosphere pressures using x-ray crystallography is a powerful method for investigating the effects of pressure on structure. Here we present results quantifying the spatial distribution of intrinsic compressibility in sperm whale myoglobin calculated from crystallographic structures solved at ambient and at 1500 atm pressures.

  20. Purification and Preliminary Crystallographic Analysis of a New Lys49-PLA2 from B. Jararacussu

    PubMed Central

    dos Santos, Marcelo L.; Fagundes, Fábio H. R.; Teixeira, Bruno R. F.; Toyama, Marcos H.; Aparicio, Ricardo

    2008-01-01

    BjVIII is a new myotoxic Lys49-PLA2 isolated from Bothrops jararacussu venom that exhibits atypical effects on human platelet aggregation. To better understand the mode of action of BjVIII, crystallographic studies were initiated. Two crystal forms were obtained, both containing two molecules in the asymmetric unit (ASU). Synchrotron radiation diffraction data were collected to 2.0 Å resolution and 1.9 Å resolution for crystals belonging to the space group P212121 (a = 48.4 Å, b = 65.3 Å, c = 84.3 Å) and space group P3121 (a = b = 55.7 Å, c = 127.9 Å), respectively. Refinement is currently in progress and the refined structures are expected to shed light on the unusual platelet aggregation activity observed for BjVIII. PMID:19325781

  1. Crystallization and preliminary X-ray crystallographic studies of dipeptidyl peptidase 11 from Porphyromonas gingivalis

    PubMed Central

    Sakamoto, Yasumitsu; Suzuki, Yoshiyuki; Iizuka, Ippei; Tateoka, Chika; Roppongi, Saori; Fujimoto, Mayu; Gouda, Hiroaki; Nonaka, Takamasa; Ogasawara, Wataru; Tanaka, Nobutada

    2015-01-01

    Dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) preferentially cleaves substrate peptides with Asp and Glu at the P1 position [NH2–P2–P1(Asp/Glu)–P1′–P2′…]. For crystallographic studies, PgDPP11 was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 1.82 Å resolution were collected from an orthorhombic crystal form belonging to space group C2221, with unit-cell parameters a = 99.33, b = 103.60, c = 177.33 Å. Structural analysis by the multi-wavelength anomalous diffraction method is in progress. PMID:25664797

  2. High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective.

    PubMed

    Wlodawer, Alexander; Li, Mi; Dauter, Zbigniew

    2017-08-10

    The appearance of ten high-resolution cryoelectron microscopy (cryo-EM) maps of proteins, ribosomes, and viruses was compared with the experimentally phased crystallographic electron density maps of four proteins. We found that maps calculated at a similar resolution by the two techniques are quite comparable in their appearance, although cryo-EM maps, even when sharpened, seem to be a little less detailed. An analysis of models fitted to the cryo-EM maps indicated the presence of significant problems in almost all of them, including incorrect geometry, clashes between atoms, and discrepancies between the map density and the fitted models. In particular, the treatment of the atomic displacement (B) factors was meaningless in almost all analyzed cryo-EM models. Stricter cryo-EM structure deposition standards and their better enforcement are needed. Published by Elsevier Ltd.

  3. Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

    PubMed Central

    Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

    2011-01-01

    Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

  4. Automating crystallographic structure solution and refinement of protein–ligand complexes

    SciTech Connect

    Echols, Nathaniel Moriarty, Nigel W. Klei, Herbert E.; Afonine, Pavel V.; Bunkóczi, Gábor; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Adams, Paul D.

    2014-01-01

    A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies. High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.

  5. Crystallographic orientation analysis in HDDR process of anisotropic Nd-Fe-B magnet powders

    NASA Astrophysics Data System (ADS)

    Takizawa, Rina; Itakura, Masaru; Katayama, Nobuhiro; Morimoto, Koichiro

    2017-07-01

    Microstructural changes and crystallographic orientation information in the hydrogenation-decomposition-desorption-recombination (HDDR) process of Nd-Fe-B alloy were investigated using electron backscatter diffraction (EBSD) and precession electron diffraction (PED) in order to understand the mechanism of anisotropy inducement in the HDDR process. Recombined Nd2Fe14B grains were found to nucleate at the interfaces between NdH2 and α-Fe grains and to have a [0 0 1]-oriented texture from the beginning of the recombination reaction. The Fe grains form with alignment of one of the <1 1 3> directions at decomposed stage. This suggests that α-Fe most likely induces texture development of recombined Nd2Fe14B.

  6. Trapping of Oxygen Vacancies at Crystallographic Shear Planes in Acceptor-Doped Pb-Based Ferroelectrics.

    PubMed

    Batuk, Dmitry; Batuk, Maria; Tsirlin, Alexander A; Hadermann, Joke; Abakumov, Artem M

    2015-12-01

    The defect chemistry of the ferroelectric material PbTiO3 after doping with Fe(III) acceptor ions is reported. Using advanced transmission electron microscopy and powder X-ray and neutron diffraction, we demonstrate that even at concentrations as low as circa 1.7% (material composition approximately ABO2.95), the oxygen vacancies are trapped into extended planar defects, specifically crystallographic shear planes. We investigate the evolution of these defects upon doping and unravel their detailed atomic structure using the formalism of superspace crystallography, thus unveiling their role in nonstoichiometry in the Pb-based perovskites. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Transfer of olivine crystallographic orientation through a cycle of serpentinisation and dehydration

    NASA Astrophysics Data System (ADS)

    Dunkel, Kristina G.; Austrheim, Håkon; Ildefonse, Benoit; Jamtveit, Bjørn

    2017-08-01

    Our ability to decipher the mechanisms behind metamorphic transformation processes depends in a major way on the extent to which crystallographic and microstructural information is transferred from one stage to another. Within the Leka Ophiolite Complex in the Central Norwegian Caledonides, prograde olivine veins that formed by dehydration of serpentinite veins in dunites exhibit a characteristic distribution of microstructures: The outer part of the veins comprises coarse-grained olivine that forms an unusual, brick-like microstructure. The inner part of the veins, surrounding a central fault, is composed of fine-grained olivine. Where the fault movement included a dilational component, optically clear, equant olivine occurs in the centre. Electron backscatter diffraction mapping reveals that the vein olivine has inherited its crystallographic preferred orientation (CPO) from the olivine in the porphyroclastic host rock; however, misorientation is weaker and associated to different rotation axes. We propose that prograde olivine grew epitaxially on relics of mantle olivine and thereby acquired its CPO. Growth towards pre-existing microfractures along which serpentinisation had occurred led to straight grain boundaries and a brick-like microstructure in the veins. When dehydration embrittlement induced slip, a strong strain localisation on discrete fault planes prevented distortion of the CPO due to cataclastic deformation; grain size reduction did not significantly modify the olivine CPO. This illustrates how a CPO can be preserved though an entire metamorphic cycle, including hydration, dehydration, and deformation processes, and that the CPO and the microstructures (e.g. grain shape) of one phase do not necessarily record the same event.

  8. Development of crystallographic texture in ultra-low carbon sheet steel

    NASA Astrophysics Data System (ADS)

    Ruiz-Aparicio, Luis J.

    The increasing usage of interstitial-free (IF) sheet steels for automotive body applications has resulted in an increasing interest in examining the behavior of these steels during hot strip mill and subsequent processing. To this end, a major program directed to study the basic hot deformation of austenite and its effect on the evolution of crystallographic texture throughout processing in Ti- and Nb/Ti IF steels was conducted. The transformation temperature Arsb3, and the critical temperatures of austenitic recrystallization, Tsb{5%} and Tsb{95%}, for these steels were determined by simulation of thermomechanical processing (TMP) in an MTS computerized system. The influence of TMP on the transformation texture behavior of a Nb/Ti- and a Ti-stabilized interstitial-free (IF) steel was studied using laboratory rolling simulation. The evolution of the crystallographic texture resulting from the gamma-> alpha transformation was followed using orientation distribution function (ODF) analysis. The results of this investigation have shown that the major texture components in the hot band microstructure of these steels are \\{ 111\\} < 110> and \\{111\\}< 112> , irrespective of the steel composition and TMP path. It is shown that the presence of these major texture orientations is strongly related to the initial austenitic grain size, processing, and method of C-stabilization. These results also show that TMP of these steels in the austenitic pancake region results in better formability properties after subsequent cold rolling and annealing. It is proposed that the initial hot band texture is responsible for this improvement as it induces more beneficial cold-rolling and annealing textures.

  9. Crystallographic structure and superconductive properties of Nb-Ti films with an artificially layered structure

    SciTech Connect

    Sato, N. )

    1990-06-15

    Artificially layered niobium-titanium (Nb-Ti) films with various thickness ratios (3/1--1/3) and periodicities (2--100 A) are made in an argon or in a mixed argon/nitrogen atmosphere by a dc magnetron sputtering method. Films with small periodicities (less than 30 A) have an artificial superlattice structure (ASL) with crystallographic coherence between constituent layers, where Nb and Ti grow epitaxially on the closest planes. The crystallographic structures of films are bcc with the (110) plane parallel to the film for films with the same or a thicker Nb layer than a Ti layer, and hcp with the (001) plane parallel to the film for films with a thinner Nb layer than a Ti layer. Films with large periodicities have an artificial superstructure (ASS) with only periodic stacking of constituent layers. Films deposited in the Ar/N atmosphere also have the artificially layered structures of ASL or ASS. The artificially layered structure is thermally stable at temperatures up to 500 {degree}C. The superconducting properties of the films depend strongly on the periodicity and thickness ratio of Nb and Ti layers. The dependence of the transition temperature on the periodicity and thickness ratio is qualitatively explained by a proximity effect with a three-region model. Films with periodicities less than 20 A, composed of the same or a thicker Nb layer than a Ti layer, show high transition temperatures (above 9.3 K). The highest {ital T}{sub {ital c}} of about 13.6 K is obtained in the film composed of monatomic layers of constituents deposited in an Ar atmosphere including 30 vol % N.

  10. Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

    PubMed Central

    Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

    2010-01-01

    The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

  11. Development of Microstructure and Crystallographic Texture in a Double-Sided Friction Stir Welded Microalloyed Steel

    NASA Astrophysics Data System (ADS)

    Rahimi, S.; Wynne, B. P.; Baker, T. N.

    2017-01-01

    The evolution of microstructure and crystallographic texture has been investigated in double-sided friction stir welded microalloyed steel, using electron backscatter diffraction (EBSD). The microstructure analyses show that the center of stirred zone reached a temperature between Ac1 and Ac3 during FSW, resulting in a dual-phase austenitic/ ferritic microstructure. The temperatures in the thermo-mechanically affected zone and the overlapped area between the first and second weld pass did not exceed the Ac1. The shear generated by the rotation probe occurs in austenitic/ferritic phase field where the austenite portion of the microstructure is transformed to a bainitic ferrite, on cooling. Analysis of crystallographic textures with regard to shear flow lines generated by the probe tool shows the dominance of simple shear components across the whole weld. The austenite texture at Ac1 - Ac3 is dominated by the B { {1bar{1}2} }< 110rangle and bar{B} { {bar{1}1bar{2}} }< bar{1}bar{1}0rangle simple shear texture components, where the bainite phase textures formed on cooling were inherited from the shear textures of the austenite phase with relatively strong variant selection. The ferrite portion of the stirred zone and the ferrites in the thermo-mechanically affected zones and the overlapped area underwent shear deformation with textures dominated by the D1 { {bar{1}bar{1}2} }< 111rangle and D2 { {11bar{2}} }< 111rangle simple shear texture components. The formation of ultrafine equiaxed ferrite with submicron grain size has been observed in the overlapped area between the first and second weld pass. This is due to continuous dynamic strain-induced recrystallization as a result of simultaneous severe shear deformation and drastic undercooling.

  12. Dependence of Fracture Toughness on Crystallographic Orientation in Single-Crystalline Cubic (β) Silicon Carbide

    SciTech Connect

    Pharr, M.; Katoh, Y.; Bei, H.

    2006-01-01

    Along with other desirable properties, the ability of silicon carbide (SiC) to retain high strength after elevated temperature exposures to neutron irradiation renders it potentially applicable in fusion and advanced fission reactors. However, properties of the material such as room temperature fracture toughness must be thoroughly characterized prior to such practical applications. The objective of this work is to investigate the dependence of fracture toughness on crystallographic orientation for single-crystalline β-SiC. X-ray diffraction was first performed on the samples to determine the orientation of the crystal. Nanoindentation was used to determine a hardness of 39.1 and 35.2 GPa and elastic modulus of 474 and 446 GPa for the single-crystalline and polycrystalline samples, respectively. Additionally, crack lengths and indentation diagonals were measured via a Vickers micro-hardness indenter under a load of 100 gf for different crystallographic orientations with indentation diagonals aligned along fundamental cleavage planes. Upon examination of propagation direction of cracks, the cracks usually did not initiate and propagate from the corners of the indentation where the stresses are concentrated but instead from the indentation sides. Such cracks clearly moved along the {1 1 0} family of planes (previously determined to be preferred cleavage plane), demonstrating that the fracture toughness of SiC is comparatively so much lower along this set of planes that the lower energy required to cleave along this plane overpowers the stress-concentration at indentation corners. Additionally, fracture toughness in the <1 1 0> direction was 1.84 MPa·m1/2, lower than the 3.46 MPa·m1/2 measured for polycrystalline SiC (which can serve as an average of a spectrum of orientations), further demonstrating that single-crystalline β-SiC has a strong fracture toughness anisotropy.

  13. Crystallization and preliminary crystallographic analysis of l-asparaginase from Erwinia carotovora

    SciTech Connect

    Wikman, Linnea E. K.; Krasotkina, Julya; Kuchumova, Anastasia; Sokolov, Nikolay N.; Papageorgiou, Anastassios C.

    2005-04-01

    Er. carotovoral-asparaginase, a potential antileukaemic agent, has been crystallized. Crystals diffract to 2.6 Å using a rotating-anode source and belong to space group P2{sub 1}, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. Bacterial l-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia for over 30 y. However, their use is limited owing to the glutaminase activity of the administered enzymes, which results in serious side effects. In contrast, l-asparaginase from Erwinia carotovora exhibits low glutaminase activity at physiological concentrations of l-asparagine and l-glutamine in the blood. Recombinant Er. carotovoral-asparaginase was crystallized in the presence of l-glutamate by the hanging-drop vapour-diffusion method using 10 mg ml{sup −1} purified enzyme, 16–18%(w/v) PEG 3350 and 0.2 M NaF. X-ray diffraction data were collected to 2.6 Å at 293 K using an in-house rotating-anode generator. The crystals belong to the monoclinic P2{sub 1} space group, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. A molecular-replacement solution has been found and refinement is currently in progress. The crystal structure may provide leads towards protein-engineering efforts aimed at safer asparaginase administration in leukaemia treatment.

  14. Pre-Exposure Prophylaxis (PrEP)

    MedlinePlus

    ... Sites Podcasts QR Codes RSS Feeds Social Bookmarking Social Network Sites Text Messaging Twitter Video Games Video Sharing ... PrEP be considered for people who are HIV-negative and at very high risk for HIV infection . ...

  15. Microstructure and martensitic transformation of Ni-Ti-Pr alloys

    NASA Astrophysics Data System (ADS)

    Zhao, Chunwang; Zhao, Shilei; Jin, Yongjun; Guo, Shaoqiang; Hou, Qingyu

    2017-09-01

    The effect of Pr addition on the microstructure and martensitic transformation behavior of Ni50Ti50- x Pr x ( x = 0, 0.1, 0.3, 0.5, 0.7, 0.9) alloys were investigated experimentally. Results show that the microstructures of Ni-Ti-Pr alloys consist of the NiTi matrix and the NiPr precipitate with the Ti solute. The martensitic transformation start temperature decreases gradually with the increase in Pr fraction. The stress around NiPr precipitates is responsible for the decrease in martensitic transformation temperature with the increase in Pr fraction in Ni-Ti-Pr alloys.

  16. The effect of crystallographic texture on stress-induced martensitic transformation in NiTi: A computational analysis.

    PubMed

    Weafer, F M; Guo, Y; Bruzzi, M S

    2016-01-01

    NiTi׳s superelasticity is exploited in a number of biomedical devices, in particular self-expanding endovascular stents. These stents are often laser-cut from textured micro-tubing; texture is the distribution of crystallographic grain orientations in a polycrystalline material which has been experimentally shown to have a marked influence on mechanical properties. This study offers a computational examination into the effect of texture on the stress-induced martensite transformation (SIMT) in a micro-dogbone NiTi specimen subject to tensile loading. Finite Element Analysis (FEA) is employed to simulate the transformational behaviour of the specimen on a micro-scale level. To represent a realistic grain structure in the FEA model, grains present in a 200µm×290µm test site located at the centre edge of the specimen were identified using Scanning Electron Microscopy (SEM). Grains are assumed to have homogenous behaviour with properties varying according to their crystallographic orientation to the loading direction. Required material properties were extracted from uniaxial stress-strain curves of single crystals for each crystallographic orientation for input into the in-built UMAT/Nitinol. The orientation of each grain in the test site was identified using Electron Back-Scatter Diffraction (EBSD) techniques. In this way, a quantitative explanation is offered to the effect of crystallographic texture on SIMT. Finally, the evolution of grains in the specimen, during the transformation process, was experimentally investigated by means of an in-situ SEM tensile test.

  17. Asymmetric cold/warm rolling simulation by crystal plasticity multi-scale finite element analysis based on crystallographic homogenization

    SciTech Connect

    Onishi, Koshiro; Sakamoto, Hidetoshi; Kuramae, Hiroyuki; Morimoto, Hideo; Nakamachi, Eiji

    2010-06-15

    The purpose of this study is forming a high formability aluminum alloy sheet metal by controlling the microcrystal structure and the texture. So asymmetric rolling is applied to the material process. Analysis method is crystal plasticity multi-scale finite element analysis based on crystallographic homogenization.

  18. To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent

    PubMed Central

    Dahanayake, Jayangika N.; Gautam, Devaki N.; Verma, Rajni; Mitchell-Koch, Katie R.

    2016-01-01

    The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results. PMID:27403032

  19. An optimized alkyl chain-based binding motif for 2D self-assembly: a comprehensive crystallographic approach.

    PubMed

    Bléger, David; Bocheux, Amandine; Kreher, David; Mathevet, Fabrice; Attias, André-Jean; Metgé, Germain; Douillard, Ludovic; Fiorini-Debuisschert, Céline; Charra, Fabrice

    2013-02-21

    Taking into account substrate crystallographic constraints, an overarching molecular binding motif has been designed to allow transferable self-assembling patterns on different substrates. This optimized clip demonstrates robust and equivalent self-assembled architectures on both highly oriented pyrolitic graphite (HOPG) and reconstructed Au(111) surfaces.

  20. PrEP: controversy, agency and ownership

    PubMed Central

    Cairns, Gus P; Race, Kane; Goicochea, Pedro

    2016-01-01

    Pre-exposure prophylaxis (PrEP) has been and continues to be an intervention that causes controversy and debate between stakeholders involved in providing or advocating for it, and within communities in need of it. These controversies extend beyond the intrinsically complex issues of making it available. In this commentary, some of the possible roots of the air of dissent and drama that accompanies PrEP are explored. The similarities between the controversies that dogged the earliest human trials of PrEP and the ones we see today in the era of licensing and implementation are explored. We outline five mediating principles or cultural norms that may influence arguments about PrEP differently. Three areas of specific concern are identified: medical risk versus benefit, distrust and fear of healthcare interventions, and fears for individual responsibility and community cohesion. The fear that PrEP may somehow represent a loss of control over one or more of these domains is suggested as an underlying factor. The development of countervailing measures, to institute greater community “ownership” of PrEP, and concomitant improvements in the sense of individual agency over sexual risk are outlined and recommended. PMID:27760689

  1. Photoluminescence properties of Pr3+ doped Bi2ZnOB2O6 microcrystals and PMMA-based composites

    NASA Astrophysics Data System (ADS)

    Jaroszewski, K.; Chrunik, M.; Głuchowski, P.; Coy, E.; Maciejewska, B.; Jastrzab, R.; Majchrowski, A.; Kasprowicz, D.

    2016-12-01

    Photoluminescence properties of red-emitting Pr3+-doped Bi2ZnOB2O6 microcrystalline powder and PMMA-based composite materials were reported. Bi2ZnOB2O6:Pr3+ powders were synthesized by means of the modified Pechini method. The morphology and crystallographic structure of Bi2ZnOB2O6:Pr3+ microcrystals were investigated by XRD and HRTEM. The PMMA-based composite materials were prepared by embedding of Bi2ZnOB2O6:Pr3+ powder in the PMMA matrix. The vibrational properties of the powder and composite systems were investigated by μ-Raman spectroscopy. Emission spectra of the samples were measured under blue (451.6 nm) and UV (320 nm) excitation. Both, the powder and composite samples show enhancement of red emission (1D2 → 3H4) and quenching of greenish-blue luminescence from 3P0 level of Pr3+ ions after excitation in UV and VIS caused by the 3P0 ∼ 1D2 non-radiative relaxation of Pr3+ ion by low-lying charge transfer state and non-radiative de-excitation through Pr3+-Bi3+ energy transfer. The response of the powder and composite samples to pulsed excitation at 451.6 nm was measured by monitoring emission from the 1D2 level (595 nm/3P0 → 3H6 transition). The determined lifetimes τ1 and τ2 of the red emission at 595 nm (1D2 → 3H4 transition) of the composite are significantly longer in comparison to powder samples. Moreover, because of the good nonlinear optical properties of the Bi2ZnOB2O6 crystals and effective luminescence of the Pr3+-doped Bi2ZnOB2O6 powders and composites, they can be very useful as bi-functional materials in the new generation of optoelectronic devices.

  2. Pr-magnetism in the quasi-skutterudite compound PrFe2Al8

    NASA Astrophysics Data System (ADS)

    Nair, Harikrishnan S.; Ogunbunmi, Michael O.; Kumar, C. M. N.; Adroja, D. T.; Manuel, P.; Fortes, D.; Taylor, J.; Strydom, A. M.

    2017-08-01

    The intermetallic compound PrFe2Al8 that possesses a three-dimensional network structure of Al polyhedra centered at the transition metal element Fe and the rare earth Pr is investigated through neutron powder diffraction and inelastic neutron scattering in order to elucidate the magnetic ground state of Pr and Fe and the crystal field effects of Pr. Our neutron diffraction study confirms long-range magnetic order of Pr below TN = 4.5 K in this compound. Subsequent magnetic structure estimation reveals a magnetic propagation vector {k} = {(\\frac{1}{2}~0~\\frac{1}{2})} with a magnetic moment value of 2.5~μB /Pr along the orthorhombic c-axis and evidence the lack of ordering in the Fe sublattice. The inelastic neutron scattering study reveals one crystalline electric field excitation near 19 meV at 5 K in PrFe2Al8. The energy-integrated intensity of the 19 meV excitation as a function of \\vert Q\\vert (\\mathringA-1) follows the square of the magnetic form factor of Pr3+ thereby confirming that the inelastic excitation belongs to the Pr sublattice. The second sum rule applied to the dynamic structure factor indicates only 1.6(2) μB evolving at the 19 meV peak compared to the 3.58 μB for free Pr3+ , indicating that the crystal field ground state is magnetic and the missing moment is associated with the resolution limited quasi-elastic line. The magnetic order occurring in Pr in PrFe2Al8 is counter-intuitive to the symmetry-allowed crystal field level scheme, hence, is suggestive of exchange-mediated mechanisms of ordering stemming from the magnetic ground state of the crystal field levels.

  3. Crystallographic Behavior of Iron Oxide Minerals in the Deformed Iron Formation of Quadrilátero Ferrífero

    NASA Astrophysics Data System (ADS)

    Duarte Lisboa, Filipe Augusto; Lagoeiro, Leonardo; Martins Graça, Leonardo; Ávila, Carlos Fernando; Ferreira Barbosa, Paola

    2016-04-01

    The Quadrilátero Ferrífero (QF) which is located in Brazil represents a mineral province of great importance for hosting Banded Iron Formation deposits (BIFs). The Alegria mine which belongs to Vale Company is located in the east part of Quadrilátero Ferrífero and it explores iron ore from a region of great structural complexity. A deformed BIF sample that presents a micro-fold on quartz and hematite bands was analyzed through Electron Backscatter Diffraction technique (EBSD) in order to relate the crystallographic orientations with the microstructures along the micro-fold envelop. For the sample orientation the Z-axis is taken parallel to the fold limb, Y-axis is perpendicular to the fold hinge and X-axis perpendicular to the YZ plane. In the limbs hematite grains are mostly stretched whereas at the hinge grains tend to be somewhat equant. On the other hand, quartz grain shapes are invariable along the fold, with a few exceptions in the hinge where grains are slightly elongated. Grains of hematite present a strong c-axis ({0001}) preferred orientation forming a subtle girdle somewhat parallel to the XY plane of the strain ellipsoid determined macroscopically (XY being the foliation plane), and a strong (<2bar1bar10>) crystallographic fabric approximately parallel to the Z-axis. Similarly, the poles to the prismatic planes ({m} or {10bar10}) also have a stronger crystallographic fabric parallel to the Z axis. It seems that there are two crossing planes for the orientation of and {m} with the two maxima at the intersection of the two planes. Typical hematite crystallographic fabrics are somewhat distinct, since {c} axis commonly forms a very strong fiber texture parallel to the pole of the foliation. Most studies regard such crystallographic texture as evidence for high activity of {c} slip. The {c} girdles observed here are common for mica grains under rigid body rotation in constriction strain, which mechanism is commonly observed in the hematite

  4. 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

  5. Longitudinal studies of patients with ANCA vasculitis demonstrate concurrent reactivity to complementary PR3 protein segments cPR3m and cPR3C and with no reactivity to cPR3N

    PubMed Central

    Hewins, Peter; Belmonte, Frances; Jennette, J Charles; Falk, Ronald J; Preston, Gloria A

    2010-01-01

    Antibodies recognizing the complement of the middle of PR3 (cPR3m) occur in ~30% of PR3-ANCA-vasculitis patients and immunization of animals with a peptide complementary to the middle of PR3 (cPR3m) induces not only anti-complementary PR3 antibodies, but also anti-PR3 antibodies derived through an anti-idiotypic response. PR3 epitopes recognized by patient ANCA however, are not restricted to the middle of PR3. This prompted us to test for antibodies that react with proteins complementary to the terminal regions of PR3 (cPR3C and cPR3N) in PR3-ANCA patients. Anti-cPR3C reactivity was detected in 28% of patients but anti-cPR3N reactivity in only 15%. Ranked anti-cPR3C and anti-cPR3m reactivity correlated in the cohort, whereas there was no significant relationship between cPR3C and cPR3N reactivity. Serial samples from three patients’ revealed that anti-cPR3C and anti-cPR3m reactivity followed a similar pattern over time. Serial samples from a fourth patient demonstrated an anti-cPR3N response without concurrent cPR3m or cPR3C reactivity. Epitope determination by mass spectrometry identified a thirteen amino acid sequence on cPR3C that contained a common binding site recognized by antibodies from three patients. This peptide sequence contains a “PHQ” motif which was reported to be the basis for cross-reactivity of anti-cPR3m antibodies with plasminogen. Why these antibodies are detected in only ~30% of the patients remains unclear. The data reveal it is not due to lack of inclusion of flanking regions of complementary PR3 during screening. Instead, quite unexpectedly, the data demonstrate that patients’ antibodies react with a restricted epitope that exists in both cPR3m and cPR3C. PMID:20712431

  6. Reactions of R(2)P-P(SiMe(3))Li with [(R'(3)P)(2)PtCl(2)]. A general and efficient entry to phosphanylphosphinidene complexes of platinum. Syntheses and structures of [(eta(2)-P=(i)Pr(2))Pt(p-Tol(3)P)(2)], [(eta(2)-P=(t)Bu(2))Pt(p-Tol(3)P)(2)], [{eta(2)-P=(N(i)Pr(2))(2)}Pt(p-Tol(3)P)(2)] and [{(Et(2)PhP)(2)Pt}(2)P(2)].

    PubMed

    Domańska-Babul, Wioleta; Chojnacki, Jaroslaw; Matern, Eberhard; Pikies, Jerzy

    2009-01-07

    The reactions of lithium derivatives of diphosphanes R(2)P-P(SiMe(3))Li (R = (t)Bu, (i)Pr, Et(2)N and (i)Pr(2)N) with [(R'(3)P)(2)PtCl(2)] (R'(3)P = Et(3)P, Et(2)PhP, EtPh(2)P and p-Tol(3)P) proceed in a facile manner to afford side-on bonded phosphanylphosphinidene complexes of platinum [(eta(2)-P=R(2))Pt(PR'(3))(2)]. The related reactions of Ph(2)P-P(SiMe(3))Li with [(R'(3)P)(2)PtCl(2)] did not yield [(eta(2)-P=PPh(2))Pt(PR'(3))(2)] and resulted mainly in the formation of [{(R'(3)P)(2)Pt}(2)P(2)], Ph(2)P-PLi-PPh(2), (Me(3)Si)(2)PLi and (Me(3)Si)(3)P. Crystallographic data are reported for the compounds [(eta(2)-P=R(2))Pt(p-Tol(3)P)(2)] (R = (t)Bu, (i)Pr, ((i)Pr(2)N)(2)P) and for [{(Et(2)PhP)(2)Pt}(2)P(2)].

  7. ESO PR Highlights in 2007

    NASA Astrophysics Data System (ADS)

    2008-01-01

    Another great year went by for ESO, the European Organisation for Astronomical Research in the Southern Hemisphere. From 1 January 2007, with the official joining of the Czech Republic, ESO has 13 member states, and since September, ESO has a new Director General, Tim de Zeeuw (ESO 03/07 and 38/07). Many scientific discoveries were made possible with ESO's telescopes. Arguably, the most important is the discovery of the first Earth-like planet in the habitable zone of a low-mass red dwarf (ESO 22/07). If there is water on this planet, then it should be liquid! ESO PR Highlights 2007 This is a clickable map. These are only some of the press releases issued by ESO in 2007. For a full listing, please go to ESO 2007 page. In our own Solar System also, astronomers made stunning breakthroughs with ESO's telescopes, observing the effect of the light from the Sun on an asteroid's rotation (ESO 11/07), describing in unprecedented detail the double asteroid Antiope (ESO 18/07), peering at the rings of Uranus (ESO 37/07), discovering a warm south pole on Neptune (ESO 41/07), showing a widespread and persistent morning drizzle of methane over the western foothills of Titan's major continent (ESO 47/07), and studying in the greatest details the wonderful Comet McNaught (ESO 05/07 and 07/07). In the study of objects slightly more massive than planets, the VLT found that brown dwarfs form in a similar manner to normal stars (ESO 24/07). The VLT made it also possible to measure the age of a fossil star that was clearly born at the dawn of time (ESO 23/07). Other discoveries included reconstructing the site of a flare on a solar-like star (ESO 53/07), catching a star smoking (ESO 34/07), revealing a reservoir of dust around an elderly star (ESO 43/07), uncovering a flat, nearly edge-on disc of silicates in the heart of the magnificent Ant Nebula (ESO 42/07), finding material around a star before it exploded (ESO 31/07), fingerprinting the Milky Way (ESO 15/07), revealing a rich

  8. PR: The State of Public Relations in Academic Libraries.

    ERIC Educational Resources Information Center

    Ford, Vikki

    1985-01-01

    Presents results of survey of 48 academic library directors on use and effectiveness of public relations (PR) programs (planned PR programs administered by one person, coordinated PR programs, favored channels of communication, importance of academic library PR). Recommendations based on survey results and review of literature are offered. (22…

  9. Penicillium roqueforti PR toxin gene cluster characterization.

    PubMed

    Hidalgo, Pedro I; Poirier, Elisabeth; Ullán, Ricardo V; Piqueras, Justine; Meslet-Cladière, Laurence; Coton, Emmanuel; Coton, Monika

    2017-03-01

    PR toxin is a well-known isoprenoid mycotoxin almost solely produced by Penicillium roqueforti after growth on food or animal feed. This mycotoxin has been described as the most toxic produced by this species. In this study, an in silico analysis allowed identifying for the first time a 22.4-kb biosynthetic gene cluster involved in PR toxin biosynthesis in P. roqueforti. The pathway contains 11 open reading frames encoding for ten putative proteins including the major fungal terpene cyclase, aristolochene synthase, involved in the first farnesyl-diphosphate cyclization step as well as an oxidoreductase, an oxidase, two P450 monooxygenases, a transferase, and two dehydrogenase enzymes. Gene silencing was used to study three genes (ORF5, ORF6, and ORF8 encoding for an acetyltransferase and two P450 monooxygenases, respectively) and resulted in 20 to 40% PR toxin production reductions in all transformants proving the involvement of these genes and the corresponding enzyme activities in PR toxin biosynthesis. According to the considered silenced gene target, eremofortin A and B productions were also affected suggesting their involvement as biosynthetic intermediates in this pathway. A PR toxin biosynthesis pathway is proposed based on the most recent and available data.

  10. Small molecules and antibodies: a means of distinguishing between PrPC and PrPSc

    USDA-ARS?s Scientific Manuscript database

    PrPSc and PrPC are isoforms, since they possess identical covalent structures and identical post-translational modifications. The same amino acid may react differently with the same chemical reagent in an isoform-dependent manner. The site of covalent modification can be identified by mass spectrom...

  11. Distinguishing between PrPC and PrPSc using small molecule reagents

    USDA-ARS?s Scientific Manuscript database

    Background/Introduction. The structural difference between PrPSc and PrPC is entirely conformational: they are isoforms. Both isoforms possess identical covalent structures and identical post-translational modifications. This means that the same amino acid can react differently with the same chemic...

  12. Distinguishing between PrPC and PrPSc using small molecule reagents(Abstract)

    USDA-ARS?s Scientific Manuscript database

    Background/Introduction. The structural difference between PrPSc and PrPC is entirely conformational: they are isoforms. Both isoforms possess identical covalent structures and identical post-translational modifications. This means that the same amino acid can react differently with the same chemica...

  13. A High-strain Flow Law for Olivine: Grain-size Sensitivity and Crystallographic Fabric

    NASA Astrophysics Data System (ADS)

    Hansen, L. N.; Zimmerman, M. E.; Kohlstedt, D. L.

    2011-12-01

    The dislocation-accommodated grain-boundary sliding regime, which has recently been recognized in deformation experiments on olivine aggregates, has important implications for the rheological characteristics of the upper mantle and for the interpretation of microstructures in naturally deformed rocks. However, previous experimental studies suffer from both the difficulty in synthesizing samples with a desired mean grain size and the limitation that crystallographic fabrics have not fully developed at low strains. We alleviate these difficulties in a series of innovative deformation experiments. Aggregates of iron-bearing olivine, hot pressed as hollow cylinders, were deformed in torsion at 1200°C in a gas-medium apparatus at constant strain rate until a steady-state shear stress was reached, which occurred by a shear strain of ~5. Since recrystallized grain size is a function of shear stress, we were able to systematically vary the mean grain size among samples by changing the controlling shear-strain rate. Above a shear strain of ~5, strain rate stepping tests were performed to determine the stress exponent. Between each strain-rate step, the strain rate was returned to the original strain rate to reset the microstructure. Experiments were stopped when the total shear strain reached ~11. Our results yield a stress exponent of ~4 and a grain size exponent of ~1, both of which agree with previous small-strain compression experiments on olivine in the dislocation-accommodated grain-boundary sliding regime. If the dependence of strain rate on grain size in the power-law flow law is removed by inserting the grain-size piezometer, the apparent stress exponent in the resulting grain size independent flow law increases to 5.2. Microstructural analyses indicate that very strong crystallographic-preferred orientation (CPO) fabrics are developed with M-indices of ~0.6. The CPO fabrics have [100] maxima sub-parallel to the shear direction and [010] maxima sub

  14. Effect of crystallographic texture and dislocation hardening on limit strain in sheet metal forming

    NASA Astrophysics Data System (ADS)

    Wen, Xiyu

    2000-10-01

    In the metal industry, sheet metals are widely used to produce packaging materials for consumer goods, for structures such as automobilse, and for building construction and transportation. The desired shape of the products is imparted by plastic deformation in either the cold or hot state. Traditionally, the prediction of the forming limit of sheet metals is based on tensile tests, simulation tests and continuum mathematical models. Continuum models used in the prediction of the plastic behavior of sheet metals are based on average values of mechanical properties such as elongation, yield strength, work hardening and work-hardening rate, which are usually derived from tensile tests. Although attempts have been made to abandon the phenomenological description of the yield function by applying the theory of crystal plasticity to calculate the yield surface of texture polycrystals and hence the limit strains, only the average properties of the microstructure (e.g., the crystallographic texture of the bulk sheet) have been taken into account. So far, there has been no model for the prediction of the strain path and the limit strain of sheet metals that takes into account the effect of individual grain orientation and the dislocation property. In this thesis, different approaches in the study of plastic deformation are reviewed from the view-point of both macroplasticity and microplasticity. Instead of relying on a unique flow rule to describe the stress and strain relationship, the role of work hardening in the instability process of sheet metal and hence the flow localization phenomenon is explored from a study of the changes in the orientation of the constituent crystallites and from the changes in the dislocation density associated with different grain orientations during the course of large biaxial deformation. The changes in the crystallographic textures of an aluminium sheet sample deformed under various stress states from plane-strain tension to equi

  15. cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer.

    PubMed Central

    Madhusudan; Trafny, E. A.; Xuong, N. H.; Adams, J. A.; Ten Eyck, L. F.; Taylor, S. S.; Sowadski, J. M.

    1994-01-01

    The crystal structure of ternary and binary substrate complexes of the catalytic subunit of cAMP-dependent protein kinase has been refined at 2.2 and 2.25 A resolution, respectively. The ternary complex contains ADP and a 20-residue substrate peptide, whereas the binary complex contains the phosphorylated substrate peptide. These 2 structures were refined to crystallographic R-factors of 17.5 and 18.1%, respectively. In the ternary complex, the hydroxyl oxygen OG of the serine at the P-site is 2.7 A from the OD1 atom of Asp 166. This is the first crystallographic evidence showing the direct interaction of this invariant carboxylate with a peptide substrate, and supports the predicted role of Asp 166 as a catalytic base and as an agent to position the serine -OH for nucleophilic attack. A comparison of the substrate and inhibitor ternary complexes places the hydroxyl oxygen of the serine 2.7 A from the gamma-phosphate of ATP and supports a direct in-line mechanism for phosphotransfer. In the binary complex, the phosphate on the Ser interacts directly with the epsilon N of Lys 168, another conserved residue. In the ternary complex containing ATP and the inhibitor peptide, Lys 168 interacts electrostatically with the gamma-phosphate of ATP (Zheng J, Knighton DR, Ten Eyck LF, Karlsson R, Xuong NH, Taylor SS, Sowadski JM, 1993, Biochemistry 32:2154-2161). Thus, Lys 168 remains closely associated with the phosphate in both complexes. A comparison of this binary complex structure with the recently solved structure of the ternary complex containing ATP and inhibitor peptide also reveals that the phosphate atom traverses a distance of about 1.5 A following nucleophilic attack by serine and transfer to the peptide. No major conformational changes of active site residues are seen when the substrate and product complexes are compared, although the binary complex with the phosphopeptide reveals localized changes in conformation in the region corresponding to the glycine

  16. Slicing the perovskite structure with crystallographic shear planes: the A(n)B(n)O(3n-2) homologous series.

    PubMed

    Abakumov, Artem M; Hadermann, Joke; Batuk, Maria; D'Hondt, Hans; Tyablikov, Oleg A; Rozova, Marina G; Pokholok, Konstantin V; Filimonov, Dmitry S; Sheptyakov, Denis V; Tsirlin, Alexander A; Niermann, Daniel; Hemberger, Joachim; Van Tendeloo, Gustaaf; Antipov, Evgeny V

    2010-10-18

    A new A(n)B(n)O(3n-2) homologous series of anion-deficient perovskites has been evidenced by preparation of the members with n = 5 (Pb(2.9)Ba(2.1)Fe(4)TiO(13)) and n = 6 (Pb(3.8)Bi(0.2)Ba(2)Fe(4.2)Ti(1.8)O(16)) in a single phase form. The crystal structures of these compounds were determined using a combination of transmission electron microscopy and X-ray and neutron powder diffraction (S.G. Ammm, a = 5.74313(7), b = 3.98402(4), c = 26.8378(4) Å, R(I) = 0.035, R(P) = 0.042 for Pb(2.9)Ba(2.1)Fe(4)TiO(13) and S.G. Imma, a = 5.7199(1), b = 3.97066(7), c = 32.5245(8) Å, R(I) = 0.032, R(P) = 0.037 for Pb(3.8)Bi(0.2)Ba(2)Fe(4.2)Ti(1.8)O(16)). The crystal structures of the A(n)B(n)O(3n-2) homologues are formed by slicing the perovskite structure with (101)(p) crystallographic shear (CS) planes. The shear planes remove a layer of oxygen atoms and displace the perovskite blocks with respect to each other by the 1/2[110](p) vector. The CS planes introduce edge-sharing connections of the transition metal-oxygen polyhedra at the interface between the perovskite blocks. This results in intrinsically frustrated magnetic couplings between the perovskite blocks due to a competition of the exchange interactions between the edge- and the corner-sharing metal-oxygen polyhedra. Despite the magnetic frustration, neutron powder diffraction and Mössbauer spectroscopy reveal that Pb(2.9)Ba(2.1)Fe(4)TiO(13) and Pb(3.8)Bi(0.2)Ba(2)Fe(4.2)Ti(1.8)O(16) are antiferromagnetically ordered below T(N) = 407 and 343 K, respectively. The Pb(2.9)Ba(2.1)Fe(4)TiO(13) and Pb(3.8)Bi(0.2)Ba(2)Fe(4.2)Ti(1.8)O(16) compounds are in a paraelectric state in the 5-300 K temperature range.

  17. Binding of bovine T194A PrPC by PrPSc-specific antibodies

    PubMed Central

    Madampage, Claudia A; Määttänen, Pekka; Marciniuk, Kristen; Brownlie, Robert; Andrievskaia, Olga; Potter, Andrew; Cashman, Neil R; Lee, Jeremy S; Napper, Scott

    2013-01-01

    Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative diseases that are based on the misfolding of a cellular prion protein (PrPC) into an infectious, pathological conformation (PrPSc). There is proof-of-principle evidence that a prion vaccine is possible but this is tempered with concerns of the potential dangers associated with induction of immune responses to a widely-expressed self-protein. By targeting epitopes that are specifically exposed upon protein misfolding, our group developed a vaccine that induces PrPSc-specific antibody responses. Here we consider the ability of this polyclonal antibody (SN6b) to bind to a mutant of PrPC associated with spontaneous prion disease. Polyclonal antibodies were selected to mimic the vaccination outcome and also explore all possible protein conformations of the recombinant bovine prion protein with mutation T194A [bPrP(T194A)]. This mutant is a homolog of the human T183A mutation of PrPC that is associated with early onset of familial dementia. With nanopore analysis, under non-denaturing conditions, we observed binding of the SN6b antibody to bPrP(T194A). This interaction was confirmed through ELISAs as well as immunoprecipitation of the recombinant and cellularly expressed forms of bPrP(T194A). This interaction did not promote formation of a protease resistant conformation of PrP in vitro. Collectively, these findings support the disease-specific approach for immunotherapy of prion diseases but also suggest that the concept of conformation-specific immunotherapy may be complicated in individuals who are genetically predisposed to PrPC misfolding. PMID:23787697

  18. Pr-magnetism in the quasi-skutterudite compound PrFe2Al8.

    PubMed

    Nair, Harikrishnan S; Ogunbunmi, Michael O; Kumar, C M N; Adroja, D T; Manuel, P; Fortes, D; Taylor, J; Strydom, A M

    2017-08-31

    The intermetallic compound PrFe2Al8 that possesses a three-dimensional network structure of Al polyhedra centered at the transition metal element Fe and the rare earth Pr is investigated through neutron powder diffraction and inelastic neutron scattering in order to elucidate the magnetic ground state of Pr and Fe and the crystal field effects of Pr. Our neutron diffraction study confirms long-range magnetic order of Pr below [Formula: see text] K in this compound. Subsequent magnetic structure estimation reveals a magnetic propagation vector [Formula: see text] with a magnetic moment value of [Formula: see text]/Pr along the orthorhombic c-axis and evidence the lack of ordering in the Fe sublattice. The inelastic neutron scattering study reveals one crystalline electric field excitation near 19 meV at 5 K in PrFe2Al8. The energy-integrated intensity of the 19 meV excitation as a function of [Formula: see text] follows the square of the magnetic form factor of [Formula: see text] thereby confirming that the inelastic excitation belongs to the Pr sublattice. The second sum rule applied to the dynamic structure factor indicates only 1.6(2) [Formula: see text] evolving at the 19 meV peak compared to the 3.58 [Formula: see text] for free [Formula: see text], indicating that the crystal field ground state is magnetic and the missing moment is associated with the resolution limited quasi-elastic line. The magnetic order occurring in Pr in PrFe2Al8 is counter-intuitive to the symmetry-allowed crystal field level scheme, hence, is suggestive of exchange-mediated mechanisms of ordering stemming from the magnetic ground state of the crystal field levels.

  19. Histidines in the octapeptide repeat of PrPC react with PrPSc at an acidic pH.

    PubMed

    Cruite, Justin T; Abalos, Gil C; Bellon, Anne; Solforosi, Laura

    2011-03-15

    Cellular PrP is actively cycled between the cell surface and the endosomal pathway. The exact site and mechanism of conversion from PrP(C) to PrP(Sc) remain unknown. We have previously used recombinant antibodies containing grafts of PrP sequence to identify three regions of PrP(C) (aa23-27, 98-110, and 136-158) that react with PrP(Sc) at neutral pH. To determine if any regions of PrP(C) react with PrP(Sc) at an acidic pH similar to that of an endosomal compartment, we tested our panel of grafted antibodies for the ability to precipitate PrP(Sc) in a range of pH conditions. At pH near or lower than 6, PrP-grafted antibodies representing the octapeptide repeat react strongly with PrP(Sc) but not PrP(C). Modified grafts in which the histidines of the octarepeat were replaced with alanines did not react with PrP(Sc). PrP(Sc) precipitated by the octapeptide at pH 5.7 was able to seed conversion of normal PrP to PrP(Sc) in vitro. However, modified PrP containing histidine to alanine substitutions within the octapeptide repeats was still converted to PrP(Sc) in N2a cells. These results suggest that once PrP has entered the endosomal pathway, the acidic environment facilitates the binding of PrP(Sc) to the octarepeat of PrP(C) by the change in charge of the histidines within the octarepeat.

  20. TSE strain differentiation in mice by immunohistochemical PrP(Sc) profiles and triplex Western blot.

    PubMed

    van Keulen, Lucien J M; Langeveld, Jan P M; Dolstra, Corry H; Jacobs, Jorg; Bossers, Alex; van Zijderveld, Fred G

    2015-10-01

    TSE strains are routinely identified by their incubation period and vacuolation profile in the brain after intracerebral inoculation and serial passaging in inbred mouse lines. There are some major drawbacks to this method that are related to the variation in vacuolation that exists in the brains of mice infected with the same TSE strain and to variation between observers and laboratories in scoring vacuolation and determining the final incubation period. We investigated the potential of PrP(Sc) immunohistochemistry and triplex Western blotting as possible alternative methods to differentiate between TSE strains. TSE reference strains ME7, 87A/87V, 22A/22C, 79A/79V and 301C/301V were intracerebrally inoculated in RIII or VM inbred mice that differ in their PrP genotype. Immunohistochemical PrP(Sc) profiles were drawn up by scanning light microscopy both on coronal and sagittal sections. On the basis of the localization of PrP(Sc) in the cerebral cortex, hippocampus, and cerebellar cortex and the overall type of PrP(Sc) staining, all TSE strains could be well differentiated from each other through their typical strain dependent characteristics. In addition, Western blot showed that the combination of glycosylation profile and 12B2 epitope content of PrP(Sc) allowed to distinguish between all reference strains except for ME7 and 22A in VM mice. TSE strains in mice can be identified on the basis of their PrP(Sc) profile alone. The potential to identify TSE strains in ruminants with these PrP(Sc) profiles after a single primary passage in mice will be the topic of future studies. © 2014 British Neuropathological Society.

  1. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. 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.

  3. A deeper insight into (Lu,Y)AG:Pr scintillator crystals

    NASA Astrophysics Data System (ADS)

    Drozdowski, W.; Wojtowicz, A. J.; Brylew, K.; Łachmański, W.; Talik, E.; Szubka, M.; Kusz, J.; Guzik, A.; Balin, K.; Kisielewski, J.; Świrkowicz, M.; Pajączkowska, A.

    2017-02-01

    Interior of Czochralski-grown (Lu,Y)AG:Pr crystals has been examined by means of several techniques, such as X-Ray Photoelectron Spectroscopy, X-Ray Diffraction, Time-of-Flight Secondary Ion Mass Spectrometry, and magnetic susceptibility measurements. Additionally, their luminescence has been monitored at various combinations of a double-beam (X-ray/IR) excitation.

  4. Study on Crystallographic Orientation Effect on Surface Generation of Aluminum in Nano-cutting

    NASA Astrophysics Data System (ADS)

    Xu, Feifei; Fang, Fengzhou; Zhu, Yuanqing; Zhang, Xiaodong

    2017-04-01

    The material characteristics such as size effect are one of the most important factors that could not be neglected in cutting the material at nanoscale. The effects of anisotropic nature of single crystal materials in nano-cutting are investigated employing the molecular dynamics simulation. Results show that the size effect of the plastic deformation is based on different plastic carriers, such as the twin, stacking faults, and dislocations. The minimum uncut chip thickness is dependent on cutting direction, where even a negative value is obtained when the cutting direction is {110}<001>. It also determines the material deformation and removal mechanism (e.g., shearing, extruding, and rubbing mechanism) with a decrease in uncut chip thickness. When material is deformed by shearing, the primary shearing zone expands from the stagnation point or the tip of stagnation zone. When a material is deformed by extruding and rubbing, the primary deformation zone almost parallels to the cutting direction and expands from the bottom of the cutting edge merging with the tertiary deformation zone. The generated surface quality relates to the crystallographic orientation and the minimum uncut chip thickness. The cutting directions of {110}<001>, {110}<1-10>, and {111}<1-10>, whose minimum uncut chip thickness is relatively small, have better surface qualities compared to the other cutting direction.

  5. Processing-Microstructure-Crystallographic Texture-Surface Property Relationships in Friction Stir Processing of Titanium

    NASA Astrophysics Data System (ADS)

    Bahl, Sumit; Nithilaksh, P. L.; Suwas, Satyam; Kailas, Satish V.; Chatterjee, Kaushik

    2017-08-01

    Friction stir processing (FSP) is a solid-state technique for microstructural modification of metallic materials. The aim of this work is to establish processing-microstructure-texture-surface properties relationship in commercially pure titanium (cp-Ti) processed by FSP under different processing conditions. The effect of processing conditions on the microstructural changes and the evolution of crystallographic texture is systematically studied. The changes in the chemical composition of the passive surface layer are characterized by x-ray photoelectron spectroscopy. The corrosion behavior of cp-Ti after FSP is evaluated in simulated body fluid and is related to the microstructure, texture and composition of passive layer. Substantial grain refinement was observed after FSP. Shear type deformation texture evolved during FSP with dynamic restoration processes weakening the overall shear texture. The corrosion resistance improved after processing at lower rotational speed due to the presence of basal planes at the surface and the incorporation of TiN in the passive layer. The results of this study suggest that surface properties of cp-Ti like passive layer and corrosion resistance are altered by FSP and can be controlled using appropriate processing parameters.

  6. Crystallographic preferred orientations may develop in nanocrystalline materials on fault planes due to surface energy interactions

    NASA Astrophysics Data System (ADS)

    Toy, Virginia G.; Mitchell, Thomas M.; Druiventak, Anthony; Wirth, Richard

    2015-09-01

    A layer of substantially noncrystalline material, composed of partially annealed nanopowder with local melt, was experimentally generated by comminution during ˜1.5 mm total slip at ˜2.5 × 10-6 m s-1, Pconf ˜ 0.5 GPa, and 450°C or 600°C, on saw cut surfaces in novaculite. The partially annealed nanopowder comprises angular grains mostly 5-200 nm diameter in a variably dense packing arrangement. A sharp transition from wall rock to partially annealed nanopowder illustrates that the nanopowder effectively localizes shear, consistent with generation of nanoparticles during initial fragmentation, not by progressive grain size reduction. Dislocation densities in nanopowder grains or immediate wall rock are not significantly high, but there are planar plastic defects spaced at 5-200 nm parallel to the host quartz grain's basal plane. We propose these plastic defects developed into through-going fractures to generate nanocrystals. The partially annealed nanopowder has a crystallographic preferred orientation (CPO) that we hypothesize developed due to surface energy interactions to maximize coincident site lattices (CSL) during annealing. This mechanism may also have generated CPOs recently described in micro/nanocrystalline calcite fault gouges.

  7. Structure of the SARS coronavirus main proteinase as an active C{sub 2} crystallographic dimer

    SciTech Connect

    Xu, Ting; Ooi, Amy; Lee, Hooi Chen; Wilmouth, Rupert; Liu, Ding Xiang; Lescar, Julien

    2005-11-01

    An orthorhombic crystal form of the SARS CoV main proteinase diffracting to a resolution of 1.9 Å is reported. The conformation of residues in the catalytic site indicates an active enzyme. The 34 kDa main proteinase (M{sup pro}) from the severe acute respiratory syndrome coronavirus (SARS-CoV) plays an important role in the virus life cycle through the specific processing of viral polyproteins. As such, SARS-CoV M{sup pro} is a key target for the identification of specific inhibitors directed against the SARS virus. With a view to facilitating the development of such compounds, crystals were obtained of the enzyme at pH 6.5 in the orthorhombic space group P2{sub 1}2{sub 1}2 that diffract to a resolution of 1.9 Å. These crystals contain one monomer per asymmetric unit and the biologically active dimer is generated via the crystallographic twofold axis. The conformation of the catalytic site indicates that the enzyme is active in the crystalline form and thus suitable for structure-based inhibition studies.

  8. Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10)

    PubMed Central

    Park, HaJeung; González, Àlex L.; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R.; Fang, Pengfei; Guo, Min; Disney, Matthew D.

    2016-01-01

    Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide 5′UCU3′/3′UCU5′ internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA. PMID:26039897

  9. On the validation of crystallographic symmetry and the quality of structures.

    PubMed

    Wang, Jimin

    2015-05-01

    In 2008, Zwart and colleagues observed that the fraction of the structures deposited in the PDB alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (NCS) was about 6%, and that this percentage was rising annually. A few years later, Poon and colleagues found that 2% of all the crystal structures in the PDB belonged to higher symmetry space groups than those assigned to them. Here, I report an analysis of the X-ray diffraction data deposited for this class of structures, which shows that most of the "pseudosymmetry" and "special NCS" that has been reported is in fact true crystallographic symmetry (CS). This distinction is important because the credibility of crystal structures depends heavily on quality control statistics such as Rfree that are unreliable when they are computed incorrectly, which they often are when CS is misidentified as "special NCS" or "pseudosymmetry". When mistakes of this kind are made, artificially low values of Rfree can give unjustified confidence in the accuracy of the reported structures.

  10. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

    PubMed Central

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    2014-01-01

    The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. PMID:24034303

  11. Crystallographic snapshots of active site metal shift in E. coli fructose 1,6-bisphosphate aldolase

    PubMed Central

    Tran, Huyen-Thi; Lee, Seon-Hwa; Ho, Thien-Hoang; Hong, Seung-Hye; Huynh, Kim-Hung; Ahn, Yeh-Jin; Oh, Deok-Kun; Kang, Lin-Woo

    2016-01-01

    Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between 1.8 Å and 2.0 Å. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2+ ion. Citrate and TRIS bound EcFBA structures showed Zn2+ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2+ within EcFBA without losing it. PMID:27733232

  12. Temperature dependent crystallographic transformations in chalcedony, SiO2, assessed in mid infrared spectroscopy.

    PubMed

    Schmidt, Patrick; Fröhlich, François

    2011-05-01

    Chalcedony consists of hydroxylated 50-100 nanometre measuring α-quartz (SiO(2)) crystallites that lose their surface silanole groups (Si-OH) upon heating between 350°C and 600°C. The loss of the chalcedony's ≈1% of silanole groups allows for the healing of water related defects in the crystallites. We investigated these crystallographic transformations using Fourier Transform mid Infrared Spectroscopy in direct transmission, Attenuated Total Reflection (ATR) and the reflectivity. We found that an absorption band that is specific for chalcedony at 555 cm(-1) disappears gradually upon heating between 350°C and 600°C. The reduction of the band is correlated to the loss of surface silanoles. This result leads to the assignment of the band to free Si-O vibrations in non bridging Si-OH groups that have a lower natural frequency than Si-O vibrations in bridging Si-O-Si. The recognition of a silanole signal in the mid infrared allows for an easy, cheap and rapid recognition of hydroxyl in chalcedony.

  13. Electrical and crystallographic characterization of CdTe grown by the vapor transport method

    NASA Astrophysics Data System (ADS)

    Boone, J. L.; Cantwell, Gene; Harsch, W. C.; Thomas, J. E.; Foreman, B. A.

    1994-05-01

    Crystallographic and electrical characterization techniques were performed on CdTe single crystal samples grown by the sublimation and physical vapor transport (SPVT) technique. The SPVT growth process described here has resulted in the routine growth of 45-50 mm diameter, 250-300 g boules of single crystal CdTe. As-grown material is p-type in the 5-10 omega cm range. Etch pit densities (EPD) are nominally 7 x 10(exp 4) cm(exp -2) along the (111) growth direction and 3 x 10(exp 4) cm(exp -2) along the (111) direction. X-ray full width at half maximum (FWHM) on recent samples is 8.6 arc sec compared to 8.5 arc sec theoretical. The as-grown p-type material displays room temperature mobility in the 80-90 cm(exp 2) V(exp -1)s(exp -1) range and displays acceptor levels due to Cd vacancies 0.045 eV above the valence band and due to Cd vacancy-donor complexes 0.16 eV above the valence band. The boules are a constant diameter over most of their length (approx. 5.5 cm) and generally display no visual or x-ray detectable twins or grain boundaries.

  14. Large magnetoresistance induced by crystallographic defects in FexTaS2 single crystals

    NASA Astrophysics Data System (ADS)

    Chen, Chih-Wei; Morosan, Emilia; Morosan's Group Team

    The search for the materials that show large magnetoresistance and the mechanisms that induce it remains challenging in both experimental and theoretical aspects. The giant magnetoresistance in one class of materials, ferromagnetic conductors, is generally attributed to the misalignments of magnetic moments, which cause spin disorder scattering. Recently, very large magnetoresistance (>60 %) was discovered in the ferromagnetic Fe-intercalated transition metal dichalcogenide, Fe0.28TaS2 [Phys. Rev. B 91, 054426(2015)]. The mechanism that led to this large magnetoresistance was suggested to be due to the deviation of Fe concentration from commensurate values (1/4 or 1/3), which caused magnetic moments' misalignments. Here we report a study of FexTaS2 crystals with x close to the commensurate values. Our results qualitatively demonstrate that crystallographic defects significantly affect magnetoresistance in FexTaS2. This provides a way to search for large magnetoresistance in more intercalated transition metal dichalcogenides. This work is supported by the Department of Defense PECASE.

  15. Crystallographic Structure of Xanthorhodopsin, the Light-Driven Proton Pump With a Dual Chromophore

    SciTech Connect

    Luecke, H.; Schobert, B.; Stagno, J.; Imasheva, E.S.; Wang, J.M.; Balashov, S.P.; Lanyi, J.K.

    2009-05-19

    Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-{angstrom} resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK{sub a} of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as {approx}45%, and the 46{sup o} angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer.

  16. Surface energy-mediated construction of anisotropic semiconductor wires with selective crystallographic polarity

    NASA Astrophysics Data System (ADS)

    Sohn, Jung Inn; Hong, Woong-Ki; Lee, Sunghoon; Lee, Sanghyo; Ku, Jiyeon; Park, Young Jun; Hong, Jinpyo; Hwang, Sungwoo; Park, Kyung Ho; Warner, Jamie H.; Cha, Seungnam; Kim, Jong Min

    2014-07-01

    ZnO is a wide band-gap semiconductor with piezoelectric properties suitable for opto-electronics, sensors, and as an electrode material. Controlling the shape and crystallography of any semiconducting nanomaterial is a key step towards extending their use in applications. Whilst anisotropic ZnO wires have been routinely fabricated, precise control over the specific surface facets and tailoring of polar and non-polar growth directions still requires significant refinement. Manipulating the surface energy of crystal facets is a generic approach for the rational design and growth of one-dimensional (1D) building blocks. Although the surface energy is one basic factor for governing crystal nucleation and growth of anisotropic 1D structures, structural control based on surface energy minimization has not been yet demonstrated. Here, we report an electronic configuration scheme to rationally modulate surface electrostatic energies for crystallographic-selective growth of ZnO wires. The facets and orientations of ZnO wires are transformed between hexagonal and rectangular/diamond cross-sections with polar and non-polar growth directions, exhibiting different optical and piezoelectrical properties. Our novel synthetic route for ZnO wire fabrication provides new opportunities for future opto-electronics, piezoelectronics, and electronics, with new topological properties.

  17. Surface energy-mediated construction of anisotropic semiconductor wires with selective crystallographic polarity

    PubMed Central

    Sohn, Jung Inn; Hong, Woong-Ki; Lee, Sunghoon; Lee, Sanghyo; Ku, JiYeon; Park, Young Jun; Hong, Jinpyo; Hwang, Sungwoo; Park, Kyung Ho; Warner, Jamie H.; Cha, SeungNam; Kim, Jong Min

    2014-01-01

    ZnO is a wide band-gap semiconductor with piezoelectric properties suitable for opto-electronics, sensors, and as an electrode material. Controlling the shape and crystallography of any semiconducting nanomaterial is a key step towards extending their use in applications. Whilst anisotropic ZnO wires have been routinely fabricated, precise control over the specific surface facets and tailoring of polar and non-polar growth directions still requires significant refinement. Manipulating the surface energy of crystal facets is a generic approach for the rational design and growth of one-dimensional (1D) building blocks1234. Although the surface energy is one basic factor for governing crystal nucleation and growth of anisotropic 1D structures, structural control based on surface energy minimization has not been yet demonstrated56789. Here, we report an electronic configuration scheme to rationally modulate surface electrostatic energies for crystallographic-selective growth of ZnO wires. The facets and orientations of ZnO wires are transformed between hexagonal and rectangular/diamond cross-sections with polar and non-polar growth directions, exhibiting different optical and piezoelectrical properties. Our novel synthetic route for ZnO wire fabrication provides new opportunities for future opto-electronics, piezoelectronics, and electronics, with new topological properties. PMID:25017476

  18. Quartz microstructures and crystallographic preferred orientation: Which shear sense do they indicate?

    NASA Astrophysics Data System (ADS)

    Kilian, Rüdiger; Heilbronner, Renée; Stünitz, Holger

    2011-10-01

    Crystallographic preferred orientation (CPO) and shape fabrics of dynamically recrystallized quartz are currently used as shear sense indicators. We show that the CPO and shape fabric in a polyphase rock do not necessarily indicate the shear sense at the global scale of the shear zone but rather at the local scale of the deforming and recrystallizing quartz aggregates. In lower amphibolite facies shear zones in the Gran Paradiso metagranodiorite, magmatic quartz grains have recrystallized dynamically by subgrain rotation and grain boundary migration and deform inside a very fine-grained feldspar-mica matrix. The quartz CPO has a peripheral [c]-axis maximum inclined synthetically with the local shear sense. The orientation of the surface fabric is related to the orientation of the [c]-axis maximum and the microscopic shear sense in the quartz aggregate. The geometry of the surface fabric ranges from monoclinic to symmetric depending on the relative contribution of grain boundary migration. It is inferred that flow partitioning between the quartz aggregates and the matrix controls the local kinematics. CPOs are only reliable shear sense indicators in polyphase rocks if the most highly strained parts are analyzed where spin of the aggregates with respect to the shear zone boundary has ceased.

  19. Crystallization and initial crystallographic characterization of the Corynebacterium glutamicum nitrilotriacetate monooxygenase component A

    SciTech Connect

    Kim, Kyung-Jin; Kim, Sujin; Lee, Sujin; Kang, Beom Sik; Lee, Heung-Soo; Oh, Tae-Kwang; Kim, Myung Hee

    2006-11-01

    The Corynebacterium glutamicum NTA monooxygenase component A protein, which plays the central role in NTA biodegradation, was crystallized. The initial X-ray crystallographic characterization is reported. Safety and environmental concerns have recently dictated the proper disposal of nitrilotriacetate (NTA). Biodegradation of NTA is initiated by NTA monooxygenase, which is composed of two proteins: component A and component B. The NTA monooxygenase component A protein from Corynebacterium glutamicum was crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium sulfate as the precipitant. X-ray diffraction data were collected to a maximum resolution of 2.5 Å on a synchrotron beamline. The crystal belongs to the monoclinic space group C2, with unit-cell parameters a = 111.04, b = 98.51, c = 171.61 Å, β = 101.94°. The asymmetric unit consists of four molecules, corresponding to a packing density of 2.3 Å{sup 3} Da{sup −1}. The structure was solved by molecular replacement. Structure refinement is in progress.

  20. Surface energy-mediated construction of anisotropic semiconductor wires with selective crystallographic polarity.

    PubMed

    Sohn, Jung Inn; Hong, Woong-Ki; Lee, Sunghoon; Lee, Sanghyo; Ku, JiYeon; Park, Young Jun; Hong, Jinpyo; Hwang, Sungwoo; Park, Kyung Ho; Warner, Jamie H; Cha, SeungNam; Kim, Jong Min

    2014-07-14

    ZnO is a wide band-gap semiconductor with piezoelectric properties suitable for opto-electronics, sensors, and as an electrode material. Controlling the shape and crystallography of any semiconducting nanomaterial is a key step towards extending their use in applications. Whilst anisotropic ZnO wires have been routinely fabricated, precise control over the specific surface facets and tailoring of polar and non-polar growth directions still requires significant refinement. Manipulating the surface energy of crystal facets is a generic approach for the rational design and growth of one-dimensional (1D) building blocks. Although the surface energy is one basic factor for governing crystal nucleation and growth of anisotropic 1D structures, structural control based on surface energy minimization has not been yet demonstrated. Here, we report an electronic configuration scheme to rationally modulate surface electrostatic energies for crystallographic-selective growth of ZnO wires. The facets and orientations of ZnO wires are transformed between hexagonal and rectangular/diamond cross-sections with polar and non-polar growth directions, exhibiting different optical and piezoelectrical properties. Our novel synthetic route for ZnO wire fabrication provides new opportunities for future opto-electronics, piezoelectronics, and electronics, with new topological properties.

  1. Inhibition of Staphyloxanthin Virulence Factor Biosynthesis in Staphylococcus aureus: In Vitro, in Vivo, and Crystallographic Results†

    PubMed Central

    Song, Yongcheng; Liu, Chia-I; Lin, Fu-Yang; No, Joo Hwan; Hensler, Mary; Liu, Yi-Liang; Jeng, Wen-Yih; Low, Jennifer; Liu, George Y.; Nizet, Victor; Wang, Andrew H.-J.; Oldfield, Eric

    2009-01-01

    The gold color of Staphylococcus aureus is derived from the carotenoid staphyloxanthin, a virulence factor for the organism. Here, we report the synthesis and activity of a broad variety of staphyloxanthin biosynthesis inhibitors that inhibit the first committed step in its biosynthesis, condensation of two farnesyl diphosphate (FPP) molecules to dehydrosqualene, catalyzed by the enzyme dehydrosqualene synthase (CrtM). The most active compounds are phosphonoacetamides that have low nanomolar Ki values for CrtM inhibition and are active in whole bacterial cells and in mice, where they inhibit S. aureus disease progression. We also report the X-ray crystallographic structure of the most active compound, N-3-(3-phenoxyphenyl)propylphosphonoacetamide (IC50 = 8 nM, in cells), bound to CrtM. The structure exhibits a complex network of hydrogen bonds between the polar headgroup and the protein, while the 3-phenoxyphenyl side chain is located in a hydrophobic pocket previously reported to bind farnesyl thiodiphosphate (FsPP), as well as biphenyl phosphonosulfonate inhibitors. Given the good enzymatic, whole cell, and in vivo pharmacologic activities, these results should help guide the further development of novel antivirulence factor-based therapies for S. aureus infections. PMID:19456099

  2. Achievement of safer palladium nanocrystals by enlargement of {100} crystallographic facets.

    PubMed

    Chang, Yun; Li, Kai; Feng, Yanlin; Cheng, Yan; Zhang, Mei; Wang, Zuankai; Wu, Zhijian; Zhang, Haiyuan

    2017-10-05

    Developing catalytic and safe nanomaterials is very necessary for the reduction of potential risk to human health; however, this strategy has been found extremely challenging because the enhancement in catalytic activity of nanomaterials is inevitably accompanied with more potent cell injury. The relationship of physicochemical properties and biological responses in catalytic nanomaterials needs to be clarified at the nano-bio interface for achieving the safe application. Herein, high-energy crystallographic facets of palladium (Pd) nanocrystals that have been known to significantly contribute to the catalytic activity were introduced to attenuate the toxicity, and the underlying mechanism was unraveled. Polyhedral Pd nanocrystals with morphology evolution from truncated octahedron to cuboctahedron and cube were prepared for elaborately tuning the extents of high-energy {100} facets, and hierarchical in vitro and in vivo biological evaluation were performed to clarify that Pd nanocrystals exposed with the more {100} facets could show the less toxicity to cells and animals. Density functional theory (DFT) calculation revealed {100} facet exposure was endowed with a strong oxygen adsorption, which weakens the breakage of the water molecule and suppresses the hazardous water dissociation and hydroxyl radical generation, which was supported by electron spin resonance (ESR)-based radical evaluation and X-ray photoelectron spectroscopy (XPS)-based oxygen identification. This means high-energy facet-based catalytic Pd nanocrystals can deliver low toxicity due to their unique surface properties.

  3. Preliminary crystallographic analysis of a possible transcription factor encoded by the mimivirus L544 gene

    PubMed Central

    Ciaccafava, Alexandre; Lartigue, Audrey; Mansuelle, Pascal; Jeudy, Sandra; Abergel, Chantal

    2011-01-01

    Mimivirus is the prototype of a new family (the Mimiviridae) of nucleocytoplasmic large DNA viruses (NCLDVs), which already include the Poxviridae, Iridoviridae, Phycodnaviridae and Asfarviridae. Mimivirus specifically replicates in cells from the genus Acanthamoeba. Proteomic analysis of purified mimivirus particles revealed the presence of many subunits of the DNA-directed RNA polymerase II complex. A fully functional pre-transcriptional complex appears to be loaded in the virions, allowing mimivirus to initiate transcription within the host cytoplasm immediately upon infection independently of the host nuclear apparatus. To fully understand this process, a systematic study of mimivirus proteins that are predicted (by bioinformatics) or suspected (by proteomic analysis) to be involved in transcription was initiated by cloning and expressing them in Escherichia coli in order to determine their three-dimensional structures. Here, preliminary crystallographic analysis of the recombinant L544 protein is reported. The crystals belonged to the orthorhombic space group C2221 with one monomer per asymmetric unit. A MAD data set was used for preliminary phasing using the selenium signal present in a selenomethionine-substituted protein crystal. PMID:21821896

  4. Synthetic, crystallographic, and computational study of copper(II) complexes of ethylenediaminetetracarboxylate ligands.

    PubMed

    Matović, Zoran D; Miletić, Vesna D; Ćendić, Marina; Meetsma, Auke; van Koningsbruggen, Petra J; Deeth, Robert J

    2013-02-04

    Copper(II) complexes of hexadentate ethylenediaminetetracarboxylic acid type ligands H(4)eda3p and H(4)eddadp (H(4)eda3p = ethylenediamine-N-acetic-N,N',N'-tri-3-propionic acid; H(4)eddadp = ethylenediamine-N,N'-diacetic-N,N'-di-3-propionic acid) have been prepared. An octahedral trans(O(6)) geometry (two propionate ligands coordinated in axial positions) has been established crystallographically for the Ba[Cu(eda3p)]·8H(2)O compound, while Ba[Cu(eddadp)]·8H(2)O is proposed to adopt a trans(O(5)) geometry (two axial acetates) on the basis of density functional theory calculations and comparisons of IR and UV-vis spectral data. Experimental and computed structural data correlating similar copper(II) chelate complexes have been used to better understand the isomerism and departure from regular octahedral geometry within the series. The in-plane O-Cu-N chelate angles show the smallest deviation from the ideal octahedral value of 90°, and hence the lowest strain, for the eddadp complex with two equatorial β-propionate rings. A linear dependence between tetragonality and the number of five-membered rings has been established. A natural bonding orbital analysis of the series of complexes is also presented.

  5. Crystallographic features of the structure of a martensite packet of the NiMn intermetallic compound

    NASA Astrophysics Data System (ADS)

    Khlebnikova, Yu. V.; Egorova, L. Yu.; Rodionov, D. P.; Belosludtseva, E. S.; Kazantsev, V. A.

    2016-06-01

    Optical microscopy, scanning electron microscopy, and X-ray diffraction are used to show that a pseudosingle crystal forms upon cooling of an alloy Ni49Mn51 single crystal below the temperature of the β→θ (bcc → fct) transformation. At room temperature, this pseudosingle crystal has the structure of tetragonal L10 martensite with parameters a = 0.3732 nm and c = 0.3537 nm and a tetragonality c/ a = 0.94775. The temperatures of the forward and reverse B2 → L10 transformations are determined. The crystallographic features of martensite packet formation are analyzed. As shown by EBSD, neighboring martensite packets always have three kinds of tetragonal martensite plates, which are in a twin position and have different tetragonality axis directions. Repeated heating and quenching of the pseudosingle crystal result in recrystallization with the formation of coarse grains. The packet structure of the tetragonal martensite is retained in this case, and the sizes of the packets formed within a grain decrease by a factor of 2-3 as compared to the initial pseudosingle crystal.

  6. Microstructures and crystallographic preferred orientation of anorthosites from Oman ophiolite and the dynamics of melt lenses

    NASA Astrophysics Data System (ADS)

    Morales, Luiz F. G.; Boudier, FrançOise; Nicolas, Adolphe

    2011-04-01

    Microstructures and crystallographic preferred orientation (CPO) of anorthosite samples interlayered in the upper and lower gabbro sections in the Oman ophiolite were analyzed in this paper. In the anorthosites registering the dynamics of the melt lenses, foliation is flat lying and starts to develop a few meters below the root zone of the sheeted dike complex (RZSDC). Microstructures and CPO of these rocks were developed in response to four different mechanisms: (1) density-controlled settling of plagioclase on the lens floor, (2) deposition of anorthosites related to convection currents, (3) melt compaction, and (4) uncompacted melt accumulation. In these anorthosites, the poles to (010) of plagioclase are parallel to the flow plane of convection, whereas the [100] axes and poles to (001) express the convection flow direction and the axis of convection rolls, respectively. The effect of subsidence of melt lens floor is recorded immediately below the RZSDC and is characterized by the rapid (but progressive) development of dipping foliation and lineation, reflecting the increase of deformation downsection. The degree of foliation and CPO development in the anorthosites is directly related to the distance of the center of the melt lenses before the subsidence starts. Despite the uncertain origin of the anorthosites from the lower gabbro section, all the samples lost the magmatic microstructural characteristics and presently are reequilibrated aggregates. However, they still preserve plagioclase CPO, where some of these patterns present similarities with the anorthosites from the upper gabbro section, but no evidence of intracrystalline deformation under high temperatures.

  7. Past and Present Crystallographic Work at the NBS/NIST Reactor

    PubMed Central

    Santoro, A.

    2001-01-01

    Neutron diffraction at NBS/NIST started soon after the NBS reactor became operational in the summer of 1969. Since that time, literally hundreds of crystal structures have been determined and refined using single crystal and powder neutron diffraction data, collected with a variety of instruments. This work has been usually done in collaboration with other NBS/NIST divisions and/or universities and industrial laboratories. In parallel with the technical developments and the experimental work, also theoretical aspects of crystal geometry have been clarified, and significant improvements in the techniques of profile refinements have been made. It is therefore understandable that a comprehensive description of all the crystallographic studies carried out up to the present is impossible under the constraints of space and time imposed by a review of this type, and, in the following sections, we will limit ourselves to give, only a brief account of the topics which, in our opinion, represent the highlights of the work carried out at the reactor. PMID:27500055

  8. Purification, crystallization and preliminary crystallographic analysis of human cystathionine β-synthase

    PubMed Central

    Oyenarte, Iker; Majtan, Tomas; Ereño, June; Corral-Rodríguez, María Angeles; Kraus, Jan P.; Martínez-Cruz, Luis Alfonso

    2012-01-01

    Human cystathionine β-synthase (CBS) is a pyridoxal-5′-phosphate-dependent hemeprotein, whose catalytic activity is regulated by S-adenosylmethionine. CBS catalyzes the β-replacement reaction of homocysteine (Hcy) with serine to yield cystathionine. CBS is a key regulator of plasma levels of the thrombogenic Hcy and deficiency in CBS is the single most common cause of homocystinuria, an inherited metabolic disorder of sulfur amino acids. The properties of CBS enzymes, such as domain organization, oligomerization degree or regulatory mechanisms, are not conserved across the eukaryotes. The current body of knowledge is insufficient to understand these differences and their impact on CBS function and physiology. To overcome this deficiency, we have addressed the crystallization and preliminary crystallographic analysis of a protein construct (hCBS516–525) that contains the full-length CBS from Homo sapiens (hCBS) and just lacks amino-acid residues 516–525, which are located in a disordered loop. The human enzyme yielded crystals belonging to space group I222, with unit-cell parameters a = 124.98, b = 136.33, c = 169.83 Å and diffracting X-rays to a resolution of 3.0 Å. The crystal structure appears to contain two molecules in the asymmetric unit which presumably correspond to a dimeric form of the enzyme. PMID:23143240

  9. Improvement of Crystallographic Quality of Electroplated Copper Thin-Film Interconnections for Through-Silicon Vias

    NASA Astrophysics Data System (ADS)

    Suzuki, Ken; Murata, Naokazu; Saito, Naoki; Furuya, Ryosuke; Asai, Osamu; Miura, Hideo

    2013-04-01

    The relationship between the electrical properties and crystallographic quality (crystallinity) of electroplated copper thin-film interconnections was investigated. The crystallinity of the grains and grain boundaries of the interconnections was evaluated on the basis of the image quality (IQ) value obtained by electron back-scatter diffraction (EBSD) analysis. The electrical properties of the interconnections vary markedly depending on their crystallinity. The crystallinity also changed markedly as functions of electroplating conditions and the annealing temperature after electroplating. Although the electro migration (EM) resistance of the annealed interconnection was improved, stress-induced migration (SM) was activated by a high residual stress after annealing. To improve electrical reliability without heat treatment after electroplating, the effects of the seed layer under the interconnections on the crystallinity were investigated. As a result, the crystallinity was improved by changing the seed layer from Cu to Ru. In addition, the decrease in current density during electroplating also improved the crystallinity. Therefore, both introducing the Ru seed layer and decreasing the current density during electroplating are effective for developing highly reliable copper interconnections.

  10. Purification and crystallographic analysis of a FAD-dependent halogenase from Streptomyces sp. JCM9888.

    PubMed

    Zhao, Yanqun; Yan, Baohua; Yang, Ting; Jiang, Jian; Wei, Heng; Zhu, Xiaofeng

    2015-08-01

    A new FAD (flavin adenine dinucleotide)-dependent halogenase HalY from Streptomyces sp. JCM9888 was reported to be involved in the regioselective halogenation of adenine. HalY is a variant B FAD-dependent halogenase that is most similar to the halogenase PltA involved in pyoluteorin biosynthesis. This study reports the overexpression and purification of HalY with an N-terminal hexahistidine tag, followed by crystallization experiments and X-ray crystallographic analysis. HalY was purified as a monomer in solution and crystallized to give X-ray diffraction to a resolution of 1.7 Å. The crystal belonged to the monoclinic space group P21, with unit-cell parameters a = 41.4, b = 113.4, c = 47.6 Å, α = γ = 90, β = 107.4°, and contained one monomer of HalY in the asymmetric unit, with a calculated Matthews coefficient of 2.3 Å(3) Da(-1) and a solvent content of 46%. The structure of the halogenase CndH was used as a search model in molecular replacement to obtain the initial model of HalY. Manual model building and structure refinement of HalY are in progress.

  11. Crystallization and preliminary crystallographic study of carnosinase CN2 from mice

    SciTech Connect

    Yamashita, Tetsuo; Unno, Hideaki; Ujita, Sayuri; Otani, Hiroto; Okumura, Nobuaki; Hashida-Okumura, Akiko; Nagai, Katsuya; Kusunoki, Masami

    2006-10-01

    Mouse carnosinase was crystallized in complex with Zn{sup 2+} or Mn{sup 2+} and the complexes are undergoing structure determination by the MAD method. Mammalian tissues contain several histidine-containing dipeptides, of which l-carnosine is the best characterized and is found in various tissues including the brain and skeletal muscles. However, the mechanism for its biosynthesis and degradation have not yet been fully elucidated. Crystallographic study of carnosinase CN2 from mouse has been undertaken in order to understand its enzymatic mechanism from a structural viewpoint. CN2 was crystallized by the hanging-drop vapour-diffusion technique using PEG 3350 as a precipitant. Crystals were obtained in complex with either Mn{sup 2+} or Zn{sup 2+}. Both crystals of CN2 belong to the monoclinic space group P2{sub 1} and have almost identical unit-cell parameters (a = 54.41, b = 199.77, c = 55.49 Å, β = 118.52° for the Zn{sup 2+} complex crystals). Diffraction data were collected to 1.7 and 2.3 Å for Zn{sup 2+} and Mn{sup 2+} complex crystals, respectively, using synchrotron radiation. Structure determination is ongoing using the multiple-wavelength anomalous diffraction (MAD) method.

  12. Structure-energy relationship in barbituric acid: a calorimetric, computational, and crystallographic study.

    PubMed

    Roux, María Victoria; Temprado, Manuel; Notario, Rafael; Foces-Foces, Concepción; Emel'yanenko, Vladimir N; Verevkin, Sergey P

    2008-08-14

    This paper reports the value of the standard (p(o) = 0.1 MPa) molar enthalpy of formation in the gas phase at T = 298.15 K for barbituric acid. The enthalpies of combustion and sublimation were measured by static bomb combustion calorimetry and transference (transpiration) method in a saturated N2 stream and a gas-phase enthalpy of formation value of -(534.3 +/- 1.7) kJ x mol(-1) was determined at T = 298.15 K. G3-calculated enthalpies of formation are in very good agreement with the experimental value. The behavior of the sample as a function of the temperature was studied by differential scanning calorimetry, and a new polymorph of barbituric acid at high temperature was found. In the solid state, two anhydrous forms are known displaying two out of the six hydrogen-bonding patterns observed in the alkyl/alkenyl derivatives retrieved from the Cambridge Crystallographic Database. The stability of these motifs has been analyzed by theoretical calculations. X-ray powder diffraction technique was used to establish to which polymorphic form corresponds to the commercial sample used in this study and to characterize the new form at high temperature.

  13. Crystallographic structure of a photoreceptor protein at 2.4 A resolution.

    PubMed

    McRee, D E; Tainer, J A; Meyer, T E; Van Beeumen, J; Cusanovich, M A; Getzoff, E D

    1989-09-01

    The first essential step in protein photoreception is the capture and storage of energy from a photon. We have recently identified and isolated, from the purple photoautotrophic bacterium, Ectothiorhodospira halophila, a 13,000-dalton photoactive yellow protein (PYP) that has a photocycle with kinetics similar to sensory rhodopsin and a very high quantum efficiency. To study the structural chemistry of protein photoreception, we determined, refined, and analyzed the crystallographic structure of PYP at 2.4 A resolution and report here that it is composed of two perpendicular antiparallel beta-sheets that enclose the chromophore. Each of the 10 beta-strands of PYP is connected directly to its nearest neighbor with +1 topology. Globally, an asymmetric distribution of side chains places aromatic and acidic side chains in an ellipsoidal band around the chromophore with a cluster of basic side chains on one side. Locally, the electron density maps place an internal lysine and the chromophore in an apparent Schiff base linkage stabilized by a buried glutamate and a tyrosine side chain. To our knowledge, the atomic resolution structure of a protein with a reversible photoisomerization has not been reported previously. Furthermore, PYP may also represent a class of proteins that bind conjugated molecules and interact with a secondary receptor system.

  14. Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases.

    PubMed

    McGregor, Nicholas; Yin, Victor; Tung, Ching-Chieh; Van Petegem, Filip; Brumer, Harry

    2017-02-01

    The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  15. Expression, crystallization and preliminary crystallographic study of GluB from Corynebacterium glutamicum

    PubMed Central

    Liu, Qingbo; Li, Defeng; Hu, Yonglin; Wang, Da-Cheng

    2013-01-01

    GluB is a substrate-binding protein (SBP) which participates in the uptake of glutamic acid in Corynebacterium glutamicum, a Gram-positive bacterium. It is part of an ATP-binding cassette (ABC) transporter system. Together with the transmembrane proteins GluC and GluD and the cytoplasmic protein GluA, which couples the hydrolysis of ATP to the translocation of glutamate, they form a highly active glutamate-uptake system. As part of efforts to study the amino-acid metabolism, especially the metabolism of glutamic acid by C. glutamicum, a bacterium that is widely used in the industrial production of glutamic acid, the GluB protein was expressed, purified and crystallized, an X-ray diffraction data set was collected to a resolution of 1.9 Å and preliminary crystallographic analysis was performed. The crystal belonged to space group P3121 or P3221, with unit-cell parameters a = b = 82.50, c = 72.69 Å. PMID:23722846

  16. Y-TZP zirconia regeneration firing: Microstructural and crystallographic changes after grinding.

    PubMed

    Ryan, Daniel Patrick Obelenis; Fais, Laiza Maria Grassi; Antonio, Selma Gutierrez; Hatanaka, Gabriel Rodrigues; Candido, Lucas Miguel; Pinelli, Ligia Antunes Pereira

    2017-07-26

    This study evaluated microstructural and crystallographic phase changes after grinding (G) and regeneration firing/anneling (R) of Y-TZP ceramics. Thirty five bars (Lava(TM) and Ice Zirkon) were divided: Y-TZP pre-sintered, control (C), regeneration firing (R), dry grinding (DG), dry grinding+regeneration firing (DGR), wet grinding (WG) and wet grinding+regeneration firing (WGR). Grinding was conducted using a diamond bur and annealing at 1,000°C. The microstructure was analyzed by SEM and the crystalline phases by X-ray diffraction (XRD). XRD showed that pre-sintered specimens contained tetragonal and monoclinic phases, while groups C and R showed tetragonal, cubic and monoclinic phases. After grinding, the cubic phase was eliminated in all groups. Annealing (DGR and WGR) resulted in only tetragonal phase. SEM showed semi-circular cracks after grinding and homogenization of particles after annealing. After grinding, surfaces show tetragonal and monoclinic phases and R can be assumed to be necessary prior to porcelain layering when grinding is performed.

  17. Sr3Bi(PO4)3:Eu2+ Luminescence, Concentration Quenching and Crystallographic Sites

    NASA Astrophysics Data System (ADS)

    Gao, Shao-Jie; Li, Ting; Zhang, Zi-Cai; Li, Pan-Lai; Wang, Zhi-Jun; Yang, Zhi-Ping

    2014-07-01

    A blue emitting phosphor Sr3Bi(PO4)3:Eu2+ is synthesized by a high-temperature solid state method, and its luminescent property is investigated. Sr3Bi(PO4)3:Eu2+ can create blue emission under the 332 radiation excitation, and the prominent luminescence in blue (423 nm) due to the 4f 5d1 →4 f7 transition of the Eu2+ ion. The crystallographic sites of the Eu2+ ion in Sr3Bi(PO4)3 are analyzed, and the 420 and 440 nm emission peaks of the Eu2+ ion are assigned to the nine-coordination and eight-coordination, respectively. The emission intensity of Sr3Bi(PO4)3:Eu2+ is influenced by the Eu2+ doping content, and the concentration quenching effect is observed. The quenching mechanism is the dipole-dipole interaction, and the critical distance of energy transfer is calculated by the concentration quenching method to be approximately 1.72 nm.

  18. Crystallographic orientation and electrode nature are key factors for electric current generation by Geobacter sulfurreducens.

    PubMed

    Maestro, Beatriz; Ortiz, Juan M; Schrott, Germán; Busalmen, Juan P; Climent, Víctor; Feliu, Juan M

    2014-08-01

    We have investigated the influence of electrode material and crystallographic structure on electron transfer and biofilm formation of Geobacter sulfurreducens. Single-crystal gold-Au(110), Au(111), Au(210)-and platinum-Pt(100), Pt(110), Pt(111), Pt(210)-electrodes were tested and compared to graphite rods. G. sulfurreducens electrochemically interacts with all these materials with different attachment kinetics and final current production, although redox species involved in the electron transfer to the anode are virtually the same in all cases. Initial bacterial colonization was fastest on graphite up to the monolayer level, whereas gold electrodes led to higher final current densities. Crystal geometry was shown to have an important influence, with Au(210) sustaining a current density of up to 1442±101μAcm(-2) at the steady state, over Au(111) with 961±94μAcm(-2) and Au(110) with 944±89μAcm(-2). On the other hand, the platinum electrodes displayed the lowest performances, including Pt(210). Our results indicate that both crystal geometry and electrode material are key parameters for the efficient interaction of bacteria with the substrate and should be considered for the design of novel materials and microbial devices to optimize energy production.

  19. Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10).

    PubMed

    Park, HaJeung; González, Àlex L; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R; Fang, Pengfei; Guo, Min; Disney, Matthew D

    2015-06-23

    Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide (5')UCU(3')/(3')UCU(5') internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA.

  20. Changes of structure and crystallographic texture of cladding tubes from austenitic steel under thermal creep testing

    NASA Astrophysics Data System (ADS)

    Perlovich, Yu; Isaenkova, M.; Fesenko, V.; Dobrokhotov, P.; Tselishchev, A.

    2016-04-01

    The process of changes in structure and crystallographic texture of cladding tubes from austenitic steel ChS68 under thermal creep testing were studied. Testing of tubes was conducted at the temperature 700 oC in the air by their stretching in axial direction under the stress 160 MPa until rupture. By data of phase and texture analysis a number of processes, accompanying plastic deformation of tubes during thermal creep tests at elevated temperature, were identified. The main texture components of original tube, as well as texture components of different parts of the tested tube are {110}<001> and {112}<111¯>. In the rupture zone the component of the texture of tension with axis <111> along the tube axis becomes stronger. This effect is connected with activation of dislocation slip in the deformed area of tested tube near the new-formed neck. At the same time the character of texture changes in the zone of tube rupture indicates to development of the dynamic recrystallization, conditioned by the total influence of all factors, which control the passage in the tube of thermal creep. In addition, it was revealed the activation of martensitic transformations in the zone of maximal deformation of tube as a result of its creep tests.

  1. Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

    PubMed

    Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

    2011-04-13

    Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Heterogeneous crystal growth of methane hydrate on its sII [001] crystallographic face.

    PubMed

    Vatamanu, Jenel; Kusalik, Peter G

    2008-02-28

    This paper presents a systematic molecular simulation study of the heterogeneous crystal growth of methane hydrate sII from supersaturated aqueous methane solutions. The growth of sII hydrate on the [001] crystallographic face is achieved through utilization of a recently proposed methodology, and rates of crystal growth of 1 A/ns were sustained for the molecular models and specific conditions employed in this work. Characteristics of the crystals grown as well as properties and structure of the interface are examined. Water cages with a 5(12)6(3) arrangement, which are improper to both sI and sII structures, are identified during the heterogeneous growth of sII methane hydrate. We show that the growth of a [001] face of sII hydrate can produce an sI crystalline structure, confirming that cross-nucleation of methane hydrate structures is possible. Defects consisting of two methane molecules trapped in large 5(12)6(4) cages and water molecules trapped in small and large cages are observed, where in one instance we have found a large 5(12)6(4) cage containing three water molecules.

  3. Functional mechanisms of the cellular prion protein (PrP(C)) associated anti-HIV-1 properties.

    PubMed

    Alais, Sandrine; Soto-Rifo, Ricardo; Balter, Vincent; Gruffat, Henri; Manet, Evelyne; Schaeffer, Laurent; Darlix, Jean Luc; Cimarelli, Andrea; Raposo, Graça; Ohlmann, Théophile; Leblanc, Pascal

    2012-04-01

    The cellular prion protein PrP(C)/CD230 is a GPI-anchor protein highly expressed in cells from the nervous and immune systems and well conserved among vertebrates. In the last decade, several studies suggested that PrP(C) displays antiviral properties by restricting the replication of different viruses, and in particular retroviruses such as murine leukemia virus (MuLV) and the human immunodeficiency virus type 1 (HIV-1). In this context, we previously showed that PrP(C) displays important similarities with the HIV-1 nucleocapsid protein and found that PrP(C) expression in a human cell line strongly reduced HIV-1 expression and virus production. Using different PrP(C) mutants, we report here that the anti-HIV-1 properties are mostly associated with the amino-terminal 24-KRPKP-28 basic domain. In agreement with its reported RNA chaperone activity, we found that PrP(C) binds to the viral genomic RNA of HIV-1 and negatively affects its translation. Using a combination of biochemical and cell imaging strategies, we found that PrP(C) colocalizes with the virus assembly machinery at the plasma membrane and at the virological synapse in infected T cells. Depletion of PrP(C) in infected T cells and microglial cells favors HIV-1 replication, confirming its negative impact on the HIV-1 life cycle.

  4. Marginal activity of progesterone receptor B (PR-B) in dogs but high incidence of mammary cancer.

    PubMed

    Gracanin, Ana; Voorwald, Fabiana A; van Wolferen, Monique; Timmermans-Sprang, Elpetra; Mol, Jan A

    2014-10-01

    Progesterone plays an important role in the normal development and carcinogenesis of the mammary gland. In vitro studies have shown that the canine progesterone receptor B (cPR-B), which is essential for mammary development in the mouse, does not transactivate reporter constructs containing progesterone response elements. Therefore, the question was raised whether the cPR-B was completely devoid of transactivation potential of endogenous progesterone regulated genes. Canine mammary cell lines expressing doxycycline-inducible cPR-B, human PR-B or a chimera in which the canine B-upstream segment (BUS) was replaced by a human BUS were treated for 24h with doxycycline, progesterone or a combination of the two. The expression profiling was subsequently performed using a dog-specific microarray and miRNA primers. Incubation of stably transfected cell lines with doxycycline or progesterone alone, did not change expression of any endogenous gene. Expression of activated human PR-B or the chimera of human BUS with the canine PR resulted in differential expression of >500 genes whereas the activated cPR-B regulated only a subset of 40 genes and to a limited extent. The relevance of the marginal transactivation potential or the consequence of a lack of cPR-B function for the carcinogenesis of mammary gland tumors is discussed.

  5. Pentavalent lanthanide nitride-oxides: NPrO and NPrO(-) complexes with N≡Pr triple bonds.

    PubMed

    Hu, Shu-Xian; Jian, Jiwen; Su, Jing; Wu, Xuan; Li, Jun; Zhou, Mingfei

    2017-05-01

    The neutral molecule NPrO and its anion NPrO(-) are produced via co-condensation of laser-ablated praseodymium atoms with nitric oxide in a solid neon matrix. Combined infrared spectroscopy and state-of-the-art quantum chemical calculations confirm that both species are pentavalent praseodymium nitride-oxides with linear structures that contain Pr≡N triple bonds and Pr=O double bonds. Electronic structure studies show that the neutral NPrO molecule features a 4f(0) electron configuration and a Pr(v) oxidation state similar to that of the isoelectronic PrO2(+) ion, while its NPrO(-) anion possesses a 4f(1) electron configuration and a Pr(iv) oxidation state. The neutral NPrO molecule is thus a rare lanthanide nitride-oxide species with a Pr(v) oxidation state, which follows the recent identification of the first Pr(v) oxidation state in the PrO2(+) and PrO4 complexes (Angew. Chem. Int. Ed., 2016, 55, 6896). This finding indicates that lanthanide compounds with oxidation states of higher than +IV are richer in chemistry than previously recognized.

  6. Frontobasal gray matter loss is associated with the TREM2 p.R47H variant

    PubMed Central

    Luis, E.O.; Ortega-Cubero, S.; Lamet, I.; Razquin, C.; Cruchaga, C.; Benitez, B.A.; Lorenzo, E.; Irigoyen, J.; Pastor, M.A.; Pastor, P.

    2014-01-01

    A rare heterozygous TREM2 variant p.R47H (rs75932628) has been associated with an increased risk for Alzheimer disease (AD). We aimed to investigate the clinical presentation, neuropsychological profile and regional pattern of gray matter and white matter loss associated with the TREM2 variant p.R47H, and to establish which regions best differentiate p.R47H carriers from noncarriers in two sample sets (Spanish and ADNI1). This was a cross-sectional study including a total number of 16 TREM2 p.R47H carriers diagnosed with AD or mild cognitive impairment (MCI), 75 AD p.R47H noncarriers and 75 cognitively intact TREM2 p.R47H noncarriers. Spanish AD TREM2 p.R47H carriers showed apraxia (9 out of 9) and psychiatric symptoms such as personality changes, anxiety, paranoia or fears more frequently than in AD noncarriers (corrected p< 0.05). For gray matter and white matter volumetric brain magnetic resonance imaging (MRI) voxel-wise analyses, we used statistical parametric mapping (SPM8) based on the General Linear Model. We used 3 different design matrices with a full factorial design. Voxel-based morphometry (VBM) analyses were performed separately in the two sample sets. The absence of inter-set statistical differences allowed us to perform joint and conjunction analyses. Independent VBM analysis of the Spanish set as well as conjunction and joint analyses revealed substantial gray matter loss in orbitofrontal cortex and anterior cingulate cortex with relative preservation of parietal lobes in AD/mild cognitive impairment (MCI) TREM2 p.R47H carriers, suggesting that TREM2 p.R47H variant is associated with certain clinical and neuroimaging AD features in addition to the increased TREM2 p.R47H atrophy in temporal lobes described previously. The high frequency of pathological behavioural symptoms, combined with a preferential fronto-basal gray matter cortical loss, suggests that frontobasal and temporal regions could be more susceptible to the deleterious biological

  7. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models.

    PubMed

    Perrakis, A; Sixma, T K; Wilson, K S; Lamzin, V S

    1997-07-01

    wARP is a procedure that substantially improves crystallographic phases (and subsequently electron-density maps) as an additional step after density-modification methods such as solvent flattening and averaging. The initial phase set is used to create a number of dummy atom models which are subjected to least-squares or maximum-likelihood refinement and iterative model updating in an automated refinement procedure (ARP). Averaging of the phase sets calculated from the refined output models and weighting of structure factors by their similarity to an average vector results in a phase set that improves and extends the initial phases substantially. An important requirement is that the native data have a maximum resolution beyond approximately 2.4 A. The wARP procedure shortens the time-consuming step of model building in crystallographic structure determination and helps to prevent the introduction of errors.

  8. Crystallographic Stability of Metastable Phase Formed by Containerless Processing in REFeO3 (RE: Rare-Earth Element)

    NASA Technical Reports Server (NTRS)

    Kuribayashi, Kazuhiko; Kumar, M. S. Vijaya

    2012-01-01

    Undercooling a melt often facilitates a metastable phase to nucleate preferentially. Although the classical nucleation theory shows that the most critical factor for forming a metastable phase is the interface free energy, the crystallographic stability is also indispensable for the phase to be frozen at ambient temperature. In compound materials such as oxides, authors have suggested that the decisive factors for forming a critical nucleus are not only the free energy difference but also the difference of the entropy of fusion between stable and metastable phases. In the present study, using REFeO3 (RE: rare-earth element) as a model material, we investigate the formation of a metastable phase from undercooled melts with respect to the competitive nucleation and crystallographical stabilities of both phases.

  9. The effects of deposition parameters on surface morphology and crystallographic orientation of electroless Ni-B coatings

    NASA Astrophysics Data System (ADS)

    Bulbul, Ferhat

    2011-02-01

    Electroless Ni-B coatings were deposited on AISI 304 stainless steels by electroless deposition method, which was performed for nine different test conditions at various levels of temperature, concentration of NaBH4, concentration of NiCl2, and time, using the Taguchi L9(34) experimental method. The effects of deposition parameters on the crystallographic orientation of electroless Ni-B coatings were investigated using SEM and XRD equipment. SEM analysis revealed that the Ni-B coatings developed six types (pea-like, maize-like, primary nodular, blackberry-like or grapes-like, broccoli-like, and cauliflower-like) of morphological structures depending on the deposition parameters. XRD results also showed that these structures exhibited different levels of amorphous character. The concentration of NaBH4 had the most dominant effect on the morphological and crystallographic development of electroless Ni-B coatings.

  10. Development of <100> crystallographic texture in magnetostrictive Fe-Ga microwires produced by in-rotating water spinning method

    NASA Astrophysics Data System (ADS)

    Lupu, N.; Lostun, M.; Corodeanu, S.; Chiriac, H.

    2011-04-01

    Fe-22.5 at.% Ga microwires with diameters ranging from 150 to 350 μm were produced by the in-rotating water spinning (INROWASP) method. All microwires were found to be polycrystalline and developed <100> crystallographic textures along the wire symmetry axis. The microwires are magnetically soft with very little coercivity and reach saturation magnetization values of 1.5 T. The largest magnetostriction value, of 185 ppm, is obtained for microwires with a diameter of 260 μm, in the absence of prestress and stress-annealing treatments. The increase/decrease of the microwires' diameter above/below 260 μm results in smaller magnetostriction values, with the minimum of 130 ppm being reached for microwires of 150 μm. The unique properties of microwires made by the INROWASP method make them attractive for further production of Fe-Ga long, continuous microwires with a specific crystallographic texture.

  11. Iron distances in hemoglobin: comparison of x-ray crystallographic and extended x-ray absorption fine structure studies

    SciTech Connect

    Fermi, G.; Perutz, M.F.; Shulman, R.G.

    1987-09-01

    A comparison is presented of the structures obtained around the iron atom in deoxyhemoglobin (Hb). The data come from extended x-ray absorption fine structure (EXAFS) studies of the iron, which gave Fe-porphyrin nitrogen distances of 2.06 +- 0.01 A, and from the most recent high-resolution x-ray crystallographic study, which gave exactly the same distance-2.06 +- 0.02 A. The distance of Fe above the plane of the porphyrin nitrogens was 0.38 +- 0.04 A from the crystallographic study; this value is not far from the upper limit of the distances 0.20 +- /sub 0.20//sup 0.10/ A calculated from the EXAFS experiment by triangulation. These distances above the nitrogen plane are shorter than those estimated in the earliest x-ray structures

  12. Crystallographic parameters and composition of unit cells of macrocyclic complexes of Zn and Co with polygalacturonic acid

    NASA Astrophysics Data System (ADS)

    Kaisheva, N. Sh.; Kaishev, A. Sh.

    2013-12-01

    Zinc and cobalt(II) pectinates are found to crystallize in hexagonal syngony. The parameters of unit cells of zinc ( a = 10.72 Å, c = 3.79 Å) and cobalt(II) ( a = 29.89 Å, c = 10.57 Å) pectinates are determined. The correctness of indexing is confirmed by the agreement between the experimental and calculated values of the crystallographic parameters, and by the number of formula units per unit cell.

  13. Crystallographic Features and State Stability of the Decagonal Quasicrystal in the Al-Co-Cu Alloy System

    NASA Astrophysics Data System (ADS)

    Nakayama, Kei; Mizutani, Akito; Koyama, Yasumasa

    2016-11-01

    In the Al-Co-Cu alloy system, both the decagonal quasicrystal with the space group of Poverline{10}m2 and its approximant Al13Co4 phase with monoclinic Cm symmetry are present around 20 at. % Co-10 at. % Cu. In this study, we examined the crystallographic features of prepared Al-(30 - x) at. % Co-x at. % Cu samples mainly by transmission electron microscopy in order to make clear the crystallographic relation between the decagonal quasicrystal and the monoclinic Al13Co4 structure. The results revealed a coexistence state consisting of decagonal quasicrystal and approximant Al13Co4 regions in Al-20 at. % Co-10 at. % Cu alloy samples. With the help of the coexistence state, the orientation relationship was established between the monoclinic Al13Co4 structure and the decagonal quasicrystal. In the determined relationship, the crystallographic axis in the quasicrystal was found to be parallel to the normal direction of the (010)m plane in the Al13Co4 structure, where the subscript m denotes the monoclinic system. Based on data obtained experimentally, the state stability of the decagonal quasicrystal was also examined in terms of the Hume-Rothery (HR) mechanism on the basis of the nearly-free-electron approximation. It was found that a model based on the HR mechanism could explain the crystallographic features such as electron diffraction patterns and atomic arrangements found in the decagonal quasicrystal. In other words, the HR mechanism is most likely appropriate for the stability of the decagonal quasicrystal in the Al-Co-Cu alloy system.

  14. Integrating Behavioral HIV Interventions into Biomedical Prevention Trials with Youth: Lessons from Chicago’s Project PrEPare

    PubMed Central

    Hosek, Sybil G.; Green, Keith R.; Siberry, George; Lally, Michelle; Balthazar, Christopher; Serrano, Pedro A.; Kapogiannis, Bill

    2013-01-01

    On the heels of several trials demonstrating the efficacy of pre-exposure prophylaxis (PrEP) and the recent approval by the FDA of the supplemental indication for Truvada as PrEP, researchers, advocates, and community providers are calling for the investigation of implementation strategies that combine behavioral interventions with biomedical prevention. This paper describes the modification and integration of an evidence-based group-level intervention into a small PrEP pilot trial with young men who have sex with men (YMSM). The behavioral intervention as well as ongoing risk reduction counseling sessions were found to be highly acceptable among a sample of racially diverse YMSM. PMID:24223514

  15. Low-temperature specific heat of the heavy-fermion superconductor PrOs4Sb12.

    PubMed

    Vollmer, R; Faisst, A; Pfleiderer, C; V Löhneysen, H; Bauer, E D; Ho, P-C; Zapf, V; Maple, M B

    2003-02-07

    We report the magnetic field dependence of the specific-heat C of single crystals of the first Pr-based heavy-fermion superconductor Pr(Os4Sb12. The variation of C at low temperature and the magnetic phase diagram inferred from C, the resistivity and magnetization provide compelling evidence of a doublet ground state. Two distinct superconducting anomalies in C indicate an unconventional superconducting state, where the splitting may arise from a weak lifting of the ground state degeneracy. In combination this identifies Pr(Os4Sb12 as a strong contender for quadrupolar pairing, i.e., superconductivity that is neither electron-phonon nor magnetically mediated.

  16. The isomeric structure of 132Pr

    NASA Astrophysics Data System (ADS)

    Alharshan, G. A.; Cullen, D. M.; Taylor, M. J.; Procter, M. G.; Lumley, N. M.; Grahn, T.; Greenless, P. T.; Hauschild, K.; Herzon, A.; Jakobsson, U.; Jones, P. M.; Julin, R.; Juutinen, S.; Ketelhut, S.; Leino, M.; Lopez-Martens, A.; Nieminen, P.; Pantanen, J.; Peura, P.; Rahkila, P.; Rinta-Antilla, S.; Ruatsalainen, P.; Sandzelius, H. M.; Saren, J.; Scholey, C.; Sorri, J.; Stolze, S.; Uusitalo, J.

    2012-09-01

    The isomeric structure of the neutron deficient nucleus 132Pr, located in the rare-earth region of the nuclear chart, has been studied with the 98Mo(40Ar,5pn)132Pr reaction at beam energies of 150, 158 and 165 MeV. The experiment was performed at the University of Jyväskylä, Finland where the 40Ar beam was accelerated onto the target by the K130 cyclotron. The JUROGAM II HPGe detector array was employed in conjunction with the RITU gas-filled recoil separator. The focal-plane chamber housed a multi wire proportional counter and a position-sensitive silicon strip detector used for the implantation and identification of recoiling nuclei. The recoil-isomer tagging technique was used to correlate the delayed decays, measured in the Planar and Clover detectors of the GREAT spectrometer, with the known prompt transitions in 132Pr. Two new delayed transitions have been observed at energies of 102 and 118 keV. The corresponding X ray peaks are consistent with Pr Kα and Kβ X rays with energies of 35.63 and 40.91 keV, respectively. The half-life of the newly established isomeric state, from which the 102 and 118-keV transitions proceed, has been measured to be 2.5(3) μs.

  17. Using PR Tools to Boost Recruitment.

    ERIC Educational Resources Information Center

    Rabbino, Irma L.

    1979-01-01

    Public relations and admissions are shown to be related. It is not necessary to use exotic PR tools to recruit students. Some suggestions include: the magic of marketing; national, local and hometown media; publications; filmstrips or cassettes; fairs and festivals; public service; and logo buttons, decals, etc. (MLW)

  18. Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

    SciTech Connect

    Hughes, Ronny C.; McFeeters, Hana; Coates, Leighton; McFeeters, Robert L.

    2014-10-15

    The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6122 with unit-cell parameters a = b = 63.62,c = 155.20 Å, α = β = 90, γ = 120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da-1. The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.

  19. Modeling the effects of ion dose and crystallographic symmetry on the morphological evolution of embedded precipitates under thermal annealing

    NASA Astrophysics Data System (ADS)

    Li, Kun-Dar

    2014-10-01

    Thermal annealing is one of the most common techniques to synthesize embedded precipitates by ion implantation process. In this study, an anisotropic phase field model is presented to investigate the effects of ion dose and crystallographic symmetry on the morphological formation and evolution of embedded precipitates during post-implantation thermal annealing process. This theoretical model provides an efficient numerical approach to understand the phenomenon of faceted precipitates formation by ion implantation. As a theoretical analysis, the interfacial energy and diffusion kinetics play prominent roles in the mechanism of atomic diffusion for the precipitates formation. With a low ion dose, faceted precipitates are developed by virtue of the anisotropic interfacial energy. As an increase of ion dose, connected precipitates with crystallographic characters on the edge are appeared. For a high ion dose, labyrinth-like nanostructures of precipitates are produced and the characteristic morphology of crystallographic symmetry becomes faint. These simulation results for the morphological evolutions of embedded precipitates by ion implantation are corresponded with many experimental observations in the literatures. The quantitative analyses of the simulations are also well described the consequence of precipitates formation under different conditions.

  20. Coupled Crystal Plasticity-Phase Field Fracture Simulation Study on Damage Evolution Around a Void: Pore Shape Versus Crystallographic Orientation

    NASA Astrophysics Data System (ADS)

    Diehl, Martin; Wicke, Marcel; Shanthraj, Pratheek; Roters, Franz; Brueckner-Foit, Angelika; Raabe, Dierk

    2017-05-01

    Various mechanisms such as anisotropic plastic flow, damage nucleation, and crack propagation govern the overall mechanical response of structural materials. Understanding how these mechanisms interact, i.e. if they amplify mutually or compete with each other, is an essential prerequisite for the design of improved alloys. This study shows—by using the free and open source software DAMASK (the Düsseldorf Advanced Material Simulation Kit)—how the coupling of crystal plasticity and phase field fracture methods can increase the understanding of the complex interplay between crystallographic orientation and the geometry of a void. To this end, crack initiation and propagation around an experimentally obtained pore with complex shape is investigated and compared to the situation of a simplified spherical void. Three different crystallographic orientations of the aluminum matrix hosting the defects are considered. It is shown that crack initiation and propagation depend in a non-trivial way on crystallographic orientation and its associated plastic behavior as well as on the shape of the pore.

  1. Study on the crystallographic orientation relationship and formation mechanism of reversed austenite in economical Cr12 super martensitic stainless steel

    SciTech Connect

    Ye, Dong; Li, Shaohong; Li, Jun; Jiang, Wen; Su, Jie; Zhao, Kunyu

    2015-11-15

    Effect of carbides and crystallographic orientation relationship on the formation mechanism of reversed austenite of economical Cr12 super martensitic stainless steel (SMSS) has been investigated mainly by transmission electron microscopy (TEM) and electron backscatter diffraction (EBSD). The results indicate that the M{sub 23}C{sub 6} precipitation and the formation of the reversed austenite have the interaction effect during tempering process in SMSS. The reversed austenite forms intensively at the sub-block boundary and the lath boundary within a misorientation range of 0–60°. M{sub 23}C{sub 6} has the same crystallographic orientation relationship with reversed austenite. There are two different kinds of formation modes for reversed austenite. One is a nondiffusional shear reversion; the other is a diffusion transformation. Both are strictly limited by crystallographic orientation relationship. The austenite variants are limited to two kinds within one packet and five kinds within one prior austenite grain. - Highlights: • Reversed austenite forms at martensite boundaries with misorientation of 0–60° • M{sub 23}C{sub 6} precipitation and reversed austenite formation have the interaction effect. • Two austenite variants with different orientations can be formed inside a packet. • Two reversed austenite formation modes: shear reversion; diffusion transformation.

  2. Coupled Crystal Plasticity-Phase Field Fracture Simulation Study on Damage Evolution Around a Void: Pore Shape Versus Crystallographic Orientation

    NASA Astrophysics Data System (ADS)

    Diehl, Martin; Wicke, Marcel; Shanthraj, Pratheek; Roters, Franz; Brueckner-Foit, Angelika; Raabe, Dierk

    2017-03-01

    Various mechanisms such as anisotropic plastic flow, damage nucleation, and crack propagation govern the overall mechanical response of structural materials. Understanding how these mechanisms interact, i.e. if they amplify mutually or compete with each other, is an essential prerequisite for the design of improved alloys. This study shows—by using the free and open source software DAMASK (the Düsseldorf Advanced Material Simulation Kit)—how the coupling of crystal plasticity and phase field fracture methods can increase the understanding of the complex interplay between crystallographic orientation and the geometry of a void. To this end, crack initiation and propagation around an experimentally obtained pore with complex shape is investigated and compared to the situation of a simplified spherical void. Three different crystallographic orientations of the aluminum matrix hosting the defects are considered. It is shown that crack initiation and propagation depend in a non-trivial way on crystallographic orientation and its associated plastic behavior as well as on the shape of the pore.

  3. Quartz deformation mechanisms during Barrovian metamorphism: Implications from crystallographic orientation of different generations of quartz in pelites

    NASA Astrophysics Data System (ADS)

    Rahimi-Chakdel, A.; Boyle, A. P.; Prior, D. J.

    2006-12-01

    The behaviour of quartz during metamorphism is studied based on two case studies from the Barrovian terrains of Sulitjelma in arctic Scandinavia and Loch Tay in the Central Highlands Dalradian of Scotland. Both terrains preserve evidence for metamorphism in pelites involving nucleation and growth of garnet at different times in the deformation history. Data are presented on the size, shape and crystallographic orientation of quartz preserved as inclusions in garnet and as grains in the surrounding matrix. While quartz-grains remain small and dispersed between mica grains, deformation appears to be dominated by grain-boundary sliding accommodated by dissolution-precipitation. At amphibolite facies, textural coarsening occurs by dissolution of small quartz grains and growth of larger quartz grains, coupled with segregation of quartz from mica. As a result, quartz deforms by dislocation creep, developing crystallographic preferred orientations (CPO) consistent with both coaxial and non-coaxial strain. Quartz CPOs with <0001> axes lying parallel to foliation and stretching direction are commonly developed, and best explained by mechanical rotation of inequant (detrital?) quartz grains. There is no evidence for selective entrapment of quartz inclusions in garnet on the basis of quartz crystallographic orientation.

  4. Measuring Acceptability and Preferences for Implementation of Pre-Exposure Prophylaxis (PrEP) Using Conjoint Analysis: An Application to Primary HIV Prevention Among High Risk Drug Users.

    PubMed

    Shrestha, Roman; Karki, Pramila; Altice, Frederick L; Dubov, Oleksandr; Fraenkel, Liana; Huedo-Medina, Tania; Copenhaver, Michael

    2017-07-10

    Although people who use drugs (PWUD) are one of the key risk populations who could benefit from the use of pre-exposure prophylaxis (PrEP), to date, little attention has been given to incorporating PrEP into HIV prevention approaches targeting this underserved group. This study investigated the acceptability of PrEP based on a number of known PrEP attributes among high-risk PWUD in a drug treatment setting. A total of 400 HIV-negative PWUD, who reported drug- and/or sex-related risk behaviors were recruited from a methadone clinic to complete a stated preference (full-profile conjoint) survey. Participants ranked the eight hypothetical PrEP program scenarios with varied combinations of six attributes related to PrEP (cost, dosing, efficacy, side-effects, treatment setting, and frequency of HIV testing). SPSS conjoint procedure was used to estimate the relative importance of each attribute and preferences across eight possible PrEP delivery programs. PrEP acceptability ranged from 30.6 to 86.3% with a mean acceptability of 56.2% across the eight hypothetical PrEP program scenarios. The PrEP program scenario with the highest acceptability had the following attribute levels: insurance covered, daily dosing, 95% effective, no side-effects, treatment at HIV clinic, and HIV testing needed every 6 months. The cost associated with PrEP was the most important attribute (relative importance score: RIS = 38.8), followed by efficacy (RIS = 20.5) and side effects (RIS = 11.9); other attributes had no significant effect. Our findings reported a high acceptability of PrEP in response to different PrEP program scenarios with different attribute profiles. As the result of having this information, researchers and policymakers will be better equipped for evidence informed targeting and dissemination efforts to optimize PrEP uptake among this underserved population.

  5. Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin.

    PubMed

    Sliwiak, Joanna; Dauter, Zbigniew; Jaskolski, Mariusz

    2016-01-01

    Hyp-1, a PR-10-fold protein from Hypericum perforatum, was crystallized in complex with melatonin (MEL). The structure confirms the conserved protein fold and the presence of three unusual ligand binding sites, two of which are internal chambers (1,2), while the third one (3) is formed as an invagination of the protein surface. The MEL ligand in site 1 is well defined while that in site 3 seems to be rotating between the side chains of Lys33 and Tyr150 that act as a molecular vise. The patch of electron density in site 2 does not allow unambiguous modeling of a melatonin molecule but suggests a possible presence of its degradation product. This pattern of ligand occupation is reproducible in repeated crystallization/structure determination experiments. Although the binding of melatonin by Hyp-1 does not appear to be very strong (for example, MEL cannot displace the artificial fluorescence probe ANS), it is strong enough to suggest a physiological role of this interaction. For example, trans-zeatin, which is a common ligand of PR-10 proteins, does not overcompete melatonin for binding to Hyp-1 as it does not affect the crystallization process of the Hyp-1/MEL complex, and among a number of potential natural mediators tested, melatonin was the only one to form a crystalline complex with Hyp-1 with the use of standard crystallization screens. Hyp-1 is the second protein in the Protein Data Bank for which melatonin binding has been demonstrated crystallographically, the first one being human quinone reductase.

  6. Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin

    PubMed Central

    Sliwiak, Joanna; Dauter, Zbigniew; Jaskolski, Mariusz

    2016-01-01

    Hyp-1, a PR-10-fold protein from Hypericum perforatum, was crystallized in complex with melatonin (MEL). The structure confirms the conserved protein fold and the presence of three unusual ligand binding sites, two of which are internal chambers (1,2), while the third one (3) is formed as an invagination of the protein surface. The MEL ligand in site 1 is well defined while that in site 3 seems to be rotating between the side chains of Lys33 and Tyr150 that act as a molecular vise. The patch of electron density in site 2 does not allow unambiguous modeling of a melatonin molecule but suggests a possible presence of its degradation product. This pattern of ligand occupation is reproducible in repeated crystallization/structure determination experiments. Although the binding of melatonin by Hyp-1 does not appear to be very strong (for example, MEL cannot displace the artificial fluorescence probe ANS), it is strong enough to suggest a physiological role of this interaction. For example, trans-zeatin, which is a common ligand of PR-10 proteins, does not overcompete melatonin for binding to Hyp-1 as it does not affect the crystallization process of the Hyp-1/MEL complex, and among a number of potential natural mediators tested, melatonin was the only one to form a crystalline complex with Hyp-1 with the use of standard crystallization screens. Hyp-1 is the second protein in the Protein Data Bank for which melatonin binding has been demonstrated crystallographically, the first one being human quinone reductase. PMID:27242869

  7. Different structural stability and toxicity of PrP(ARR) and PrP(ARQ) sheep prion protein variants.

    PubMed

    Paludi, Domenico; Thellung, Stefano; Chiovitti, Katia; Corsaro, Alessandro; Villa, Valentina; Russo, Claudio; Ianieri, Adriana; Bertsch, Uwe; Kretzschmar, Hans A; Aceto, Antonio; Florio, Tullio

    2007-12-01

    The polymorphisms at amino acid residues 136, 154, and 171 in ovine prion protein (PrP) have been associated with different susceptibility to scrapie: animals expressing PrP(ARQ) [PrP(Ala136/Arg154/Gln171)] show vulnerability, whereas those that express PrP(ARR) [PrP(Ala136/Arg154/Arg171)] are resistant to scrapie. The aim of this study was to evaluate the in vitro toxic effects of PrP(ARR) and PrP(ARQ) variants in relation with their structural characteristics. We show that both peptides cause cell death inducing apoptosis but, unexpectedly, the scrapie resistant PrP(ARR) form was more toxic than the scrapie susceptible PrP(ARQ) variant. Moreover, the alpha-helical conformation of PrP(ARR) was less stable than that of PrP(ARQ) and the structural determinants responsible of these different conformational stabilities were characterized by spectroscopic analysis. We observed that PrP toxicity was inversely related to protein structural stability, being the unfolded conformation more toxic than the native one. However, the PrP(ARQ) variant displays a higher propensity to form large aggregates than PrP(ARR). Interestingly, in the presence of small amounts of PrP(ARR), PrP(ARQ) aggregability was reduced to levels similar to that of PrP(ARR). Thus, in contrast to PrP(ARR) toxicity, scrapie transmissibility seems to reside in the more stable conformation of PrP(ARQ) that allows the formation of large amyloid fibrils.

  8. Using crystallographic shear to reduce lattice thermal conductivity: high temperature thermoelectric characterization of the spark plasma sintered Magnéli phases WO2.90 and WO2.722.

    PubMed

    Kieslich, Gregor; Veremchuk, Igor; Antonyshyn, Iryna; Zeier, Wolfgang G; Birkel, Christina S; Weldert, Kai; Heinrich, Christophe P; Visnow, Eduard; Panthöfer, Martin; Burkhardt, Ulrich; Grin, Yuri; Tremel, Wolfgang

    2013-10-07

    Engineering of nanoscale structures is a requisite for controlling the electrical and thermal transport in solids, in particular for thermoelectric applications that require a conflicting combination of low thermal conductivity and low electrical resistivity. We report the thermoelectric properties of spark plasma sintered Magnéli phases WO2.90 and WO2.722. The crystallographic shear planes, which are a typical feature of the crystal structures of Magnéli-type metal oxides, lead to a remarkably low thermal conductivity for WO2.90. The figures of merit (ZT = 0.13 at 1100 K for WO2.90 and 0.07 at 1100 K for WO2.722) are relatively high for tungsten-oxygen compounds and metal oxides in general. The electrical resistivity of WO2.722 shows a metallic behaviour with temperature, while WO2.90 has the characteristics of a heavily doped semiconductor. The low thermopower of 80 μV K(-1) at 1100 K for WO2.90 is attributed to its high charge carrier concentration. The enhanced thermoelectric performance for WO2.90 compared to WO2.722 originates from its much lower thermal conductivity, due to the presence of crystallographic shear and dislocations in the crystal structure. Our study is a proof of principle for the development of efficient and low-cost thermoelectric materials based on the use of intrinsically nanostructured materials rather than artificially structured layered systems to reduce lattice thermal conductivity.

  9. Achieving high-pressure and high-temperature within a TEM: Crystallographic defects as hosts for concentrating and storing carbon deep within Earth

    NASA Astrophysics Data System (ADS)

    Wu, J.; Buseck, P. R.

    2013-12-01

    Transmission electron microscopy in combination with in-situ high-pressure and high-temperature measurements is uniquely able to provide high-resolution data about materials under conditions resembling those in Earth's interior. By using nanocontainers of graphitized carbon, it is possible to achieve pressures and temperatures up to 40 GPa and 1200 °C, respectively. A wide range of relatively simple minerals and mineral analogs have been examined using this approach. By studying alpha-PbO2-type titanium dioxide (TiO2) and perovskite-structured nickel-doped lanthanum chromate (LaCr0.5Ni0.5O3), we show the influence of crystallographic defects in concentrating and storing carbon within these analogs to minerals occurring deep inside Earth. Such in-situ observations are impossible by using existing conventional high-pressure techniques. Figure 1. Temporal compression sequence of an anatase nanocrystal with two visible fault planes inside a multi-walled graphitic cage. (a)-(g) The times indicated in each panel are from the start of irradiation. Pressure was generated by shrinkage of the cage resulting from displacement damage by electrons (30 A/cm2) at 770 C. The disappearance of anatase (101) planes and emergence of alpha-PbO2-type TiO2 (110) planes indicates a phase transition between (e) and (f) (see insets).

  10. Crystallographic control on early stages of cataclasis in carbonate fault gouges

    NASA Astrophysics Data System (ADS)

    Demurtas, Matteo; Smith, Steven A. F.; Fondriest, Michele; Spagnuolo, Elena; Di Toro, Giulio

    2017-04-01

    Carbonates are a recurring lithology in most of active seismic areas worldwide, such as the Apennines (Italy). Here, typical fault products are gouges and cataclasites made of mixtures of carbonate minerals (i.e., calcite and dolomite) that occasionally exhibit a foliation. Natural fault gouges often contain minerals with strong anisotropies, such as cleavage surfaces in phyllosilicates and carbonates. Therefore, the understanding of the role of such anisotropies during shearing is important to develop realistic microphysical models of brittle fragmentation and grain size reduction. Here we present results of microstructural and coupled EDS-EBSD (Energy Dispersive Spectroscopy - Electron Backscattered Diffraction) analysis on mixtures (50/50wt%) of calcite-dolomite gouges deformed experimentally in a rotary shear apparatus (SHIVA, INGV-Rome) at room temperature under constant normal stress of 17.5 MPa and slip rates of 30 µm/s to 1 m/s. The EDS-EBSD analysis was focused on the gouge layer underlying the slip zone, which has been previously demonstrated to accommodate low finite shear strain during deformation. At all investigated slip rates, calcite develops a crystallographic preferred orientation (CPO) on the (0001) plane, with the c-axis inclined subparallel to the principal stress and the [-1-120] direction forming a girdle perpendicular to it. Texture strength typically increases with slip rate and appears not to be influenced by the presence of water or foliation development in the gouge during deformation. Misorientation analysis suggests twinning as the principal crystallographic active deformation mechanism. Instead, dolomite grains do not develop a CPO. Microfractures are closely spaced, mainly oriented subparallel to the principal stress and rarely exploit calcite twin planes. The latter typically occur at high angle with respect to fractures, are oriented consistently with the sense of shear and almost orthogonal to the principal stress. Calcite grains

  11. Sterically Hindered Chiral Organometallic Complexes: AN X-Ray Crystallographic, NMR Spectroscopic and Ehmo Study.

    NASA Astrophysics Data System (ADS)

    Malisza, Krisztina Laura

    Sterically crowded organometallic complexes present fascinating problems of structure and molecular dynamics. Tetrahedral clusters such as (RCequivCR ^')rm(C_5H_5)_2M _2(CO)_4, where M = Mo or W, crystallize in conformations possessing three terminal carbonyls while the fourth is semi-bridging. However, these ligands undergo a rapid exchange process which can be followed by variable -temperature NMR spectroscopy. When the R substituent is derived from a chiral natural product, the low temperature NMR spectra reveal the presence of diastereomers which are interconvertible via rotations of the organometallic vertices. The fluxional behaviour of tetrahedral clusters containing such vertices as Co(CO)_3, Fe(CO)_3 or rm(C_5H _5)Mo(CO)_2 can be rationalized by means of molecular orbital calculations at the extended Huckel level of approximation. These studies show that the barriers to vertex rotation can usually be traced to one principal orbital interaction in each case. However, in rm(C_5H_5)_2Mo_2(CO) _4(R-CequivC-R) clusters, the barriers are primarily steric in character. The ability of transition metal clusters to delocalize electronic charge is well known and, in principle, could be used to stabilize intermediates of biochemical significance. Treatment of 2-methylcyclopentanone with an alkyne anion was carried out in order to generate 1-alkynyl-2-methylcyclopentanols in which the methyl and alkynyl groups are trans diaxial; the aim was to mimic the "D"-ring of the steroidal contraceptive mestranol. In fact, the major epimer was the one in which the methyl and alkynyl substituents were disposed in a cis manner. The conformation of 2-methyl-1-phenylethynylcyclopentanol 47 was elucidated by two-dimensional NMR techniques. Moreover, the structure of 47 and also of its rm Co _2(CO)_6 derivative have been determined crystallographically. Protonation of the dicobalt or dimolybdenum complexes of 47 lead to stable cations; treatment of these cations with nucleophiles

  12. Bandcrossing of magnetic rotation bands in Pr137

    NASA Astrophysics Data System (ADS)

    Agarwal, Priyanka; Kumar, Suresh; Singh, Sukhjeet; Sinha, Rishi Kumar; Dhal, Anukul; Muralithar, S.; Singh, R. P.; Madhavan, N.; Kumar, Rakesh; Bhowmik, R. K.; Malik, S. S.; Pancholi, S. C.; Chaturvedi, L.; Jain, H. C.; Jain, A. K.

    2007-08-01

    The odd mass nucleus Pr137 has been studied to high spins in order to investigate the magnetic rotation phenomenon in mass 130 region using the Sn122(F19,4n)Pr137 reaction at a beam energy of 80 MeV. A known ΔI=1 band has been extended to Jπ=47/2- with the addition of three new transitions. Directional Correlation of Oriented Nuclei (DCO) ratios and linear polarization measurements have been performed to assign the multipolarities of gamma transitions and the spins and parities of the energy levels in this band, now established as the M1 band. The combination of M1 transitions along with cross over E2 transitions have been observed in this band for the first time. The experimentally deduced B(M1)/B(E2) ratios show a decrease with increasing spin after band-crossing suggesting magnetic rotation. TAC calculations for the 3qp: πh11/2⊗ν(h11/2)-2 configuration reproduce the experimental observations in the lower spin part of the ΔI=1 band and the 5qp: πh11/2(g7/2)2⊗ν(h11/2)-2 configuration reproduces the ΔI=1 band at higher spins; the crossing of the bands based on the two configuration leads to a back-bending also. Theoretical calculations also support a magnetic rotation nature for both the configurations.

  13. A crystallographic study of the binding of 13 metal ions to two related RNA duplexes

    PubMed Central

    Ennifar, Eric; Walter, Philippe; Dumas, Philippe

    2003-01-01

    Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at ‘Hoogsteen’ sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson–Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium. PMID:12736317

  14. Unintended consequences? Water molecules at biological and crystallographic protein-protein interfaces.

    PubMed

    Ahmed, Mostafa H; Habtemariam, Mesay; Safo, Martin K; Scarsdale, J Neel; Spyrakis, Francesca; Cozzini, Pietro; Mozzarelli, Andrea; Kellogg, Glen E

    2013-12-01

    The importance of protein-protein interactions (PPIs) is becoming increasingly appreciated, as these interactions lie at the core of virtually every biological process. Small molecule modulators that target PPIs are under exploration as new therapies. One of the greatest obstacles faced in crystallographically determining the 3D structures of proteins is coaxing the proteins to form "artificial" PPIs that lead to uniform crystals suitable for X-ray diffraction. This work compares interactions formed naturally, i.e., "biological", with those artificially formed under crystallization conditions or "non-biological". In particular, a detailed analysis of water molecules at the interfaces of high-resolution (≤2.30 Å) X-ray crystal structures of protein-protein complexes, where 140 are biological protein-protein complex structures and 112 include non-biological protein-protein interfaces, was carried out using modeling tools based on the HINT forcefield. Surprisingly few and relatively subtle differences were observed between the two types of interfaces: (i) non-biological interfaces are more polar than biological interfaces, yet there is better organized hydrogen bonding at the latter; (ii) biological associations rely more on water-mediated interactions with backbone atoms compared to non-biological associations; (iii) aromatic/planar residues play a larger role in biological associations with respect to water, and (iv) Lys has a particularly large role at non-biological interfaces. A support vector machines (SVMs) classifier using descriptors from this study was devised that was able to correctly classify 84% of the two interface types. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Local dynamics of proteins and DNA evaluated from crystallographic B factors

    PubMed Central

    Schneider, Bohdan; Gelly, Jean-Christophe; de Brevern, Alexandre G.; Černý, Jiří

    2014-01-01

    The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res. 42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified. PMID:25195754

  16. Crystallographic texture and microstructural changes in fusion welds of recrystallized Zry-4 rolled plates

    NASA Astrophysics Data System (ADS)

    Moya Riffo, A.; Vicente Alvarez, M. A.; Santisteban, J. R.; Vizcaino, P.; Limandri, S.; Daymond, M. R.; Kerr, D.; Okasinski, J.; Almer, J.; Vogel, S. C.

    2017-05-01

    This work presents a detailed characterization of the microstructural and crystallographic texture changes observed in the transition region in a weld between two Zircaloy-4 cold rolled and recrystallized plates. The microstructural study was performed by optical microscopy under polarized light and scanning electron microscopy (SEM). Texture changes were characterized at different lengthscales: in the micrometric size, orientation imaging maps (OIM) were constructed by electron backscatter diffraction (EBSD), in the millimetre scale, high energy XRD experiments were done at the Advanced Photon Source (USA) and compared to neutron diffraction texture determinations performed in the HIPPO instrument at Los Alamos National Laboratory. In the heat affected zone (HAZ) we observed the development of Widmanstätten microstructures, typical of the α(hcp) to β(bcc) phase transformation. Associated with these changes a rotation of the c-poles is found in the HAZ and fusion zone. While the base material shows the typical texture of a cold rolled plate, with their c-poles pointing 35° apart from the normal direction of the plate in the normal-transversal line, in the HAZ, c-poles align along the transversal direction of the plate and then re-orient along different directions, all of these changes occurring within a lengthscale in the order of mm. The evolution of texture in this narrow region was captured by both OIM and XRD, and is consistent with previous measurements done by Neutron Diffraction in the HIPPO diffractometer at Los Alamos National Laboratory, USA. The microstructural and texture changes along the HAZ were interpreted as arising due to the effect of differences in the cooling rate and β grain size on the progress of the different α variants during transformation. Fast cooling rates and large β grains are associated to weak variant selection during the β->α transformation, while slow cooling rates and fine β grains result in strong variant selection.

  17. Mimicking of Estradiol Binding by Flame Retardants and Their Metabolites: A Crystallographic Analysis

    PubMed Central

    Gosavi, Rajendrakumar A.; Knudsen, Gabriel A.; Birnbaum, Linda S.

    2013-01-01

    Background: Brominated flame retardants (BFRs), used in many types of consumer goods, are being studied because of concerns about possible health effects related to endocrine disruption, immunotoxicity, reproductive toxicity, and neurotoxicity. Tetrabromobisphenol A (TBBPA), the most widely used BFR, and human metabolites of certain congeners of polybrominated diphenyl ether (e.g., 3-OH-BDE-47) have been suggested to inhibit estrogen sulfotransferase, potentially affecting estrogen metabolism. Objectives: Our primary goal was to understand the structural mechanism for inhibition of the hormone-metabolizing enzyme estrogen sulfotransferase by certain BFRs. We also sought to understand various factors that facilitate the binding of flame retardants in the enzyme binding pocket. Methods: We used X-ray crystallography to obtain atomic detail of the binding modes of TBBPA and 3-OH-BDE-47 to estrogen sulfotransferase for comparison with binding of the endogenous substrate estradiol. Results: The crystal structures reveal how BFRs mimic estradiol binding as well as the various interactions between the compounds and protein residues that facilitate its binding. In addition, the structures provide insights into the ability of the sulfotransferase substrate binding pocket to accommodate a range of halogenated compounds that satisfy minimal structural criteria. Conclusions: Our results show how BFRs or their metabolites can bind to and inhibit a key hormone-metabolizing enzyme, potentially causing endocrine disruption. Citation: Gosavi RA, Knudsen GA, Birnbaum LS, Pedersen LC. 2013. Mimicking of estradiol binding by flame retardants and their metabolites: a crystallographic analysis. Environ Health Perspect 121:1194–1199; http://dx.doi.org/10.1289/ehp.1306902 PMID:23959441

  18. Biochemical and Crystallographic Analysis of Substrate Binding and Conformational Changes in Acetyl-CoA Synthetase

    SciTech Connect

    Reger,A.; Carney, J.; Gulick, A.

    2007-01-01

    The adenylate-forming enzymes, including acyl-CoA synthetases, the adenylation domains of non-ribosomal peptide synthetases (NRPS), and firefly luciferase, perform two half-reactions in a ping-pong mechanism. We have proposed a domain alternation mechanism for these enzymes whereby, upon completion of the initial adenylation reaction, the C-terminal domain of these enzymes undergoes a 140{sup o} rotation to perform the second thioester-forming half-reaction. Structural and kinetic data of mutant enzymes support this hypothesis. We present here mutations to Salmonella enterica acetyl-CoA synthetase (Acs) and test the ability of the enzymes to catalyze the complete reaction and the adenylation half-reaction. Substitution of Lys609 with alanine results in an enzyme that is unable to catalyze the adenylate reaction, while the Gly524 to leucine substitution is unable to catalyze the complete reaction yet catalyzes the adenylation half-reaction with activity comparable to the wild-type enzyme. The positions of these two residues, which are located on the mobile C-terminal domain, strongly support the domain alternation hypothesis. We also present steady-state kinetic data of putative substrate-binding residues and demonstrate that no single residue plays a dominant role in dictating CoA binding. We have also created two mutations in the active site to alter the acyl substrate specificity. Finally, the crystallographic structures of wild-type Acs and mutants R194A, R584A, R584E, K609A, and V386A are presented to support the biochemical analysis.

  19. Identification of succinic semialdehyde reductases from Geobacter: expression, purification, crystallization, preliminary functional, and crystallographic analysis

    SciTech Connect

    Zhang, Yanfeng; Gao, Xiaoli; Zheng, Yi; Garavito, R. Michael

    2012-04-30

    Succinic semialdehyde reductase (SSAR) is an important enzyme involved in {gamma}-aminobutyrate (GABA) metabolism. By converting succinic semialdehyde (SSA) to {gamma}-hydroxybutyrate (GHB), the SSAR facilitates an alternative pathway for GABA degradation. In this study, we identified SSARs from Geobacter sulfurreducens and Geobacter metallireducens (GsSSAR and GmSSAR, respectively). The enzymes were over-expressed in Escherichia coli and purified to near homogeneity. Both GsSSAR and GmSSAR showed the activity of reducing SSA using nicotinamide adenine dinucleotide phosphate as a co-factor. The oligomeric sizes of GsSSAR and GmSSAR, as determined by analytical size exclusion chromatography, suggest that the enzymes presumably exist as tetramers in solution. The recombinant GsSSAR and GmSSAR crystallized in the presence of NADP{sup +}, and the resulting crystals diffracted to 1.89 {angstrom} (GsSSAR) and 2.25 {angstrom} (GmSSAR) resolution. The GsSSAR and GmSSAR crystals belong to the space groups P2{sub 1}22{sub 1} (a = 99.61 {angstrom}, b = 147.49 {angstrom}, c = 182.47 {angstrom}) and P1 (a = 75.97 {angstrom}, b = 79.14 {angstrom}, c = 95.47 {angstrom}, {alpha} = 82.15{sup o}, {beta} = 88.80{sup o}, {gamma} = 87.66{sup o}), respectively. Preliminary crystallographic data analysis suggests the presence of eight protein monomers in the asymmetric units for both GsSSAR and GmSSAR.

  20. Phosphate tungsten bronze series: crystallographic and structural properties of low-dimensional conductors.

    PubMed

    Roussel, P; Pérez, O; Labbé, P

    2001-10-01

    Phosphate tungsten bronzes have been shown to be conductors of low dimensionality. A review of the crystallographic and structural properties of this huge series of compounds is given here, corresponding to the present knowledge of the different X-ray studies and electron microscopy investigations. Three main families are described, monophosphate tungsten bronzes, Ax(PO2)4(WO3)2m, either with pentagonal tunnels (MPTBp) or with hexagonal tunnels (MPTBh), and diphosphate tungsten bronzes, Ax(P2O4)2(WO3)2m, mainly with hexagonal tunnels (DPTBh). The general aspect of these crystal structures may be described as a building of polyhedra sharing oxygen corners made of regular stacking of WO3-type slabs with a thickness function of m, joined by slices of tetrahedral PO4 phosphate or P2O7 diphosphate groups. The relations of the different slabs with respect to the basic perovskite structure are mentioned. The structural description is focused on the tilt phenomenon of the WO6 octahedra inside a slab of WO3-type. In this respect, a comparison with the different phases of the WO3 crystal structures is established. The various modes of tilting and the different possible connections between two adjacent WO3-type slabs involve a great variety of structures with different symmetries, as well as the existence of numerous twins in MPTBp's. Several phase transitions, with the appearance of diffuse scattering and modulation phenomena, were analysed by X-ray scattering measurements and through the temperature dependence of various physical properties for the MPTBp's. The role of the W displacements within the WO3-type slabs, in two modulated structures (m = 4 and m = 10), already solved, is discussed. Finally, the complexity of the structural aspects of DPTBh's is explained on the basis of the average structures which are the only ones solved.